blob_id stringlengths 40 40 | directory_id stringlengths 40 40 | path stringlengths 6 214 | content_id stringlengths 40 40 | detected_licenses listlengths 0 50 | license_type stringclasses 2 values | repo_name stringlengths 6 87 | snapshot_id stringlengths 40 40 | revision_id stringlengths 40 40 | branch_name stringclasses 15 values | visit_date timestamp[us]date 2016-08-04 09:00:04 2023-09-05 17:18:33 | revision_date timestamp[us]date 1998-12-11 00:15:10 2023-09-02 05:42:40 | committer_date timestamp[us]date 2005-04-26 09:58:02 2023-09-02 05:42:40 | github_id int64 436k 586M ⌀ | star_events_count int64 0 12.3k | fork_events_count int64 0 6.3k | gha_license_id stringclasses 7 values | gha_event_created_at timestamp[us]date 2012-11-16 11:45:07 2023-09-14 20:45:37 ⌀ | gha_created_at timestamp[us]date 2010-03-22 23:34:58 2023-01-07 03:47:44 ⌀ | gha_language stringclasses 36 values | src_encoding stringclasses 17 values | language stringclasses 1 value | is_vendor bool 1 class | is_generated bool 1 class | length_bytes int64 5 10.4M | extension stringclasses 15 values | filename stringlengths 2 96 | content stringlengths 5 10.4M |
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11377ff06b755c5d421dd5c10a3c8a347b4996eb | 449d555969bfd7befe906877abab098c6e63a0e8 | /2708/CH16/EX16.4/ex_16_4.sce | b9e2e6a326711c9f5ef3b13a9f2491491af55c7d | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 372 | sce | ex_16_4.sce | //Example 16.4 //de-broglie wavelength of neutrons
clc;
clear;
//given data :
k=1.38D-23;// Boltzmann's Constant in joules per K
T=27;// temperature in degree
m=1.67D-27;// mass of neutron in kg
h=6.62D-34;// plank's constant in joules-sec
T=T+273;// to convert in K
lamda=h/sqrt(2*m*k*T);// De-broglie Wavelength in m
disp(lamda,"De-broglie Wavelength in m")
|
4e33e8aed6410d30887056b3f3fd88bf282b5d18 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1322/CH17/EX17.9/145ex2.sce | b6f13be203b482c6707e19ba73985201c8a03cbd | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 630 | sce | 145ex2.sce |
clear;
clc;
close;
//let x km/hr is avg. speed for 1st journey
//as velocity=distance/time, time for 1st journey is 84/x hrs
//speed for return journey is 84/(x+4).from given data, this is <1/2 hr than the 1st time
x=poly(0,'x');
//In algebraic form,(84/x)-(84/(x+4))=1/2
y=(84/x)-(84/(x+4))-1/2; //y=0. so, numerator=0
x=roots(numer(y));
//velocity can't be in negatives.take +ve root
disp("avg. speed for 1st journey is x=24km/h")
distance=84;//given
velocity=24;//found
time=distance/velocity;//time for 1st journey
time1=distance/(velocity+4);//time for 2nd journey
mprintf("total_time=%fhours",time+time1)
|
d2864d420e251661a20e613e806439e70280dbab | 449d555969bfd7befe906877abab098c6e63a0e8 | /1859/CH8/EX8.12/exa_8_12.sce | b436277527db16b18857168102a62ae86da0ef7e | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 559 | sce | exa_8_12.sce | // Exa 8.12
clc;
clear;
close;
// Given data
// Part (a)
d_v0= 0;
Dv=6;
fie= asind(d_v0/Dv);
disp(fie,"Phase angle of first figure in degree")
// Part (b)
d_v0= 3;
Dv=6;
fie= asind(d_v0/Dv);
disp(fie,"Phase angle of second figure in degree")
// Part (c)
d_v0= 5;
Dv=5;
fie= asind(d_v0/Dv);
disp(fie,"Phase angle of third figure in degree")
// Part (d)
d_v0= 3;
Dv=5;
fie= asind(d_v0/Dv);
// since ellipse is in 2nd and fourth quartes so the valid value of phase angle
fie= 180-fie
disp(fie,"Phase angle of forth figure in degree")
|
26d9f077d39d8c6b3cad4a35950d8cad64ef07a4 | e964e170c140080bfdc45c1e423e436b86d7c1b7 | /Titration and demo/2 demo SHOCKS/EP_demo.sce | 8d5bb346ba834a776a36b7b7b53621829199a53c | [] | no_license | GNilsonne/gebra_stim | 647b6b8663bf825c606ace960f3343497b4fb3ad | 1ad944fc973ad296dba8502e1e10539fcc487408 | refs/heads/master | 2021-01-12T12:01:55.417785 | 2017-10-20T16:56:36 | 2017-10-20T16:56:36 | 69,223,164 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 3,027 | sce | EP_demo.sce | #define files
scenario = "EP_demo";
pcl_file = "EP_demo.pcl";
#standard settings
scenario_type = fMRI;
pulses_per_scan = 1;
pulse_code = 115;
active_buttons = 5;
button_codes = 1,2,3,4,5;
response_logging = log_active; # log only if response is expected
response_matching = simple_matching;
default_output_port = 1; # parallel port
response_port_output = false;
write_codes = true;
pulse_width = 1; # duration of shock, will be changed in pcl
default_background_color = 100, 100, 100; # gray
default_font_size = 40;
default_text_color = 255,255,255;
default_font = "Arial";
#####################################################
begin;
#####################################################
#Stimuli
picture {} default;
picture {text {caption = "+"; font_size=100; font_color = 255,255,255,;}; x=0;y=0;} fixation_cross;
TEMPLATE "template.tem";
text { caption = "XXX";
font_size =20;
preload = false;
} gap;
# RANGE OF RATING SCALE #
array{
text {caption = "0";};
text {caption = "100";};
} number;
# QUESTION ABOVE RATING SCALE #
array{
text { caption = "Hur ont gjorde det?";};
text { caption = "Hur obehagligt var det för dig?";};
} questions;
# RATING SCALE #
picture {
box { height = 10; width = 200; color = 255,255,255; };
x = 0; y = 0;
box { height = 50; width = 5;color = 255,255,255; };
x = 0; y = 0;
text gap;
x = -200; y = 0;
text gap;
x = 200; y = 0;
text gap;
x=0; y=150;
}scale;
#######################################################
# Define trials
#######################################################
# FIXATION CROSS #
trial {
all_responses = false;
trial_duration = stimuli_length;
trial_type = fixed;
stimulus_event{
picture fixation_cross;
time = 0;
duration = 4000;
code="fixation_cross";
} ev_fixation_cross;
} tr_fixation_cross;
# BLANK SCREEN #
trial {
all_responses = false;
trial_duration = stimuli_length;
trial_type = fixed;
stimulus_event{
picture default;
time = 0;
duration = 4000;
code="blank";
} ev_blank;
} tr_blank;
# CONDITION TRIAL #
trial {
trial_duration = stimuli_length;
trial_type = fixed;
all_responses = false;
stimulus_event{ #condition
picture {
text {caption = "condition";}; x = 0; y = 0;
} pic_condition;
time=0;
duration = 500;
code = "condition";
} ev_condition;
}tr_condition;
# SHOCK #
trial {
trial_duration = stimuli_length;
trial_type = fixed;
all_responses = false;
stimulus_event{ #shock picture
picture {
text {caption = "condition";}; x = 0; y = 0;
} pic_shock;
time=0;
duration = 2000;
code = "shockpic";
} ev_shockpic;
stimulus_event{
nothing {};
code = "Shock";
deltat = 0;
#port_code = 1;
code_width = 1; # Will be changed in pcl
} ev_shock;
} tr_shock;
# RATING SCALE #
trial {
all_responses = true;
trial_duration = stimuli_length;
trial_type = fixed;
} tr_rate;
######################### |
3b32493b6cf1fef70390c2fbb14f203ab4d565ce | 59e7c95649eb8894e1d6f0bcac3ca7ea2b023217 | /Matriz Multiplicada.sce | ce91d44b025284c1759f658552c54677ab9747f2 | [] | no_license | nascimento-luciano/Scilab-Matlab | cb5ee9d97df3ed0f4311573df0fd37a88b3394d8 | 1cba42b68cc7954ff4c7dd6b13c7d8e6bd3d039e | refs/heads/main | 2023-03-19T21:06:18.691193 | 2021-03-18T00:57:29 | 2021-03-18T00:57:29 | 348,877,701 | 1 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 196 | sce | Matriz Multiplicada.sce | //
a =[1 2; 3 4; 5 6];
b = [1 2 3; 4 5 6];
for i=1:3
for j=1:3
c(i,j) =0;
for k=1:2
c(i,j =c(i,j)+a(i,k)*b(k,j);
end
end
end
disp(c);
|
faa9e0d95a75da9d893dd5c608a46d88352a5f11 | 8217f7986187902617ad1bf89cb789618a90dd0a | /browsable_source/2.4/Unix-Windows/scilab-2.4/macros/m2sci/sci_text.sci | 92e33db4f7cb6ad7bfccd811b73cd70a35e1cb0d | [
"LicenseRef-scancode-public-domain",
"LicenseRef-scancode-warranty-disclaimer"
] | permissive | clg55/Scilab-Workbench | 4ebc01d2daea5026ad07fbfc53e16d4b29179502 | 9f8fd29c7f2a98100fa9aed8b58f6768d24a1875 | refs/heads/master | 2023-05-31T04:06:22.931111 | 2022-09-13T14:41:51 | 2022-09-13T14:41:51 | 258,270,193 | 0 | 1 | null | null | null | null | UTF-8 | Scilab | false | false | 471 | sci | sci_text.sci | function [stk,txt,top]=sci_text()
// Copyright INRIA
txt=[]
if rhs==3 then
str=stk(top)(1)
x=stk(top-2)(1)
y=stk(top-1)(1)
stk=list('xstring'+rhsargs([x,y,str]),'0','0','0','0')
elseif rhs==0 then
stk=list(' ','-2','0','0','0')
else
str=stk(top)(1)
z1=stk(top-1)(1)
y1=stk(top-2)(1)
x1=stk(top-3)(1)
x=gettempvar(1)
y=gettempvar(2)
txt=lhsargs([x,y])+' = geom3d'+rhsargs([x1,y1,z1])
stk=list('xstring'+rhsargs([x,y,str]),'0','0','0','0')
end
|
d96868e5a3b471a932c78832de031544bd9b9962 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3753/CH5/EX5.8/Ex5_8.sce | bab31cff6b714defa717b7f89b548468e1a22be1 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 247 | sce | Ex5_8.sce | //Example 5.8, Page number 5.30
clc;clear;close
// variable declaration
V=2.405//unitless
lamda=1.3 // in m
N_a=0.05//unitless
// Calculations
a_max=(V*lamda)/(2*%pi*N_a) // in m
// Result
printf("Maximum core radius = %.2f micro-m",(a_max))
|
bfffbf99d5fba0058e9c83b9f40d4c05607b6427 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3760/CH3/EX3.5/Ex3_5.sce | 5d835efab6c78e6d0a77a709c63691caa9b1b33a | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 1,406 | sce | Ex3_5.sce | clc;
p=4; // number of pole
f=50; // frequency of supply
ns=420; // stator turns
nr=240; // rotor turns
F=30*10^-3; // flux per pole
kw=0.96; // winding factor for both stator and rotor
nsph=ns/3; // stator turn per phase
nrph=nr/3; // rotor turn per phase
es=sqrt(2)*%pi*f*kw*nsph*F; // stator turn per phase
disp('case a');
// rotor is stationary
s=1; // at standstill slip=1
er=sqrt(2)*%pi*f*kw*nrph*F;
printf('frequency of EMF in stator is %f Hz\n',f);
printf('frequency of EMF in rotor is %f Hz\n',f);
printf('Per phase stator EMF is %f V\n',es);
printf('Per phase rotor EMF is %f V\n',er);
disp('case b');
sr=1440; // speed of rotor in rpm in direction of rotating flux
Ns=(120*f)/p; // speed of rotating flux
s=(Ns-sr)/Ns; // slip
fr=s*f; // frequency of EMF in rotor
er=sqrt(2)*%pi*fr*kw*nrph*F;
printf('frequency of EMF in stator is %f Hz\n',f);
printf('frequency of EMF in rotor is %f Hz\n',fr);
printf('Per phase stator EMF is %f V\n',es);
printf('Per phase rotor EMF is %f V\n',er);
disp('case c');
sr=1440; // speed of rotor in rpm opposite to the direction of rotating flux
s=(Ns+sr)/Ns; // slip
fr=s*f; // frequency of EMF in rotor
er=sqrt(2)*%pi*fr*kw*nrph*F;
printf('frequency of EMF in stator is %f Hz\n',f);
printf('frequency of EMF in rotor is %f Hz\n',fr);
printf('Per phase stator EMF is %f V\n',es);
printf('Per phase rotor EMF is %f V\n',er);
|
c9bd301e449c277c97fafe261265d5402b57ffc9 | 2eac84edf941c64588fef76f10d02309aabcb2fb | /System/Scilab/Scripts/createModel.sci | d8f2427a3de6f4fa77f1ca16c6279b3c3f179aff | [
"BSD-3-Clause"
] | permissive | AlexisTM/X2C | fdd93bd33b931ea448ba516f5e3f9af6a5149a6a | 31f39b598afe271a7fd46ef1ee9e06c410b1120c | refs/heads/master | 2021-08-07T04:26:24.391617 | 2017-11-07T14:34:33 | 2017-11-07T14:34:33 | 109,844,123 | 1 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 12,553 | sci | createModel.sci | // Copyright (c) 2017, Linz Center of Mechatronics GmbH (LCM) http://www.lcm.at/
// All rights reserved.
//
// This file is licensed according to the BSD 3-clause license as follows:
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of the "Linz Center of Mechatronics GmbH" and "LCM" nor
// the names of its contributors may be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
// WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL "Linz Center of Mechatronics GmbH" BE LIABLE FOR ANY
// DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
// (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
// LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// This file is part of X2C. http://www.mechatronic-simulation.org/
// $LastChangedRevision: 1111 $
// $LastChangedDate:: 2017-02-28 14:18:07 +0100#$
//
// Function to create Xcos model from XML file.
// Parameters:
// xmlName - XML name
function [] = createModel(xmlName)
funcprot(0);
// import necessary java classes
jimport at.lcm.x2c.core.structure.Model;
jimport at.lcm.x2c.core.structure.ControlBlock;
// get file separator
fs = filesep();
// get current directory
curDir = pwd();
try
// get model information
newModel = jnewInstance(Model);
jinvoke(newModel, "readFromXml", xmlName);
modelName = jinvoke(newModel, "getModelName");
catch
mprintf("Error reading xml %s\n", xmlName);
mprintf("ERROR: %s\n", lasterror());
return;
end
// Scaling factor for block size
scale = 20;
try
// setup diagram structure
scs_m = scicos_diagram(); // create diagram
scs_m.props.title = modelName; // give diagram a name
cnt = 0;
// add blocks from X2C Basic library
cnt = cnt + 1;
execstr("scs_m.objs(" + string(cnt) + ") = x2c_CommunicatorStart('"define'");"); // load block into model
sz = scs_m.objs(cnt).graphics.sz * scale;
scs_m.objs(cnt).graphics.sz = sz; // resize block to a suitable size
scs_m.objs(cnt).graphics.orig = [0*scale, sz(2)+2*scale]; // set position of block in model
cnt = cnt + 1;
execstr("scs_m.objs(" + string(cnt) + ") = x2c_ModelTransformation('"define'");"); // load block into model
sz = scs_m.objs(cnt).graphics.sz * scale;
scs_m.objs(cnt).graphics.sz = sz; // resize block to a suitable size
scs_m.objs(cnt).graphics.orig = [10*scale, sz(2)+2*scale]; // set position of block in model
cnt = cnt + 1;
execstr("scs_m.objs(" + string(cnt) + ") = x2c_ProjectDocumentation('"define'");"); // load block into model
sz = scs_m.objs(cnt).graphics.sz * scale;
scs_m.objs(cnt).graphics.sz = sz; // resize block to a suitable size
scs_m.objs(cnt).graphics.orig = [20*scale, sz(2)+2*scale]; // set position of block in model
// add main system clock
cnt = cnt + 1;
execstr("scs_m.objs(" + string(cnt) + ") = CLOCK_c('"define'");"); // load block into model
sz = scs_m.objs(cnt).graphics.sz * scale;
scs_m.objs(cnt).graphics.sz = sz; // resize block to a suitable size
scs_m.objs(cnt).graphics.orig = [30*scale, sz(2)+2*scale]; // set position of block in model
Ts = jinvoke(newModel, "getSampleTime");
// TODO: enter sample time in clock
//scs_m.objs(cnt).graphics.exprs = Ts;
// process all inports
Inports = jinvoke(newModel, "getInports");
vertOffset = 0;
horiOffset = 0;
//for i = 1:Inports.length // NOTE: for some strange reason this does not work!
i=0;
while i < Inports.length
i = i + 1;
cnt = cnt + 1;
// get general block information
curBlockLib = jinvoke(Inports(i), "getLibraryName");
curBlockType = jinvoke(Inports(i), "getName");
curBlockMask = jinvoke(Inports(i), "getMask");
curBlockName = jinvoke(Inports(i), "getMaskName");
curXcosName = getXcosBlockName(curBlockLib, curBlockType);
// get scilab block information
execstr("scs_m.objs(" + string(cnt) + ") = "+ curXcosName + "('"define'");"); // load block into model
sz = scs_m.objs(cnt).graphics.sz * scale;
vertOffset = vertOffset - (sz(2)+scale);
exprs = scs_m.objs(cnt).graphics.exprs;
// set block label
exprs(4) = curBlockName; // fourth entry is the block label
// set parameter values (implementation and sample time factor )
curMaskParameterNames = jinvoke(curBlockMask, "getMaskParameterNames");
len = size(curMaskParameterNames);
if len(2) == 2
// first parameter is DataType
curMaskParam = jinvoke(curBlockMask, "getMaskParameter", curMaskParameterNames(1));
curMaskParamVal = jinvoke(curMaskParam, "getValue");
exprs(7) = curMaskParamVal; // 7th entry is implementation
// TODO: check if ok (visiualization seems odd, is code generation possible?)
// second parameter is ts_fact
curMaskParam = jinvoke(curBlockMask, "getMaskParameter", curMaskParameterNames(2));
curMaskParamVal = jinvoke(curMaskParam, "getValue");
exprs(10) = curMaskParamVal; // 10th entry is adjustable field of first parameter
else
disp('Warning: Parameter ' + curMaskParameterNames(j) + 'could not be entered for block ' + curBlockName + " because data structure of Inports has changed!")
end
// position block in model
scs_m.objs(cnt).graphics.sz = sz; // resize block to a suitable size
scs_m.objs(cnt).graphics.orig = [horiOffset, vertOffset]; // set position of block in model
scs_m.objs(cnt).graphics.exprs = exprs; // set block name
end
// process all regular blocks
Blocks = jinvoke(newModel, "getControlBlocks");
vertOffset = 0;
horiOffset = 15*scale;
//for i = 1:Blocks.length // NOTE: for some strange reason this does not work!
i=0;
while i < Blocks.length
i = i + 1;
cnt = cnt + 1;
// get general block information
curBlockLib = jinvoke(Blocks(i), "getLibraryName");
curBlockType = jinvoke(Blocks(i), "getName");
curBlockMask = jinvoke(Blocks(i), "getMask");
curBlockName = jinvoke(Blocks(i), "getMaskName");
curXcosName = getXcosBlockName(curBlockLib, curBlockType);
// get scilab block information
execstr("scs_m.objs(" + string(cnt) + ") = "+ curXcosName + "('"define'");"); // load block into model
sz = scs_m.objs(cnt).graphics.sz * scale;
vertOffset = vertOffset - (sz(2)+scale);
exprs = scs_m.objs(cnt).graphics.exprs;
// set block label
exprs(4) = curBlockName; // fourth entry is the block label // TODO: consider subsystems/superblocks!
// set implementation
exprs(7) = jinvoke(Blocks(i), "getUsedImplName");
// set parameter values (sample time factor included)
curMaskParameterNames = jinvoke(curBlockMask, "getMaskParameterNames");
len = size(curMaskParameterNames);
for j=1:len(2)
curMaskParam = jinvoke(curBlockMask, "getMaskParameter", curMaskParameterNames(j));
curMaskParamVal = jinvoke(curMaskParam, "getValue");
if isnum(curMaskParamVal)
exprs(10+(j-1)*4) = curMaskParamVal; // 10th entry is adjustable field of first parameter // TODO: check for arrays!
else
exprs(11+(j-1)*4) = curMaskParamVal; // 11th entry is value field of first parameter // TODO: check for combo boxes!
end
end
// position block in model
scs_m.objs(cnt).graphics.sz = sz; // resize block to a suitable size
scs_m.objs(cnt).graphics.orig = [horiOffset, vertOffset]; // set position of block in model
scs_m.objs(cnt).graphics.exprs = exprs; // set block name
end
// process all outports
Outports = jinvoke(newModel, "getOutports");
vertOffset = 0;
horiOffset = 30*scale;
//for i = 1:Outports.length // NOTE: for some strange reason this does not work!
i=0;
while i < Outports.length
i = i + 1;
cnt = cnt + 1;
// get general block information
curBlockLib = jinvoke(Outports(i), "getLibraryName");
curBlockType = jinvoke(Outports(i), "getName");
curBlockMask = jinvoke(Outports(i), "getMask");
curBlockName = jinvoke(Outports(i), "getMaskName");
curXcosName = getXcosBlockName(curBlockLib, curBlockType);
// get scilab block information
execstr("scs_m.objs(" + string(cnt) + ") = "+ curXcosName + "('"define'");"); // load block into model
sz = scs_m.objs(cnt).graphics.sz * scale;
vertOffset = vertOffset - (sz(2)+scale);
exprs = scs_m.objs(cnt).graphics.exprs;
// set block label
exprs(4) = curBlockName; // fourth entry is the block label
// set parameter values (implementation and sample time factor )
curMaskParameterNames = jinvoke(curBlockMask, "getMaskParameterNames");
len = size(curMaskParameterNames);
if len(2) == 2
// first parameter is DataType
curMaskParam = jinvoke(curBlockMask, "getMaskParameter", curMaskParameterNames(1));
curMaskParamVal = jinvoke(curMaskParam, "getValue");
exprs(7) = curMaskParamVal; // 7th entry is implementation
// TODO: check if ok (visiualization seems odd, is code generation possible?)
// second parameter is ts_fact
curMaskParam = jinvoke(curBlockMask, "getMaskParameter", curMaskParameterNames(2));
curMaskParamVal = jinvoke(curMaskParam, "getValue");
exprs(10) = curMaskParamVal; // 10th entry is adjustable field of first parameter
else
disp('Warning: Parameter ' + curMaskParameterNames(j) + 'could not be entered for block ' + curBlockName + " because data structure of Outports has changed!")
end
// position block in model
scs_m.objs(cnt).graphics.sz = sz; // resize block to a suitable size
scs_m.objs(cnt).graphics.orig = [horiOffset, vertOffset]; // set position of block in model
scs_m.objs(cnt).graphics.exprs = exprs; // set block name
end
// open Xcos model
xcos(scs_m);
// // create Xcos instance
// sdh = jinvoke(ScilabDirectHandler, "acquire")
// diagram = jnewInstance(XcosDiagram);
// diag = jinvoke(sdh, "readDiagram", diagram, "scs_m");
//
// jinvoke(diag, "saveDiagram");
//
// // release instance
// jinvoke(sdh, "release");
//
// mprintf("Xcos model %s successfully created.\n",modelName);
catch
mprintf("Error creating model %s\n", modelName);
mprintf("ERROR: %s\n", lasterror());
end
endfunction
|
edbcf4e3dd3c2602738db54d71f25f6fcc180935 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1991/CH2/EX2.19/19.sce | b67b4d159fda91c7f324c4013788f92d2465f6c4 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 285 | sce | 19.sce | clc
clear
//input
m=5*10^24//mass of earth
g1=6.7*10^-11
//calculation
r=((6.7*10^-11*5*10^24*(3600*24)^2)/(4*%pi^2))^(1/3)//orbit radius
v=(2*%pi*r)/(3600*24)//linear velocity
//output
printf("the orbit radius is %3.3f",r)
printf("\n the linear velocity is %3.3f ms^-1",v)
|
164606cd705a61c50f31675e9918b9c6183308e6 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1752/CH6/EX6.7/exa6_7.sce | c7130ca232a31ccf8bfa5814ca2204daf7cfe67d | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 577 | sce | exa6_7.sce | //Exa 6.7
clc;
clear;
close;
//given data
L=3;// in m
delta=0;
hx='10*x^(-1/4)'
// (a) Average heat transfer coefficient
h=1/L*integrate(hx,'x',delta,L);
disp("(a) Average heat transfer coefficient is : "+string(h)+" W/m^2K")
// (b) Heat transfer rate
A=3*.3;// in m^2
Tp=170;// plate temp. in degree C
Tg=30;// gas temp. in degree C
del_T=Tp-Tg;
q=h*A*del_T;// in W
disp("(b) Heat transfer rate is : "+string(q)+" W")
// (c)
x=2;// in m
qx_by_A= 10*x^(-1/4)*(Tp-Tg);
disp("Local heat flux 2 m from the leading edge is : "+string(qx_by_A)+" W/m^2");
|
ae5d29bf413f84ba227c0b918e304d5ba5ab60c1 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1652/CH19/EX19.5/19_5.sce | 2a62fb5b7e2a8ebd3edcd1a06d7e9b9ff21a23a6 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 215 | sce | 19_5.sce | clc
//Initialization of variables
c=0.5 //M
c1=0.000025 //M
D2=0.280
D1=0.417
//calculations
c2=D2*c1/(D1)
dC=c1-c2
SCN=c- 6*c2 -4*dC
K=dC*SCN^2 /c2
//results
printf("Kc for dissociation = %.2f M^2",K)
|
e3b6774e25d1b6770e57b6175c9aecd5db950d02 | 449d555969bfd7befe906877abab098c6e63a0e8 | /2123/CH5/EX5.34/Exa_5_35.sce | dfe975ba70e0a0908a83e034074b9facce5b6b81 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 267 | sce | Exa_5_35.sce | //Example No. 5.35
clc;
clear;
close;
format('v',9);
//Given Data :
V1=200;//V
N1=940;//rpm
Ra=0.02;//ohm
Ia=100;//A
N2=500;//rpm
Eb1=V1-Ia*Ra;//V
//Eb1/Eb2=N1/N2
//Eb2=V2-Ia*Ra;//V
V2=Eb1*N2/N1+Ia*Ra;//V
cycle=V2/V1;
disp(cycle,"Duty cycle : ");
|
aefc884d1478d3f1f8da272a4508a282153971e5 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1646/CH5/EX5.39/Ch05Ex39.sce | 13c30142fe877ad902bca8c3cfd7c8a94127fc30 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 402 | sce | Ch05Ex39.sce | // Scilab Code Ex5.39: Page:315 (2011)
clc;clear;
theta = 11;....// Optical rotation of sugar solution, degrees
l = 20;....// Length of the tube, cm
S = 66;....// Specific rotation of sugar solution, degrees
c = theta*10/(l*S); // The concentration of sugar solution, g/cc
printf("\nThe strength of the solution = %6.4f g/cc", c);
// Result
// The strength of the solution = 0.0833 g/cc
|
f594d4b0ca9ca4a6689a5afe68955ff5d9836c28 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3648/CH6/EX6.6/Ex6_6.sce | 2470cbdc54db927b5c2cdf4ad7acf93acbea3e57 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 474 | sce | Ex6_6.sce | //Example 6_6
clc();
clear;
//To calculate the speed of the pellet before collision
h=0.30 //units in meters
g=9.8 //units in meters/sec^2
v=sqrt(2*g*h) //units in meters/sec
m1=2 //units in Kgs
m2=0.010 //units in kgs
v10=((m1+m2)*v)/m2 //units in meters/sec
printf("The speed of the pelet before collision is V10=%d meters/sec",v10)
//In textbook the answer is printed wrong as V10=486 meters/sec the correct answer is V10=487 meters/sec
|
0b428131d6308c0a9fa5e8531b6d774ebb320f2f | 449d555969bfd7befe906877abab098c6e63a0e8 | /278/CH23/EX23.20/ex_23_20.sce | 0e9e35a43e462d2ca6bcf8093bc7aaa2f0f9157a | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 797 | sce | ex_23_20.sce | //find
clc
//solution
//given
dx1=15//mm
n1=10
D1=40//mm
d1=5//mm
n2=8
D2=30//mm
d2=4//mm
W=400//N
G=84000//N/mm^2
//comprssion of each spring
P1=dx1*G*d1^4/(8*D1^3*n1)//N
R=W-P1//remaining load istaken by both spring
//P2=P1*dx2/dx1=10.27*dx2
//dx2=8*W2*D2^3/(G*d2^4)=0.08*W2
//W2=12.5*dx2
//P2+W2=W-P1
dx2=(W-P1)/(22.77)//mm
P2=10.27*dx2
printf("total deflection is,%f mm\n",dx1+dx2)
W1=P1+P2
printf("load on outr spring is,%f N\n",W1)
W2=12.5*dx2
printf("load shared by innr spring is,%f N\n",W2)
C1=D1/d1
C2=D2/d2
K1=(4*C1-1)/(4*C1-4)+(0.615/C1)
K2=(4*C2-1)/(4*C2-4)+(0.615/C2)
t1=K1*8*W1*D1/(%pi*d1^3)//N/mm^2
t2=K2*8*W2*D2/(%pi*d2^3)//N/mm^2
printf("stress induced in outr spring is,%f N/mm^2\n",t1)
printf("strss induce in iner spring is,%f N/mm^2\n",t2)
|
fe5e58bb5922adebbbe448b72b950e0cc3be654e | 449d555969bfd7befe906877abab098c6e63a0e8 | /3630/CH4/EX4.1/Ex4_1.sce | 54cab93a7b9063fc817606367795e1eebcfe3e05 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 172 | sce | Ex4_1.sce | clc;
Vin=12; //volt
RL=5100; //ohm
Rs=1000; //ohm
VL=(RL/(RL+Rs))*Vin ; //volt //voltage divide rule
disp('Vpk',VL,"VL=");//The answers vary due to round off error
|
d51f1ebf17d5992543126b665cd1aa8df6403f24 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3630/CH17/EX17.13/Ex17_13.sce | 7bc16f629c620801124937a86aa8c9ebdd663ebf | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 96 | sce | Ex17_13.sce | clc;
XL=3160;
Rw=25;
Q=XL/Rw;
disp(' ',Q,"Q=");//The answers vary due to round off error
|
5a854018e4e871b01bbc7805666454509e7f09ec | 936c3b35ba232dc3649cc1c6275365a215b2b00d | /estimation_par_discretisation.sce | e03d5d47560377767235490c65af86bb02b8c26b | [] | no_license | Pierre-Edouard/Projet-modal-sna | 7adb267a560af6286807a0a4330f83898a9fc11c | e73a5361f4b081c7c5c019fc48fcab91206db0c3 | refs/heads/master | 2016-09-05T18:30:16.523787 | 2013-05-17T14:15:08 | 2013-05-17T14:15:08 | null | 0 | 0 | null | null | null | null | ISO-8859-1 | Scilab | false | false | 3,496 | sce | estimation_par_discretisation.sce | //------------------------------------------------------------------------------
// Estimations utilisant la simulation par discrétisation en temps
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
// Evolution de l'espérance de l'encombrement avec le temps
//------------------------------------------------------------------------------
//
// lambda (reel) : Parametre de la loi d'arrivee des paquets
// mu (reel) : Parametre de la loi de la duree d'envoie des paquets
// t (vecteur ligne) : Temps pour lesquels estimer l'espérance de l'encombrement.
// h : (reel) Pas de la discrétisation en temps.
// nbsimulations : (entier) Le nombre de simulations utilisées pour calculer
// l'espérance.
//
// E (vecteur ligne) : Les espérances correspondant aux temps t.
//
function E=esperanceDiscr(lambda, mu, t, h, nbSimulations)
tmax = t($)
[T,X] = trajectoireDiscrete(lambda, mu, tmax, h, nbSimulations)
Y = []
for i=1:nbSimulations
[ind, occ, inf] = dsearch(t, T)
Y = [Y; X(i, ind)]
end
E = sum(Y, 'r')/nbSimulations
endfunction
//------------------------------------------------------------------------------
// Simulation du temps de saturation.
//------------------------------------------------------------------------------
//
// lambda (reel) : Parametre de la loi d'arrivee des paquets
// mu (reel) : Parametre de la loi de la duree d'envoie des paquets
// h : (reel) Pas de la discrétisation en temps.
// nbSimulation (entier) : Nombre de simulations a effectuer.
// N (entier) : Taille de la mémoire tampon.
//
// Tn (vecteur ligne) : Les temps de saturation données par les simulations
//
function Tn=tempsDeSaturationDiscr(lambda, mu, h, nbSimulations, N)
n = 1000
X = zeros(nbSimulations, 1)
Tn = zeros(nbSimulations, 1)
F = ones(nbSimulations, 1)
Ones = ones(nbSimulations, 1)
while or(F)
i = 1
IncrA = 1*(grand(nbSimulations, n, 'def')<=(lambda*h))
IncrD = (-1)*(grand(nbSimulations, n, 'def')<=(mu*h))
while or(F) & (i<=n)
X = X + F.*(IncrA(:,i).*(X==0) + (IncrD(:,i) + IncrA(:,i)).*(X>0))
Tn = Tn + F.*Ones
F = X<N
i = i+1
end
end
Tn = (Tn*h)'
endfunction
//------------------------------------------------------------------------------
// Estimation de la probabilité de saturation avant un temps donné.
//------------------------------------------------------------------------------
//
// lambda (reel) : Parametre de la loi d'arrivee des paquets
// mu (reel) : Parametre de la loi de la duree d'envoie des paquets
// h : (reel) Pas de la discrétisation en temps.
// nbSimulation (entier) : Nombre de simulations a effectuer.
// N (entier) : Taille de la mémoire tampon.
// S (reel) : Le temps S dans la définition de la probabilité (cf énoncé)
//
// pS (reel) : Estimation de la probabilité de saturation de la mémoire tampon
// avant le temps S.
//
function pS=probabiliteSatDiscr(lambda, mu, h, nbSimulations, N, S)
Tn = tempsDeSaturationDiscr(lambda, mu, h, nbSimulations, N)
pS = sum(Tn<S)/nbSimulations
endfunction
//n = 1000
//t = linspace(0, n, n+1)
//E = esperanceDiscr(0.5, 0.5, t, 1, 500)
//plot(t,E)
//
//Tn = tempsDeSaturationDiscr(0.55, 0.5, 0.1, 1000, 50)
//disp(sum(Tn)/1000)
disp(probabiliteSatDiscr(0.6, 0.5, 0.1, 1000, 50, 400)) |
c5b87790cf203644583d53455d68744901627226 | 449d555969bfd7befe906877abab098c6e63a0e8 | /2087/CH14/EX14.20/example14_20.sce | 35e840ad219044a17c96a2ee46ce5ef0e7eeb017 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 465 | sce | example14_20.sce |
//example14.20
//design a regime channel
clc;funcprot(0);
//given
Q=100; //discharge
f=1.1; //silt factor
s=1/2; //side slope
V=(Q*f^2/140)^(1/6);
A=Q/V;
P=4.75*Q^0.5;
D=(P-(P^2-6.944*A)^0.5)/3.472;
B=P-2.236*D;
R=5*V^2/(2*f);
S=f^(5/3)/(3340*Q^(1/6));
B=round(B*10)/10;
D=round(D*100)/100;
mprintf("Width of channel section=%f m.",B);
mprintf("\nDepth of channel section=%f m.",D);
mprintf("\nBed slope=%f.",S);
|
c0934d2c6082e70de0c3bccf20acc9b3331cdf16 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3407/CH10/EX10.7/Ex10_7.sce | 7942aaeef8bf2b41804f8da68cf810446089bf5d | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 834 | sce | Ex10_7.sce | clear;
clc;
funcprot(0);
//given data
//data from Exampla 10.5
Z = 3;//number of blades
D = 30;//rotor diameter in m
J = 5.0;//tip-speed ratio
l = 1.0;//blade chord in m
beta = 2;//pitch angle in deg
omega = 2.5;//in rad/s
rho = 1.2;//density in kg/m^3
cx1 = 7.5;//in m/s
sum_var1 = 6.9682;//from Table 10.3
sum_var2 = 47.509*10^-3;//from Table 10.4
//Calculations
X = sum_var1*0.5*rho*Z*l*0.5*D*cx1^2;
tau = sum_var2*0.5*rho*Z*l*(omega^2)*(0.5*D)^4;
P = tau*omega;
A2 = 0.25*%pi*D^2;
P0 = 0.5*rho*A2*cx1^3;
Cp = P/P0;
zeta = (27/16)*Cp;
//Results
printf('The total axial force = %d N.',X);
printf('\n The torque = %.3f *10^3 Nm.',tau/1000);
printf('\n The power developed = %.3f kW.',P/1000);
printf('\n The power coefficient = %.3f',Cp);
printf('\n The relative power coefficient = %.3f',zeta);
|
735b12ce9ab3b2e95e03a50af2ef0ef528021eef | 449d555969bfd7befe906877abab098c6e63a0e8 | /858/CH5/EX5.1/example_1.sce | 9015d394da864cd8a8cd25ba235caced955b7c0e | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 262 | sce | example_1.sce | clc
clear
printf("example 5.1 page number 171\n\n")
//to find the rate of heat loss
A=5*4 //in m2
T1=100; //in K
T2=30; //in K
delta_T=T1-T2;
x=0.25 //in m
k=0.70 //in W/mK
Q=k*A*(delta_T/x);
printf("rate of heat loss = %f W",Q)
|
da958efa1f07d323cc0798ebbc340a85dbc470dd | 449d555969bfd7befe906877abab098c6e63a0e8 | /431/CH5/EX5.6/EX5_6.sce | 54c46f7b4afcbbbc7d1fdd4ec40adb54bc9adefb | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 945 | sce | EX5_6.sce | //chapter 5
//example 5.6
//page 428
clear;
clc;
disp("example 5.6");
printf("\n");
slots=144; //number of slots
ph=3; //3-phase machine
P=16; //number of poles
Cp=10; //number of conducters per slot
Fp=0.03; //flux per pole
Ns=375; //synchronous speed
fre=(Ns*P)/120; //frequency
printf("frequency=%d\n\n",fre);
m=slots/(P*ph); //number of slots per pole per phase
printf("number of slots per pole per phase,m= %d\n",m);
SA_m=360/slots; //slot angle mechanical
SA_e=(P/2)*SA_m; //slot angle electrical
k_p=1 //no short pitching
printf("short pitch= %d\n",k_p);
k_d=sind((m*SA_e)/2)/(m*sind(SA_e/2));
printf("distribution factor= %f\n",k_d);
T=(slots*10)/(2*ph);
printf("number of turns per phase,T= %d\n",T);
E=4.44*Fp*fre*T*k_d*k_p;
printf("RMS value of induced emf per phase,E= %fV\n",E);
printf("induced emf across the linesis %fV \n",(sqrt(3)*E)); |
5d779ed70d0908c0acd1b5c359a1f635379fa781 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1382/CH5/EX5.22/EX_5_22.sce | ed68c43921bdc1873056d01306e7dc8b725ce12b | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 942 | sce | EX_5_22.sce | // Example 5.21:mid band gain and upper 3 db frequency
clc;
clear;
close;
Cpi=40;//in pico farad
Vt=26;//voltage in milli volts
Beta=150;//
Icq=1;//current in milli ampere
rpi= ((Beta*Vt)/Icq)*10^-3;//
gm=(Icq/Vt)*10^3;//transconductance in mili ampere per volt
rs=1;//in killo ohms
re=0.5;//in killo ohms
g=(rs*re)/(rs+re);//
m=rpi/(1+Beta);//
tpi= ((m*g)/(m+g))*Cpi*10^-7;//
fh1=(1/(2*%pi*tpi*10^4));//first 3-db upper cut off frequency in mega hertz
Rc=4.7;//collector resistance in killo ohms
Rl=10;//load resistance in killo ohms
Rld= (Rc*Rl)/(Rc+Rl);//
Cmu=3;//capacitance in pico farad
R1= 50;// in kilo ohms
R2= 5;// in kilo ohms
Rb= (R1*R2)/(R1+R2);
fh2=(1/(2*%pi*Cmu*10^-8*Rld*10^3))*10^-2;//second 3-db upper cut off frequency in mega hertz
x=(m*re)/(m+re);///
Avm=(gm*Rld*x)/(x+rs);//
disp(fh1,"3-db upper cut off frequency in mega hertz is")
disp(fh2,"second 3-db upper cut off frequency in mega hertz")
disp(Avm,"MIDBAND GAIN")
|
5683defd3465e5ee0334c452ae9a257a2d13e18b | 1bb72df9a084fe4f8c0ec39f778282eb52750801 | /test/TEC9.prev.tst | c9c8f09e3b905c5c19da9c3805a5a668948b6511 | [
"Apache-2.0",
"LicenseRef-scancode-unknown-license-reference"
] | permissive | gfis/ramath | 498adfc7a6d353d4775b33020fdf992628e3fbff | b09b48639ddd4709ffb1c729e33f6a4b9ef676b5 | refs/heads/master | 2023-08-17T00:10:37.092379 | 2023-08-04T07:48:00 | 2023-08-04T07:48:00 | 30,116,803 | 2 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 3,869 | tst | TEC9.prev.tst | Expanding for base=2, level=4, reasons+features=base,same,similiar invall,norm
Refined variables=u,v
[0+1u,0+1v]: unknown -> [1] [0,0] 20u+4u²-130v+8u*v-56v²-8v³-98
---------------- level 0
expanding queue[0]^-1,meter=[2,2]: 20u+4u²-130v+8u*v-56v²-8v³-98
[0+2u,1+2v]: unknown -> [1] [0,1] 14u+4u²-133v+8u*v-80v²-16v³-73
[1+2u,1+2v]: unknown -> [2] [1,1] 18u+4u²-129v+8u*v-80v²-16v³-65
endexp[0]
---------------- level 1
expanding queue[1]^0,meter=[2,2]: 14u+4u²-133v+8u*v-80v²-16v³-73
[0+4u,3+4v]: unknown -> [3] [0,1] 22u+8u²-341v+16u*v-256v²-64v³-151
[2+4u,3+4v]: unknown -> [4] [1,1] 30u+8u²-333v+16u*v-256v²-64v³-138
endexp[1]
expanding queue[2]^0,meter=[2,2]: 18u+4u²-129v+8u*v-80v²-16v³-65
[1+4u,3+4v]: unknown -> [5] [0,1] 26u+8u²-337v+16u*v-256v²-64v³-145
[3+4u,3+4v]: unknown -> [6] [1,1] 34u+8u²-329v+16u*v-256v²-64v³-130
endexp[2]
---------------- level 2
expanding queue[3]^1,meter=[2,2]: 22u+8u²-341v+16u*v-256v²-64v³-151
[0+8u,7+8v]: unknown -> [7] [0,1] 38u+16u²-1045v+32u*v-896v²-256v³-406
[4+8u,7+8v]: unknown -> [8] [1,1] 54u+16u²-1029v+32u*v-896v²-256v³-383
endexp[3]
expanding queue[4]^1,meter=[2,2]: 30u+8u²-333v+16u*v-256v²-64v³-138
[2+8u,3+8v]: unknown -> [9] [0,0] 30u+16u²-333v+32u*v-512v²-256v³-69
[6+8u,3+8v]: unknown -> [10] [1,0] 46u+16u²-317v+32u*v-512v²-256v³-50
endexp[4]
expanding queue[5]^2,meter=[2,2]: 26u+8u²-337v+16u*v-256v²-64v³-145
[1+8u,7+8v]: unknown -> [11] [0,1] 42u+16u²-1041v+32u*v-896v²-256v³-401
[5+8u,7+8v]: unknown -> [12] [1,1] 58u+16u²-1025v+32u*v-896v²-256v³-376
endexp[5]
expanding queue[6]^2,meter=[2,2]: 34u+8u²-329v+16u*v-256v²-64v³-130
[3+8u,3+8v]: unknown -> [13] [0,0] 34u+16u²-329v+32u*v-512v²-256v³-65
[7+8u,3+8v]: unknown -> [14] [1,0] 50u+16u²-313v+32u*v-512v²-256v³-44
endexp[6]
---------------- level 3
expanding queue[7]^3,meter=[2,2]: 38u+16u²-1045v+32u*v-896v²-256v³-406
[0+16u,7+16v]: unknown -> [15] [0,0] 38u+32u²-1045v+64u*v-1792v²-1024v³-203
[8+16u,7+16v]: unknown -> [16] [1,0] 70u+32u²-1013v+64u*v-1792v²-1024v³-176
endexp[7]
expanding queue[8]^3,meter=[2,2]: 54u+16u²-1029v+32u*v-896v²-256v³-383
[4+16u,15+16v]: unknown -> [17] [0,1] 86u+32u²-3589v+64u*v-3328v²-1024v³-1282
[12+16u,15+16v]: unknown -> [18] [1,1] 118u+32u²-3557v+64u*v-3328v²-1024v³-1231
endexp[8]
expanding queue[9]^4,meter=[2,2]: 30u+16u²-333v+32u*v-512v²-256v³-69
[2+16u,11+16v]: unknown -> [19] [0,1] 62u+32u²-2125v+64u*v-2560v²-1024v³-585
[10+16u,11+16v]: unknown -> [20] [1,1] 94u+32u²-2093v+64u*v-2560v²-1024v³-546
endexp[9]
expanding queue[10]^4,meter=[2,2]: 46u+16u²-317v+32u*v-512v²-256v³-50
[6+16u,3+16v]: unknown -> [21] [0,0] 46u+32u²-317v+64u*v-1024v²-1024v³-25
[14+16u,3+16v]: unknown -> [22] [1,0] 78u+32u²-285v+64u*v-1024v²-1024v³+6
endexp[10]
expanding queue[11]^5,meter=[2,2]: 42u+16u²-1041v+32u*v-896v²-256v³-401
[1+16u,15+16v]: unknown -> [23] [0,1] 74u+32u²-3601v+64u*v-3328v²-1024v³-1297
[9+16u,15+16v]: unknown -> [24] [1,1] 106u+32u²-3569v+64u*v-3328v²-1024v³-1252
endexp[11]
expanding queue[12]^5,meter=[2,2]: 58u+16u²-1025v+32u*v-896v²-256v³-376
[5+16u,7+16v]: unknown -> [25] [0,0] 58u+32u²-1025v+64u*v-1792v²-1024v³-188
[13+16u,7+16v]: unknown -> [26] [1,0] 90u+32u²-993v+64u*v-1792v²-1024v³-151
endexp[12]
expanding queue[13]^6,meter=[2,2]: 34u+16u²-329v+32u*v-512v²-256v³-65
[3+16u,11+16v]: unknown -> [27] [0,1] 66u+32u²-2121v+64u*v-2560v²-1024v³-581
[11+16u,11+16v]: unknown -> [28] [1,1] 98u+32u²-2089v+64u*v-2560v²-1024v³-540
endexp[13]
expanding queue[14]^6,meter=[2,2]: 50u+16u²-313v+32u*v-512v²-256v³-44
[7+16u,3+16v]: unknown -> [29] [0,0] 50u+32u²-313v+64u*v-1024v²-1024v³-22
[15+16u,3+16v]: unknown -> [30] [1,0] 82u+32u²-281v+64u*v-1024v²-1024v³+11
endexp[14]
---------------- level 4
Maximum level 4 [31] mod 2: 20u+4u²-130v+8u*v-56v²-8v³-98
|
87bc289aac11274b169dc4619e261b6017b0ad8f | ec4baa93e05d00692537e43a827243c1c13a0c09 | /assignment_0/Exercise0-Group8/solid_color.sce | e232a85ceb6f10625e316e7e5b6a2b15bfa7eebc | [] | no_license | Arbaba/IntroGraphics | ea9fb95681275daed383fedc4b82dfd3eabe4224 | 79835a8be5a289c3b04d1213c6a227e6409b66a8 | refs/heads/master | 2022-01-09T06:46:03.086861 | 2019-05-02T11:01:39 | 2019-05-02T11:01:39 | 171,872,971 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 63 | sce | solid_color.sce | camera 0 0 0 0 1 0 0 1 0 45 512 512
background 0.4 0.2 0.7
|
167b64185876c1cfe5c4478e77d355028d54eed3 | 449d555969bfd7befe906877abab098c6e63a0e8 | /2615/CH16/EX85.9/85.sce | 60f86d7e55b02ed15ebdbd66403111e2aafd570c | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 216 | sce | 85.sce | clc
//initialisation of variables
z=60//mm
l=15//mm
h=5//mm
h1=1.2*h//mm
h2=0.5//mm
//CALCULATIONS
m=l/%pi//mm
s=h2*%pi//mm
D=h*(60+2)//mm
//RESULTS
printf('the tooth pitch value of the model=% f mm',D)
|
969b3419afd40cdfadabfb70f6b732c6d08952a1 | 93e9a36e786acf5555736d2b9dede7b40bbca71e | /Inverted Pendulum.sce | fff64dae79e29562c77569a272121b51d5a259bf | [] | no_license | TechnikLachmann43278/Inverted-Pendulum | d4b8eec6a18b38d9bccf16ad51eaf963e23bf823 | 82b389f47b13772f8da7c7658bc4560a24820af1 | refs/heads/master | 2020-08-11T06:16:56.199428 | 2019-10-15T07:33:30 | 2019-10-15T07:33:30 | 214,508,550 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 2,151 | sce | Inverted Pendulum.sce | clear;
// Rad
m1= 0.07;
r = 0.04;
J1 = 1/2*m1*r*r;
// Aufbau
m2 = 1.5;
l = 0.03;
b = 0.07;
h = 0.1;
J2 = 1/12*m2*(b*b+h*h);
g=9.81;
P = 80 ;
Kd = 5;
Kom = 3;
Ki = 1;
phisoll=0.0;
function f=integrieren(t, y)
phi1 = y(1);
om1 = y(2);
phi2 = y(3);
om2 = y(4);
eInteg=y(5);
e = phisoll + phi2;
M = P * phi2 + Kd*om2 + Kom * om1 +Ki*eInteg;
if(M>0.8)
M=0.8;
end
if(M<-0.8)
M=-0.8;
end
A = l*sin(phi2);
B = l*cos(phi2);
MatrixA = [ (-m1*r*r)/J1 - 1, 0, 1, 0;
0, -1, 0, 1;
(-m2*r*r)/J1, 0, (-m2*B*B)/J2 - 1, (-m2*A*B)/J2;
0, 0, (-m2*A*B)/J2, (-m2*A*A)/J2 - 1 ];
Matrixb = [m1*r*M/J1;
-m1*g;
(m2*r*M)/J1 - (m2*B*M)/J2 - (m2*A*om2*om2);
(-m2*A*M)/J2 + m2*B*om2*om2 - m2*g ];
FZ = inv(MatrixA)*Matrixb;
Fx1 = FZ(1);
Fx2 = FZ(3);
Fy2 = FZ(4);
f(1) = om1;
f(2) = (r*Fx1 + M)/J1;
f(3) = om2;
f(4) = (A*Fy2 + B*Fx2 - M)/J2;
f(5) = e;
endfunction
t0 = 0;
y0 = [0,0,0.2,0,0]';
t = linspace(0,1,100);
y = ode(y0,t0,t,integrieren);
plot(t,y(1,:)',t,y(3,:)');
legend("phi1","phi2",pos = 2) ;
//Optimierung
function err=berechneFehler(x)
P=x(1);
Kd=x(2);
Kom=x(3);
Ki=x(4);
t = linspace(0,1,100);
y0 = [0,0,0.2,0,0]';
t0 = 0;
y = ode(y0,t0,t,integrieren);
err = sum(y(2,:).*y(2,:));
endfunction
P = 80 ;
Kd = 5;
Kom = 3;
Ki = 1;
x0=[P;Kd;Kom;Ki]; // Startpunkt eventuell zufaellig waehlen
ug = [0;0;0;0]; // untere Schranke fuer x
og = [1000;100;100;100]; // obere Schranke fuer x
[fopt, xopt] = optim(list(NDcost,berechneFehler),'b',ug,og,x0);
P=xopt(1);
Kd=xopt(2);
Kom=xopt(3);
Ki=xopt(4);
t0 = 0;
y0 = [0,0,0.2,0,0]';
t = linspace(0,1,100);
y = ode(y0,t0,t,integrieren);
xset("window",2);
clf;
plot(t,y(1,:)',t,y(3,:)');
legend("phi1","phi2",pos = 2) ;
|
444ad05a5349f580ebb455d065bbc0855259bb95 | 1bb72df9a084fe4f8c0ec39f778282eb52750801 | /test/L05.prev.tst | acc80aeccb101496c1ceea6094995f1552d1186d | [
"Apache-2.0",
"LicenseRef-scancode-unknown-license-reference"
] | permissive | gfis/ramath | 498adfc7a6d353d4775b33020fdf992628e3fbff | b09b48639ddd4709ffb1c729e33f6a4b9ef676b5 | refs/heads/master | 2023-08-17T00:10:37.092379 | 2023-08-04T07:48:00 | 2023-08-04T07:48:00 | 30,116,803 | 2 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 712 | tst | L05.prev.tst | . twice: 10 3 18 19 => 16 23 41 44, determinant -35?
3 2 1 -2
-1 -1 2 0
-2 2 2 1
2 2 1 0
next==
det=-35
minDet=[5,-5,0,20], det2=-35
. twice: 14 17 7 20 => 37 27 30 46, determinant -66?
3 2 3 -3
-2 2 3 0
2 -3 -1 3
3 -1 3 0
next==
det=-66
minDet=[-27,-45,12,-23], det2=-66
. twice: 19 18 21 28 => 97 86 95 134, determinant -1!
3 3 2 -2
1 1 1 1
0 1 1 2
2 3 2 0
next==
det=-1
minDet=[1,2,-4,1], det2=-1
. unknown: 1 2 3 => 1 2 3, determinant -9999
1 2 3
4 5 6
7 8 9
next!=
det=0
minDet=[-3,6,-3], det2=0
. unknown: 1 2 => 1 2 , determinant -9999
1 2
4 5
next!=
det=-3
minDet=[5,-4], det2=-3
. unknown: 7 => 7 , determinant -9999
7
next!=
det=7
minDet=[1], det2=7
|
34d386e1a3597a8abe4964dc09bab8cefed68eb3 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1076/CH8/EX8.2/8_2.sce | d181978cabe790e92d330f7b366ed230b4482c49 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 213 | sce | 8_2.sce | clear;
clc;
V=33;
V=V/sqrt(3);
T=35;
x=1;
r=V/(T * x);
R= %e * r;
t=R-r;
mprintf("\nMost economical conductor radius = %.3f cm", fix(R*1000)/1000);
mprintf("\nInsulation Thickness = %.3f cm", t);
|
707debad24b5193fcbfc8eca699bb813ef13c391 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1271/CH12/EX12.24/example12_24.sce | d396e9c0a17ec5fc3ea378262b330be093a84e9f | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 346 | sce | example12_24.sce | clc
// Given that
E = 200 // energy released per fission in Mev
m = 1 // mass of U(235) in kg
// Sample Problem 24 on page no. 12.40
printf("\n # PROBLEM 24 # \n")
printf("Standard formula used \n")
printf(" E_total = E*N_0/n \n")
E_ = E * 1.6e-13
k = E_ * 6.023e26 * m / 235
printf("\n Energy released by fission of 1 kg of U(235)is %e J.",k)
|
082be206d8031eda878cb56c6274afb65d001551 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1226/CH20/EX20.12/EX20_12.sce | 92057e6a79d12c01d1edb643d8f65c767f2021c0 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 1,431 | sce | EX20_12.sce | clc;funcprot(0);//EXAMPLE 20.12
// Initialisation of Variables
n=2;........//No of cylinders
ma=16;........//Mass of air supplied per min in kg
p1=1;........//Suction pressure in bar
t1=288;.......//Suction temperature in K
k=0.04;.......//Clearance ratio
ni=1.3;........//Compression index
R=0.287;........//Gas constant in kJ/kgK
N=2000;........//Engine rpm
p3=7;...........//Delivery pressure in bar
rld=1.2;...........//Ratio of stroke to bore for compressor cylinder and engine cylinder
etamech=0.82;.........//Mechanical efficiency of engine
pmb=5.5;..........//Mean effective pressure in bar in engine
ne=4;.............//No of engine cylinders
//Calculations
Vs=(((ma/n)*R*1000*t1)/(p1*10^5*N))/((1+k)-(k*((p3/p1)^(1/ni))));
Dc=(Vs/((%pi/4)*rld))^(1/3);.........//Diameter of compressor cylinder in m
Lc=rld*Dc;.............//Stroke of the compressor cylinder in m
disp(Dc*1000,"Diameter of compressor cylinder in mm:")
disp(Lc*1000,"Stroke of compressor cylinder in mm:")
IP=(ni/(ni-1))*(ma/60)*R*t1*(((p3/p1)^((ni-1)/ni))-1);......//Indicated power of the compressor in kW
BP=IP/etamech;...............//Brake power of the engine in kW
De=((BP*60*1000)/(ne*pmb*10^5*rld*(%pi/4)*N))^(1/3);......//Diameter of the engine cylinder in m
Le=rld*De;...........//Stroke of the engine cylinder in m
disp(De*1000,"Diameter of engine cylinder in mm:")
disp(Le*1000,"Stroke of engine cylinder in mm:")
|
128fca2bf5740c5b45ce55cc633ddb235eff6b13 | a62e0da056102916ac0fe63d8475e3c4114f86b1 | /set5/s_Digital_Signal_Processing_R._Babu_52.zip/Digital_Signal_Processing_R._Babu_52/CH3/EX3.30/Example3_30.sce | 95758b3a3bae3bb94e94ee7e76d8947592519c33 | [] | no_license | hohiroki/Scilab_TBC | cb11e171e47a6cf15dad6594726c14443b23d512 | 98e421ab71b2e8be0c70d67cca3ecb53eeef1df6 | refs/heads/master | 2021-01-18T02:07:29.200029 | 2016-04-29T07:01:39 | 2016-04-29T07:01:39 | null | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 288 | sce | Example3_30.sce | errcatch(-1,"stop");mode(2);//Example 3.30
//Program to Calculate N from given data
//fm=5000Hz
//df=50Hz
//t=0.5sec
;
;
;
fm=5000 //Hz
df=50 //Hz
t=0.5 //sec
N1=2*fm/df;
N=2;
while N<=N1, N=N*2,end
//Displaying the value of N in command window
disp(N,"N=");
exit();
|
3763ad0604029c05d58c59fcb42c1cc40fa9d8e2 | ac1f8441b0319b4a391cd5a959bd3bb7988edfa7 | /data/news2015/news2015/SplitsNEWS15/EnHe/enhe.0.tst | 361fb6eff4e45687578b10431b73c3d01bc540ce | [
"MIT"
] | permissive | SaeedNajafi/transliterator | 4d58b8604fa31f52ee2dce7845e002a18214fd5e | 523a087b777a5d6eec041165dabb43848f6222e6 | refs/heads/master | 2021-09-18T17:02:59.083727 | 2018-07-17T06:01:21 | 2018-07-17T06:01:21 | 129,796,130 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 28,858 | tst | enhe.0.tst | a c c a d e m i a א ק א ד י מ י ה
a c c r a א ק ר א
a d e l s t e i n א ד ל ס ט י ן
a d i v a s i א ד י ב א ס י
a j a x א י ג ' א ק ס
a k i h i t o א ק י ה י ט ו
a k l ע ק ל
a l a n א ל ן
a l a n s a r i א ל א נ ס א ר י
a l b a y y a t i א ל ב א י א ט י
a l b i א ל ב י
a l e k s a n d e r א ל ק ס נ ד ר
a l e x a n d r i n a א ל ק ס א נ ד ר י נ א
a l f r e d o א ל פ ר י ד ו
a l j a b a l א ל ג ' ב ל
a l k a n e א ל ק י י ן
a l l a m ע ל א ם
a l v i n א ל ו ו י ן
a m a r ע מ א ר
a m o s ע מ ו ס
a n n i e א נ י
a r i s t i d e s א ר י ס ט י ד י ס
a r u t z ע ר ו ץ
a s h c r o f t א ש ק ר ו פ ט
a s h e r א ש ר
a s h k e n a z i א ש כ נ ז י
a s p a r a g i n e א ס פ א ר א ג י ן
a s s a f ע ס א ף
a s u n c i o n א ס ו נ ס י ו ן
a t a h u a l p a א ט א ו א ל פ א
a t h a n a s i u s א ת נ א ס י ו ס
a v o g a d r o א ב ו ג א ד ר ו
a y r t o n א י ר ט ו ן
a z i z o u ע ז י ז ו
b a ב א
b a a r t m a n ב א ר ט מ א ן
b a d i r ב א ד ר
b a d r a n ב ד ר א ן
b a g a y o k o ב א ג א י ו ק ו
b a g g i o ב א ג ' י ו
b a g h d a d i ב ג ד א ד י
b a h j a ב ה ג ' א
b a i k a l ב א י ק א ל
b a k k a t i ב ק א ט י
b a k r i ב ק ר י
b a l d e ב א ל ד י
b a l h o u s ב ל ח ו ס
b a l l a c k ב א ל א ק
b a l t a ב א ל ט א
b a l t i m o r e ב א ל ט י מ ו ר
b a n g a l o r e ב א נ ג א ל ו ר
b a r b a d o s ב א ר ב א ד ו ס
b a r b o s a ב א ר ב ו ס א
b a r r a n c o s ב א ר א נ ק ו ס
b a r r a n q u i l l a ב א ר א נ ק ו י ל א
b a r t o l o m e u ב א ר ת ו ל ו מ י ו
b a t l l e s ב א ט ל ס
b a t t a ב א ט א
b a t t i r ב ט י ר
b e e r n a e r t ב י ר נ א ר ט
b e g a g ב ג א ג
b e l i z e ב ל י ז
b e l l i n i ב י ל י נ י
b e l l i o n ב ל י ו ן
b e l o z o g l u ב י ל ו ז ו ג ל ו
b e n e l u x ב נ י ל ו ק ס
b e n n o ב י נ ו
b e n n y ב נ י
b e n t o ב י נ ט ו
b e r k m a n ב י ר ק מ א ן
b e r n a r d i n o ב ר נ א ר ד י נ ו
b e r t o n i ב י ר ט ו נ י
b e s t ב ס ט
b e y n i e ב י י נ י
b i d a t s u ב י ד א ט ס ו
b i l h a r z ב י ל ה א ר ץ
b l u m ב ל ו ם
b o e i n g ב ו א י נ ג
b o l o n i ב ו ל ו נ י
b o m i s ב ו מ י ס
b o n n i s s e l ב ו נ י ס ל
b o n o ב ו נ ו
b o r d i n ב ו ר ד י ן
b o r e a n a z ב ו ר י נ א ז
b o r i s ב ו ר י ס
b o r k ב ו ר ק
b o r r e l l i ב ו ר י ל י
b o r u ב ו ר ו
b o s a c k i ב ו ס א צ ק י
b o u a b ב ו ע ב
b o u b o u l i n a ב ו ב ו ל י נ א
b r a g a ב ר א ג א
b r a m a n t e ב ר א מ א נ ט י
b r a n d t ב ר א נ ט
b r a n s o n ב ר א נ ס ו ן
b r e n t ב ר י נ ט
b r i s t o l ב ר י ס ט ו ל
b r o d e r i c k ב ר ו ד ר י ק
b u b l e ב ו ב ל ה
b u c k l e y ב א ק ל י
b u e l l ב י ו א ל
b u e n o s ב ו י נ ו ס
b u g z i l l a ב ג ז י ל א
b u l j a n ב ו ל י א ן
b u r r e l l ב ו ר י ל
b u r t o n ב ו ר ט ן
b u r u n d i ב ו ר ו נ ד י
b u s c e m i ב ו ש י מ י
c a b r i l l o ק א ב ר י ל ו
c a b r i n i ק א ב ר י נ י
c a h o r s ק א ה ו ר
c a l a b r i a ק א ל א ב ר י א
c a l d e r ק א ל ד ר
c a m e l ק א מ ל
c a m e l o t ק א מ ל ו ט
c a m e r o o n ק א מ י ר ו ן
c a n n a ק א נ א
c a p p a d o c i a ק א פ א ד ו ק י א
c a r b o n i c ק ר ב ו נ י ק
c a r d e n o s a ק א ר ד י נ ו ס א
c a r d i n a l ק א ר ד י נ ל
c a r d o z o ק א ר ד ו ז ו
c a r l t o n ק א ר ל ט ו ן
c a r r ק א ר
c a r r e r o ק א ר י ר ו
c a s a n o v a ק א ס א נ ו ב א
c a v a l i e r i ק א ב א ל י י ר י
c a y e t a n o ק א י ט א נ ו
c e n a ס י נ א
c e n t ס נ ט
c e n t a u r i ס נ ט ו ר י
c h a m a n g a צ ' א מ א נ ג א
c h a m b e r l a i n צ ' י י מ ב ר ל י ן
c h a n o v צ ' א נ ו ב
c h a n s a צ ' א נ ס א
c h e i k h ש י ך
c h i l e m b e צ ' י ל מ ב י
c h r i s t a ק ר י ס ט א
c i p o l l a צ ' י פ ו ל א
c i p r i a n ק י פ ר י א ן
c l e m e n c e ק ל י מ י נ ס
c l y d e ק ל י י ד
c o a s t ק ו ס ט
c o b a i n ק ו ב י י ן
c o b e n o ק ו ב י נ ו
c o c i s ק ו ק י ס
c o h a d e ק ו ה י י ד
c o h n ק ו ן
c o l o m b i a ק ו ל ו מ ב י א
c o l u m b u s ק ו ל ו מ ב ו ס
c o n s t a b l e ק ו נ ס ט א ב ל
c o p e n h a g e n ק ו פ נ ה א ג ן
c o r i a ק ו ר י א
c o r l e o n e ק ו ר ל י ו נ י
c o r s e t t i ק ו ר ס י ט י
c o u l i b a l y ק ו ל י ב א ל י
c r a y f o r d ק ר י י פ ו ר ד
c r a y s t o n ק ר י י ס ט ו ן
c r e m e r ק ר י מ ר
c r o n b a c h ק ר ו נ ב א ך
c r o u c h ק ר א ו ט ש
c r v e n k o v s k i ק ר ב י נ ק ו ב ס ק י
c u b ק א ב
c u r r o ק ו ר ו
c u r t i n ק ו ר ט י ן
c u r t i s s ק ו ר ט י ס
c u s a c k ק ו ז א ק
c u t t y ק א ט י
c y r i l l i c ס י ר י ל י ק
c z e s l a w צ ' י ס ל א ב
d a g h e r ד א ג ר
d a h l a n ד ח ל א ן
d a i h a t s u ד א י ה א ט ס ו
d a k o t a ד א ק ו ט א
d a m a n a k i s ד א מ א נ א ק י ס
d a n ד ן
d a n u b e ד א נ ו ב
d a s a y e v ד א ס א י י ב
d a u g h t r y ד ו ט ר י
d a v i d e ד ב י ד
d a v i e s ד י י ב י ז
d e g a s ד י ג א
d e i r ד י ר
d e k e l ד ק ל
d e l p h i ד י ל פ י
d e m i d o v ד מ י ד ו ב
d e n h o l m ד נ ה ו ל ם
d e n m a r k ד נ מ א ר ק
d e r i p a s k a ד י ר י פ א ס ק א
d e v a l l ד י ב א ל
d h i a b ד י א ב
d i a b l o ד י א ב ל ו
d i a m a n t i n o ד י א מ א נ ט י נ ו
d i e t e r ד י ט ר
d i m o n a ד י מ ו נ ה
d i n i ד י נ י
d i n u ד י נ ו
d i o g o ד י ו ג ו
d i s n e y ד י ז נ י
d i y a r b a k r ד י א ר ב ק ר
d j e l l o u l ג ' ל ו ל
d o c h e r t y ד ו ק י ר ט י
d o h e r t y ד ו י ר ט י
d o r i ד ו ר י
d o r o t h y ד ו ר ו ת י
d o r s i n ד ו ר ס ן
d o u r o ד ו ר ו
d r a g o n a i r ד ר א ג ו נ י י ר
d r a m a n e ד ר א מ א ן
d u b e r r y ד ו ב ר י
d u b l i n ד ב ל י ן
d u d a m e l ד ו ד א מ י ל
d u f f ד א ף
d u h a m e l ד ו ה א מ ל
e d i e א ד י
e l b a r a d e i א ל ב ר א ד ע י
e l d a d א ל ד ד
e l i s t a א ל י ס ט א
e l r i c h א ל ר י ט ש
e l s a m n i א ל ס מ נ י
e l s h a f e i א ל ש א פ ע י
e m a d ע מ א ד
e m i l y א מ י ל י
e m m a א י מ א
e n n i o א נ י ו
e s p i r i t o א ס פ י ר י ט ו
e s s a m ע ס א ם
f a l k e n m a y e r פ א ל ק י נ מ א י ר
f a l l a j פ ל א ג '
f a r a h פ א ר ח
f a r r o k h z a d פ ר ו כ ז א ד
f e h r פ י ה ר
f e n d i פ י נ ד י
f e r l i t o פ ר ל י ט ו
f i e n n e s פ י א נ ס
f i l m פ י ל ם
f i r m a n פ ר מ א ן
f i s k פ י ס ק
f i s t o n פ י ס ט ו ן
f l o h e פ ל ו ה
f o g g i a פ ו ג ' י א
f o r s s k a l פ ו ר ס ק א ל
f o r t פ ו ר ט
f o u i n e פ ו י ן
f r a n c i s c o פ ר א נ ס י ס ק ו
f r a n j o פ ר א נ י ו
f r a n k y פ ר א נ ק י
f r e i e r פ ר י י ר
f r i d a פ ר י ד ה
f r i e d m a n n פ ר י ד מ א ן
f u k u d a פ ו ק ו ד א
f u k u i פ ו ק ו י
f u k u n i s h i פ ו ק ו נ י ש י
f u l פ ו ל
f u l t o n פ ו ל ט ו ן
f u s i פ ו ז י
g a l a l ג ל א ל
g a n d h i ג א נ ד י
g a n g e s ג א נ ג ' ז
g a n i s ג א נ י ס
g a r g o ג א ר ג ו
g a r i b a l d i ג א ר י ב א ל ד י
g a s k e l l ג א ס ק ל
g a s s a m a ג א ס א מ א
g a t t u s o ג א ט ו ס ו
g a u d i ג א ו ד י
g e n g h i n i ג י נ ג י נ י
g e o r g y ג ' ו ר ג ' י
g e r a r d ג ' ר א ר ד
g e r c a l i u ג י ר ק א ל י ו
g e r o n i m o ג ' ר א נ י מ ו
g h i o n e a ג י ו נ י א
g i a c o m o ג ' א ק ו מ ו
g i l b o a ג ל ב ו ע
g i n s b u r g ג י נ ס ב ו ר ג
g n a k o ג נ א ק ו
g o a ג ו א
g o r a n ג ו ר א ן
g o r i n g ג ו ר י נ ג
g r a n i t e ג ר א נ י ט
g r e a v e s ג ר י ב ז
g r e n a d a ג ר י נ א ד א
g r e y ג ר י י
g r i s ג ר י ס
g r n e m e y e r ג ר נ מ י י ר
g r z e g o r z ג ר ז י ג ו ר ז
g u a r i n o ג ו א ר י נ ו
g u c c i o n e ג ו צ ' י ו ן
g u i s c a r d ג י ס ק א ר ד
h a a s e ה א ס י
h a b a s h ח ב ש
h a d d o c k ה א ד ו ק
h a i ה א י
h a i d e r ח י ד ר
h a i t h a m ה א י ת ם
h a l f o r d ה א ל פ ו ר ד
h a m e e d ח מ י ד
h a m e r ה א מ ר
h a m m e t t ה א מ י ט
h a m p d e n ה א מ פ ד ן
h a n b a l ח נ ב ל
h a n i y e h ה נ י ה
h a n k e ה א נ ק י
h a n n i ה א נ י
h a n t u c h o v a ה א נ ט ש ו ב א
h a r b ח א ר ב
h a r d a w a y ה א ר ד א ו י י
h a r l o w ה א ר ל ו
h a r r e l s o n ה א ר ל ס ו ן
h a r t m a n ה א ר ט מ א ן
h a s e n c l e v e r ה א ס נ ק ל י ב ר
h a s h e m i a n ה א ש מ י א ן
h a u s m a n n ה א ו ס מ א ן
h a w t h o r n e ה א ו ת ו ר ן
h e b e r t ה י ב י ר ט
h e i d i ה א י ד י
h e i k o ה י י ק ו
h e i n e ה א י נ ה
h e i s e n b e r g ה י י ז נ ב י ר ג
h e m d a n ח מ ד א ן
h e n r i ה נ ר י
h e r a k l i o n ה י ר א ק ל י ו ן
h e r b i n ה ר ב ן
h e r z o g ה ר צ ו ג
h i a m ה י א ם
h i d e a k i ה י ד י א ק י
h i k a r u ה י ק א ר ו
h i l l a r y ה י ל א ר י
h i r o k i ה י ר ו ק י
h i r s c h ה י ר ש
h i r s i ה י ר ס י
h l e b ה ל י ב
h o c h u ה ו צ ' ו
h o l d e r l i n ה ו ל ד ר ל י ן
h o l i d a y ה ו ל י ד א י
h o l m e s ה ו ל מ ז
h o l z e n b e i n ה ו ל ז נ ב א י ן
h o n g ה ו נ ג
h o p k i n s ה ו פ ק י נ ס
h o r o w i t z ה ו ר ו ב י ץ
h o s h i ה ו ש י
h o s i c ה ו ס י ט ש
h o s k i n s ה ו ס ק י נ ס
h o u g h t o n ה ו ט ו ן
h u b b a r d ה ו ב א ר ד
h u l a g u ה ו ל א ג ו
h u s a i n ח ו ס י י ן
h u s a y n ח ו ס י י ן
h u s t o n ה י ו ס ט ן
h u t h ה ו ת
h u y g e n s ה ו ג י נ ס
h y o r i ה י ו ר י
h y u n d a i ה י ו נ ד א י
i b e r i a א י ב י ר י א
i d r i s א י ד ר י ס
i m s a a d א מ ס א ע ד
i n d i a n א י נ ד י א ן
i n d i a n a א י נ ד י א נ א
i r a k l e i o א י ר א ק ל י ו
i r o q u o i s א י ר ו ק ו י ס
i s a m ע י ס א ם
i s m e t ע י ס מ ט
i s t a n b u l א י ס ט נ ב ו ל
i v o א י ב ו
j a b o t i n s k y ג ' ב ו ט נ ס ק י
j a i r z i n h o ג ' א ר ז י נ י ו
j a l o o ג ' א ל ו
j a m e l ג ' א מ ל
j a m i e ג ' י י מ י
j a n i n e ג ' א נ י ן
j a r o s l a v י א ר ו ס ל א ב
j a s m i l a י א ס מ י ל א
j a w e d ג ' א ו ו ד
j e r m a i n e ג ' ר מ י י ן
j e r r y ג ' ר י
j e s s e ג ' ס י
j o e l ג ' ו ל
j o h a n n a י ו ה נ א
j o h a r ג ' ו ה ר
j u n a y d ג ' ו נ י י ד
j u n i n h o ג ' ו נ י נ ה ו
j u s t i n ג ' א ס ט ן
j u u s o י ו ס ו
k a d l e c ק א ד ל י ץ
k a f i ק א פ י
k a h a l a n i ק ה ל א נ י
k a h a n a כ ה נ א
k a i a ק א י א
k a j a v a ק א י א ו ו א
k a j i ק א ג ' י
k a j i u r a ק א ג ' י ו ר א
k a k u ק א ק ו
k a l a n g a ק א ל א נ ג א
k a l i l i l o ח ל י ל י ל ו
k a l o u ק א ל ו
k a n t h e r ק א נ ת ר
k a p i t s a ק א פ י ט ס א
k a p l a n ק פ ל א ן
k a p l i n s k y ק א פ ל י נ ס ק י
k a p s i s ק א פ ס י ס
k a r a g o u n i s ק א ר א ג ו נ י ס
k a r e m b e u ק א ר י מ ב ו
k a r i n ק א ר י ן
k a r l o f f ק א ר ל ו ף
k a r l o v y ק א ר ל ו ב י
k a r p e n k o ק א ר פ י נ ק ו
k a s d i ק א ס ד י
k a s e y ק י י ס י
k a t h e r i n e ק א ת ר י ן
k a t h l e e n ק א ת ל י ן
k a t s i n a ק א ט ס י נ א
k a t s u r a ק א צ ו ר א
k e e g a n ק י ג א ן
k e i t a ק י י ט א
k e l l y ק י ל י
k e n n e d y ק י נ י ד י
k e r i ק י ר י
k h o u r y ח ו ר י
k h u r t s i l a v a ח ו ר ט ס י ל א ב א
k i e r a n ק י ר א ן
k i l a ק י ל א
k i m ק י ם
k i n g ק י נ ג
k l a n ק ל א ן
k l u g ק ל ו ג
k o e c h n e r ק ו ש נ י ר
k o f i ק ו פ י
k o h n ק ו ן
k o k i c h i ק ו ק י צ ' י
k o m o d o ק ו מ ו ד ו
k o n e ק ו נ י
k o n s t a n t i n o u ק ו נ ס ט א נ ט י נ ו
k o o l h a a s ק ו ל ה א ס
k o r k m a z ק ו ר ק מ א ז
k o r u t u r k ק ו ר ו ט ו ר ק
k o t a r b a ק ו ט א ר ב א
k o t l e r ק ו ט ל ר
k o t o k u ק ו ט ו ק ו
k r a m n i k ק ר א מ נ י ק
k r e m e r s ק ר י מ ר ז
k r e m n i t z ק ר מ נ י ץ
k r i m ק ר י ם
k r o l d r u p ק ר ו ל ד ר ו פ
k r u g e r ק ר ו ג ר
k r z y n o w e k ק ר ז י נ ו ו י ק
k u n t a r ק ו נ ט א ר
k u r d i s t a n ק ו ר ד י ס ט א ן
k y d ק י ד
l a c a r n e ל א ק א ר ן
l a d a ל א ד א
l a h a d ל ח ד
l a h o u d ל ח ו ד
l a j o s ל א י ו ס
l a m b o u r d e ל א מ ב ו ר ד
l a m i a ל א מ י א
l a n c e l o t ל א נ ס ל ו ט
l a n d r y ל א נ ד ר י
l a n d s t e i n e r ל א נ ד ש ט א י נ ר
l a n s i n g ל א נ ס י נ ג
l a r o u i ל ע ר ו י
l a r s ל א ר ס
l a s t ל א ס ט
l a t h a n ל א ת א ן
l a t i n a ל א ט י נ א
l a u r e n ל ו ר ן
l a v r a ל א ב ר א
l a z a r o n i ל א ז א ר ו נ י
l e o n e ל י ו ן
l e o n e l ל י ו נ ל
l e p i l l e r ל י פ י ל י ר
l e s l i e ל י ס ל י
l i a m ל י א ם
l i d o c a i n e ל י ד ו ק א י ן
l i e d h o l m ל י ד ה ו ל ם
l i l i a n ל י ל י א ן
l i m a n ל י מ א ן
l i n c o l n ל י נ ק ו ל ן
l i n d e l o f ל י נ ד ל ו ף
l i n u s ל א י נ ו ס
l i n u x ל י נ ו ק ס
l i o t t a ל א י ו ט א
l i t a ל י ט א
l i t t l e ל י ט ל
l i v i o ל י ו ו י ו
l o c h h e a d ל ו ק ה ד
l o c k l e a r ל ו ק ל י ר
l o t h a i r ל ו ת י י ר
l o u s ל ו ס
l u c a ל ו ק א
l u c i u s ל ו ס י ו ס
l u d o v i c ל ו ד ו ב י ק
l u l e ל ו ל י
l u m u m b a ל ו מ ו מ ב א
l u r z ל ו ר ז
l u s s e n h o f f ל ו ס י נ ה ו ף
m a c c o b y מ א ק ו ב י
m a c h i n e מ א ש י ן
m a c i e j מ א ס י ג '
m a d e i r a מ א ד י ר א
m a d r u z z o מ א ד ר ו צ ו
m a h l e r מ א ה ל ר
m a h m u d מ ח מ ו ד
m a h y a d i מ א ה י א ד י
m a i l l o l מ א י ו ל
m a i m o n מ א י מ ו ן
m a l k o מ א ל ק ו
m a m m e r i מ ע מ ר י
m a n d a מ א נ ד א
m a n n i n מ א נ י ן
m a n n i n g e r מ א נ י נ ג ר
m a r c e l l o מ א ר צ ' ל ו
m a r c o n i מ א ר ק ו נ י
m a r i a n a מ א ר י א נ א
m a r i l y n מ א ר י ל י ן
m a r i n מ א ר י ן
m a r i n a מ א ר י נ א
m a r i o מ א ר י ו
m a r k מ א ר ק
m a r k k u מ א ר ק ו
m a r l b o r o u g h מ א ר ל ב ו ר ו
m a r l e n e מ א ר ל י ן
m a r l o n מ א ר ל ו ן
m a r v i n מ א ר ו י ן
m a r y מ ר י
m a s a h i r o מ א ס א ה י ר ו
m a s a r u מ א ס א ר ו
m a s a r y k מ א ז א ר י ק
m a s a y o s h i מ א ס א י ו ש י
m a s s a m a s s o מ א ס א מ א ס ו
m a t a r מ ט ר
m a t h i j s e n מ א ת י ס ן
m a t i l d a מ א ט י ל ד א
m a t i s s e מ א ט י ס
m a t o v i n o v i c מ א ט ו ב י נ ו ב י ט ש
m a u r o y מ ו ר ו י
m a x מ א ק ס
m a x i m i l i a n מ א ק ס י מ י ל י א ן
m a z o w i e c k i מ א ז ו י ק י
m c b r i d e מ ק ב ר א י ד
m c c a r t h y מ ק א ר ת י
m c f a d d e n מ ק פ א ד י ן
m c g r a w מ א ק ג ר א ו
m c n a b מ א ק נ א ב
m d l e d l e מ ד ל י ד ל י
m e d v e d e v מ י ד ב י ד י ב
m e g מ י ג
m e l p o m e n e מ י ל פ ו מ י נ י
m e n a c h e m מ נ ח ם
m e n e g a z z o מ י נ י ג א ז ו
m e n i c h e l l i מ נ י ק י ל י
m e r i d a מ י ר י ד א
m e r i d o r מ ר י ד ו ר
m e r i e m e מ ר י א ם
m e r o m מ ר ו ם
m e s z o l y מ י ס ז ו ל י
m e z e y מ י ז י
m i c h e l l e מ י ש ל
m i c h e ľ מ י כ י ל
m i k e y מ א י ק י
m i k i m o t o מ י ק י מ ו ט ו
m i l a n o מ י ל א נ ו
m i l l i c h i p מ י ל י צ ' י פ
m i l l s מ י ל ז
m i l o s z מ י ל ו ש
m i n a m b r e s מ י נ א מ ב ר י ס
m i n a r מ י נ א ר
m i n a v a n d מ י נ א ו א נ ד
m i r a n מ י ר א ן
m i s s o u r i מ י ז ו ר י
m i t s u b i s h i מ י ט ס ו ב י ש י
m i y u מ י ו
m i y u k i מ י ו ק י
m l a d i c מ ל א ד י ט ש
m o k d a d מ ו ק ד א ד
m o l d o v a n מ ו ל ד ו ב א ן
m o n g e מ ו נ ג
m o n t m a r t r e מ ו נ ט מ א ר ט ר
m o n t t מ ו נ ט
m o r a d i מ ו ר א ד י
m o r a v c i k מ ו ר א ב צ ' י ק
m o r a v i a מ ו ר א ב י א
m o r s e מ ו ר ס
m o s h e מ ש ה
m o u l o u d מ ו ל ו ד
m p h e l a מ פ י ל א
m u d h a f a r מ ו ז פ ר
m u d r i k מ ו ד ר י ק
m u i n מ ו ע י ן
m u k h t a r א ל מ ו כ ט א ר
m u l e n g a מ ו ל י נ ג א
m u r e n מ ו ר ן
m u s a m p a מ ו ס א מ פ א
m w a r u w a r i מ ו א ר ו ו א ר י
m y l e s מ א י ל ז
m y s k i n a מ י ס ק י נ א
n a f t i נ פ ט י
n a m i e נ א מ י
n a o r נ א ו ר
n a r e n d r a נ א ר י נ ד ר א
n a r e y נ א ר י
n a s h e e d נ א ש י ד
n a z a r נ ז א ר
n a z i k נ א ז י ק
n e e s o n נ י ס ו ן
n e f z i נ פ ז י
n e o t נ י ו ת
n e r e o נ י ר י ו
n e u m a n n נ ו י מ א ן
n i c c o l o נ י ק ו ל ו
n i c o נ י ק ו
n i c o l e נ י ק ו ל
n i c o l e t נ י ק ו ל ה
n i g h y נ א י
n i k o l a o s נ י ק ו ל א ו ס
n i l s s o n נ י ל ס ו ן
n i m e i r y נ מ י י ר י
n i n o m i y a נ י נ ו מ י א
n i t z a נ י צ ה
n i z a m נ י ז א ם
n o b e l נ ו ב ל
n o b u y u k i נ ו ב ו י ו ק י
n o g l y נ ו ג ל י
n o r d s t r o m נ ו ר ד ס ט ר ו ם
n o r i a k i נ ו ר י א ק י
n o r o d o m נ ו ר ו ד ו ם
n o r t o n נ ו ר ט ן
n o s r a t i נ ו ס ר ט י
n u m a נ ו מ א
n y a n d o r o נ י א נ ד ו ר ו
o b l a s t א ו ב ל א ס ט
o c t a n e א ו ק ט א ן
o k e l l o א ו ק י ל ו
o m a a r ע ו מ ר
o r e g o n א ו ר י ג ו ן
o r l a n d o n i א ו ר ל א נ ד ו נ י
o t i א ו ט י
o u e d ו ד
p a g e פ י י ג '
p a l a t i n a t e פ א ל א ט י נ י י ט
p a l l a d i n o פ א ל א ד י נ ו
p a l m e פ א ל ם
p a n u c c i פ א נ ו צ ' י
p a p a s פ א פ א ס
p a p i n פ א פ י ן
p a r פ א ר
p a r i e t t i פ א ר י א ט י
p a r k o u r פ א ר ק ו ר
p a r m e n i d e s פ א ר מ נ י ד ס
p a s t e r n a k פ א ס ט ר נ א ק
p a s t e u r פ א ס ט ו ר
p a t a g o n i a פ א ט א ג ו נ י א
p a t r i c k פ א ט ר י ק
p a t t e r s o n פ א ט י ר ס ו ן
p e a r l פ י ר ל
p e g u y פ י ג ו י
p e r e z פ י ר י ז
p e t r a פ י ט ר א
p h a n r i t פ א נ ר י ט
p h i l i p p o u s s i s פ י ל י פ ו ס י ס
p h o t o s h o p פ ו ט ו ש ו פ
p i o l a פ י ו ל א
p i o t r פ י ו ט ר
p i r a e u s פ י ר א ו ס
p i s i n פ י ס י ן
p j a n i c פ י א נ י ט ש
p l e s s e r s פ ל י ס י ר ז
p l o i e s t i פ ל ו י ס ט י
p o l g a r פ ו ל ג א ר
p o l o פ ו ל ו
p o p p e r פ ו פ ר
p o r t m a n פ ו ר ט מ א ן
p o r u s h פ ו ר ו ש
p o t s d a m פ ו ט ס ד א ם
p r a t i פ ר א ט י
p r o y a s פ ר ו י א ס
p y g m a l i o n פ י ג מ א ל י ו ן
q a b b a n i ק ב א נ י
q a n a ק א נ א
q u e i r o z ק י ר ו ז
q u e u d r u e ק ו ד ר ו
q u i n n ק ו י ן
q u z m a n ק ו ז מ א ן
r a b i n d r a n a t h ר א ב נ ד ר א נ א ת
r a d h i ר א ד י
r a e d ר א א ד
r a e m o n ר א י מ ו ן
r a m i ר א מ י
r a m s a y ר א מ ס י י
r a m z y ר מ ז י
r a n d ר א נ ד
r a v i n ר א ב י ן
r a w h i ר א ו ח י
r e c i f e ר ס י פ י
r e d k n a p p ר י ד נ א פ
r e g a n ר י ג ן
r e g u e i r o ר י ג י י ר ו
r e i k i ר י י ק י
r e i n d e r s ר י י נ ד י ר ס
r e j e w s k i ר ג ' ו ס ק י
r e l m y ר י ל מ י
r e m e t t e r ר י מ י ט י ר
r e m e z ר מ ז
r e n s e n b r i n k ר י נ ס י נ ב ר י נ ק
r e p ר פ
r e v i e ר י ב י
r e x h e p i ר ק פ י
r h e e ר י
r i ר י
r i c a r d o ר י ק א ר ד ו
r i j s b e r g e n ר י ס ב י ר ג ן
r i m i n i ר י מ י נ י
r i m o n ר י מ ו ן
r i n a ר י נ א
r i n c o n ר י נ ק ו ן
r i q u e l m e ר י ק י ל מ י
r i y a s h i ר י א ש י
r o c h e t e a u ר ו צ ' י ט ו
r o d n e y ר ו ד נ י
r o h r ר ו ה ר
r o m a n i a ר ו מ י י נ י ה
r o m e r o ר ו מ י ר ו
r o m i n a ר ו מ י נ א
r o m u a l d ר ו מ א ל ד
r o n e n ר ו נ ן
r o o n e y ר ו נ י
r o s e n b e r g ר ו ז נ ב ר ג
r u h l ר ו ל
r u m e r ר ו מ ר
r u w i ר ו י
r u y ר ו י
r y a n ר א י א ן
r y o k o ר י ו ק ו
r y u j i ר י ו ג ' י
s a b a h ס ב א ח
s a f i n a ס א פ י נ ה
s a f r a n e k ס א פ ר א נ י ק
s a g n a ס א נ י א
s a i o n j i ס א י ו נ ג ' י
s a i p a n ס א י פ א ן
s a l a m ס ל א ם
s a l a m p e s s y ס א ל א מ פ ס י
s a l f o r d ס א ל פ ו ר ד
s a l i b i ס ל י ב י
s a l i f ס א ל י ף
s a l o m o n ס א ל ו מ ו ן
s a l v a ס א ל ב א
s a n b a r ס נ ב ר
s a n d r a ס א נ ד ר א
s a n d r o ס א נ ד ר ו
s a n t i l l a n a ס א נ ט י ל א נ ה
s a n t o s ס א נ ט ו ס
s a r d i n i a ס ר ד י נ י א
s a t o r u ס א ט ו ר ו
s a t s u k i ס א צ ו ק י
s a u v a g e ס ו ב א ג '
s a y a k o ס א י א ק ו
s a y e d ס י י ד
s a y y i d ס א י י ד
s c h a c h t ש א כ ט
s c h m i d ש מ י ד
s c h m i t t ש מ י ט
s c h r o e d e r ש ר ו ד ר
s c h u m a n n ש ו מ א ן
s c h w a r t z ש ו א ר ץ
s c h w a r t z m a n ש ו א ר m מ ן
s e d a r o u s ס י ד א ר ו ס
s e g a ס ג א
s e i d a t h ס י י ד א ת
s e r z h ס י ר ז '
s h a f i k ש פ י ק
s h a h n a m e h ש א ה נ א מ ה
s h a m e k h ש א מ ך
s h a m k h a n i ש א מ כ א נ י
s h a m m a s ש מ א ס
s h a t i l i ש א ט י ל י
s h a u k a t ש א ו ק א ט
s h a w k y ש ו ק י
s h e r l o c k ש ר ל ו ק
s h e r m a n ש ר מ א ן
s h i k i b u ש י ק י ב ו
s h i n a w a t r a ש י נ א ו א ט ר א
s h o r e y ש ו ר י
s i l w a n ס י ל ו א ן
s i n g h ס י נ ג
s i o n k o ס י ו נ ק ו
s i r k i n ס י ר ק ן
s i r o u s ס י ר ו ס
s i s l e y ס י ס ל י
s i x ס י ק ס
s k i l e s ס ק א י ל ז
s k o b l a r ס ק ו ב ל א ר
s l a v k o ס ל א ב ק ו
s m a l l e y ס מ ו ל י
s m u s h ס מ א ש
s o d e r b e r g ס ו ד ר ב י ר ג
s o h r a b ס ו ה ר א ב
s o l o w ס ו ל ו
s o m ס ו ם
s o n d e r g a a r d ס ו נ ד ר ג א ר ד
s o n u ס ו נ ו
s o n y ס ו נ י
s o r o s ס ו ר ו ס
s o u a d ס ו ע א ד
s o y i n k a ס ו י נ ק א
s p e c t o r ס פ ק ט ו ר
s p i r o ס פ י ר ו
s t a l l o n e ס ט א ל ו ן
s t a n d f e s t ס ט א נ ד פ י ס ט
s t a n i s l a w ס ט א נ י ס ל ו
s t e f a n i a ס ט י פ א נ י א
s t e n d a r d o ס ט י נ ד א ר ד ו
s t e p h a n o p o u l o s ס ט י פ א נ ו פ ו ל ו ס
s t e p n e y ס ט י פ נ י י
s t i f t e r ס ט י פ ט ר
s t i l l e r ס ט י ל ר
s t o i c h i t a ס ט ו י ק י ט א
s t r a t f o r d ס ט ר א ט פ ו ר ד
s t r a u s s ס ט ר א ו ס
s t r o u s t r u p ס ט ר ו ס ט ר ו פ
s t u d e n t ס ט ו ד נ ט
s u a z o ס ו א ז ו
s u f y a n ס ו פ י א ן
s u g i t a ס ו ג י ט א
s u m m e r b e e ס א מ ר ב י
s u m m e r s ס א מ ר ז
s u r j a k ס ו ר י א ק
s u z a n n e ס ו ז א ן
s w a n k ס ו א נ ק
t ט
t a a r a b t ט א ר א ב ט
t a d i c ט א ד י ט ש
t a d i r a n ט א ד י ר א ן
t a d m o r ט ד מ ו ר
t a h e y y a ט ח י ה
t a k a g i ט א ק א ג י
t a k a h a t a ט א ק א ה א ט א
t a r t u ט א ר ט ו
t a t a r s t a n ט א ט א ר ס ט א ן
t a u p o ט א ו פ ו
t a y e ט א י
t e m p e l h o f ט מ פ ל ה ו ף
t e m s a m a n i ט מ ס מ א נ י
t e n e r i f e ט נ ר י ף
t e r e s h k o v a ט ר ש ק ו ב א
t e r t u l l i a n ט ר ט ל י א ן
t h e e r a w e s i n ת י ר א ו ו ס י ן
t h i o ת י ו
t h o m ט ו ם
t h o r ת ו ר
t i m m y ט י מ י
t i m o r i m ט י מ ו ר י ם
t i r a s p o l ט י ר א ס פ ו ל
t i s e l i u s ט י ס י ל י ו ס
t o n e g a w a ט ו נ י ג א ו א
t o n g ט ו נ ג
t o o m e y ט ו מ י
t o s h i m i c h i ט ו ש י מ י ט ש י
t o t m a ט ו ט מ א
t o u j a n ט ו ג ' א ן
t r a p a n i ט ר א פ א נ י
t r i e r ט ר י ר
t r o n d h e i m ט ר ו נ ד ה א י ם
t r o o s t ט ר ו ס ט
t s u j i צ ו ג ' י
t u m a r t ט ו מ א ר ט
t u n c a y ט ו נ ק י י
t u r b o ט ו ר ב ו
t u r k i s h ט ו ר ק י ש
t z i p i צ י פ י
u c h i d a א ו צ ' י ד א
u n i l e v e r י ו נ י ל י ב ר
u t a d a א ו ט א ד א
v a l d a n o ו א ל ד א נ ו
v a n g e l i s ו א נ ג י ל י ס
v a r n h a g e n ו א ר נ ה א ג ן
v a s h t i ו ש ת י
v a s i l i ع א ס י ל י
v a s i l i s ו א ס י ל י ס
v e l i k o ו ל י ק ו
v e n e z i a ו י נ י ז י א
v e n e z u e l a ו נ ז ו י ל א
v e r e d ו ר ד
v e r m e l h i n h o ו ר מ י ל ה י נ ו
v e r n e r ו ר נ ר
v e s e l i n ו ס י ל י ן
v i e w ו י ו
v i l l e g a s ו י ל י ג א ס
v i l l e t t e ו י ל י ט
v i n g a d a ו י נ ג א ד א
v i o l a ו י ו ל א
v i o l e a u ו י ו ל ו
v i z e k ו י ז י ק
v l a d i k a v k a z ו ל א ד י ק א ב ק א ז
v l a d i m i r ו ל א ד י מ י ר
v o l d e m o r t ו ו ל ד מ ו ר ט
v u j a n o v i c ב ו י א נ ו ב י ט ש
v u j o v i c ב ו י ו ב י ט ש
v y n t r a ו י נ ט ר א
w a d e ו י י ד
w a l e s a ו א ל י ס א
w a n g c h u c k ו א נ ג צ ' ו ק
w e i z m a n ו י צ מ ן
w e n d e e ו נ ד י
w e n t w o r t h ו נ ט ו ו ר ת
w e r n e r ו ר נ ר
w i e n e r ו י נ ר
w i e r t z ו י ר ץ
w i n d h o e k ו י נ ד ה ו ק
w i n t e r ו י נ ט ר
w i s c o n s i n ו י ס ק ו נ ס ן
w i t s c h g e ו י ט ס ט ש ג
w o o d g a t e ו ו ד ג י י ט
w o o d s ו ו ד ז
w o o d v i l l e ו ו ד ב י ל
x a b i ש א ב י
x i n ז י ן
y a d e י א ד
y a k u t s k י א ק ו ט ס ק
y a n g o n י א נ ג ו ן
y a r k o n i י ר ק ו נ י
y a s s e r י א ס ר
y e h u d י ה ו ד
y o a n י ו א ן
y o r k י ו ר ק
y o s h i h i r o י ו ש י ה י ר ו
y o s h i n a k a י ו ש י נ א ק א
y u i י ו י
y u i c h i י ו י צ ' י
y u m i י ו מ י
y u n י ו ן
y u s u f י ו ס ו ף
z a h i r ז א ה י ר
z a l e s s k y ז א ל ס ק י
z a n e t t i ז א נ י ט י
z a v e n ז א ב י ן
z a y d u n ז י י ד ו ן
z e n g a ז נ ג א
z e n k o ז י נ ק ו
z e r k a ז ר ק א
z e r o u a l i ז ר ו א ל י
z h a o ז ' א ו
z i y i ז י י
z o l t a n ז ו ל ט א ן
z o r i n ז ו ר י ן
z o r r o ז ו ר ו
z o u b e i r ז ו ב י ר
z u a b i ז ו ע ב י
z u b e i d i ז ו ב י י ד י
z u h r ז ו ה ר
z u r a b ז ו ר א ב
z v a r t n o t s ז ב א ר ט נ ו ט ס
|
b3680996d497aec928ea491c7f3c10e371685230 | 9bc415d58bf063a1bca303fea640e644333dbdbd | /Scilab/Sinais_e_Sistemas/respol.sci | 3749afa6aae8548d7fa092d13af453611ff3890e | [] | no_license | Roast-Lord/SMGcodes | 36e55be6c1cc17af91ab2e3f5117c78684f20604 | b75107be829fb4373dc1bc4b8696fe4b9cec437a | refs/heads/main | 2023-07-05T05:25:50.557705 | 2021-08-17T17:46:25 | 2021-08-17T17:46:25 | 301,012,145 | 1 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 551 | sci | respol.sci | // Computation of residues
// 4 . 5
// Numerator and denominator coefficients
// are passed in decreasing powers of z ( say )
//[res pol q]=respol(flip(coeff(Hz(2))),flip(coeff(Hz(3))))
function [ res , pol , q ] = respol ( num , den )
len = length ( num ) ;
if num ( len ) == 0
num = num (1: len -1) ;
end
[ resi ,q ] = pfe ( num , den ) ;
res = resi (: ,2) ;
res = int ( res ) + ( clean ( res - int ( res ) ,1.d -04) ) ;
pol = resi (: ,1) ;
pol = int ( pol ) + ( clean ( pol - int ( pol ) ,1.d -04) ) ;
endfunction ;
|
205ebb9d105653bb9938e12eac8a2e82145d4d2d | 449d555969bfd7befe906877abab098c6e63a0e8 | /1106/CH5/EX5.4/ex5_4.sce | f12d7767a99550d5cebf8d724ae38d0646dc0991 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 446 | sce | ex5_4.sce | // Example 5.4, Page No-251
clear
clc
Vref=1.5
// Part A
Vpp=5
Vnp=2.5
Vc=Vnp + Vref
printf('\nCapacitor voltage Vc= %.1f V', Vc)
// Part B
Vopeak=Vnp + Vref +Vpp
printf('\nPeak value of clamped output voltage Vo(peak)= %.1f V', Vopeak)
// Part C
Voc=0.7 + Vref
printf('\nOp-amp output voltage during charging Vo= %.1f V', Voc)
// Part D
Vd=Vref-Vopeak
printf('\nMaximum differential input voltage Vd= %.1f V', Vd)
|
37ac02bc2f03f81a9186597372e89e9e23394181 | 931df7de6dffa2b03ac9771d79e06d88c24ab4ff | /My First Map.sce | be5b4aef779cdbf98ffd50394449f173a37b65d5 | [] | no_license | MBHuman/Scenarios | be1a722825b3b960014b07cda2f12fa4f75c7fc8 | 1db6bfdec8cc42164ca9ff57dd9d3c82cfaf2137 | refs/heads/master | 2023-01-14T02:10:25.103083 | 2020-11-21T16:47:14 | 2020-11-21T16:47:14 | null | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 48,108 | sce | My First Map.sce | Name=My First Map
PlayerCharacters=Camera Man
BotCharacters=crocbot.bot
IsChallenge=true
Timelimit=60.0
PlayerProfile=Camera Man
AddedBots=crocbot.bot
PlayerMaxLives=0
BotMaxLives=0
PlayerTeam=1
BotTeams=0
MapName=test101.map
MapScale=4.0
BlockProjectilePredictors=true
BlockCheats=true
InvinciblePlayer=false
InvincibleBots=false
Timescale=1.0
BlockHealthbars=false
TimeRefilledByKill=0.0
ScoreToWin=1000.0
ScorePerDamage=0.0
ScorePerKill=1.0
ScorePerMidairDirect=0.0
ScorePerAnyDirect=0.0
ScorePerTime=0.0
ScoreLossPerDamageTaken=0.0
ScoreLossPerDeath=0.0
ScoreLossPerMidairDirected=0.0
ScoreLossPerAnyDirected=0.0
ScoreMultAccuracy=true
ScoreMultDamageEfficiency=false
ScoreMultKillEfficiency=false
GameTag=aim
WeaponHeroTag=Pistol
DifficultyTag=3
AuthorsTag=Tropics
BlockHitMarkers=false
BlockHitSounds=false
BlockMissSounds=true
BlockFCT=false
Description=idk
GameVersion=1.0.6.2
ScorePerDistance=0.0
[Aim Profile]
Name=Default
MinReactionTime=0.3
MaxReactionTime=0.4
MinSelfMovementCorrectionTime=0.001
MaxSelfMovementCorrectionTime=0.05
FlickFOV=30.0
FlickSpeed=1.5
FlickError=15.0
TrackSpeed=3.5
TrackError=3.5
MaxTurnAngleFromPadCenter=75.0
MinRecenterTime=0.3
MaxRecenterTime=0.5
OptimalAimFOV=30.0
OuterAimPenalty=1.0
MaxError=40.0
ShootFOV=15.0
VerticalAimOffset=0.0
MaxTolerableSpread=5.0
MinTolerableSpread=1.0
TolerableSpreadDist=2000.0
MaxSpreadDistFactor=2.0
[Bot Profile]
Name=crocbot
DodgeProfileNames=Stop
DodgeProfileWeights=1.0
DodgeProfileMaxChangeTime=5.0
DodgeProfileMinChangeTime=1.0
WeaponProfileWeights=1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0
AimingProfileNames=Default;Default;Default;Default;Default;Default;Default;Default
WeaponSwitchTime=3.0
UseWeapons=true
CharacterProfile=croc
SeeThroughWalls=false
[Character Profile]
Name=Camera Man
MaxHealth=0.1
WeaponProfileNames=pistol;;;;;;;
MinRespawnDelay=0.1
MaxRespawnDelay=5.0
StepUpHeight=75.0
CrouchHeightModifier=0.5
CrouchAnimationSpeed=1.0
CameraOffset=X=0.000 Y=0.000 Z=0.000
HeadshotOnly=false
DamageKnockbackFactor=8.0
MovementType=Base
MaxSpeed=0.0
MaxCrouchSpeed=500.0
Acceleration=16000.0
AirAcceleration=16000.0
Friction=8.0
BrakingFrictionFactor=2.0
JumpVelocity=0.0
Gravity=3.0
AirControl=0.25
CanCrouch=true
CanPogoJump=false
CanCrouchInAir=false
CanJumpFromCrouch=false
EnemyBodyColor=X=255.000 Y=0.000 Z=0.000
EnemyHeadColor=X=255.000 Y=255.000 Z=255.000
TeamBodyColor=X=0.000 Y=0.000 Z=255.000
TeamHeadColor=X=255.000 Y=255.000 Z=255.000
BlockSelfDamage=false
InvinciblePlayer=true
InvincibleBots=false
BlockTeamDamage=false
AirJumpCount=0
AirJumpVelocity=800.0
MainBBType=Cylindrical
MainBBHeight=230.0
MainBBRadius=55.0
MainBBHasHead=true
MainBBHeadRadius=45.0
MainBBHeadOffset=0.0
MainBBHide=false
ProjBBType=Cylindrical
ProjBBHeight=230.0
ProjBBRadius=55.0
ProjBBHasHead=true
ProjBBHeadRadius=45.0
ProjBBHeadOffset=0.0
ProjBBHide=true
HasJetpack=true
JetpackActivationDelay=0.2
JetpackFullFuelTime=99.0
JetpackFuelIncPerSec=10.0
JetpackFuelRegensInAir=true
JetpackThrust=6000.0
JetpackMaxZVelocity=400.0
JetpackAirControlWithThrust=0.25
AbilityProfileNames=;;;
HideWeapon=false
AerialFriction=0.0
StrafeSpeedMult=1.0
BackSpeedMult=1.0
RespawnInvulnTime=0.0
BlockedSpawnRadius=0.0
BlockSpawnFOV=0.0
BlockSpawnDistance=0.0
RespawnAnimationDuration=0.5
AllowBufferedJumps=true
BounceOffWalls=false
LeanAngle=0.0
LeanDisplacement=0.0
AirJumpExtraControl=0.0
ForwardSpeedBias=1.0
HealthRegainedonkill=0.0
HealthRegenPerSec=0.0
HealthRegenDelay=0.0
JumpSpeedPenaltyDuration=0.0
JumpSpeedPenaltyPercent=0.0
ThirdPersonCamera=false
TPSArmLength=300.0
TPSOffset=X=0.000 Y=150.000 Z=150.000
BrakingDeceleration=2048.0
VerticalSpawnOffset=0.0
[Character Profile]
Name=croc
MaxHealth=100.0
WeaponProfileNames=;;;;;;;
MinRespawnDelay=0.5
MaxRespawnDelay=0.5
StepUpHeight=75.0
CrouchHeightModifier=0.5
CrouchAnimationSpeed=1.0
CameraOffset=X=0.000 Y=0.000 Z=0.000
HeadshotOnly=false
DamageKnockbackFactor=8.0
MovementType=Base
MaxSpeed=0.0
MaxCrouchSpeed=500.0
Acceleration=100.0
AirAcceleration=16000.0
Friction=8.0
BrakingFrictionFactor=4.0
JumpVelocity=750.0
Gravity=2.0
AirControl=0.125
CanCrouch=false
CanPogoJump=true
CanCrouchInAir=false
CanJumpFromCrouch=false
EnemyBodyColor=X=255.000 Y=0.000 Z=0.000
EnemyHeadColor=X=255.000 Y=255.000 Z=255.000
TeamBodyColor=X=0.000 Y=0.000 Z=255.000
TeamHeadColor=X=255.000 Y=255.000 Z=255.000
BlockSelfDamage=false
InvinciblePlayer=false
InvincibleBots=false
BlockTeamDamage=false
AirJumpCount=0
AirJumpVelocity=800.0
MainBBType=Spheroid
MainBBHeight=110.0
MainBBRadius=55.0
MainBBHasHead=false
MainBBHeadRadius=45.0
MainBBHeadOffset=0.0
MainBBHide=false
ProjBBType=Spheroid
ProjBBHeight=50.0
ProjBBRadius=25.0
ProjBBHasHead=false
ProjBBHeadRadius=45.0
ProjBBHeadOffset=0.0
ProjBBHide=true
HasJetpack=false
JetpackActivationDelay=0.2
JetpackFullFuelTime=4.0
JetpackFuelIncPerSec=1.0
JetpackFuelRegensInAir=false
JetpackThrust=6000.0
JetpackMaxZVelocity=400.0
JetpackAirControlWithThrust=0.25
AbilityProfileNames=;;;
HideWeapon=true
AerialFriction=0.05
StrafeSpeedMult=1.0
BackSpeedMult=1.0
RespawnInvulnTime=0.0
BlockedSpawnRadius=0.0
BlockSpawnFOV=0.0
BlockSpawnDistance=0.0
RespawnAnimationDuration=0.0
AllowBufferedJumps=true
BounceOffWalls=false
LeanAngle=0.0
LeanDisplacement=0.0
AirJumpExtraControl=0.0
ForwardSpeedBias=1.0
HealthRegainedonkill=0.0
HealthRegenPerSec=0.0
HealthRegenDelay=0.0
JumpSpeedPenaltyDuration=0.0
JumpSpeedPenaltyPercent=0.0
ThirdPersonCamera=false
TPSArmLength=300.0
TPSOffset=X=0.000 Y=150.000 Z=150.000
BrakingDeceleration=2048.0
VerticalSpawnOffset=0.0
[Dodge Profile]
Name=Stop
MaxTargetDistance=2500.0
MinTargetDistance=750.0
ToggleLeftRight=false
ToggleForwardBack=false
MinLRTimeChange=0.2
MaxLRTimeChange=0.5
MinFBTimeChange=0.2
MaxFBTimeChange=0.5
DamageReactionChangesDirection=true
DamageReactionChanceToIgnore=0.0
DamageReactionMinimumDelay=0.1
DamageReactionMaximumDelay=0.15
DamageReactionCooldown=1.0
DamageReactionThreshold=0.0
DamageReactionResetTimer=0.1
JumpFrequency=0.0
CrouchInAirFrequency=0.0
CrouchOnGroundFrequency=0.0
TargetStrafeOverride=Ignore
TargetStrafeMinDelay=0.125
TargetStrafeMaxDelay=0.25
MinProfileChangeTime=0.0
MaxProfileChangeTime=0.0
MinCrouchTime=0.1
MaxCrouchTime=0.1
MinJumpTime=0.0
MaxJumpTime=0.0
LeftStrafeTimeMult=1.0
RightStrafeTimeMult=1.0
StrafeSwapMinPause=0.1
StrafeSwapMaxPause=0.1
BlockedMovementPercent=0.5
BlockedMovementReactionMin=0.125
BlockedMovementReactionMax=0.2
[Weapon Profile]
Name=pistol
Type=Hitscan
ShotsPerClick=1
DamagePerShot=100000.0
KnockbackFactor=4.0
TimeBetweenShots=0.01
Pierces=false
Category=SemiAuto
BurstShotCount=1
TimeBetweenBursts=0.5
ChargeStartDamage=10.0
ChargeStartVelocity=X=500.000 Y=0.000 Z=0.000
ChargeTimeToAutoRelease=2.0
ChargeTimeToCap=1.0
ChargeMoveSpeedModifier=1.0
MuzzleVelocityMin=X=2000.000 Y=0.000 Z=0.000
MuzzleVelocityMax=X=2000.000 Y=0.000 Z=0.000
InheritOwnerVelocity=0.0
OriginOffset=X=0.000 Y=0.000 Z=0.000
MaxTravelTime=5.0
MaxHitscanRange=100000.0
GravityScale=1.0
HeadshotCapable=true
HeadshotMultiplier=2.0
MagazineMax=0
AmmoPerShot=1
ReloadTimeFromEmpty=0.5
ReloadTimeFromPartial=0.5
DamageFalloffStartDistance=100000.0
DamageFalloffStopDistance=100000.0
DamageAtMaxRange=25.0
DelayBeforeShot=0.0
HitscanVisualEffect=None
ProjectileGraphic=Ball
VisualLifetime=0.1
WallParticleEffect=Gunshot
HitParticleEffect=Flare
BounceOffWorld=false
BounceFactor=0.5
BounceCount=0
HomingProjectileAcceleration=0.0
ProjectileEnemyHitRadius=1.0
CanAimDownSight=false
ADSZoomDelay=0.0
ADSZoomSensFactor=0.7
ADSMoveFactor=1.0
ADSStartDelay=0.0
ShootSoundCooldown=0.08
HitSoundCooldown=0.08
HitscanVisualOffset=X=0.000 Y=0.000 Z=-50.000
ADSBlocksShooting=false
ShootingBlocksADS=false
KnockbackFactorAir=4.0
RecoilNegatable=false
DecalType=1
DecalSize=15.0
DelayAfterShooting=0.0
BeamTracksCrosshair=false
AlsoShoot=
ADSShoot=
StunDuration=0.0
CircularSpread=true
SpreadStationaryVelocity=0.0
PassiveCharging=false
BurstFullyAuto=true
FlatKnockbackHorizontal=0.0
FlatKnockbackVertical=0.0
HitscanRadius=0.0
HitscanVisualRadius=1.0
TaggingDuration=0.0
TaggingMaxFactor=1.0
TaggingHitFactor=1.0
ProjectileTrail=None
RecoilCrouchScale=1.0
RecoilADSScale=1.0
PSRCrouchScale=1.0
PSRADSScale=1.0
ProjectileAcceleration=0.0
AccelIncludeVertical=false
AimPunchAmount=0.0
AimPunchResetTime=0.05
AimPunchCooldown=0.5
AimPunchHeadshotOnly=false
AimPunchCosmeticOnly=false
MinimumDecelVelocity=0.0
PSRManualNegation=false
PSRAutoReset=true
AimPunchUpTime=0.05
AmmoReloadedOnKill=0
CancelReloadOnKill=false
FlatKnockbackHorizontalMin=0.0
FlatKnockbackVerticalMin=0.0
ADSScope=No Scope
ADSFOVOverride=72.099998
ADSFOVScale=Quake/Source
ADSAllowUserOverrideFOV=true
ForceFirstPersonInADS=true
ZoomBlockedInAir=false
ADSCameraOffsetX=0.0
ADSCameraOffsetY=0.0
ADSCameraOffsetZ=0.0
Explosive=false
Radius=500.0
DamageAtCenter=100.0
DamageAtEdge=100.0
SelfDamageMultiplier=0.5
ExplodesOnContactWithEnemy=false
DelayAfterEnemyContact=0.0
ExplodesOnContactWithWorld=false
DelayAfterWorldContact=0.0
ExplodesOnNextAttack=false
DelayAfterSpawn=0.0
BlockedByWorld=false
SpreadSSA=1.0,1.0,-1.0,5.0
SpreadSCA=1.0,1.0,-1.0,5.0
SpreadMSA=1.0,1.0,-1.0,5.0
SpreadMCA=1.0,1.0,-1.0,5.0
SpreadSSH=0.0,0.1,0.0,0.0
SpreadSCH=1.0,1.0,-1.0,5.0
SpreadMSH=0.0,0.1,0.0,0.0
SpreadMCH=1.0,1.0,-1.0,5.0
MaxRecoilUp=0.0
MinRecoilUp=0.0
MinRecoilHoriz=0.0
MaxRecoilHoriz=0.0
FirstShotRecoilMult=1.0
RecoilAutoReset=false
TimeToRecoilPeak=0.05
TimeToRecoilReset=0.35
AAMode=0
AAPreferClosestPlayer=false
AAAlpha=1.0
AAMaxSpeed=360.0
AADeadZone=0.0
AAFOV=360.0
AANeedsLOS=true
TrackHorizontal=true
TrackVertical=true
AABlocksMouse=false
AAOffTimer=0.0
AABackOnTimer=0.0
TriggerBotEnabled=false
TriggerBotDelay=0.0
TriggerBotFOV=1.0
StickyLock=false
HeadLock=false
VerticalOffset=0.0
DisableLockOnKill=false
UsePerShotRecoil=false
PSRLoopStartIndex=0
PSRViewRecoilTracking=0.45
PSRCapUp=9.0
PSRCapRight=4.0
PSRCapLeft=4.0
PSRTimeToPeak=0.175
PSRResetDegreesPerSec=40.0
UsePerBulletSpread=false
PBS0=0.0,0.0
[Map Data]
reflex map version 8
global
entity
type WorldSpawn
String32 targetGameOverCamera end
UInt8 playersMin 1
UInt8 playersMax 16
brush
vertices
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-44.000000 252.000000 196.000000
faces
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brush
vertices
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faces
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faces
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faces
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type CameraPath
UInt8 posLerp 2
UInt8 angleLerp 2
entity
type Effect
Vector3 position 0.000000 256.000000 0.000000
String64 effectName internal/misc/reflectionprobe
entity
type PlayerSpawn
Vector3 position -12.000000 94.000000 -121.000000
Bool8 teamB 0
Bool8 modeCTF 0
Bool8 modeFFA 0
Bool8 modeTDM 0
Bool8 mode1v1 0
Bool8 modeRace 0
Bool8 mode2v2 0
entity
type PlayerSpawn
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Bool8 initialSpawn 0
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Bool8 modeRace 0
Bool8 mode2v2 0
entity
type PlayerSpawn
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Bool8 teamA 0
Bool8 initialSpawn 0
Bool8 modeCTF 0
Bool8 modeFFA 0
Bool8 modeTDM 0
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Bool8 modeRace 0
Bool8 mode2v2 0
entity
type PlayerSpawn
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Bool8 mode2v2 0
entity
type PlayerSpawn
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Bool8 teamA 0
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entity
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Bool8 modeRace 0
Bool8 mode2v2 0
entity
type PlayerSpawn
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Bool8 teamA 0
Bool8 initialSpawn 0
Bool8 modeCTF 0
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Bool8 modeTDM 0
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Bool8 modeRace 0
Bool8 mode2v2 0
entity
type PlayerSpawn
Vector3 position -120.000000 40.000000 196.000000
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Bool8 teamA 0
Bool8 initialSpawn 0
Bool8 modeCTF 0
Bool8 modeFFA 0
Bool8 modeTDM 0
Bool8 mode1v1 0
Bool8 modeRace 0
Bool8 mode2v2 0
entity
type PlayerSpawn
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Bool8 modeRace 0
Bool8 mode2v2 0
entity
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Bool8 teamA 0
Bool8 initialSpawn 0
Bool8 modeCTF 0
Bool8 modeFFA 0
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Bool8 modeRace 0
Bool8 mode2v2 0
entity
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Bool8 mode2v2 0
entity
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Bool8 mode2v2 0
entity
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Bool8 modeCTF 0
Bool8 modeFFA 0
Bool8 modeTDM 0
Bool8 mode1v1 0
Bool8 modeRace 0
Bool8 mode2v2 0
entity
type PlayerSpawn
Vector3 position -16.000000 80.000000 196.000000
Vector3 angles 180.000000 0.000000 90.000000
Bool8 teamA 0
Bool8 initialSpawn 0
Bool8 modeCTF 0
Bool8 modeFFA 0
Bool8 modeTDM 0
Bool8 mode1v1 0
Bool8 modeRace 0
Bool8 mode2v2 0
entity
type PlayerSpawn
Vector3 position -72.000000 92.000000 196.000000
Vector3 angles 180.000000 0.000000 90.000000
Bool8 teamA 0
Bool8 initialSpawn 0
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Bool8 modeTDM 0
Bool8 mode1v1 0
Bool8 modeRace 0
Bool8 mode2v2 0
|
3f35817fa851029992b1f84e308c16537d15cff0 | 449d555969bfd7befe906877abab098c6e63a0e8 | /26/CH6/EX6.5.7/6_5_7.sce | aa8773a5f32254128098283487694f9f26854e4d | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 736 | sce | 6_5_7.sce | disp('The co-efficient matrix is:')
a=[1 -2;-1 2;0 3;2 5]
disp(a,'A=')
disp('The RHS is:')
b=[3;1;-4;2]
disp(b,'b=')
disp('Product of transpose of A and A=')
p1=a'*a
disp(p1)
disp('Product of transpose of A and b=')
p2=a'*b
disp('Forming an augmented matrix to solve the normal equations')
p=[p1 p2]
disp(p)
disp('performing row operations')
disp('R2=R2-R1')
p(2,:)=p(2,:)-p(1,:)
disp(p)
disp('R1=R1/6 and R2=R2/36')
p(1,:)=p(1,:)/6
p(2,:)=p(2,:)/36
disp(p)
disp('R1=R1-R2')
p(1,:)=p(1,:)-p(2,:)
disp(p)
disp('Hence, the solution is:')
disp(p(:,3))
x=p(:,3)
disp('The least square error is=||Ax-b||')
disp('Ax-b=')
disp(a*x-b)
c=a*x-b
s=0
for i=1:4
s=s+c(i,1)^2
end
disp('||Ax-b||=')
disp(sqrt(s)) |
9126210f00bb2a4f936162a1667ac554aaecf289 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3840/CH7/EX7.5/Ex7_5.sce | 1ef24399c20727e01a9c042e19d419a452579697 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 278 | sce | Ex7_5.sce | clear
//
//
//
//Variable declaration
d=0.1 //diameter(m)
i=0.5 //current(ampere)
//Calculation
r=d/2 //radius of atom(m)
mew=i*%pi*r**2 //magnetic moment(A-m**2)
//Result
printf("\n magnetic moment is %0.2f *10**-3 A-m**2",mew*10**3)
|
9babbbd47962ad35c54480620ef9d3fd5da4d044 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1309/CH4/EX4.3/ch4_3.sce | b78cb8e36fd6030a11e21fa53e7d7bfa41941e9c | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 2,286 | sce | ch4_3.sce | clc;
clear;
printf("\t\t\tChapter4_example3\n\n\n");
hc=30;
L=0.24;
k=1.25;
c=890;
rou=550;
Bi=hc*L/k;
alpha=k/(rou*c);
printf("The value of diffusivity is %.2e sq.m/s",alpha);
Tc=150;
T_inf=600;
T_i=50;
printf("\nThe Biot number is %.2f,",Bi);
if Bi<0.1 then
n=0;
else if Bi>0.1 then
n=1;
end
end
select n
case 0 then
disp('The Lumped capacity approach is applicable');
case 1 then
disp('Since value of Biot number is greater than 0.1, Lumped capacity approach would not give accurate results, so figure 4.6 is to be used');
reciprocal_Bi=1/Bi;
dimensionless_temp=(Tc-T_inf)/(T_i-T_inf);
Fo=0.4; //the value of Fourier Number from figure 4.6(a)
t=L^2*Fo/alpha;
printf("The required time is %d s = %.1f hr",t,t/3600);
end
// reading values of dimensionless temperature from figure 4.6(b) using reciprocal of Biot number
x_per_L=[0 0.2 0.4 0.6 0.8 0.9 1.0];
[n,m]=size(x_per_L);
printf("\nThe choosen values of x/L are: \n");
disp(x_per_L);
printf("\n Values for dimensionless temperature for corresponding values of x/L:")
dim_T=[1.0 .97 .86 .68 .48 .36 .24]; // value for dimensionless temperature for corresponding value of x/L
disp(dim_T);
printf("the temperature profile with distance is\n");
printf("\tx/L\t\t");
for j=1:m
printf("%.2f\t",x_per_L(1,j));
end
printf("\n");
printf("(T-T_inf)/T_i-T_inf)\t");
for i=1:m
printf("%.2f\t",dim_T(i));
end
T=zeros(1,m);
x=zeros(1,m);
for i=1:m
T(1,i)=dim_T(1,i)*dimensionless_temp*(T_i-T_inf)+T_inf;
x(1,i)=x_per_L(1,i)*L;
end
printf("\n\tx,cm\t\t");
for i=1:m
X(1,i)=x(1,i)*100;
printf("%.1f\t",X(1,i));
end
printf("\nT, degree celsius\t");
for i=1:m
printf("%d\t",T(1,i));
end
plot2d(X,T,rect=[0,0,24,600]);
a=gca();
newticks=a.x_ticks;
newticks(2)=[0;4;8;12;16;20;24];
newticks(3)=['0';'4';'8';'12';'16';'20';'24'];
a.x_ticks=newticks;
newticks1=a.y_ticks;
newticks1(2)=[0;100;200;300;400;500;600];
newticks1(3)=['0';'100';'200';'300';'400';'500';'600'];
a.y_ticks=newticks1;
xlabel('x,cm');
ylabel('t,degree celsius');
title('Temperature profile in the 24-cm slab after 2.5 hr.');
filename='Temperature profile in the 24-cm slab after 2.5 hr.';
xgrid(1);
xs2jpg(0,filename);
|
c25fda311740bae34ca95b7b2b86e4f05c56fec0 | 872b5ff8852c926ca1261037de07449db7ac51db | /area-03/cap12/aprox-derivada_encontre_coeficientes.sce | 2fb0480523a3aff465522701210808bb146d66bb | [] | no_license | BerdaSantos/numeric-calculus | 20e4c50d9f66f8582e89533a5101f597df6665ec | 0698409e7fa4158d6f7dd7e4d60f8a38538b3335 | refs/heads/master | 2020-05-14T18:07:02.017600 | 2018-11-23T01:50:38 | 2018-11-23T01:50:38 | null | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 502 | sce | aprox-derivada_encontre_coeficientes.sce | // Os x sao os pontos onde a f(x) e' calculada
// Fx(xn) = [C1Fn-1 + C2Fn+0 + C3Fn+1] / H
// ^ ^ ^ ^
n = 2; // indice do coeficiente que multiplica o Fn
x(1) = -1;
x(2) = 0;
x(3) = 1;
//x(4) = ...
// Daqui pra baixo nao muda pra esse padrao de aprox de derivada
b(1) = 0;
b(2) = 1;
b(3) = 2*x(n);
// b(4)=3*x(n)^2
for i=1:3
M(1,i) = 1;
M(2,i) = x(i);
M(3,i) = x(i)^2;
// M(4,i)=x(i)^3
end
c = inv(M)*b;
S = c(1)^2 + c(2)^2 + c(3)^2; // +c(4)^2
disp(c);
|
a520b4e248fad2e8d04e2039db2253d1499e051f | 449d555969bfd7befe906877abab098c6e63a0e8 | /1670/CH10/EX10.38/10_38.sce | 0b5b597690081e26a1b911feae09a7547281f6d4 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 447 | sce | 10_38.sce | //Example 10.38
//Finite Difference Method
//Page no. 354
clc;close;clear;
h=0.25;
y(1)=0;
deff('y=f2(x,y)','y=x+y')
for i=1:3
x(i)=i*h
end
A=[0,1,0;1,0,1;0,1,0]
j=1;
for i=1:3
A(i,i)=-(2-h^2*x(i)^2)
end
for i=1:3
B(i,1)=0
if i==3 then
B(3,1)=-1
end
printf('\ny%i %gy%i + y%i = %g\n',i-1,A(i,i),i,i+1,B(i,1))
end
C=inv(A)*B;
printf('\n\n')
for i=1:3
printf('\ny%i = %g\n',i,C(i))
end |
98db354728b503d377816403ef5a190617415b69 | 449d555969bfd7befe906877abab098c6e63a0e8 | /2609/CH2/EX2.5/ex_2_5.sce | 4fbab02faa22b3307b2ec09c3c0182f6af3f0492 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 508 | sce | ex_2_5.sce | ////Ex 2.5
clc;
clear;
close;
format('v',5);
Beta=100;//unitless
VBE=0.715;VD1=0.715;//V
VZ=6.2;//V
VT=26;//mV
IZt=41;//mA
VCC=10;//V
VEE=10;//V
RE=2.7;//kohm
RC=4.7;//kohm
VB=-VEE+VZ+VD1;//V
VE=VB-VBE;//V
IE3=(VE-(-VEE))/(RE);//mA
IT=IE3;//mA
ICQ=IT/2;//mA(let ICQ1=ICQ2=ICQ)
VCEQ=VCC+VBE-ICQ*RC;//V
Q=[ICQ VCEQ];//[mA V](Q point)
disp(Q,"Q point (ICQ(mA), VCEQ(V)) is ");
re=2*VT/IT;//ohm
Ad=-RC*1000/re;//unitless
Rid=2*Beta*re/1000;//kohm
disp(Ad,"Ad");
disp(Rid,"Rid(kohm)");
|
8f539ceb469d86268da762356d70fe72d58a9f8c | 899cecef18712265c22e100bf72286df1ec5fb65 | /Asgn1/Q1.sci | a2ddbb5e7996b4b66413eb7e812fe5dd15981cca | [] | no_license | ajaykumarkannan/Speech-Signal-Processing-and-Coding | 449679bef8bdf0215e96521163774f88d8a6b41e | c1d371b2866239a89312a0f64db3d61cc0b1011c | refs/heads/master | 2020-05-17T17:02:33.143586 | 2012-11-15T12:48:40 | 2012-11-15T12:48:40 | null | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 1,690 | sci | Q1.sci | scf();
// Non-Stationary Signal
[y, Fs, bits] = wavread('Sound1.wav');
y = y(1,:); // Had recorded in stereo - Converting to mono
// Taking a portion of the input signal
y = y(1,182680:200000);
y = y./(abs(max(y))); // Normalizing the signal
// Taking 30ms worth of signal
noSamples = Fs * 30 /1000;
y1 = y(1:noSamples);
Yt = 20*log10(abs(fftshift(fft(y1))));
Yt = Yt / abs(max(Yt)); // Normalizing
N = length(Yt);
F = -(N/2):(-1 + N/2);
F = Fs * F / N;
subplot(3,2,3); plot2d(y1); title('Non-Stationary Signal - Time Domain Plot');
subplot(3,2,4); plot2d(F(N/2:N-1), Yt(N/2:N-1)); title('Non-Stationary Signal - Frequency Domain Plot');
a = get("current_axes");
a.data_bounds = [0,min(Yt);24000, max(Yt)];
y1 = y(noSamples+1:2*noSamples);
Yt = 20*log10(abs(fftshift(fft(y1))));
Yt = Yt / abs(max(Yt)); // Normalizing
N = length(Yt);
F = -(N/2):(-1 + N/2);
F = Fs * F / N;
subplot(3,2,5); plot2d(y1); title('Non-Stationary Signal - Time Domain Plot - Shifted');
subplot(3,2,6); plot2d(F(N/2:N-1), Yt(N/2:N-1)); title('Non-Stationary Signal - Frequency Domain Plot - Shifted');
a = get("current_axes");
a.data_bounds = [0,min(Yt);24000, max(Yt)];
// Stationary Signal
// Sum of two sine waves i.e. x = a*sin(b*t)+c*sin(d*t)
t = 0:0.1:noSamples;
a = 5;
b = 0.7;
c = 2;
d = 0.2;
x = a*sin(b*t)+c*sin(d*t);
Xt = 20*log10(abs(fftshift(fft(x))));
Xt = Xt/abs(max(Xt)); // Normalizing
N = length(Xt);
F = -(N/2):(-1 + N/2);
F = Fs * F / N;
subplot(3,2,1); plot2d(x); title('Stationary Signal - Time Domain Plot');
subplot(3,2,2); plot2d(F(N/2:(N-1)), Xt(N/2:(N-1))); title('Stationary Signal - Frequency Domain Plot');
a = get("current_axes");
a.data_bounds = [0,min(Xt);24000, max(Xt)];
|
ee33c3dc311071d0fa47c08a6c45f2e15065cbd1 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3793/CH4/EX4.11/exp_4_11.sce | 78b7ca2800b4dd735b724b05958a5e96ed235b1e | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 740 | sce | exp_4_11.sce | clear;
clc;
L=.35/(2*%pi*50);
C=4.2*10^(-6)/(2*%pi*50);
Zc=sqrt(L/C);
bet=2*%pi*50*sqrt(L*C);
disp(bet);
V=1;
X=1;
step=600/20;
x=600:-step:0;
y=(((cos(bet*x))+(%i*(sin(bet*x))/X)))*V;
plot(x,abs(y),'k');
set(gca(),"auto_clear","off");
X=.25;
y=(((cos(bet*x))+(%i*(sin(bet*x))/X)))*V;
plot(x,abs(y),'-k');
X=.5;
y=(((cos(bet*x))+(%i*(sin(bet*x))/X)))*V;
plot(x,abs(y),'k.');
X=1.25;
y=(((cos(bet*x))+(%i*(sin(bet*x))/X)))*V;
plot(x,abs(y),'k*');
X=1.5;
y=(((cos(bet*x))+(%i*(sin(bet*x))/X)))*V;
plot(x,abs(y),'kdiamond');
xlabel('Distance from receiving end in km' );
ylabel('Sending end voltage in pu');
title("Voltage profile of a three phase tramsmission line");
set(gca(),"auto_clear","on");
|
0bdd836c29fc5adb8844233cc6ad7c912d80f663 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1658/CH27/EX27.4/Ex27_4.sce | 9a5eba1941629e91d665582f4bfa84a8ccfe6d15 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 123 | sce | Ex27_4.sce | clc;
//e.g 27.4
Vo=12.5;
Vin1=1.5;
Vin=0.25;
AV=Vo/Vin;
disp(AV);
AV1=Vo/Vin1;
beta=((AV/AV1)-1)/AV;
disp(beta);
|
1f2fc32441e3986105979d4897d3ddc695a8a4f6 | 449d555969bfd7befe906877abab098c6e63a0e8 | /213/CH10/EX10.26/10_26.sce | d5c94a135d14b78e2eab65cade947116dfdc7693 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 889 | sce | 10_26.sce | //To find dimensions of clutch plate
clc
//Given:
P=100 //kW
N=2400 //rpm
T=500*1000 //N-mm
p=0.07 //N/mm^2
mu=0.3
Ns=8 //Number of springs
k=40 //Stiffness, N/mm
n=2
//Solution:
//Calculating the inner radius of the friction plate
r2=(T/(n*mu*2*%pi*p*(1.25-1)*(1.25+1)/2))^(1/3) //mm
//Calculating the outer radius of the friction plate
r1=1.25*r2 //mm
//Calculating the total stiffness of the springs
s=k*Ns //N/mm
//Calculating the intensity of pressure
C=p*r2 //N/mm
//Calculating the axial force required to engage the clutch
W=2*%pi*C*(r1-r2) //N
//Calculating the initial compression in the springs
IC=W/s //Initial compression in the springs, mm
//Results:
printf("\n\n Outer radius of the friction plate, r1 = %.1f mm.\n",r1)
printf(" Inner radius of the friction plate, r2 = %d mm.\n",r2)
printf(" Initial compression in the springs = %.1f mm.\n\n",IC) |
75d8773edca9ecfa685e32a5b648c7a5013cf19d | 449d555969bfd7befe906877abab098c6e63a0e8 | /3651/CH1/EX1.11/Ex1_11.sce | bb4c4de9a8aad0b5ca97ef35d5f8989cec338e5a | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 288 | sce | Ex1_11.sce | //variable declaration
n=4
A=63.55 //Atomic wt. of NaCl
N=6.02*10**26 //Avagadro number
rho=8930 //density
//Calculations
a=((n*A)/(N*rho))**(1/3) //Lattice Constant
//Result
printf('lattice constant, a=%0.3f nm',(a*10**9))
|
bec872dc58e31dfd052a51e44298192f6423d1bc | b39dfe4655bc09a15e7cf35b887e89ef12f4c8e5 | /Atividade 2/Tarefa 2 - Análise da voz/PME3402_Grupo13_Atividade2_Tarefa2.sce | de12347ac9cbc84778583481755f048fcf07d1f2 | [] | no_license | vitoramr/PME3402-Laboratorio-de-Medicao-e-Controle-Discreto | 6a57131edff44859fb5c2c1c5b0dea0cc37735da | 8228b3ae442a3bb64208c924afc0daf418abe3c2 | refs/heads/master | 2023-01-09T23:08:48.007029 | 2020-11-19T22:43:27 | 2020-11-19T22:43:27 | 288,795,340 | 1 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 18,278 | sce | PME3402_Grupo13_Atividade2_Tarefa2.sce | /*
==============================================================
Escola Politécnica da USP
PME3402 - Laboratório de Medição e Controle Discreto
--------------------------------------------------------------
ATIVIDADE 2 TAREFA 2
Análise espectral do som de vogais
--------------------------------------------------------------
GRUPO 13
Membros:
Tiago Vieira de Campos Krause
Vinicius Rosario Dyonisio
Vítor Albuquerque Maranhao Ribeiro
Vitória Garcia Bittar
---------------------------------------------------------------
Professores responsáveis:
Edilson Hiroshi Tamai
Flávio Trigo
===============================================================
INSTRUÇÕES PARA RODAR O PROGRAMA
Antes de rodar o programa, siga os seguintes passos
1) Certifique-se de que o Scilab está aberto na pasta "/Atividade 2 - Análise da voz/" em que o programa se encontra
2) Certifique-se de que os áudios encontram-se na pasta "/Atividade 2 - Análise da voz/Dados", dentro da pasta atual do programa
3) Rode o programa
*/
//LIMPEZA DE MEMÓRIA
clear; // Limpeza de variáveis
clc; // Limpeza do console
xdel(winsid()) // Fecha as janelas abertas
// ============================================================
// INICIALIZAÇÃO DE VARIÁVEIS E PARÂMETROS
/*
Para armazenar os valores dos arquivos de som, como tinhamos muitos áudios,
seria inefetivo criar uma variável para cada áudio, além do fato de dificultar
a análise adicionando mais audios.
Assim, concatenamos os arquivos de som em seus respectivos vetores. Contudo,
como cada arquivo de som tem diferentes tamanhos, ou número de elementos,
o concatenamento direto não era possível.
Para contornar isso, analisamos os espectros de frequência dos sinais e
verificamos que os áudios tinham valores baixos em suas frequências para um número
de elementos alto, e decidimos fixar o número de elementos da fft armazenados para
cada dado.
Porém, como a escala de frequência de cada transformada de Fourier depende do
número de elementos do vetor original, também criamos uma variável para armazenar
este número de elementos
*/
fa = 44100; //[Hz] Frequência de amostragem dos microfones
N_elementos = 800;
// ============================================================
// CARREGAMENTO DOS DADOS
// Obtendo os caminhos de cada arquivo de som
base_path = pwd(); // Diretório atual onde o programa está
s = filesep(); // Separador de arquivos para o OS atual ( '\' para Windows e '/' para Linux)
data_directory = base_path + s + 'Dados';
// Lista do caminho da cada arquivo de som
a_aberto_filespath = listfiles(data_directory + s + '*A.wav'); // Lista de todos os arquivos com fim 'A.wav'
a_fechado_filespath = listfiles(data_directory + s + '*Â.wav'); // Lista de todos os arquivos com fim 'Â.wav'
e_aberto_filespath = listfiles(data_directory + s + '*É.wav'); // Lista de todos os arquivos com fim 'É.wav'
e_fechado_filespath = listfiles(data_directory + s + '*Ê.wav'); // Lista de todos os arquivos com fim 'Ê.wav'
i_aberto_filespath = listfiles(data_directory + s + '*I.wav'); // Lista de todos os arquivos com fim 'I.wav'
o_aberto_filespath = listfiles(data_directory + s + '*Ó.wav'); // Lista de todos os arquivos com fim 'Ó.wav'
o_fechado_filespath = listfiles(data_directory + s + '*Ô.wav'); // Lista de todos os arquivos com fim 'Ô.wav'
// Tratamento dos dados e concatenamento dos arquivos de som nos seus respectivos vetores
function [audio_fft, audio_psd, freq_audio] = leitura_audios(nomes_dos_arquivos)
/*
Recebe "nomes_dos_arquivos" uma lista de m elementos com as strings contendo
a localização dos m arquivos que contêm os áudios de formato .wav
Lê esses arquivos armazenando em matrizes os N_elementos primeiros valores da:
FFT, PSD e Vetor de frequências do áudio.
Tamanho das matrizes de output: m_audios x N_elementos
*/
audio_fft = [];
audio_psd = [];
freq_audio = [];
for i = 1:size(nomes_dos_arquivos,1) // Para cada um dos m arquivos de áudio presentes na lista de nomes
[audio_t, fs] = wavread(nomes_dos_arquivos(i)); // Leitura do arquivo de áudio e da sua frequência de amostragem
N = size(audio_t,2); // Número de elementos do arquivo
audio_f = fft(audio_t(1,:),-1); // FFT do sinal temporal
pot_audio_f = ( 1.0/(fs*N) ) * (abs(audio_f) ).^2 ; // Potência espectral do sinal
audio_fft = [audio_fft;
abs(audio_f(1:N_elementos))]; // Para possibilitar o concatenamento, pega-se apenas os primeiros N_elementos da FFT
audio_psd = [audio_psd;
pot_audio_f(1:N_elementos)]; // Armazenamento da PSD do sinal
freq_audio = [freq_audio;
(fs/N)*(0:N_elementos-1) ]; // Armazena-se também a escala de frequência do sinal, até o tamanho N_elementos
end
endfunction
//Exemplo para compreensão das variáveis:
//a_aberto --> Tamanho: (m_audios x N_elementos). Matriz com o Espectro de cada áudio falando "A" (aberto)
//a_aberto_pot --> Tamanho: (m_audios x N_elementos). Matriz com a PSD de cada áudio falando "A" (aberto)
//f_a_aberto --> Tamanho: (m_audios x N_elementos). Matriz com a escala de frequência para cada áudio falando "A" (aberto)
[a_aberto , a_aberto_pot , f_a_aberto ] = leitura_audios(a_aberto_filespath);
[a_fechado, a_fechado_pot, f_a_fechado] = leitura_audios(a_fechado_filespath);
[e_aberto , e_aberto_pot , f_e_aberto ] = leitura_audios(e_aberto_filespath);
[e_fechado, e_fechado_pot, f_e_fechado] = leitura_audios(e_fechado_filespath);
[i_aberto , i_aberto_pot , f_i_aberto ] = leitura_audios(i_aberto_filespath);
[o_aberto , o_aberto_pot , f_o_aberto ] = leitura_audios(o_aberto_filespath);
[o_fechado, o_fechado_pot, f_o_fechado] = leitura_audios(o_fechado_filespath);
// ============================================================
// TRATAMENTO DOS DADOS
// Vizualização do espectro de cada um dos áudios para a vogal "A" (aberto)
fig1 = scf(1);
fig1.color_map = rainbowcolormap(size(a_aberto,1)); // Escala de cores para os plots
for i = 1:size(a_aberto,1) // Para cada áudio da matriz "A" aberto
subplot(2,2,i) // Plota uma figura 2x2 com 4 gráficos
plot(f_a_aberto(i,:),a_aberto(i,:)); // Gráficos de f x Espectro do sinal
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
title('Figura 1.' + string(i) + ': Espectro de frequências do áudio ' + string(i) + ' para a vogal A (aberta)')
xlabel('f (Hz)');
ylabel('|H(f)|');
end
/*
Como é visível na figura 1, os audios possuem amplitudes muito distintas. Isso
ocorre, pois os áudio provêm de diferentes fontes, já que cada celular possui
sensores diferentes com arquiteturas diferentes e cada pessoa e gravação possui
volumes diferentes.
Dessa forma, como o interesse é comparar os áudios para identificar as diferentes
frequências de cada vogal, faz-se necessária a normalização dos valores obtidos.
Isso é feito dividindo o valor de cada áudio pela sua norma em L2 para que todos
os áudios adquiram norma igual a 1.
Além disso, utilizaremos na comparação os valores da PSD normalizados, pois estas
mostraram-se distinguir melhor as frequências que mais influenciam no áudio
*/
function matriz_normalizada = normaliza_audios(matriz_de_audio)
/*
Normaliza as linhas de uma matriz dividindo seus valores pela norma em L2 de sua respectiva linha
*/
matriz_normalizada = zeros(matriz_de_audio);
for i = 1:size(matriz_de_audio,1); //Para cada áudio que o possui
norma = norm(matriz_de_audio(i,:)); // Calcula a norma da linha
matriz_normalizada(i,:) = matriz_de_audio(i,:)./norma; //Dividindo cada valor do da linha por sua norma
end
endfunction
// Normalização dos vetores
// Inicializando os vetores normalizados como vetores de zeros
a_aberto_normalizado = normaliza_audios(a_aberto_pot) ;
a_fechado_normalizado = normaliza_audios(a_fechado_pot);
e_aberto_normalizado = normaliza_audios(e_aberto_pot) ;
e_fechado_normalizado = normaliza_audios(e_fechado_pot);
i_aberto_normalizado = normaliza_audios(i_aberto_pot) ;
o_aberto_normalizado = normaliza_audios(o_aberto_pot) ;
o_fechado_normalizado = normaliza_audios(o_fechado_pot);
// ============================================================
// PLOTAGEM DOS GRÁFICOS
// Análise geral das vogais
fig2 = scf(2);
fig2.color_map = rainbowcolormap(size(a_aberto,1));
subplot(4,2,1)
xtitle('Figura 2.1: Densidade de frequência normalizada dos áudios para a vogal: A (aberto)' , 'f (Hz)','PSD normalizada');
for i = 1:size(a_aberto_normalizado,1)
plot(f_a_aberto(i,:),a_aberto_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
//legend(['Vítor', 'Vitória','Vinicius', 'Tiago'])
subplot(4,2,2)
xtitle('Figura 2.2: Densidade de frequência normalizada dos áudios para a vogal: A (fechado)' , 'f (Hz)','PSD normalizada');
for i = 1:size(a_fechado,1)
plot(f_a_fechado(i,:),a_fechado_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
subplot(4,2,3)
xtitle('Figura 2.3: Densidade de frequência normalizada dos áudios para a vogal: É (aberto)' , 'f (Hz)','PSD normalizada');
for i = 1:size(e_aberto,1)
plot(f_e_aberto(i,:),e_aberto_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
subplot(4,2,4)
xtitle('Figura 2.4: Densidade de frequência normalizada dos áudios para a vogal: Ê (fechado)' , 'f (Hz)','PSD normalizada');
for i = 1:size(e_fechado,1)
plot(f_e_fechado(i,:),e_fechado_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
subplot(4,2,5)
xtitle(' Figura 2.5: Densidade de frequência normalizada dos áudios para a vogal: Ó (aberto)' , 'f (Hz)','PSD normalizada');
for i = 1:size(o_aberto,1)
plot(f_o_aberto(i,:),o_aberto_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
subplot(4,2,6)
xtitle('Figura 2.6: Densidade de frequência normalizada dos áudios para a vogal: Ô (fechado)' , 'f (Hz)','PSD normalizada');
for i = 1:size(o_fechado,1)
plot(f_o_fechado(i,:),o_fechado_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
subplot(4,2,7)
xtitle('Figura 2.7: Densidade de frequência normalizada dos áudios para a vogal: I (Aberto)' , 'f (Hz)','PSD normalizada');
for i = 1:size(i_aberto,1)
plot(f_i_aberto(i,:),i_aberto_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
// Análise específica das vogais
// A aberto normalizado
fig3 = scf(3);
fig3.color_map = rainbowcolormap(size(a_aberto,1));
for i = 1:size(a_aberto_normalizado,1)
subplot(2,2,i)
xtitle('Figura 3.' + string(i) + ': PSD normalizada do audio ' + string(i) + ' para a Vogal: A (aberto)' , 'f (Hz)','PSD normalizada');
plot(f_a_aberto(i,:),a_aberto_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
// A fechado normalizado
fig4 = scf(4);
fig4.color_map = rainbowcolormap(size(a_fechado,1));
for i = 1:size(a_fechado_normalizado,1)
subplot(2,2,i)
xtitle('Figura 4.' + string(i) + ': PSD normalizada do audio ' + string(i) + ' para a Vogal: A (fechado)' , 'f (Hz)','PSD normalizada');
plot(f_a_fechado(i,:),a_fechado_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
// E aberto normalizado
fig5 = scf(5);
fig5.color_map = rainbowcolormap(size(e_aberto,1));
for i = 1:size(e_aberto_normalizado,1)
subplot(2,2,i)
xtitle('Figura 5.' + string(i) + ': PSD normalizada do audio ' + string(i) + ' para a Vogal: E (aberto)' , 'f (Hz)','PSD normalizada');
plot(f_e_aberto(i,:),e_aberto_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
// E fechado normalizado
fig6 = scf(6);
fig6.color_map = rainbowcolormap(size(e_fechado,1));
for i = 1:size(e_fechado_normalizado,1)
subplot(2,2,i)
xtitle('Figura 6.' + string(i) + ': PSD normalizada de cada audio para a Vogal: E (fechado)' , 'f (Hz)','PSD normalizada');
plot(f_e_fechado(i,:),e_fechado_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
// I normalizado
fig7 = scf(7);
fig5.color_map = rainbowcolormap(size(i_aberto,1));
for i = 1:size(i_aberto_normalizado,1)
subplot(2,2,i)
xtitle('Figura 7.' + string(i) + ': PSD normalizada do audio ' + string(i) + ' para a Vogal: I' , 'f (Hz)','PSD normalizada');
plot(f_i_aberto(i,:),i_aberto_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
// O aberto normalizado
fig8 = scf(8);
fig8.color_map = rainbowcolormap(size(o_aberto,1));
for i = 1:size(o_aberto_normalizado,1)
subplot(2,2,i)
xtitle('Figura 8.' + string(i) + ': PSD normalizada do audio ' + string(i) + ' para a Vogal: O (aberto)' , 'f (Hz)','PSD normalizada');
plot(f_o_aberto(i,:),o_aberto_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
// O fechado normalizado
fig9 = scf(9);
fig9.color_map = rainbowcolormap(size(o_fechado,1));
for i = 1:size(o_fechado_normalizado,1)
subplot(2,2,i)
xtitle('Figura 9.' + string(i) + ': PSD normalizada do audio ' + string(i) + ' para a Vogal: O (fechado)' , 'f (Hz)','PSD normalizada');
plot(f_o_fechado(i,:),o_fechado_normalizado(i,:));
plot_propriedades = gce();
plot_propriedades.children.foreground = i; // Mudando as cores a cada elemento
end
// ============================================================
// ANÁLISE DOS RESULTADOS
/*
Quanto mais baixa a frequência, mais grave é o som.
A faixa de voz masculina costuma variar entre 80 Hz e 150 Hz, sendo a média da
frequência da voz dos homens adultos brasileiros é de 113 Hz. A faixa feminina
varia entre 150 Hz e 250 Hz.
Analisando os gráficos gerados e normalizados, primeiramente observa-se que há
grande diferença nas frequências atingidas por cada áudio mesmo que para uma
mesma vogal, isso pode ser consequência de eventuais ruídos captados na gravaação
e diferenças nos timbres de voz, como por exemplo a mesma vogal pronunciada por
uma voz feminina e uma voz masculina. Porém mesmo com esse ruídos é possível
observar certos padrões.
Primeiramente olhando as figuras 3.1 a 3.4, observa-se que para todos os membro há
picos próximo do 200 Hz e algum sinal na faixa de 300-350 Hz, sendo provavelmente
a frequência natural e o harmônico respectivamente para essa faixa de áudio.
O mesmo é observado para a vogal  (Fechado), indicando a similaridade entre os sons
porém aparece também para 3 das 4 faixas de áudio um pico em frequências mais
graves (100-200 Hz) indicando que o som tende a ser mais grave do que para o caso
do A aberto.
Para a vogal E aberta a tendência é haver um pico próximo a 200 Hz (Frequência natural)
e um outro próximo a 450 Hz (Harmônico).
Comparando a vogal E aberta com a vogal E fechada O pico em torno de 200 Hz decresce em e
o pico de 450 Hz aumenta a intensidade e descola para mais próximo de 350 Hz para indicando
que o som se torna um pouco mais grave.
Para a vogal I há um pico na faixa 200-300 Hz para todos os áudios gravados, e aparece
em 3 das 4 gravações um segundo pico na faixa de 400-500 Hz indicando que esse som tende
a ser mais agudo que a vogal A.
Para a vogal O acontece o mesmo que para a vogal E com um pico em torno de 200 Hz que diminui a
intensidade da caso aberto para o fechado e um pico na faixa de 400 a 500 Hz que tenda a se deslocar
para a esquerda e aumentar em intensidade para 3 dos 4 áudios.
É interessante também observar que a faixa de áudio do membro do grupo Vitor, indicado pelo índice x.3
de cor azul clara tende a apresentar menos frequências graves quando comparado com os demais, isso pode
estar associado a alguma característica do medidor ou a uma voz naturalmente mais grave que dos demais.
Um fenômeno parecido acontece para o membro de grupo Vitória, porém com uma concentração maior de
frequências agudas, isso pode estar associado ao fato de ser o único membro feminino do grupo
apreesentando uma voz mais aguda que os demais membros.
Não é possível identificar a vogal gravada a partir do espectro principalmente pelo fato de have uma
variação significativa entre uma medição e outra e ao fato das diferentes vogais apresentarem picos
em regiões parecidas, como exemplo todos as vogais medidas apresentaram pico em torno de 200 Hz para
pelo menos uma parcela das faixas de áudio analisadas.
*/
|
fbad4b6d86eeea7d5555fa1b9d3d4fd029f0eac8 | 009e6209a86f0838f0faca8a33b2c162e5d1a7a6 | /src/scripts/particionUniforme.sce | 440ec011fa2f658723a1a8d91738785a57df9bf4 | [] | no_license | MoisesU/MESO-MetodosNumericos | 90a62a31e3213c50dec55228ceca7ce034cfbb7c | 17fe0efa1690ac93f36799a12a9f9c99f1ab94a4 | refs/heads/main | 2023-06-02T05:51:03.641326 | 2021-06-20T03:18:17 | 2021-06-20T03:18:17 | 306,203,044 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 268 | sce | particionUniforme.sce | function [res, tab] = particionUniforme(f, a, b, rect)
h = (b - a)/rect
tab = []
x = a
res = 0
for i=1:1:rect
tab(1, i) = x;
tab(2, i) = f(x);
x = x + h;
res = res + tab(2, i);
end
res = res * h;
endfunction
|
32aa69a2b19ba1a1e92e4e4834235757fa075ea6 | 2e676e3b1cebfbb9d20f9b935ceacd507c57d36a | /Octave/octave-4.2.1/share/octave/4.2.1/etc/tests/fixed/prefer.tst | e3fa45b98a139e891fee15da315d8f8ec9f67256 | [] | no_license | vohrahul/ML-ang-coursera | 239469e763b290aa178b7aa8a86eda08e4e7f4be | 4c24fd2ecfb9f3de7df15e3a9f75627f782f9915 | refs/heads/master | 2022-12-28T03:45:54.810173 | 2020-10-16T12:33:25 | 2020-10-16T12:33:25 | 304,620,441 | 1 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 4,657 | tst | prefer.tst | ## Copyright (C) 2006-2017 John W. Eaton
##
## This file is part of Octave.
##
## Octave is free software; you can redistribute it and/or modify it
## under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or (at
## your option) any later version.
##
## Octave is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with Octave; see the file COPYING. If not, see
## <http://www.gnu.org/licenses/>.
%!test
%! m = [3 2];
%! assert (all (m == (3:-1:2)));
%!test
%! m = [3,
%! 2];
%! assert (all (m == (3:-1:2)'));
%!test
%! a = 2;
%! assert ([a - 1], 1);
%!test
%! m = [3,2];
%! fail ("[m ']");
%!assert (all ([3 2] == (3:-1:2)))
%!assert (all ([3, 2] == (3:-1:2)))
%!test
%! m = [3,2];
%! assert (all ([m (1)] == (3:-1:1)));
%!test
%! m = [3,2];
%! assert ([m(1)],3);
%!test
%! a = 2;
%! assert ([a- 1], 1);
%!test
%! a = 1;
%! assert (all ([a -1] == (1:-2:-1)));
%!test
%! wsn = warning ("query", "Octave:str-to-num");
%! warning ("off", "Octave:str-to-num");
%! assert ("d" + 0, 100);
%! warning (wsn.state, "Octave:str-to-num");
%!test
%! wsn = warning ("query", "Octave:str-to-num");
%! warning ("on", "Octave:str-to-num");
%! fail ("'d' + 0", "warning");
%! warning (wsn.state, "Octave:str-to-num");
%!test
%! wir = warning ("query", "Octave:imag-to-real");
%! warning ("off", "Octave:imag-to-real");
%! assert (eye (1+i), 1);
%! warning (wir.state, "Octave:imag-to-real");
%!test
%! wir = warning ("query", "Octave:imag-to-real");
%! warning ("on", "Octave:imag-to-real");
%! fail ("eye (1+i)", "warning");
%! warning (wir.state, "Octave:imag-to-real");
%!test
%! wrre = warning ("query", "Octave:resize-on-range-error");
%! warning ("off", "Octave:resize-on-range-error");
%! clear a;
%! a(2) = 1; a(3) = 2;
%! assert (all (a == [0,1,2]));
%! warning (wrre.state, "Octave:resize-on-range-error");
%!test
%! clear a;
%! a(1) = 1; a(2) = 2;
%! assert (all (a == [1,2]));
%!test
%! ped = print_empty_dimensions ();
%! print_empty_dimensions (0);
%! a = cell (1, 1);
%! b = type ("-q", "a");
%! assert (!isempty (findstr (b{1}, "[]")));
%! assert (isempty (findstr (b{1} ,"[](0x0)")));
%! print_empty_dimensions (ped);
%!test
%! ped = print_empty_dimensions ();
%! print_empty_dimensions (1);
%! a = cell (1, 1);
%! b = type ("-q", "a");
%! assert (!isempty (findstr (b{1}, "[](0x0)")));
%! print_empty_dimensions (ped);
%!assert (all (size (inv ([])) == [0, 0]))
%!assert (all (svd ([]) == zeros (0, 1)))
%!test
%! sp = save_precision ();
%! save_precision (1);
%! x = pi;
%! nm = tempname ();
%! save ("-text", nm, "x");
%! clear x;
%! load (nm);
%! unlink (nm);
%! assert (x,3);
%! save_precision (sp);
%!test
%! sp = save_precision ();
%! save_precision (5);
%! x = pi;
%! nm = tempname ();
%! save ("-text", nm, "x");
%! clear x;
%! load (nm);
%! unlink (nm);
%! assert (x, 3.1416);
%! save_precision (sp);
%% FIXME: How to capture standard output for comparison?
%!function f ()
%! 1
%!endfunction
%!#test
%! sf = silent_functions ();
%! silent_functions (0);
%! f
%! assert (??);
%! silent_functions (sf);
%% FIXME: Same problem as above!!!
%!function f ()
%! 1
%!endfunction
%!#test
%! sf = silent_functions ();
%! silent_functions (1);
%! f
%! assert (??);
%! silent_functions (sf);
%!test
%! wndz = warning ("query", "Octave:neg-dim-as-zero");
%! warning ("on", "Octave:neg-dim-as-zero");
%! fail ("eye (-1) == []", "warning", "converting negative dimension");
%! warning (wndz.state, "Octave:neg-dim-as-zero");
%!test
%! wndz = warning ("query", "Octave:neg-dim-as-zero");
%! warning ("off", "Octave:neg-dim-as-zero");
%! assert (all (size (eye (-1)) == [0, 0]));
%! warning (wndz.state, "Octave:neg-dim-as-zero");
%!test
%! watv = warning ("query", "Octave:assign-as-truth-value");
%! warning ("on", "Octave:assign-as-truth-value");
%! fail ("if (x = 1) 1; endif", "warning", "assignment used as truth value");
%! warning (watv.state, "Octave:assign-as-truth-value");
%!test
%! wdbz = warning ("query", "Octave:divide-by-zero");
%! warning ("off", "Octave:divide-by-zero");
%! assert (isinf (1/0));
%! warning (wdbz.state, "Octave:divide-by-zero");
%!test
%! wdbz = warning ("query", "Octave:divide-by-zero");
%! warning ("on", "Octave:divide-by-zero");
%! a = 1;
%! b = 0;
%! fail ("isinf (a/b);", "warning", "division by zero");
%! warning (wdbz.state, "Octave:divide-by-zero");
|
782b69cf9e58959f50972c65a83bd2c3af9f69a6 | cd227ab3e84ec2423b0c65d66ced9003ea032200 | /SCUMI/Mixed/ErrFile/err.mix2.sci | 97a0ab5e01a3f3cc34461ce80aeea01d01c903b2 | [] | no_license | seanken/sc_compare_helpers | 24d4e5aabc04036c2830e75c69c5c895d9592752 | e5e9c2e93ba7b85f6a30176bb32a761a6c28eaab | refs/heads/master | 2020-04-05T13:15:46.004764 | 2018-11-09T17:36:57 | 2018-11-09T17:36:57 | 156,894,365 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 773,975 | sci | err.mix2.sci | mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1': No such file or directory
/var/spool/uger-8.5.5/uger-c030/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/uger-c030/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/uger-c030/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/uger-c030/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/comb.2.fastq.gz': No such file or directory
2018-09-27 08:45:46,129: INFO: Cell barcode in configure file
2018-09-27 08:45:46,130: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/uger-c030/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/results.star_align.bam: No such file or directory
2018-09-27 08:45:48,372: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell1/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/comb.2.fastq.gz': No such file or directory
2018-09-27 09:24:49,600: INFO: Cell barcode in configure file
2018-09-27 09:24:49,602: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/results.star_align.bam: No such file or directory
2018-09-27 09:24:57,453: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell2/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/comb.2.fastq.gz': No such file or directory
2018-09-27 09:25:20,504: INFO: Cell barcode in configure file
2018-09-27 09:25:20,506: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/results.star_align.bam: No such file or directory
2018-09-27 09:25:28,378: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell3/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/comb.2.fastq.gz': No such file or directory
2018-09-27 09:25:51,928: INFO: Cell barcode in configure file
2018-09-27 09:25:51,930: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/results.star_align.bam: No such file or directory
2018-09-27 09:25:59,897: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell4/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/comb.2.fastq.gz': No such file or directory
2018-09-27 09:26:23,901: INFO: Cell barcode in configure file
2018-09-27 09:26:23,904: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/results.star_align.bam: No such file or directory
2018-09-27 09:26:32,262: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell5/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/comb.2.fastq.gz': No such file or directory
2018-09-27 09:26:53,862: INFO: Cell barcode in configure file
2018-09-27 09:26:53,864: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/results.star_align.bam: No such file or directory
2018-09-27 09:27:02,156: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell6/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/comb.2.fastq.gz': No such file or directory
2018-09-27 09:27:17,745: INFO: Cell barcode in configure file
2018-09-27 09:27:17,747: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/results.star_align.bam: No such file or directory
2018-09-27 09:27:21,088: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell7/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/comb.2.fastq.gz': No such file or directory
2018-09-27 09:27:37,666: INFO: Cell barcode in configure file
2018-09-27 09:27:37,668: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/results.star_align.bam: No such file or directory
2018-09-27 09:27:45,766: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell8/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/comb.2.fastq.gz': No such file or directory
2018-09-27 09:28:04,300: INFO: Cell barcode in configure file
2018-09-27 09:28:04,302: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/results.star_align.bam: No such file or directory
2018-09-27 09:28:07,470: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell9/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/comb.2.fastq.gz': No such file or directory
2018-09-27 09:28:18,570: INFO: Cell barcode in configure file
2018-09-27 09:28:18,571: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/results.star_align.bam: No such file or directory
2018-09-27 09:28:21,803: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell10/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/comb.2.fastq.gz': No such file or directory
2018-09-27 09:28:35,497: INFO: Cell barcode in configure file
2018-09-27 09:28:35,499: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/results.star_align.bam: No such file or directory
2018-09-27 09:28:38,940: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell11/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/comb.2.fastq.gz': No such file or directory
2018-09-27 09:28:51,508: INFO: Cell barcode in configure file
2018-09-27 09:28:51,510: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/results.star_align.bam: No such file or directory
2018-09-27 09:28:55,816: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell12/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/comb.2.fastq.gz': No such file or directory
2018-09-27 09:29:16,455: INFO: Cell barcode in configure file
2018-09-27 09:29:16,457: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/results.star_align.bam: No such file or directory
2018-09-27 09:29:24,775: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell13/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/comb.2.fastq.gz': No such file or directory
2018-09-27 09:29:47,351: INFO: Cell barcode in configure file
2018-09-27 09:29:47,358: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/results.star_align.bam: No such file or directory
2018-09-27 09:29:55,749: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell14/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/comb.2.fastq.gz': No such file or directory
2018-09-27 09:30:22,780: INFO: Cell barcode in configure file
2018-09-27 09:30:22,782: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/results.star_align.bam: No such file or directory
2018-09-27 09:30:30,954: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell15/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/comb.2.fastq.gz': No such file or directory
2018-09-27 09:30:53,321: INFO: Cell barcode in configure file
2018-09-27 09:30:53,323: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/results.star_align.bam: No such file or directory
2018-09-27 09:31:02,269: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell16/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/comb.2.fastq.gz': No such file or directory
2018-09-27 09:31:26,477: INFO: Cell barcode in configure file
2018-09-27 09:31:26,479: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/results.star_align.bam: No such file or directory
2018-09-27 09:31:34,580: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell17/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/comb.2.fastq.gz': No such file or directory
2018-09-27 09:31:56,194: INFO: Cell barcode in configure file
2018-09-27 09:31:56,197: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/results.star_align.bam: No such file or directory
2018-09-27 09:32:05,169: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell18/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/comb.2.fastq.gz': No such file or directory
2018-09-27 09:32:30,785: INFO: Cell barcode in configure file
2018-09-27 09:32:30,787: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/results.star_align.bam: No such file or directory
2018-09-27 09:32:38,700: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell19/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/comb.2.fastq.gz': No such file or directory
2018-09-27 09:33:01,967: INFO: Cell barcode in configure file
2018-09-27 09:33:01,970: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/results.star_align.bam: No such file or directory
2018-09-27 09:33:09,872: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell20/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/comb.2.fastq.gz': No such file or directory
2018-09-27 09:33:31,365: INFO: Cell barcode in configure file
2018-09-27 09:33:31,367: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/results.star_align.bam: No such file or directory
2018-09-27 09:33:39,305: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell21/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/comb.2.fastq.gz': No such file or directory
2018-09-27 09:34:02,181: INFO: Cell barcode in configure file
2018-09-27 09:34:02,183: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/results.star_align.bam: No such file or directory
2018-09-27 09:34:10,157: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell22/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/comb.2.fastq.gz': No such file or directory
2018-09-27 09:34:33,161: INFO: Cell barcode in configure file
2018-09-27 09:34:33,164: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/results.star_align.bam: No such file or directory
2018-09-27 09:34:40,995: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell23/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/comb.2.fastq.gz': No such file or directory
2018-09-27 09:35:05,725: INFO: Cell barcode in configure file
2018-09-27 09:35:05,727: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/results.star_align.bam: No such file or directory
2018-09-27 09:35:13,962: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell24/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/comb.2.fastq.gz': No such file or directory
2018-09-27 09:35:39,166: INFO: Cell barcode in configure file
2018-09-27 09:35:39,168: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/results.star_align.bam: No such file or directory
2018-09-27 09:35:47,256: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell25/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/comb.2.fastq.gz': No such file or directory
2018-09-27 09:36:09,376: INFO: Cell barcode in configure file
2018-09-27 09:36:09,379: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/results.star_align.bam: No such file or directory
2018-09-27 09:36:17,905: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell26/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/comb.2.fastq.gz': No such file or directory
2018-09-27 09:36:40,702: INFO: Cell barcode in configure file
2018-09-27 09:36:40,704: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/results.star_align.bam: No such file or directory
2018-09-27 09:36:48,664: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell27/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/comb.2.fastq.gz': No such file or directory
2018-09-27 09:37:12,817: INFO: Cell barcode in configure file
2018-09-27 09:37:12,820: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/results.star_align.bam: No such file or directory
2018-09-27 09:37:20,609: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell28/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/comb.2.fastq.gz': No such file or directory
2018-09-27 09:37:44,104: INFO: Cell barcode in configure file
2018-09-27 09:37:44,105: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/results.star_align.bam: No such file or directory
2018-09-27 09:37:51,936: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell29/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/comb.2.fastq.gz': No such file or directory
2018-09-27 09:38:06,924: INFO: Cell barcode in configure file
2018-09-27 09:38:06,926: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/results.star_align.bam: No such file or directory
2018-09-27 09:38:10,119: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell30/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/comb.2.fastq.gz': No such file or directory
2018-09-27 09:38:20,968: INFO: Cell barcode in configure file
2018-09-27 09:38:20,969: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/results.star_align.bam: No such file or directory
2018-09-27 09:38:24,176: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell31/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/comb.2.fastq.gz': No such file or directory
2018-09-27 09:38:35,729: INFO: Cell barcode in configure file
2018-09-27 09:38:35,730: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/results.star_align.bam: No such file or directory
2018-09-27 09:38:39,054: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell32/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/comb.2.fastq.gz': No such file or directory
2018-09-27 09:38:53,401: INFO: Cell barcode in configure file
2018-09-27 09:38:53,402: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/results.star_align.bam: No such file or directory
2018-09-27 09:38:56,852: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell33/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/comb.2.fastq.gz': No such file or directory
2018-09-27 09:39:08,069: INFO: Cell barcode in configure file
2018-09-27 09:39:08,071: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/results.star_align.bam: No such file or directory
2018-09-27 09:39:11,241: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell34/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/comb.2.fastq.gz': No such file or directory
2018-09-27 09:39:23,276: INFO: Cell barcode in configure file
2018-09-27 09:39:23,278: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/results.star_align.bam: No such file or directory
2018-09-27 09:39:26,450: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell35/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/comb.2.fastq.gz': No such file or directory
2018-09-27 09:39:36,835: INFO: Cell barcode in configure file
2018-09-27 09:39:36,837: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/results.star_align.bam: No such file or directory
2018-09-27 09:39:40,682: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell36/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/comb.2.fastq.gz': No such file or directory
2018-09-27 09:39:54,023: INFO: Cell barcode in configure file
2018-09-27 09:39:54,025: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/results.star_align.bam: No such file or directory
2018-09-27 09:39:57,386: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell37/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/comb.2.fastq.gz': No such file or directory
2018-09-27 09:40:09,838: INFO: Cell barcode in configure file
2018-09-27 09:40:09,839: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/results.star_align.bam: No such file or directory
2018-09-27 09:40:13,196: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell38/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/comb.2.fastq.gz': No such file or directory
2018-09-27 09:40:25,561: INFO: Cell barcode in configure file
2018-09-27 09:40:25,563: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/results.star_align.bam: No such file or directory
2018-09-27 09:40:28,843: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell39/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/comb.2.fastq.gz': No such file or directory
2018-09-27 09:40:47,748: INFO: Cell barcode in configure file
2018-09-27 09:40:47,750: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/results.star_align.bam: No such file or directory
2018-09-27 09:40:55,801: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell40/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/comb.2.fastq.gz': No such file or directory
2018-09-27 09:41:11,704: INFO: Cell barcode in configure file
2018-09-27 09:41:11,707: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/results.star_align.bam: No such file or directory
2018-09-27 09:41:15,433: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell41/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/comb.2.fastq.gz': No such file or directory
2018-09-27 09:41:27,411: INFO: Cell barcode in configure file
2018-09-27 09:41:27,414: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/results.star_align.bam: No such file or directory
2018-09-27 09:41:30,802: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell42/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/comb.2.fastq.gz': No such file or directory
2018-09-27 09:41:43,291: INFO: Cell barcode in configure file
2018-09-27 09:41:43,293: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/results.star_align.bam: No such file or directory
2018-09-27 09:41:46,886: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell43/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/comb.2.fastq.gz': No such file or directory
2018-09-27 09:42:03,047: INFO: Cell barcode in configure file
2018-09-27 09:42:03,049: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/results.star_align.bam: No such file or directory
2018-09-27 09:42:06,973: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell44/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/comb.2.fastq.gz': No such file or directory
2018-09-27 09:42:18,137: INFO: Cell barcode in configure file
2018-09-27 09:42:18,139: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/results.star_align.bam: No such file or directory
2018-09-27 09:42:21,792: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell45/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/comb.2.fastq.gz': No such file or directory
2018-09-27 09:42:33,604: INFO: Cell barcode in configure file
2018-09-27 09:42:33,606: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/results.star_align.bam: No such file or directory
2018-09-27 09:42:37,601: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell46/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/comb.2.fastq.gz': No such file or directory
2018-09-27 09:42:49,142: INFO: Cell barcode in configure file
2018-09-27 09:42:49,144: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/results.star_align.bam: No such file or directory
2018-09-27 09:42:53,052: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell47/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/comb.2.fastq.gz': No such file or directory
2018-09-27 09:43:05,594: INFO: Cell barcode in configure file
2018-09-27 09:43:05,595: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/results.star_align.bam: No such file or directory
2018-09-27 09:43:09,636: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell48/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/comb.2.fastq.gz': No such file or directory
2018-09-27 09:43:26,550: INFO: Cell barcode in configure file
2018-09-27 09:43:26,552: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/results.star_align.bam: No such file or directory
2018-09-27 09:43:30,146: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell49/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/comb.2.fastq.gz': No such file or directory
2018-09-27 09:43:41,044: INFO: Cell barcode in configure file
2018-09-27 09:43:41,046: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/results.star_align.bam: No such file or directory
2018-09-27 09:43:44,743: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell50/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/comb.2.fastq.gz': No such file or directory
2018-09-27 09:43:57,490: INFO: Cell barcode in configure file
2018-09-27 09:43:57,491: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/results.star_align.bam: No such file or directory
2018-09-27 09:44:01,357: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell51/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/comb.2.fastq.gz': No such file or directory
2018-09-27 09:44:14,216: INFO: Cell barcode in configure file
2018-09-27 09:44:14,218: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/results.star_align.bam: No such file or directory
2018-09-27 09:44:18,206: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell52/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/comb.2.fastq.gz': No such file or directory
2018-09-27 09:44:30,386: INFO: Cell barcode in configure file
2018-09-27 09:44:30,388: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/results.star_align.bam: No such file or directory
2018-09-27 09:44:34,708: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell53/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/comb.2.fastq.gz': No such file or directory
2018-09-27 09:44:50,292: INFO: Cell barcode in configure file
2018-09-27 09:44:50,293: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/results.star_align.bam: No such file or directory
2018-09-27 09:44:54,509: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell54/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/comb.2.fastq.gz': No such file or directory
2018-09-27 09:45:09,290: INFO: Cell barcode in configure file
2018-09-27 09:45:09,291: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/results.star_align.bam: No such file or directory
2018-09-27 09:45:12,716: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell55/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/comb.2.fastq.gz': No such file or directory
2018-09-27 09:45:25,816: INFO: Cell barcode in configure file
2018-09-27 09:45:25,818: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/results.star_align.bam: No such file or directory
2018-09-27 09:45:29,350: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell56/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/comb.2.fastq.gz': No such file or directory
2018-09-27 09:45:43,442: INFO: Cell barcode in configure file
2018-09-27 09:45:43,444: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/results.star_align.bam: No such file or directory
2018-09-27 09:45:47,067: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell57/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/comb.2.fastq.gz': No such file or directory
2018-09-27 09:45:59,946: INFO: Cell barcode in configure file
2018-09-27 09:45:59,948: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/results.star_align.bam: No such file or directory
2018-09-27 09:46:03,559: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell58/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/comb.2.fastq.gz': No such file or directory
2018-09-27 09:46:14,580: INFO: Cell barcode in configure file
2018-09-27 09:46:14,581: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/results.star_align.bam: No such file or directory
2018-09-27 09:46:17,934: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell59/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/comb.2.fastq.gz': No such file or directory
2018-09-27 09:46:30,778: INFO: Cell barcode in configure file
2018-09-27 09:46:30,779: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/results.star_align.bam: No such file or directory
2018-09-27 09:46:33,965: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell60/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/comb.2.fastq.gz': No such file or directory
2018-09-27 09:46:46,523: INFO: Cell barcode in configure file
2018-09-27 09:46:46,525: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/results.star_align.bam: No such file or directory
2018-09-27 09:46:49,931: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell61/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/comb.2.fastq.gz': No such file or directory
2018-09-27 09:47:01,805: INFO: Cell barcode in configure file
2018-09-27 09:47:01,807: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/results.star_align.bam: No such file or directory
2018-09-27 09:47:05,197: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell62/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/comb.2.fastq.gz': No such file or directory
2018-09-27 09:47:15,073: INFO: Cell barcode in configure file
2018-09-27 09:47:15,074: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/results.star_align.bam: No such file or directory
2018-09-27 09:47:18,463: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell63/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/comb.2.fastq.gz': No such file or directory
2018-09-27 09:47:32,324: INFO: Cell barcode in configure file
2018-09-27 09:47:32,326: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/results.star_align.bam: No such file or directory
2018-09-27 09:47:36,842: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell64/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/comb.2.fastq.gz': No such file or directory
2018-09-27 09:47:52,590: INFO: Cell barcode in configure file
2018-09-27 09:47:52,591: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/results.star_align.bam: No such file or directory
2018-09-27 09:47:56,985: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell65/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/comb.2.fastq.gz': No such file or directory
2018-09-27 09:48:13,170: INFO: Cell barcode in configure file
2018-09-27 09:48:13,172: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/results.star_align.bam: No such file or directory
2018-09-27 09:48:17,547: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell66/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/comb.2.fastq.gz': No such file or directory
2018-09-27 09:48:33,933: INFO: Cell barcode in configure file
2018-09-27 09:48:33,934: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/results.star_align.bam: No such file or directory
2018-09-27 09:48:38,221: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell67/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/comb.2.fastq.gz': No such file or directory
2018-09-27 09:48:57,233: INFO: Cell barcode in configure file
2018-09-27 09:48:57,235: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/results.star_align.bam: No such file or directory
2018-09-27 09:49:01,869: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell68/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/comb.2.fastq.gz': No such file or directory
2018-09-27 09:49:24,188: INFO: Cell barcode in configure file
2018-09-27 09:49:24,190: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/results.star_align.bam: No such file or directory
2018-09-27 09:49:32,481: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell69/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/comb.2.fastq.gz': No such file or directory
2018-09-27 09:49:51,062: INFO: Cell barcode in configure file
2018-09-27 09:49:51,063: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/results.star_align.bam: No such file or directory
2018-09-27 09:49:55,596: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell70/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/comb.2.fastq.gz': No such file or directory
2018-09-27 09:50:10,609: INFO: Cell barcode in configure file
2018-09-27 09:50:10,612: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/results.star_align.bam: No such file or directory
2018-09-27 09:50:15,245: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell71/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/comb.2.fastq.gz': No such file or directory
2018-09-27 09:50:36,052: INFO: Cell barcode in configure file
2018-09-27 09:50:36,054: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/results.star_align.bam: No such file or directory
2018-09-27 09:50:43,924: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell72/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/comb.2.fastq.gz': No such file or directory
2018-09-27 09:51:07,099: INFO: Cell barcode in configure file
2018-09-27 09:51:07,101: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/results.star_align.bam: No such file or directory
2018-09-27 09:51:15,132: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell73/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/comb.2.fastq.gz': No such file or directory
2018-09-27 09:51:35,209: INFO: Cell barcode in configure file
2018-09-27 09:51:35,210: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/results.star_align.bam: No such file or directory
2018-09-27 09:51:43,023: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell74/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/comb.2.fastq.gz': No such file or directory
2018-09-27 09:52:04,156: INFO: Cell barcode in configure file
2018-09-27 09:52:04,158: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/results.star_align.bam: No such file or directory
2018-09-27 09:52:12,255: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell75/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/comb.2.fastq.gz': No such file or directory
2018-09-27 09:52:33,308: INFO: Cell barcode in configure file
2018-09-27 09:52:33,310: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/results.star_align.bam: No such file or directory
2018-09-27 09:52:41,369: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell76/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/comb.2.fastq.gz': No such file or directory
2018-09-27 09:53:05,013: INFO: Cell barcode in configure file
2018-09-27 09:53:05,015: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/results.star_align.bam: No such file or directory
2018-09-27 09:53:13,578: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell77/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/comb.2.fastq.gz': No such file or directory
2018-09-27 09:53:34,013: INFO: Cell barcode in configure file
2018-09-27 09:53:34,015: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/results.star_align.bam: No such file or directory
2018-09-27 09:53:42,083: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell78/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/comb.2.fastq.gz': No such file or directory
2018-09-27 09:54:03,766: INFO: Cell barcode in configure file
2018-09-27 09:54:03,769: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/results.star_align.bam: No such file or directory
2018-09-27 09:54:11,877: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell79/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/comb.2.fastq.gz': No such file or directory
2018-09-27 09:54:36,583: INFO: Cell barcode in configure file
2018-09-27 09:54:36,585: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/results.star_align.bam: No such file or directory
2018-09-27 09:54:44,404: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell80/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/comb.2.fastq.gz': No such file or directory
2018-09-27 09:55:06,379: INFO: Cell barcode in configure file
2018-09-27 09:55:06,380: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/results.star_align.bam: No such file or directory
2018-09-27 09:55:14,141: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell81/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/comb.2.fastq.gz': No such file or directory
2018-09-27 09:55:50,241: INFO: Cell barcode in configure file
2018-09-27 09:55:50,243: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/results.star_align.bam: No such file or directory
2018-09-27 09:55:58,465: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell82/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/comb.2.fastq.gz': No such file or directory
2018-09-27 09:56:20,720: INFO: Cell barcode in configure file
2018-09-27 09:56:20,722: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/results.star_align.bam: No such file or directory
2018-09-27 09:56:29,280: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell83/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/comb.2.fastq.gz': No such file or directory
2018-09-27 09:56:49,199: INFO: Cell barcode in configure file
2018-09-27 09:56:49,200: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/results.star_align.bam: No such file or directory
2018-09-27 09:56:52,747: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell84/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/comb.2.fastq.gz': No such file or directory
2018-09-27 09:57:09,921: INFO: Cell barcode in configure file
2018-09-27 09:57:09,923: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/results.star_align.bam: No such file or directory
2018-09-27 09:57:17,693: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell85/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/comb.2.fastq.gz': No such file or directory
2018-09-27 09:57:39,330: INFO: Cell barcode in configure file
2018-09-27 09:57:39,332: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/results.star_align.bam: No such file or directory
2018-09-27 09:57:46,984: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell86/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/comb.2.fastq.gz': No such file or directory
2018-09-27 09:58:10,169: INFO: Cell barcode in configure file
2018-09-27 09:58:10,171: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/results.star_align.bam: No such file or directory
2018-09-27 09:58:17,905: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell87/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/comb.2.fastq.gz': No such file or directory
2018-09-27 09:58:42,819: INFO: Cell barcode in configure file
2018-09-27 09:58:42,821: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/results.star_align.bam: No such file or directory
2018-09-27 09:58:55,577: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell88/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/comb.2.fastq.gz': No such file or directory
2018-09-27 09:59:20,803: INFO: Cell barcode in configure file
2018-09-27 09:59:20,805: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/results.star_align.bam: No such file or directory
2018-09-27 09:59:28,631: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell89/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/comb.2.fastq.gz': No such file or directory
2018-09-27 09:59:58,164: INFO: Cell barcode in configure file
2018-09-27 09:59:58,166: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/results.star_align.bam: No such file or directory
2018-09-27 10:00:06,613: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell90/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/comb.2.fastq.gz': No such file or directory
2018-09-27 10:00:26,196: INFO: Cell barcode in configure file
2018-09-27 10:00:26,198: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/results.star_align.bam: No such file or directory
2018-09-27 10:00:33,717: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell91/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/comb.2.fastq.gz': No such file or directory
2018-09-27 10:00:56,426: INFO: Cell barcode in configure file
2018-09-27 10:00:56,429: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/results.star_align.bam: No such file or directory
2018-09-27 10:01:04,393: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell92/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/comb.2.fastq.gz': No such file or directory
2018-09-27 10:01:26,846: INFO: Cell barcode in configure file
2018-09-27 10:01:26,847: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/results.star_align.bam: No such file or directory
2018-09-27 10:01:34,452: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell93/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/comb.2.fastq.gz': No such file or directory
2018-09-27 10:01:52,593: INFO: Cell barcode in configure file
2018-09-27 10:01:52,595: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/results.star_align.bam: No such file or directory
2018-09-27 10:01:56,829: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell94/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/comb.2.fastq.gz': No such file or directory
2018-09-27 10:02:17,543: INFO: Cell barcode in configure file
2018-09-27 10:02:17,545: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/results.star_align.bam: No such file or directory
2018-09-27 10:02:25,364: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell95/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/comb.2.fastq.gz': No such file or directory
2018-09-27 10:02:46,822: INFO: Cell barcode in configure file
2018-09-27 10:02:46,824: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/results.star_align.bam: No such file or directory
2018-09-27 10:02:54,896: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell96/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/comb.2.fastq.gz': No such file or directory
2018-09-27 10:03:16,871: INFO: Cell barcode in configure file
2018-09-27 10:03:16,873: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/results.star_align.bam: No such file or directory
2018-09-27 10:03:25,762: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell97/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/comb.2.fastq.gz': No such file or directory
2018-09-27 10:03:45,908: INFO: Cell barcode in configure file
2018-09-27 10:03:45,910: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/results.star_align.bam: No such file or directory
2018-09-27 10:03:53,912: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell98/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/comb.2.fastq.gz': No such file or directory
2018-09-27 10:04:16,819: INFO: Cell barcode in configure file
2018-09-27 10:04:16,821: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/results.star_align.bam: No such file or directory
2018-09-27 10:04:24,646: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell99/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/comb.2.fastq.gz': No such file or directory
2018-09-27 10:04:49,091: INFO: Cell barcode in configure file
2018-09-27 10:04:49,093: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/results.star_align.bam: No such file or directory
2018-09-27 10:04:57,068: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell100/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/comb.2.fastq.gz': No such file or directory
2018-09-27 10:05:19,967: INFO: Cell barcode in configure file
2018-09-27 10:05:19,969: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/results.star_align.bam: No such file or directory
2018-09-27 10:05:27,917: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell101/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/comb.2.fastq.gz': No such file or directory
2018-09-27 10:05:51,323: INFO: Cell barcode in configure file
2018-09-27 10:05:51,325: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/results.star_align.bam: No such file or directory
2018-09-27 10:05:59,081: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell102/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/comb.2.fastq.gz': No such file or directory
2018-09-27 10:06:22,540: INFO: Cell barcode in configure file
2018-09-27 10:06:22,542: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/results.star_align.bam: No such file or directory
2018-09-27 10:06:30,275: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell103/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/comb.2.fastq.gz': No such file or directory
2018-09-27 10:06:49,518: INFO: Cell barcode in configure file
2018-09-27 10:06:49,520: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/results.star_align.bam: No such file or directory
2018-09-27 10:06:56,791: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell104/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/comb.2.fastq.gz': No such file or directory
2018-09-27 10:07:16,540: INFO: Cell barcode in configure file
2018-09-27 10:07:16,542: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/results.star_align.bam: No such file or directory
2018-09-27 10:07:23,874: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell105/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/comb.2.fastq.gz': No such file or directory
2018-09-27 10:07:45,008: INFO: Cell barcode in configure file
2018-09-27 10:07:45,010: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/results.star_align.bam: No such file or directory
2018-09-27 10:07:52,893: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell106/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/comb.2.fastq.gz': No such file or directory
2018-09-27 10:08:15,873: INFO: Cell barcode in configure file
2018-09-27 10:08:15,874: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/results.star_align.bam: No such file or directory
2018-09-27 10:08:23,403: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell107/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/comb.2.fastq.gz': No such file or directory
2018-09-27 10:08:41,868: INFO: Cell barcode in configure file
2018-09-27 10:08:41,870: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/results.star_align.bam: No such file or directory
2018-09-27 10:08:49,407: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell108/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/comb.2.fastq.gz': No such file or directory
2018-09-27 10:09:10,247: INFO: Cell barcode in configure file
2018-09-27 10:09:10,249: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/results.star_align.bam: No such file or directory
2018-09-27 10:09:17,792: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell109/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/comb.2.fastq.gz': No such file or directory
2018-09-27 10:09:40,707: INFO: Cell barcode in configure file
2018-09-27 10:09:40,708: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/results.star_align.bam: No such file or directory
2018-09-27 10:09:48,147: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell110/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/comb.2.fastq.gz': No such file or directory
2018-09-27 10:10:12,553: INFO: Cell barcode in configure file
2018-09-27 10:10:12,555: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/results.star_align.bam: No such file or directory
2018-09-27 10:10:19,685: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell111/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/comb.2.fastq.gz': No such file or directory
2018-09-27 10:10:43,356: INFO: Cell barcode in configure file
2018-09-27 10:10:43,357: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/results.star_align.bam: No such file or directory
2018-09-27 10:10:50,969: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell112/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:11:00,624: INFO: Cell barcode in configure file
2018-09-27 10:11:00,626: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/results.star_align.bam: No such file or directory
2018-09-27 10:11:03,632: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell113/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/comb.2.fastq.gz': No such file or directory
2018-09-27 10:11:13,185: INFO: Cell barcode in configure file
2018-09-27 10:11:13,186: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/results.star_align.bam: No such file or directory
2018-09-27 10:11:16,070: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell115/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:11:21,191: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell114'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/comb.2.fastq.gz': No such file or directory
2018-09-27 10:11:28,722: INFO: Cell barcode in configure file
2018-09-27 10:11:28,723: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/results.star_align.bam: No such file or directory
2018-09-27 10:11:31,595: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117': No such file or directory
bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell116/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/comb.2.fastq.gz': No such file or directory
2018-09-27 10:11:43,515: INFO: Cell barcode in configure file
2018-09-27 10:11:43,516: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/results.star_align.bam: No such file or directory
2018-09-27 10:11:46,441: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell118/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:11:51,141: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell117'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/comb.2.fastq.gz': No such file or directory
2018-09-27 10:11:58,786: INFO: Cell barcode in configure file
2018-09-27 10:11:58,788: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/results.star_align.bam: No such file or directory
2018-09-27 10:12:02,002: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120': No such file or directory
bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell119/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/comb.2.fastq.gz': No such file or directory
2018-09-27 10:12:14,332: INFO: Cell barcode in configure file
2018-09-27 10:12:14,334: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/results.star_align.bam: No such file or directory
2018-09-27 10:12:17,020: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121'
q/Cell120/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell121/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:12:21,285: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell120/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:12:29,753: INFO: Cell barcode in configure file
2018-09-27 10:12:29,754: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/results.star_align.bam: No such file or directory
2018-09-27 10:12:32,633: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is no/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell122/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:12:39,939: INFO: Cell barcode in configure file
2018-09-27 10:12:39,941: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/results.star_align.bam: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/comb.2.fastq.gz': No such file or directory
2018-09-27 10:12:45,300: INFO: Cell barcode in configure file
2018-09-27 10:12:45,301: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/results.star_align.bam: No such file or directory
2018-09-27 10:12:48,204: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell124/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell123/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/comb.2.fastq.gz': No such file or directory
2018-09-27 10:13:00,473: INFO: Cell barcode in configure file
2018-09-27 10:13:00,474: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/results.star_align.bam: No such file or directory
2018-09-27 10:13:03,747: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125'
broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell125/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:13:07,405: INFO: Cell barcode in configure file
2018-09-27 10:13:07,407: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/results.star_align.bam: No such file or directory
2018-09-27 10:13:11,484: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell126/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:13:17,040: INFO: Cell barcode in configure file
2018-09-27 10:13:17,042: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/results.star_align.bam: No such file or directory
2018-09-27 10:13:19,998: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is no/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell127/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:13:27,642: INFO: Cell barcode in configure file
2018-09-27 10:13:27,644: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/results.star_align.bam: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/comb.2.fastq.gz': No such file or directory
2018-09-27 10:13:33,214: INFO: Cell barcode in configure file
2018-09-27 10:13:33,215: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/results.star_align.bam: No such file or directory
2018-09-27 10:13:36,166: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell129/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell128/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/comb.2.fastq.gz': No such file or directory
2018-09-27 10:13:54,348: INFO: Cell barcode in configure file
2018-09-27 10:13:54,351: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/results.star_align.bam: No such file or directory
2018-09-27 10:13:57,073: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131'
q/Cell130/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell131/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:14:01,559: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell130/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:14:10,157: INFO: Cell barcode in configure file
2018-09-27 10:14:10,158: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/results.star_align.bam: No such file or directory
2018-09-27 10:14:13,038: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132'
broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell132/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:14:16,849: INFO: Cell barcode in configure file
2018-09-27 10:14:16,850: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/results.star_align.bam: No such file or directory
2018-09-27 10:14:20,908: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell133/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:14:25,884: INFO: Cell barcode in configure file
2018-09-27 10:14:25,885: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/results.star_align.bam: No such file or directory
2018-09-27 10:14:29,163: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell135': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell134/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/comb.2.fastq.gz': No such file or directory
2018-09-27 10:14:36,817: INFO: Cell barcode in configure file
2018-09-27 10:14:36,819: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell135/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell135/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell135/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell135/results.star_align.bam: No such file or directory
2018-09-27 10:14:40,127: INFO: Cell barcode in configure file
2018-09-27 10:14:40,128: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/results.star_align.bam: No such file or directory
2018-09-27 10:14:43,370: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell135/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell135/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell136/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138': No such file or directory
e
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/results.star_align.bam: No such file or directory
2018-09-27 10:14:58,613: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137'
5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell137/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:15:04,599: INFO: Cell barcode in configure file
2018-09-27 10:15:04,601: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/results.star_align.bam: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/comb.2.fastq.gz': No such file or directory
2018-09-27 10:15:09,987: INFO: Cell barcode in configure file
2018-09-27 10:15:09,989: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/results.star_align.bam: No such file or directory
2018-09-27 10:15:11,954: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138'
2018-09-27 10:15:13,640: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell139/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell138/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141': No such file or directory
e
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/results.star_align.bam: No such file or directory
2018-09-27 10:15:28,842: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140'
5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell140/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:15:34,903: INFO: Cell barcode in configure file
2018-09-27 10:15:34,906: INFO: UMI in config fil/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/comb.1.fastq.gz: No such file or directory
c(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/results.star_align.bam: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/comb.2.fastq.gz': No such file or directory
2018-09-27 10:15:39,384: INFO: Cell barcode in configure file
2018-09-27 10:15:39,385: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/results.star_align.bam: No such file or directory
2018-09-27 10:15:42,702: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell142/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell143': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell141/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:15:53,150: INFO: Cell barcode in configure file
2018-09-27 10:15:53,152: INFO: UMI in config fil/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/comb.1.fastq.gz: No such file or directory
c(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell143/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell143/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell143/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell143/results.star_align.bam: No such file or directory
2018-09-27 10:15:56,389: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell143'
5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell143/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell143/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/comb.2.fastq.gz': No such file or directory
2018-09-27 10:16:02,638: INFO: Cell barcode in configure file
2018-09-27 10:16:02,640: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/results.star_align.bam: No such file or directory
2018-09-27 10:16:05,689: INFO: Cell barcode in configure file
2018-09-27 10:16:05,690: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/results.star_align.bam: No such file or directory
2018-09-27 10:16:08,622: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell145/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell144/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147': No such file or directory
e
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/results.star_align.bam: No such file or directory
2018-09-27 10:16:23,984: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146'
5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell146/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell148': No such file or directory
2018-09-27 10:16:30,879: INFO: Cell barcode in configure file
2018-09-27 10:16:30,881: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/results.star_align.bam: No such file or directory
2018-09-27 10:16:34,565: INFO: Cell barcode in configure file
2018-09-27 10:16:34,566: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell148/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell148/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell148/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell148/results.star_align.bam: No such file or directory
2018-09-27 10:16:37,588: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell148'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell148/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell148/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell149': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell147/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150': No such file or directory
e
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell149/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell149/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell149/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell149/results.star_align.bam: No such file or directory
2018-09-27 10:16:52,395: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell149'
5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell149/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell149/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/comb.2.fastq.gz': No such file or directory
2018-09-27 10:16:59,273: INFO: Cell barcode in configure file
2018-09-27 10:16:59,275: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/results.star_align.bam: No such file or directory
2018-09-27 10:17:02,571: INFO: Cell barcode in configure file
2018-09-27 10:17:02,572: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/results.star_align.bam: No such file or directory
2018-09-27 10:17:05,488: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell151/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell150/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153': No such file or directory
e
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/results.star_align.bam: No such file or directory
2018-09-27 10:17:20,462: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152'
5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell152/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/comb.1.fastq.gz: No such file or directory
hg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/results.star_align.bam: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/comb.2.fastq.gz': No such file or directory
2018-09-27 10:17:31,118: INFO: Cell barcode in configure file
2018-09-27 10:17:31,119: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/results.star_align.bam: No such file or directory
2018-09-27 10:17:34,020: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell154/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell155': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell153/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156': No such file or directory
e
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell155/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell155/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell155/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell155/results.star_align.bam: No such file or directory
2018-09-27 10:17:48,598: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell155'
5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell155/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell155/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:17:55,414: INFO: Cell barcode in configure file
2018-09-27 10:17:55,416: INFO: UMI in config fil/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/comb.1.fastq.gz: No such file or directory
c(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/results.star_align.bam: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/comb.2.fastq.gz': No such file or directory
2018-09-27 10:17:59,522: INFO: Cell barcode in configure file
2018-09-27 10:17:59,524: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/results.star_align.bam: No such file or directory
2018-09-27 10:18:02,433: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/results.star_align.bam.featureCounts.bam
tmp/ssimmons/scumi/mixed2/SciSeq/Cell156'
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell157/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell156/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:18:13,752: INFO: Cell barcode in configure file
2018-09-27 10:18:13,753: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/results.star_align.bam: No such file or directory
2018-09-27 10:18:16,715: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158'
broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell158/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell160': No such file or directory
2018-09-27 10:18:24,293: INFO: Cell barcode in configure file
2018-09-27 10:18:24,295: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/results.star_align.bam: No such file or directory
2018-09-27 10:18:28,229: INFO: Cell barcode in configure file
2018-09-27 10:18:28,231: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell160/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell160/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell160/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell160/results.star_align.bam: No such file or directory
2018-09-27 10:18:31,173: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell160'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell160/results.star_align.bam.featureCounts.bam
tmp/ssimmons/scumi/mixed2/SciSeq/Cell159'
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell160/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell159/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162': No such file or directory
e
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/results.star_align.bam: No such file or directory
2018-09-27 10:18:44,733: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161'
5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell161/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/comb.2.fastq.gz': No such file or directory
2018-09-27 10:18:51,861: INFO: Cell barcode in configure file
2018-09-27 10:18:51,863: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/results.star_align.bam: No such file or directory
2018-09-27 10:18:55,289: INFO: Cell barcode in configure file
2018-09-27 10:18:55,290: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/results.star_align.bam: No such file or directory
2018-09-27 10:18:58,226: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell163/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/comb.2.fastq.gz': No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell162/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:19:09,162: INFO: Cell barcode in configure file
2018-09-27 10:19:09,163: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/results.star_align.bam: No such file or directory
2018-09-27 10:19:12,115: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/comb.1.fastq.gz: No such file or directory
ll last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell164/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/comb.2.fastq.gz': No such file or directory
2018-09-27 10:19:22,327: INFO: Cell barcode in configure file
2018-09-27 10:19:22,328: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/results.star_align.bam: No such file or directory
2018-09-27 10:19:25,290: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell166/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:19:30,577: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/comb.2.fastq.gz': No such file or directory
2018-09-27 10:19:36,317: INFO: Cell barcode in configure file
2018-09-27 10:19:36,318: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/results.star_align.bam: No such file or directory
2018-09-27 10:19:39,254: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167'
/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell165/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/results.star_align./var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/comb.1.fastq.gz: No such file or directory
module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell167/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/comb.2.fastq.gz': No such file or directory
2018-09-27 10:19:49,466: INFO: Cell barcode in configure file
2018-09-27 10:19:49,467: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/results.star_align.bam: No such file or directory
2018-09-27 10:19:52,448: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell169/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:19:57,147: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/comb.2.fastq.gz': No such file or directory
2018-09-27 10:20:03,660: INFO: Cell barcode in configure file
2018-09-27 10:20:03,661: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/results.star_align.bam: No such file or directory
2018-09-27 10:20:06,626: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170'
/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell168/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/comb.1.fastq.gz: No such file or directory
ll last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell170/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/comb.2.fastq.gz': No such file or directory
2018-09-27 10:20:17,743: INFO: Cell barcode in configure file
2018-09-27 10:20:17,745: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/results.star_align.bam: No such file or directory
2018-09-27 10:20:20,698: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell172/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:20:25,844: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/comb.2.fastq.gz': No such file or directory
2018-09-27 10:20:31,961: INFO: Cell barcode in configure file
2018-09-27 10:20:31,962: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/results.star_align.bam: No such file or directory
2018-09-27 10:20:34,969: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173'
/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell171/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/results.star_align./var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/comb.1.fastq.gz: No such file or directory
module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell173/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/comb.2.fastq.gz': No such file or directory
2018-09-27 10:20:45,531: INFO: Cell barcode in configure file
2018-09-27 10:20:45,532: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/results.star_align.bam: No such file or directory
2018-09-27 10:20:48,516: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell175/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:20:53,884: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/comb.2.fastq.gz': No such file or directory
2018-09-27 10:20:59,498: INFO: Cell barcode in configure file
2018-09-27 10:20:59,499: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/results.star_align.bam: No such file or directory
2018-09-27 10:21:02,409: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176'
/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell174/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/results.star_align./var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/comb.1.fastq.gz: No such file or directory
module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell176/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/comb.2.fastq.gz': No such file or directory
2018-09-27 10:21:13,560: INFO: Cell barcode in configure file
2018-09-27 10:21:13,562: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/results.star_align.bam: No such file or directory
2018-09-27 10:21:16,467: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell178/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:21:21,595: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/comb.2.fastq.gz': No such file or directory
2018-09-27 10:21:28,175: INFO: Cell barcode in configure file
2018-09-27 10:21:28,177: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/results.star_align.bam: No such file or directory
2018-09-27 10:21:31,222: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179'
/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell177/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/comb.1.fastq.gz: No such file or directory
ll last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell179/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/comb.2.fastq.gz': No such file or directory
2018-09-27 10:21:41,588: INFO: Cell barcode in configure file
2018-09-27 10:21:41,589: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/results.star_align.bam: No such file or directory
2018-09-27 10:21:44,495: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell181/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:21:50,455: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/comb.2.fastq.gz': No such file or directory
2018-09-27 10:21:56,399: INFO: Cell barcode in configure file
2018-09-27 10:21:56,400: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/results.star_align.bam: No such file or directory
2018-09-27 10:21:59,347: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182'
/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell180/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/results.star_align./var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/comb.1.fastq.gz: No such file or directory
module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell182/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/comb.2.fastq.gz': No such file or directory
2018-09-27 10:22:09,682: INFO: Cell barcode in configure file
2018-09-27 10:22:09,683: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/results.star_align.bam: No such file or directory
2018-09-27 10:22:12,692: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell184/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:22:18,271: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/comb.2.fastq.gz': No such file or directory
2018-09-27 10:22:23,989: INFO: Cell barcode in configure file
2018-09-27 10:22:23,990: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/results.star_align.bam: No such file or directory
2018-09-27 10:22:26,942: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185'
/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell183/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/results.star_align./var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/comb.1.fastq.gz: No such file or directory
module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell185/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/comb.2.fastq.gz': No such file or directory
2018-09-27 10:22:38,579: INFO: Cell barcode in configure file
2018-09-27 10:22:38,581: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/results.star_align.bam: No such file or directory
2018-09-27 10:22:41,578: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell187/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:22:46,358: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/comb.2.fastq.gz': No such file or directory
2018-09-27 10:22:51,609: INFO: Cell barcode in configure file
2018-09-27 10:22:51,611: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/results.star_align.bam: No such file or directory
2018-09-27 10:22:54,626: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188'
/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell186/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/comb.1.fastq.gz: No such file or directory
ll last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell188/results.star_align.bam.featureCounts.bam`: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/comb.2.fastq.gz': No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/comb.2.fastq.gz': No such file or directory
2018-09-27 10:23:05,212: INFO: Cell barcode in configure file
2018-09-27 10:23:05,213: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/results.star_align.bam: No such file or directory
2018-09-27 10:23:08,258: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190'
cts/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell190/results.star_align.bam.featureCounts.bam`: No such file or directory
2018-09-27 10:23:13,379: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189'
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/comb.2.fastq.gz': No such file or directory
2018-09-27 10:23:18,111: INFO: Cell barcode in configure file
2018-09-27 10:23:18,112: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c001/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/results.star_align.bam: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell189/results.star_align.bam.featureCounts.bam`: No such file or directory
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell191/results.star_align.bam.featureCounts.bam`: No such file or directory
mkdir: cannot create directory `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 70: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/comb.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 71: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/comb.2.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 81: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/results.1.fastq.gz: No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 82: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/results.2.fastq.gz: No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/comb.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/comb.2.fastq.gz': No such file or directory
2018-09-27 10:23:30,670: INFO: Cell barcode in configure file
2018-09-27 10:23:30,672: INFO: UMI in config file
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 13, in merge_fastq
cb_count=cb_count, num_thread=num_thread)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 78, in format_fastq
fastq_out_file = write_fastq(fastq_out)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/fastq_io.py", line 33, in write_fastq
fastq_file = gzip.open(fastq, mode='wb')
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/results.fastq.gz'
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/results.1.fastq.gz': No such file or directory
rm: cannot remove `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/results.2.fastq.gz': No such file or directory
/var/spool/uger-8.5.5/ugerbm-c003/job_scripts/5615885: line 96: /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/results.star_align.bam: No such file or directory
2018-09-27 10:23:33,834: INFO: Running featureCounts to annotate alignments.
ERROR: temporary directory is not writable: '/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192'
[E::hts_open_format] Failed to open file /broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/results.star_align.bam.featureCounts.bam
Traceback (most recent call last):
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/bin/scumi", line 165, in <module>
args.func(args)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/run.py", line 47, in count_umi
cell_barcode_whitelist=cell_barcode_whitelist)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 402, in count_feature
barcode_parser, first_cb, read_mode = _construct_barcode_regex(bam)
File "/ahg/regevdata/projects/sc_compare/software/miniconda3/envs/scumi/lib/python3.6/site-packages/scumi/scumi.py", line 343, in _construct_barcode_regex
bam_file = AlignmentFile(bam, mode=read_mode)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/broad/hptmp/ssimmons/scumi/mixed2/SciSeq/Cell192/results.star_align.bam.featureCounts.bam`: No such file or directory
|
6ae8d3e31b2352952b1eca4bfb64bb4a7a41d3b7 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1271/CH20/EX20.18/example20_18.sce | ff70654eea36a74bcc29feff172782776df06bb2 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 358 | sce | example20_18.sce | clc
// Given that
Z = 79 // atomic no. of anticathode
R = 1.097e7 // Rydberg constant in m^-1
c = 3e8 // speed of light in m/sec
// Sample Problem 18 on page no. 20.13
printf("\n # PROBLEM 18 # \n")
printf("Standard formula used \n ")
printf(" nu = a*(Z-b)^2 ........Moseley law \n")
f = 3/4 * (R * c) * (Z-1)^2
printf("\n Frequency of k line is %e Hz.",f)
|
ea784248ecc543a24b9a459eb33bb2570e3ba735 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3821/CH10/EX10.4/Example10_4.sce | 8a01ed8f86e7851c1c2d3cad273a351bbd1a471a | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 792 | sce | Example10_4.sce | //////Chapter 10 Properties Of Steam
////Example 10.4 Page No:185
///
////#Input data
clc;
clear;
P=15; //Absolute pressure in bar
//From steam table (pressure basis at 15 bar)
ts=198.3; //In degree celsius
hf=844.7; //In KJ/Kg
hfg=1945.2; //In KJ/Kg
hg=2789.9; //In KJ/Kg
tsup=300; //In degree celsius
x=0.8;
Cps=2.3;
hg=2789.9;
//Calculation
h1=hf+x*hfg; //Enthalpy of wet steam in KJ/KG
h=hg; //Enthalpy of dry and saturated steam in KJ/KG
h2=hg+Cps*(tsup-ts); //Enthalpy of superheated steam in KJ/KG
//Output
printf('Enthalpy of wet steam=%f KJ/Kg \n ",h1);
printf('Enthalpy of dry and saturated steam=%f KJ/Kg \n ',h);
printf('Enthalpy of superheated steam= %f KJ/Kg \n ',h2);
|
90256478afc8ec59197f785e255236f06b1f81a8 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1754/CH3/EX3.6/Exa3_6.sce | 7701e5ff2da289781a4948157adf31c4b0e7a1f6 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 484 | sce | Exa3_6.sce | //Exa 3.6
clc;
clear;
close;
//Given data :
RC=10;//in kohm
hfe=330;//unitless
hie=4.5;//in kOhm
//RS<<hie
AVM=hfe*RC*10^3/(hie*10^3+RC*10^3);//unitless
AVM1=AVM;//Gain of 1st stage
AVM2=AVM;//Gain of 2nd stage
AVM3=hfe*RC*10^3/(hie*10^3);//unitless(//Gain of 3rd stage)
OverallGain=AVM1*AVM2*AVM3;//unitless
disp(AVM,"Gain in mid frequeny range : ");
disp("This is the gain of 1st and 2nd stage.")
disp(OverallGain,"Overall Voltage gain for mid frequency range : "); |
ed283a5eb8dd764919418241e9e3d1ebb36bbee9 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1820/CH10/EX10.1/Example10_1.sce | 52fc514ffa11820e8369fca416d39036e0c5707b | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 888 | sce | Example10_1.sce | // ELECTRIC POWER TRANSMISSION SYSTEM ENGINEERING ANALYSIS AND DESIGN
// TURAN GONEN
// CRC PRESS
// SECOND EDITION
// CHAPTER : 10 : PROTECTIVE EQUIPMENT AND TRANSMISSION SYSTEM PROTECTION
// EXAMPLE : 10.1 :
clear ; clc ; close ; // Clear the work space and console
// GIVEN DATA
X_d = 0.14*%i ; // Reactance of generator in pu
E_g = 1*exp(%i*0*%pi/180) ;
S_B = 25*10^3 ; // voltage in kVA
V_BL_V = 13.8 ; // low voltage in kV
// CALCULATIONS
I_f = E_g/X_d ; // Subtransient fault current in pu
I_BL_V = S_B/( sqrt(3)*V_BL_V) ; // Current base for low-voltage side
I_f1 = abs(I_f)*I_BL_V ; // magnitude of fault current in A
// DISPLAY RESULTS
disp("EXAMPLE : 10.1 : SOLUTION :-") ;
printf("\n Subtransient fault current for 3-Φ fault in per units = pu \n") ; disp(I_f) ;
printf("\n Subtransient fault current for 3-Φ fault in ampere = %.f A \n",I_f1) ;
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ac597fc06fa24289c9d8693fa2f14b84acc602c9 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1922/CH2/EX2.4/2_4.sce | b9341b14d42056de7132b2550514f3a2d581acf5 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 314 | sce | 2_4.sce | clc
clear
//Initialization of variables
basis= 1 //kmol ammonia
P=10^6 //pa
a=4.19
b=0.0373
R=8314.3
Tc=405.5
Pc=11.28*10^6
//calculations
disp("case a")
disp("Using vandwerwaals equation, ")
disp("(P+a/v^2)*(V-b) = R*T, on solving by trail and error method,")
V=3
printf("Volume = %d m^3/kmol",V)
|
0e76cbb9db07a7752710b37ff59b262e203ef957 | 449d555969bfd7befe906877abab098c6e63a0e8 | /2210/CH1/EX1.5/1_5.sce | 4fdf18e9b365fc3c4098ba8772bc1fe8a0c6c3f7 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 648 | sce | 1_5.sce | //Chapter 1, Example 1.5
clc
n=100 //no of coil turns
a=8*10^-5 //effective cross-sectional area in metre
ur=200 //relative permeability
uo=4*%pi*10^-7 //permeability, of air
ao=60*%pi/180 //angle of incidence of magnetic field
f=10^6 //frequency in hertz
E=100*10^-6 //electric field strength in V/m
z=377 //wave impedance in ohm
//calculation
w=2*%pi*f
erms=n*w*ur*uo*a*(E/z)*cos(ao)
printf("r.m.s open circuit voltage induced = %.3f uV",erms*10^6)
|
b8c4a79f76a8c94ebd921044434f3d6f5d6e46d2 | 089894a36ef33cb3d0f697541716c9b6cd8dcc43 | /NLP_Project/test/tweet/bow/bow.3_2.tst | 182f874ae23bf22d69689b8e4b3d644f3999f625 | [] | no_license | mandar15/NLP_Project | 3142cda82d49ba0ea30b580c46bdd0e0348fe3ec | 1dcb70a199a0f7ab8c72825bfd5b8146e75b7ec2 | refs/heads/master | 2020-05-20T13:36:05.842840 | 2013-07-31T06:53:59 | 2013-07-31T06:53:59 | 6,534,406 | 0 | 1 | null | null | null | null | UTF-8 | Scilab | false | false | 35,194 | tst | bow.3_2.tst | 3 10:0.1111111111111111 13:1.0 17:0.6666666666666666 28:0.045454545454545456 59:0.6666666666666666 61:0.5 63:0.16666666666666666 82:0.13333333333333333 89:0.125 96:0.5 100:0.16666666666666666 108:1.0 110:1.0 153:1.0 168:0.25 208:1.0 234:0.05263157894736842 264:1.0 327:1.0 363:2.0 719:0.3333333333333333 722:0.5 949:1.0 1287:0.5 1288:1.0 1960:1.0 2183:1.0 2646:1.0 2836:1.0 3329:1.0 5152:1.0 5486:1.0 5887:1.0 6042:0.5 6051:1.0 7378:1.0
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3 11:0.14285714285714285 28:0.045454545454545456 30:0.07692307692307693 39:0.25 40:1.0 43:0.09090909090909091 59:0.3333333333333333 64:0.3333333333333333 68:0.14285714285714285 83:0.2 115:1.0 284:1.0 297:0.5 616:1.0 2254:1.0 3202:1.0 3956:1.0 4810:0.5 4817:0.07692307692307693 5009:1.0 8251:1.0
3 7:0.5 11:0.7142857142857143 14:1.3333333333333333 19:0.5 28:0.045454545454545456 30:0.038461538461538464 43:0.09090909090909091 46:1.0 83:0.1 90:0.030303030303030304 168:0.25 259:0.5 369:0.2 390:1.0 394:1.0 416:0.5 518:1.0 568:1.0 636:0.5 756:0.2 804:1.0 1083:0.3333333333333333 1287:0.5 1296:1.0 1370:1.0 1374:1.0 1447:1.0 2065:1.0 2182:1.0 2183:1.0 3016:1.0 3311:1.0 3920:1.0 4825:1.0 4904:1.0 5102:1.0 5603:1.0 5840:0.5 6599:1.0 7850:1.0 8488:1.0
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3 10:0.3333333333333333 18:0.5 19:0.5 23:1.0 28:0.045454545454545456 30:0.15384615384615385 39:0.25 59:0.3333333333333333 68:0.2857142857142857 82:0.06666666666666667 109:1.0 135:0.5 138:0.5 142:0.5 263:0.16666666666666666 264:1.0 265:0.09090909090909091 313:0.3333333333333333 349:0.5 353:0.2 419:0.5 443:1.0 676:1.0 876:0.5 949:1.0 1365:1.0 2055:0.6666666666666666 2299:1.0 2738:1.0 3325:0.05263157894736842 4744:1.0 4825:1.0 4964:1.0 5190:1.0 5603:1.0 5604:1.0 5983:1.0 7103:1.0 7988:1.0
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3 30:0.038461538461538464 46:1.0 56:0.07692307692307693 59:0.6666666666666666 61:0.5 64:0.3333333333333333 100:0.16666666666666666 388:1.0 703:1.0 769:1.0 1708:1.0 2023:1.0 2432:1.0 2548:1.0 3242:1.0 4363:1.0 4817:0.07692307692307693 4880:0.14285714285714285 4956:1.0 5064:1.0 5376:0.5 5700:1.0 5998:1.0 6551:1.0 7935:1.0
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3 28:0.045454545454545456 30:0.15384615384615385 59:0.6666666666666666 88:1.0 96:1.0 100:0.16666666666666666 212:1.0 264:1.0 300:1.0 326:0.2222222222222222 394:1.0 484:1.0 719:0.3333333333333333 1024:1.0 1625:1.0 1793:1.0 2287:1.0 2908:2.0 2912:1.0 3447:0.5 3462:0.5 4817:0.07692307692307693 4978:1.0 5088:1.0 5093:1.0 5263:0.5 5841:1.0 6797:1.0 7921:1.0
3 4:1.0 10:0.1111111111111111 11:0.14285714285714285 14:0.3333333333333333 30:0.07692307692307693 43:0.18181818181818182 90:0.030303030303030304 258:1.0 380:0.25 616:1.0 1083:0.3333333333333333 1366:1.0 1683:1.0 2078:1.0 2245:0.5 5326:1.0 5327:1.0 5623:1.0 6860:1.0 7405:1.0
3 6:1.0 11:0.2857142857142857 17:0.3333333333333333 30:0.07692307692307693 46:1.0 59:0.6666666666666666 68:0.14285714285714285 69:0.3333333333333333 82:0.06666666666666667 153:1.0 186:1.0 300:1.0 517:0.14285714285714285 548:1.0 568:1.0 676:1.0 804:1.0 1411:1.0 3636:0.5 4817:0.07692307692307693 4935:1.0 5813:1.0 7505:1.0
3 30:0.07692307692307693 39:0.25 46:2.0 63:0.3333333333333333 90:0.030303030303030304 100:0.16666666666666666 117:1.0 217:2.0 230:1.0 234:0.05263157894736842 263:0.16666666666666666 265:0.09090909090909091 277:1.0 288:1.0 531:0.5 815:0.16666666666666666 1255:1.0 1955:0.5 2638:1.0 2768:0.25 3288:1.0 4242:1.0 4880:0.14285714285714285 4931:1.0 5311:1.0 5476:1.0 5603:1.0 5604:1.0 5835:1.0 7380:1.0 8487:1.0
3 37:1.0 39:0.25 46:1.0 83:0.1 352:0.03333333333333333 829:1.0 879:1.0 948:1.0 1467:1.0 2066:1.0 4756:1.0 4880:0.14285714285714285 5575:1.0 5603:1.0 5604:1.0 7016:1.0 7436:1.0 8533:1.0
3 10:0.1111111111111111 11:0.14285714285714285 28:0.045454545454545456 30:0.11538461538461539 39:0.25 40:1.0 43:0.09090909090909091 46:3.0 56:0.07692307692307693 59:0.3333333333333333 83:0.2 126:0.2 135:0.5 156:0.5 160:0.3333333333333333 204:1.0 237:1.0 265:0.09090909090909091 286:0.1 297:0.5 368:0.25 390:1.0 394:1.0 513:1.0 531:0.5 587:1.0 612:1.0 619:1.0 786:1.0 875:1.0 1149:1.0 1171:1.0 1207:1.0 1623:1.0 1912:1.0 3338:1.0 4100:1.0 4104:1.0 4130:1.0 5060:1.0 5853:1.0 6703:1.0 6960:1.0
3 30:0.07692307692307693 39:0.25 43:0.09090909090909091 173:0.5 230:1.0 286:0.1 349:0.5 513:1.0 1144:0.09090909090909091 1165:1.0 1927:0.2 2079:1.0 4880:0.14285714285714285 5192:1.0 6766:1.0
3 11:0.14285714285714285 17:0.3333333333333333 39:0.25 43:0.09090909090909091 46:1.0 48:0.3333333333333333 59:0.6666666666666666 68:0.14285714285714285 135:1.0 168:0.25 174:1.0 354:1.0 414:1.0 568:1.0 834:1.0 1974:1.0 3325:0.05263157894736842 5124:1.0 5235:1.0 5603:1.0 5604:1.0 6802:1.0 7513:1.0 7787:1.0 8071:1.0
3 4:1.0 10:0.1111111111111111 11:0.42857142857142855 13:1.0 28:0.045454545454545456 30:0.11538461538461539 39:0.25 43:0.09090909090909091 212:1.0 234:0.05263157894736842 385:1.0 411:1.0 636:0.5 804:1.0 947:0.5 1083:0.3333333333333333 1096:1.0 1342:1.0 1518:1.0 2023:1.0 2280:1.0 2381:1.0 2480:1.0 2849:1.0 3660:1.0 4104:1.0 5038:1.0 5488:1.0 5584:1.0 5603:1.0 5604:1.0
3 10:0.3333333333333333 11:0.2857142857142857 19:0.5 30:0.15384615384615385 39:0.25 43:0.09090909090909091 46:1.0 61:0.5 64:0.3333333333333333 100:0.5 160:0.3333333333333333 393:1.0 419:0.5 501:1.0 656:1.0 1337:1.0 1404:1.0 1683:1.0 2171:1.0 4880:0.14285714285714285 4881:1.0 4964:1.0 4987:1.0 5449:1.0 6180:1.0 6194:1.0 6197:1.0 6198:1.0 6216:1.0
3 14:0.3333333333333333 28:0.045454545454545456 43:0.09090909090909091 56:0.07692307692307693 63:0.16666666666666666 126:0.2 153:1.0 156:0.5 416:0.5 619:1.0 1096:1.0 1248:1.0 1322:1.0 1354:1.0 1370:1.0 1447:1.0 2052:1.0 2182:1.0 2694:1.0 4817:0.07692307692307693 4956:1.0 4961:1.0 4962:1.0 5043:1.0 5603:1.0 5604:1.0 6124:1.0 6845:3.0 7510:1.0
|
f3b4682b0a392ad67d817fb8d3365147f3c174ee | 449d555969bfd7befe906877abab098c6e63a0e8 | /479/CH8/EX8.1/Example_8_1.sce | 88a273668f01997abaafdf4e48cec64902f82abe | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 739 | sce | Example_8_1.sce | //Chemical Engineering Thermodynamics
//Chapter 8
//Third Law of Thermodynamics
//Example 8.1
clear;
clc;
//Given
C_ps = 0.1;//Molal heat capacity of copper at 20 K
Ti = 0;//Initial temperature in K
Tf = 20;//melting point in K
Tb = 300;//boiling point in K
//To calculate the absolute entropy of copper at 300 K
//From equation 8.4(page no 164)
a = C_ps/(Tf^3);// a is the charateristic constant
C_p = [0.1 0.80 1.94 3.0 3.9 5.0];
//T1 = log(T);
T1 = [1.301 1.6021 1.7782 1.9031 2.000 2.1761];
plot(T1,C_p);
xtitle("C_p vs T1","T1","Cp");
// Area under the curve is given as
A = 7.82;
//From equation 8.5(page no 164)
S = (a*((Tf^3)/3))+A;
mprintf('The absolute entropy of copper is %f Kcal/Kgmole',S);
//end |
3ced7a4ecfce43154c1ccc00a219f5c7a714aaed | 449d555969bfd7befe906877abab098c6e63a0e8 | /1962/CH2/EX2.7/example2_7.sce | 1cf6c18a7b71b0a818d044c96e6c8b4b1f1a5ba2 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 342 | sce | example2_7.sce | //example 2.7
//page 67
clc; funcprot(0);
//initialisation of variable
A=2;
pi=3.14;
Gamma=9810;
theta=pi/3;
ybar=0.75+sin(pi/3);
Ig=2^3/12;//moment of inertia
//part1
F=Gamma*A*ybar;//force
disp(F,"Total Force (N)=");
//part2
hbar=ybar+Ig*(sin(theta))^2/A/ybar;//centroid
disp(hbar,"depth of center of pressure(m)=");
clear
|
4e96e5b9fe5ab321668ae58e1c9960a38165bdaa | 449d555969bfd7befe906877abab098c6e63a0e8 | /45/CH4/EX4.9/exmple_4_9.sce | 8bafd0a6f9d10bdbfdaf05d42c86d343e2f3b393 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 577 | sce | exmple_4_9.sce | //example 4.9
clc;
clear;
sel = input(' Enter the values of ABCD :');
a=sel;
q=1;
while(a>0) // finding the decimal equivlent
r=modulo(a,10);
b(1,q)=r;
a=a/10;
a=floor(a);
q=q+1;
end
f=0;
for m=1:q-1
c=m-1
f = f + b(1,m)*(2^c);
end
if f >9 then //checking the invalid condition
disp('Its a invalid input. Therefore,none of the LEDs is on because all outputs lines are high' );
else //displaying the LED no if the inputs are valid
printf('\n LED %d lights up all. All other LEDs remain off because the other outputs are high.',f);
end
|
b26b974d3112e6f21fe58ae790a84374cce28091 | 449d555969bfd7befe906877abab098c6e63a0e8 | /2951/CH6/EX6.3.A/additional_ex_3.sce | cab6cd299dc67aa730b0515eebd33b297714a1aa | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 910 | sce | additional_ex_3.sce | clc;
clear;
q=1.6*10^(-19);// electron charge
Ieq=5;//equivalent shot noise current in uA
Bn=8;//bandwidth in MHz
Rn=200;
Rs=100;//resistance in ohms
k=1.38*10^(-23);// boltzman constant
T=290;//temperature in K
Vs=10// RMS signal source volatage in uV
In=sqrt(2*Ieq*q*Bn);
Vni=Rs*In;//shot noise voltage
Vns=sqrt(4*Rs*k*T*Bn*10^(6));//thermal noise volatge from source
//change in answer due to calculation error in book
Vne=sqrt(4*Rn*k*T*Bn*10^(6));//noise voltage by equivalent noise resistance
Vn=sqrt(Vni^2+Vns^2+Vne^2);// total noise voltage
SNR=20*log10(Vs*10^(-6)/Vn);
disp("shot noise voltage(in V) is ");
disp(Vni);
disp("thermal noise voltage from source(in V) is");
disp(Vns);
disp("noise voltage by equivalent noise resistance(in V) is");
disp(Vne);
disp("total noise voltage at the input(in V) is");
disp(Vn);
disp("SNR (in dB) is");
disp(SNR);
|
ccde99a4b1ea5140c1de94aad85c1497c689130a | 449d555969bfd7befe906877abab098c6e63a0e8 | /132/CH4/EX4.5/Example4_5.sce | 64899aa5fcf6b5a2fa8009463bb602cd14a373d2 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 397 | sce | Example4_5.sce | //Example 4.5
//Program to determine Capacitance of Varactor Diode if the
//Reverse-Bias Voltage is increased from 4V to 8V
clear;
clc ;
close ;
//Given Circuit Data
Ci=18*10^(-12);//i.e. 18 pF
Vi=4; //Volts
Vf=8; //Volts
//Calculation
K=Ci*sqrt(Vi);
Cf=K/sqrt(Vf);
//Displaying The Results in Command Window
printf("\n\t The Final Value of Capacitance is C = %f pF .",Cf/10^(-12)); |
03f5280044ae1424e7c08821b6698d7a2c65adee | 527c41bcbfe7e4743e0e8897b058eaaf206558c7 | /Positive_Negative_test/Netezza-Base-StatisticalFunctions/FLFracRank-NZ-01.tst | 3a11030cc5d17ee7dde702de785ca794744f93e5 | [] | no_license | kamleshm/intern_fuzzy | c2dd079bf08bede6bca79af898036d7a538ab4e2 | aaef3c9dc9edf3759ef0b981597746d411d05d34 | refs/heads/master | 2021-01-23T06:25:46.162332 | 2017-07-12T07:12:25 | 2017-07-12T07:12:25 | 93,021,923 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 3,477 | tst | FLFracRank-NZ-01.tst | -- Fuzzy Logix, LLC: Functional Testing Script for DB Lytix functions on Netezza
--
-- Copyright (c): 2014 Fuzzy Logix, LLC
--
-- NOTICE: All information contained herein is, and remains the property of Fuzzy Logix, LLC.
-- The intellectual and technical concepts contained herein are proprietary to Fuzzy Logix, LLC.
-- and may be covered by U.S. and Foreign Patents, patents in process, and are protected by trade
-- secret or copyright law. Dissemination of this information or reproduction of this material is
-- strictly forbidden unless prior written permission is obtained from Fuzzy Logix, LLC.
-- Functional Test Specifications:
--
-- Test Category: Basic Statistics
--
-- Test Unit Number: FL-Netezza-01
--
-- Name(s): FLFracRank
--
-- Description: Scalar function that returns the fractional rank.
-- Applications:
--
-- Signature: FLFracRank(A INTEGER,
-- B INTEGER)
--
-- Parameters: See Documentation
--
-- Return value: DOUBLE PRECISION
--
-- Last Updated: 07-11-2017
--
-- Author: Diptesh Nath,Kamlesh Meena
--
-- BEGIN: TEST SCRIPT
\time
--.run file=../PulsarLogOn.sql
--.set width 2500
-- BEGIN: POSITIVE TEST(s)
---- Positive Test 1: Returns expected result
--- Return expected results, Good
SELECT p.Rank,
FLFracRank(p.Rank, COUNT(*)) AS FracRank
FROM
(
SELECT a.GroupID,
a.ObsID,
RANK() OVER (PARTITION BY 1 ORDER BY a.NUM_VAL ASC)
FROM tblHypoTest a
) AS p
GROUP BY p.Rank;
---- Positive Test 2: FrackRank should be the same as oRank since All Freq = 1
--- Return expected results, Good
SELECT a.SerialVal AS oRank, 1 AS oFreq, FLFracRank(a.SerialVal, 1)
FROM fzzlSerial a
WHERE a.SerialVal <= 10;
-- END: POSITIVE TEST(s)
-- BEGIN: NEGATIVE TEST(s)
---- Negative Test 1: No data
--- No Output
SELECT FLFracRank(a.SerialVal, a.SerialVal)
FROM fzzlSerial a
WHERE a.SerialVal <= -1;
---- Negative Test 2: Original rank with Invalid Freqs
--- Still return values, need to check if the input table is valid or not
SELECT a.SerialVal AS oRank, a.SerialVal AS oFreq, FLFracRank(a.SerialVal, a.SerialVal)
FROM fzzlSerial a
WHERE a.SerialVal <= 10;
---- Negative Test 3: Condition Test (pRank >0): Zero and Negative Rank
--- Return expected error, Good
SELECT FLFracRank(a.SerialVal - 1, 1)
FROM fzzlSerial a
WHERE a.SerialVal <= 10;
SELECT FLFracRank(a.SerialVal * -1, 1)
FROM fzzlSerial a
WHERE a.SerialVal <= 10;
---- Negative Test 4: Condition Test (pFreq >0): Zero Freq
--- Return expected error, Good
SELECT FLFracRank(a.SerialVal, 0)
FROM fzzlSerial a
WHERE a.SerialVal <= 10;
---- Negative Test 5: Condition Test (pFreq >0): Negative Freq
--- Return expected error, Good
SELECT FLFracRank(a.SerialVal, -1)
FROM fzzlSerial a
WHERE a.SerialVal <= 10;
---- Negative Test 6: Invalid Data Type(BIGINT): Non-Integer Rank
--- Return expected error, Good
SELECT FLFracRank(a.RandVal, 1)
FROM fzzlSerial a
WHERE a.SerialVal <= 10;
---- Negative Test 7: Invalid Data Type(BIGINT): Non_Integer Freq
--- Return expected error, Good
SELECT FLFracRank(a.SerialVal, 1.0)
FROM fzzlSerial a
WHERE a.SerialVal <= 10;
-- END: NEGATIVE TEST(s)
\time
-- END: TEST SCRIPT
---- Negative Test 8: Bad input in partition
SELECT p.Rank,
FLFracRank(p.Rank, COUNT(*)) AS FracRank
FROM
(
SELECT a.GroupID,
a.ObsID,
RANK() OVER (PARTITION BY 1 ORDER BY a.NUM ASC)
FROM tblHypoTest a
) AS p
GROUP BY p.Rank;
-- END: NEGATIVE TEST(s)
\time
-- END: TEST SCRIPT
|
866afaf8c9b8b8379609c5389d96bae3de94f24d | 449d555969bfd7befe906877abab098c6e63a0e8 | /659/CH3/EX3.5/exm3_5.sce | 93136c7b1ea8245da5eba1381b87d6e549f725e6 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 308 | sce | exm3_5.sce | // Example 3.5
//Output of program shows round-off errors that can occur in computation of floating point numbers
//Sum of n terms of 1/n
count=1;
sum1=0;
n=input("Enter value of n:");
term=1.0/n;
while(count<=n)
sum1=sum1+term;
count=count+1;
end
printf("Sum= %f",sum1); |
ac216dd7575c61a8538de553e20a4e3012d993a6 | 78de1b37ac7fbc77bc00584d6677402639eb8ccf | /Ex_9_5_a.sce | d1d12b0a96e333864dbcaf712e1c55e343967f9d | [] | no_license | devanshmody/c-c-programs | de25f17728b488bb5245342338d303d968f2ee05 | 7405239f4fc792a1382d7726cb1aaeffc3e740a8 | refs/heads/main | 2023-04-16T14:11:06.271935 | 2021-05-05T09:39:48 | 2021-05-05T09:39:48 | 364,526,778 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 287 | sce | Ex_9_5_a.sce | //Example 9.5.a
clc;clear;close;
z=poly(0,'z');
s=poly(0,'s');
Hz=3*(2*z^2+5*z+4)/(2*z+1)/(z+2);
H=pfss(Hz/z);
for k=1:length(H)
H(k)=clean(H(k));
H1(k)=z*horner(H(k),z);
end
disp(Hz,'System Function H(z)=');
disp(H1,'System Function for parallel realisation Hk(z)='); |
472f29d2a54e23fcfdb5930cc00046b7e4d5c6cd | 449d555969bfd7befe906877abab098c6e63a0e8 | /3020/CH13/EX13.2/ex13_2.sce | 2443f2d64e1386f50feb8fcea87ce2af4b355067 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 206 | sce | ex13_2.sce | clc;
clear all;
h = 4; // Miller indices
k = 3; // Miller indices
l = 0; // Miller indices
a = 2e-10; // In meters
d = a/(sqrt(h^2+k^2+l^2));
disp('m',d,'The interplanar spacing for the plane is ')
|
25e3e1523144a741880cf720f3192ba392e728cc | 449d555969bfd7befe906877abab098c6e63a0e8 | /23/CH13/EX13.12/Example_13_12.sce | 36abb49227698c1d07fb35f33c05d5411def3a22 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 2,727 | sce | Example_13_12.sce | clear;
clc;
//To find Approx Value
function[A]=approx(V,n)
A=round(V*10^n)/10^n;//V-Value n-To what place
funcprot(0)
endfunction
function[Q]=IDCPH(T0,T,dA,dB,dC,dD)
t=T/T0;
Q=(dA+((dB/2)*T0*(t+1))+((dC/3)*T0*T0*((t^2)+t+1))+(dD/(t*T0*T0)))*(T-T0)
funcprot(0);
endfunction
function[Q]=IDCPS(T0,T,dA,dB,dC,dD)
t=T/T0;
Q=((dA)*log(t))+(((dB*T0)+(((dC*T0*T0)+(dD/(t*t*T0*T0)))*(t+1)/2))*(t-1))
funcprot(0);
endfunction
//Example 13.12
//Caption : Program to Find the Product Composition for Two Reactions
T0=298.16;//[K]
T1=750;//[K]
R=8.314;
P=1.2;//[bar]
//C4H10 --> C2H4 + C2H6 (I)
//C4H10 --> C3H6 + CH4 (II)
//Values From Table C.1 At T=298.15K
A_butane=1.935;
A_ethene=1.424;
A_ethane=1.131;
A_propene=1.637;
A_methane=1.702;
B_butane=36.915*10^-3;
B_ethene=14.394*10^-3;
B_ethane=19.225*10^-3;
B_propene=22.706*10^-3;
B_methane=9.081*10^-3;
C_butane=-11.402*10^-6;
C_ethene=-4.392*10^-6;
C_ethane=-5.561*10^-6;
C_propene=-6.915*10^-6;
C_methane=-2.164*10^-6;
D_butane=0;
D_ethene=0;
D_ethane=0;
D_propene=0;
D_methane=0;
dA_I=A_ethene+A_ethane-A_butane;
dA_II=A_methane+A_propene-A_butane;
dB_I=B_ethene+B_ethane-B_butane;
dB_II=B_methane+B_propene-B_butane;
dC_I=C_ethene+C_ethane-C_butane;
dC_II=C_methane+C_propene-C_butane;
dD_I=D_ethene+D_ethane-D_butane;
dD_II=D_methane+D_propene-D_butane;
// Values from Table C.4 at T=298.15K
H_butane=-125790;//[J/mol]
H_ethene=52510;//[J/mol]
H_ethane=-83820;//[J/mol]
H_propene=19710;//[J/mol]
H_methane=-74520;//[J/mol]
G_butane=-16570;//[J/mol]
G_ethene=68460;//[J/mol]
G_ethane=-31855;//[J/mol]
G_propene=62205;//[J/mol]
G_methane=-50460;//[J/mol]
dHo_I=H_ethene+H_ethane-H_butane
dHo_II=H_methane+H_propene-H_butane
dGo_I=G_ethene+G_ethane-G_butane
dGo_II=G_methane+G_propene-G_butane
I1_I=approx(IDCPH(T0,T1,dA_I,dB_I,dC_I,dD_I),3)
I1_II=approx(IDCPH(T0,T1,dA_II,dB_II,dC_II,dD_II),3)
I2_I=approx(IDCPS(T0,T1,dA_I,dB_I,dC_I,dD_I),5)
I2_II=approx(IDCPS(T0,T1,dA_II,dB_II,dC_II,dD_II),5)
//Using Eqn 13.18
//dG_418/RT=((dGo - dHo)/RTo)+(dHo/RT)+((1/T)*I1)-I2 c1=dG_418/RT
c1_I=approx(((dGo_I-dHo_I)/(R*T0))+(dHo_I/(R*T1))+((1/T1)*I1_I)-I2_I,4)
c1_II=approx(((dGo_II-dHo_II)/(R*T0))+(dHo_II/(R*T1))+((1/T1)*I1_II)-I2_II,4)
K_I=approx(exp(-c1_I),4)
K_II=approx(exp(-c1_II),4)
k=(K_II/K_I)^0.5;
e_I=approx(((K_I/P)/(1+(K_I*(1/P)*(1+k)*(1+k))))^0.5,4);
e_II=approx(k*e_I,4);
n_C4H10=1-e_I-e_II;
n_C2H4=e_I;
n_C2H6=e_I;
n_C3H6=e_II;
n_CH4=e_II;
nt=n_C4H10+n_C2H4+n_C2H6+n_C3H6+n_CH4;
y_C4H10=approx(n_C4H10/nt,4);
y_C2H4=approx(n_C2H4/nt,4);
y_C2H6=approx(n_C2H6/nt,4);
y_C3H6=approx(n_C3H6/nt,4);
y_CH4=approx(n_CH4/nt,4);
y=[y_C4H10 y_C2H4 y_C2H6 y_C3H6 y_CH4];
disp(y,' Y_C4H10 Y_C2H4 Y_C2H6 Y_C3H6 Y_CH4')
//End |
933c8ca6f2de229858f83e9daa62a3032efd8b08 | 9b68b3d73b63ebcbfe18cc9a4aa8e91c84833a84 | /tests/libs/hdf5/test-h5-wrappers-new/C/H5G/testfiles/110/h5ex_g_iterate.tst | 66a4ae927ff240ea08aec04511468eb4a1b42ba5 | [
"LicenseRef-scancode-llnl",
"LicenseRef-scancode-hdf4",
"LicenseRef-scancode-unknown-license-reference",
"Apache-2.0",
"LicenseRef-scancode-warranty-disclaimer"
] | permissive | openhpc/ohpc | 17515db5082429eb9f250f12bf242b994beb715f | 725a1f230434d0f08153ba1a5d0a7418574f8ae9 | refs/heads/3.x | 2023-08-19T02:15:14.682630 | 2023-08-18T19:33:51 | 2023-08-18T19:34:18 | 43,318,561 | 827 | 247 | Apache-2.0 | 2023-09-14T01:22:18 | 2015-09-28T18:20:29 | C | UTF-8 | Scilab | false | false | 80 | tst | h5ex_g_iterate.tst | Objects in root group:
Dataset: DS1
Datatype: DT1
Group: G1
Dataset: L1
|
7aa7a9a448702507c0b2ebcaf6c1bcd7ac72142f | 449d555969bfd7befe906877abab098c6e63a0e8 | /2339/CH4/EX4.9.1/Ex4_9.sce | 85d41dae4df97cd0a2c6ec08ab315161b46dde90 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 242 | sce | Ex4_9.sce | clc
clear
//For throttling H1=H2
//At 11 bar
Hf=781.3; //in kJ/kg
Hfg=2000.4; //in kJ/kg
//At 1 bar
Hg=2675.5; //in kJ/kg
x=(Hg-Hf)/Hfg;
printf('The Dryness Fraction: %3.3f kJ/kg',x);
printf('\n');
|
24e95ca0218421d495192d9688d0be078b991208 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1571/CH11/EX11.3/Chapter11_Example3.sce | a6ca170c77a799ea950469476441be61fd3f36e7 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 445 | sce | Chapter11_Example3.sce | clc
clear
//INPUT
i=1.18;//current in amperes
e=20;//potential difference across its ends in volts
j=4.2;//joules constant in joule/cal
a=2*10^4;//area of the slab in sq.cm
t=5;//thickness of the plate in cm
t1=12.5;//temperature at hot side in K
t2=0;//temperature at cold side in k
//CALCULATIONS
k=e*i*t/(j*a*(t1-t2));//thermal conductivity in cgs unit
//OUTPUT
mprintf('thermal conductivity of slab is %3.5f cgs unit',k)
|
18665a71dd128f1ae2ea76210a4e7665437ab0e4 | 449d555969bfd7befe906877abab098c6e63a0e8 | /632/CH9/EX9.18/example9_18.sce | 08cffe04f2999da798e5a8743383679fe0a446ee | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 711 | sce | example9_18.sce | //clc()
F = 100;//kg
//F, D and W be the flow rates of the feed, the distillate and bottom product resp., xf , xd and xw be the mole fraction of methanol in the fee, distillate and the bottom product resp.
xf = 0.20;
xd = 0.97;
xw = 0.02;
//using, F = D + W and F*xf + D*xd + W*xw,we get
D = 18.95;//kg/h
W = 81.05;//kg/h
R = 3.5;
//R = L / D
//for distillate = 1kg
D1 = 1;//kg
L = R*D1;
//Taking balance around the condenser,
G = L + D1;
mcondensed = G * D / F;
disp("kg",D,"(a)Amount of distillate = ")
disp("kg",W," Amount of Bottom Product = ")
disp("kg",G,"(b)Amount of vapour condensed per kg of distillate = ")
disp("kg",mcondensed,"(c)Amount of vapour condensed per kg of feed = ") |
d2eba57cd7dee3ddad380cff5c38397ef6bb2b8e | a62e0da056102916ac0fe63d8475e3c4114f86b1 | /set11/s_Fundamentals_Of_Optics_F._A._Jenkins_And_H._E.white_3480.zip/Fundamentals_Of_Optics_F._A._Jenkins_And_H._E.white_3480/CH5/EX5.3/Ex5_3.sce | 54150cdc63115c2a5241df9531388ef771fe401f | [] | no_license | hohiroki/Scilab_TBC | cb11e171e47a6cf15dad6594726c14443b23d512 | 98e421ab71b2e8be0c70d67cca3ecb53eeef1df6 | refs/heads/master | 2021-01-18T02:07:29.200029 | 2016-04-29T07:01:39 | 2016-04-29T07:01:39 | null | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 146 | sce | Ex5_3.sce | errcatch(-1,"stop");mode(2);//Example 5.3, Page 111
n=1
n11=1.3
f11=4.333//in cm
HN=f11*((n11-n)/n11)
printf("Nodal length is %f cm",HN)
exit();
|
b1a768abbeb6f0f816c7d266542bf9493bbf4845 | a62e0da056102916ac0fe63d8475e3c4114f86b1 | /set14/s_Linear_Control_Systems_B._S._Manke__29.zip/Linear_Control_Systems_B._S._Manke__29/CH7/EX7.19.3/exa7_19_3.sce | c2e7b5caa8008f1f87ef807a09a5fb77bb775c9c | [] | no_license | hohiroki/Scilab_TBC | cb11e171e47a6cf15dad6594726c14443b23d512 | 98e421ab71b2e8be0c70d67cca3ecb53eeef1df6 | refs/heads/master | 2021-01-18T02:07:29.200029 | 2016-04-29T07:01:39 | 2016-04-29T07:01:39 | null | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 505 | sce | exa7_19_3.sce | mode(2);errcatch(-1,"stop");driver("GIF");//caption:stability_using_bode_plot
//example 7.19.3
//page 283
s=%s;
g=(48*(s+10))/(s*(s+20)*(s^2+2.4*s+16));
G=syslin('c',g)
fmin=0.01;
fmax=100;
bode(G, fmin, fmax)
show_margins(G)
gm=g_margin(G)
pm=p_margin(G)
disp(gm,"gain_margin=");
disp(pm,"phase_margin=");
disp("since gain and phase margin are both positive so system is stable")
xinit('/home/fossee/Downloads/tbc_graphs/Linear_Control_Systems_B._S._Manke__29/exa7_19_3');xend();exit();
|
fbed50b097dc720e9928cb7d3be2262eb34eac4d | 449d555969bfd7befe906877abab098c6e63a0e8 | /1541/CH2/EX2.22/Chapter2_Example22.sce | b38a87c55794888889724273964ada76794ad2e1 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 757 | sce | Chapter2_Example22.sce | //Chapter-2, Example 2.22, Page 2.40
//=============================================================================
clc
clear
//INPUT DATA
L2=7500;//Load on secondary in W
V2=220;//Secondary voltage in V
cosq=0.8;//Power factor
R2=0.05;//Secondary resistance in ohm
X2=0.75;//Secondary reactance in ohm
V2i=200;//Secondary voltage in V
//CALCULATIONS
I2=(L2/(V2*cosq));//Secondary current in A
q=acosd(cosq);//Phase angle in degree
I2c=complex((I2*cosd(q)),(I2*sind(-q)));//I2 in complex form
Z2=complex(R2,X2);
E2=(V2i+(I2c*Z2));//Induced imf in V
a1=real(E2);
a2=imag(E2);
//OUTPUT
mprintf('Induced emf in the secondary is %3.2f+j%3.2f',a1,a2)
//=================================END OF PROGRAM==============================
|
859e040e52c86d4f734b4b55071e16c5d1c45a72 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3740/CH3/EX3.6/Ex3_6.sce | ae6adf851549a3fe84a40ba514428bb470288733 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 529 | sce | Ex3_6.sce | //Optoelectronics - An Introduction, 2nd Edition by J. Wilson and J.F.B. Hawkes
//Example 3.5
//OS=Windows XP sp3
//Scilab version 5.5.2
clc;
clear;
//given
nOmega=1.5019;//refractive index corresponding to the ray of frequency Omega
n2Omega=1.4802;//refractive index corresponding to the ray of frequency 2*Omega
Lambda0=0.8e-6;//vacuum wavelength at the fundamental frequency in m
lc=Lambda0/(4*(nOmega-n2Omega));//Coherence length in m
mprintf("\n lc = %.1e m",lc);//The answers vary due to round off error
|
306d557bdafab7ac1cb1c027b215bd84fb626986 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3821/CH7/EX7.8/Example7_8.sce | 0214e40133c3925e42c76da1956625f267263454 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 727 | sce | Example7_8.sce | ///Chapter No 7 Fluid Mechanics
////Example 7.8 Page No:118
/// Find Power required to maintain the speed of upper plate
//Input data
clc;
clear;
dy=1.5*10^-4; //Two horizontal plates are placed in m
mu=0.12; //Space between plates Ns/m**2
A=2.5; //Upper area is required to move in m**2
du=0.6; //Speed rerlated to lower plate in m/s
////(1)Calculation
tau=mu*(du/dy); //Shear stress N/m**2
F=tau*A; //Force in N
P=F*du; //Power required to maintain the speed of upper plate in W
//Output
printf('Shear stress=%f N/m^2 \n ',tau);
printf('Force=%f N \n ',F);
printf('Power required to maintain the speed of upper plate=%f W \n ',P);
|
4f6b18f9befe63de6f0e2ba4a86e0b15faf6ac3e | 932d6f0f83a2eaed579be193b551589dc6674c52 | /montas.sce | 626ff4a3ba0008141ce5aba6f1038979cfcb5b56 | [] | no_license | JossueRenteria/Raudel | 31f69ca750031b1515034155bce6109a358ca46d | 664c502976a9430a4215b25454d3cb38f3c810fc | refs/heads/master | 2016-08-12T20:00:55.727841 | 2015-11-28T19:17:16 | 2015-11-28T19:17:16 | 47,035,904 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 382 | sce | montas.sce | function conejos()
m=1
h=1
cm=0
ch=0
ma=zeros(50,6)
for i=1:50
ma(i,1)=i;
ma(i,2)=cm+m;
m= ma(i,2)
ma(i,3)=ch+h;
h= ma(i,3)
ma(i,4)=m*3;
cm= ma(i,4)
ma(i,5)=h*3;
ch= ma(i,5)
ma(i,6)=((ma(i,2))+(ma(i,3))+(ma(i,4))+(ma(i,5)));
end
disp(ma)
endfunction
|
27e29f4c08dc952b96e127dbd3b4f316e55b770b | 449d555969bfd7befe906877abab098c6e63a0e8 | /2459/CH11/EX11.5/Ex11_5.sce | 3b17431c6c2ae15700a67946f51ecf953454c37a | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 148 | sce | Ex11_5.sce | //chapter11
//example11.5
//page205
Ie=1 //mA
alpha=0.92
Icbo=50d-3 //mA
Ic=alpha*Ie+Icbo
printf("collector current = %.3f mA \n",Ic)
|
2860a1796f0aab693037694f7c9edb90960c8e26 | 449d555969bfd7befe906877abab098c6e63a0e8 | /462/CH2/EX2.36.a/ex_2_36_a.sce | 6a6bb7cfcc6f2e24c6c0677476007f3b2f8b0d7d | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 471 | sce | ex_2_36_a.sce | //example 2.36(a)//
//subtraction of hexadecimal number//
clc
//clears the screen//
clear
//clears already existing variables//
x=hex2dec('3F')
//hexadecimal to deciimal conversion//
y=hex2dec('5C')
z=x-y
//subtraction//
t=z*-1
t1=dec2hex(t)
//answer in hexadecimal form(modulus)//
t2=bitcmp(t,8)
//complement//
t3=t2+1
//2's complement//
a=dec2bin(t3)
//answer in 2's complement form
disp('result of subtraction in 2''s compliment form is:')
disp(a) |
ae6aa4fbaf3b4051e758efb1b3a6ec8ce5e245d4 | 449d555969bfd7befe906877abab098c6e63a0e8 | /3802/CH4/EX4.3/Ex4_3.sce | c884f6ef44381751e2eec9a7a30785016b4e4b48 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 741 | sce | Ex4_3.sce | //Book Name:Fundamentals of Electrical Engineering
//Author:Rajendra Prasad
//Publisher: PHI Learning Private Limited
//Edition:Third ,2014
//Ex4_3.sce
clc;
clear;
r=[-0.03 0.01 0.04];
r_dash=[0.03 0.08 -0.02];
Q1=129e-9;
Q2=110e-6;
epsilon_not=1/(36*%pi*1e9);
a=r-r_dash; //r and r_dash are the position of two charges
b=a.^2;
c=b(1,1)+b(1,2)+b(1,3);
d=sqrt(c); //b,c,d are assumed alphabets for calculating magnitude of difference of r and r'
F=(Q1*Q2)/(4*%pi*epsilon_not*d^2);
printf("\n The force on Q2=%2.1f N \n",F)
Ir=a/d;
F1=Ir*F;
printf("\n Force interms of i,j,k vector coefficient is")
disp(F1)
//There is a error in the book for calculating F value
//So answer given in the book is wrong
|
2fd40c77210465080fee650cac381a1c1b060505 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1627/CH4/EX4.5/Ex4_5.sce | f2372c71a9ab2c32e5b350596c9af512dff28562 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 245 | sce | Ex4_5.sce | clc
//initialisation of variables
p=8000*10^-3//liters/min
r=15*10^-2//cm
v=2.5//m
//CALCULATIONS
V1=(4*(p)*(1/60))/(%pi*(r)^2)//m/s
D=sqrt(4*(p)*(1/60)/(%pi*v))*100//cm
//RESULTS
printf('The diameter of the suction line is=% f cm',D)
|
aa4c0c9dccb15507b7c8ef789168f7ad5fe0ea0a | 449d555969bfd7befe906877abab098c6e63a0e8 | /3733/CH3/EX3.1/Ex3_1.sce | fbb48f4449cd13aa47ff55e1d6564fbb60dc6b4a | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 3,275 | sce | Ex3_1.sce | // Example 3_1
clc;funcprot(0);
// Given data
m=[1 2 3 4 5 6 7 8 9 10 11 12];// Month for load curve
R_a=[40 30 30 20 20 160 180 180 100 80 50 50];// The run off for river A is given in millions of cu-m per month
R_b=[50 50 60 80 100 100 90 90 70 60 60 60];// The run off for river B is given in millions of cu-m per month
H_a=80;// The head available for river A in m
H_b=82;// The head available for river B in m
// Calculation
m=[0 0 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12];// Month for load curve
R_a=[0 40 40 30 30 30 30 20 20 20 20 160 160 180 180 180 180 100 100 80 80 50 50 50 50 190];//The run off for river A is given in millions of cu-m per month for load curve
R_b=[0 50 50 50 50 60 60 80 80 100 100 100 100 90 90 90 90 70 70 60 60 60 60 60 60 190];//The run off for river B is given in millions of cu-m per month for load curve
subplot(2,1,1);
xtitle('Fig.Prob.3.1.(a)');
plot(m',R_a','b',m',R_b','r');
a=gca();
a.x_ticks.labels=["0","J","F","M","A","M","J","J","A","S","O","N","D"];
a.x_ticks.locations=[0;1;2;3;4;5;6;7;8;9;10;11;12];
legend('Hydrograph of river A','Hydrograph of river B');
D_a=[20 30 40 50 80 100 160 180];// Discharge in millions of cu-m. per month
M_a=[12 10 8 7 5 4 3 2];// No.of months during which flow is available
D_b=[50 60 70 80 90 100];// Discharge in millions of cu-m. per month
M_b=[12 10 6 5 4 2];// No.of months during which flow is available
for(i=1:8)
T_a(i)=(M_a(i)/12)*100;
end
for(j=1:6)
T_b(j)=(M_b(j)/12)*100;
end
subplot(2,1,2);
xtitle('Fig.Prob.3.1.(b)');
plot(T_a,D_a','b',T_b,D_b','g');
legend('Flow duration curve for river A','Flow duration curve for river B');
//(a)
Q_a=(R_a(1)+R_a(2)+R_a(3)+R_a(4)+R_a(5)+R_a(6)+R_a(7)+R_a(8)+R_a(9)+R_a(10)+R_a(11)+R_a(12))/12;// The average flow per month of river A in millions of cu-m. per month
Q_b=(R_b(1)+R_b(2)+R_b(3)+R_b(4)+R_b(5)+R_b(6)+R_b(7)+R_b(8)+R_b(9)+R_b(10)+R_b(11)+R_b(12))/12;// The average flow per month of river A in millions of cu-m. per month
P_a=Q_a*H_a;// The power developed
P_b=Q_b*H_b;// The power developed
P_r=P_a/P_b;// Power ratio
if(P_a>P_b)
printf('\n(a)As P_a>P_b,the river A is more suitable for storage type power plant');
else
printf('\n(a)As P_b>P_a,the river B is more suitable for storage type power plant');
end
//(b)From Fig.Prob.3.1(a),The flow available for 85% of the time in year
Q_b=59.5;// millions of cu-m per month
Q_a=29;// millions of cu-m per month
P_b=Q_b*H_b;
P_a=Q_a*H_a;
if(P_b>P_a)
printf('\n(b)The site of river B is more suitable than the site of river A for run-off river power plant');
else
printf('\n(b)The river A is more suitable than the site of river B for run-off river power plant');
end
//(c)when 60% time of the year,the run off is required from both the rivers,thenfrom Fig.Prob.3.1(b),
Q_a=47;// millions of cu-m per month
Q_b=66;// millions of cu-m per month
Q_r=Q_a/Q_b;// Flow ratio
P_a=Q_a*H_a;// The power developed
P_b=Q_b*H_b;// The power developed
P_r=P_a/P_b;// Power ratio
printf('\n(c)Flow ratio=%0.3f \n Power ratio=%0.3f',Q_r,P_r);
printf('\n(d)From Fig.Prob.3.1(b),At 43 percentage of time,the run off rate of both sites is same');
// The answer vary due to round off error
|
7139a59eb94f7da721af01c13e654498913e664e | 08fe4df45181e37cb84ba1610cdfb219b4142434 | /macros/buildmacros.sce | 07ee7686f173bcc2e81eddf8b11ca65426df24a9 | [] | no_license | gzq763199198/AutoGenHelpToolBox | 17c7db64547e0e196806464f47b788d6ae33bf2e | c85275e8a7a1cd2ab3e19db5b283e9d1e9502843 | refs/heads/master | 2021-02-17T04:02:18.470172 | 2020-03-05T04:35:44 | 2020-03-05T04:35:44 | 245,069,411 | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 83 | sce | buildmacros.sce |
tbx_build_macros("AutoGenHelpToolBox",get_absolute_file_path("buildmacros.sce"));
|
244092cb9da0253737a843b88e545119cdba711c | 1bb72df9a084fe4f8c0ec39f778282eb52750801 | /test/SH12.prev.tst | 1136d994bd3026fcf736ff39fb7b37f757be9abb | [
"Apache-2.0",
"LicenseRef-scancode-unknown-license-reference"
] | permissive | gfis/ramath | 498adfc7a6d353d4775b33020fdf992628e3fbff | b09b48639ddd4709ffb1c729e33f6a4b9ef676b5 | refs/heads/master | 2023-08-17T00:10:37.092379 | 2023-08-04T07:48:00 | 2023-08-04T07:48:00 | 30,116,803 | 2 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 266 | tst | SH12.prev.tst | expression: x=a+log(0.001)*b + floor(3.14^2)
postfix1: ;x;a;log(;0.001;log);b;*;+;floor(;3.14;2;^;floor);+;=
rebuilt1: x=a+log(0.001)*b+floor(3.14^2)
postfix2: ;x;a;log(;0.001;log);b;*;+;floor(;3.14;2;^;floor);+;=
rebuilt2: x=a+log(0.001)*b+floor(3.14^2)
same
|
2bfe0b2e42efc1e124ccac34a48faec5ffe2d491 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1964/CH15/EX15.3/ex15_3.sce | 727e2f5301a7479fa3c32b83b8248a3e354ee864 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 499 | sce | ex15_3.sce | //Chapter-15, Example 15.3, Page 493
//=============================================================================
clc
clear
//INPUT DATA
x1=112;//in decimal form
x2=253;//in decimal form
//CALCULATIONS
y1=dec2base(x1,16)//converting decimal to hexadecimal
y2=dec2base(x2,16)//converting decimal to hexadecimal
disp(y1);
disp(y2);
//=================================END OF PROGRAM=======================================================================================================
|
cfea11c58d46acce37b662302ff589fd2c77460b | 449d555969bfd7befe906877abab098c6e63a0e8 | /3760/CH4/EX4.42/Ex4_42.sce | 8952674cdb3b8fa7a05c41bf79dfffcd4df2944d | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 563 | sce | Ex4_42.sce | clc;
N=1000; // speed of dc series motor
v=250; // supply from mains
i=50; // current drawn from mains
r=0.6; // armature + field resistance
rg=4.4; // additional resistance
// field flux is proportional to armature current
Ea1=v-i*r; // counter EMF at 1000 rpm
// Ea2=v-(n2/20)*(r+rg) where Ea2 is counter EMf at speed n2 . taking ratio of Ea2/Ea1 we obtain a quadratic equation in n2 whose terms are given by
t1=(Ea1*i)/N;
t2=(N*i)*((r+rg)/(N/i));
t3=-(N*i*v);
p=[ t1 t2 t3];
n=roots(p);
printf('New speed of motor is %f rpm',ceil(n(2)));
|
c0df80d0da0181e524e4ac19be1239aab5d47dd2 | e04f3a1f9e98fd043a65910a1d4e52bdfff0d6e4 | /New LSTMAttn Model/.data/lemma-split/DEVELOPMENT-LANGUAGES/oto-manguean/azg.tst | 326022d2b3ccb777322da38a258181fbd1b6e6cf | [] | no_license | davidgu13/Lemma-vs-Form-Splits | c154f1c0c7b84ba5b325b17507012d41b9ad5cfe | 3cce087f756420523f5a14234d02482452a7bfa5 | refs/heads/master | 2023-08-01T16:15:52.417307 | 2021-09-14T20:19:28 | 2021-09-14T20:19:28 | 395,023,433 | 3 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 97,128 | tst | azg.tst | n⁵ndɛʔ³⁵ V;PFV;SG;2;PST
n⁵ndɛʔ³⁵ V;SBJV;PL;1+INCL
n⁵ndɛʔ³⁵ V;IPFV;PL;3;PRS
n⁵ndɛʔ³⁵ V;PROG;PL;3;PST
n⁵ndɛʔ³⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndɛʔ³⁵ V;PROG;PL;1+EXCL;PST
n⁵ndɛʔ³⁵ V;IRR;PL;3;FUT
n⁵ndɛʔ³⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndɛʔ³⁵ V;IPFV;SG;1;PRS
n⁵ndɛʔ³⁵ V;IRR;PL;1+INCL;FUT
n⁵ndɛʔ³⁵ V;IRR;SG;1;FUT
n⁵ndɛʔ³⁵ V;PROG;PL;1+INCL;FUT
n⁵ndɛʔ³⁵ V;PFV;PL;3;PST
n⁵ndɛʔ³⁵ V;SBJV;SG;1
n⁵ndɛʔ³⁵ V;IRR;SG;2;FUT
n⁵ndɛʔ³⁵ V;PROG;PL;3;FUT
n⁵ndɛʔ³⁵ V;PFV;PL;1+EXCL;PST
n⁵ndɛʔ³⁵ V;PROG;SG;3;FUT
n⁵ndɛʔ³⁵ V;IPFV;SG;3;PRS
n⁵ndɛʔ³⁵ V;PROG;SG;1;FUT
n⁵ndɛʔ³⁵ V;SBJV;PL;3
n⁵ndɛʔ³⁵ V;PROG;SG;2;FUT
n⁵ndɛʔ³⁵ V;IRR;SG;3;FUT
n⁵ndɛʔ³⁵ V;PROG;SG;1;PST
n⁵ndɛʔ³⁵ V;PROG;PL;1+INCL;PST
n⁵ndɛʔ³⁵ V;PROG;SG;3;PST
n⁵ndɛʔ³⁵ V;PFV;SG;3;PST
n⁵ndɛʔ³⁵ V;SBJV;SG;2
n⁵ndɛʔ³⁵ V;IPFV;SG;2;PRS
n⁵ndɛʔ³⁵ V;SBJV;SG;3
n⁵ndɛʔ³⁵ V;PFV;SG;1;PST
n⁵ndɛʔ³⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndɛʔ³⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndɛʔ³⁵ V;SBJV;PL;1+EXCL
n⁵ndɛʔ³⁵ V;PFV;PL;1+INCL;PST
n⁵ndɛʔ³⁵ V;PROG;SG;2;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;SG;3;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;SG;3;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IRR;SG;3;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;SG;1;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IPFV;SG;1;PRS
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;SBJV;PL;1+EXCL
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;SBJV;SG;2
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IPFV;PL;3;PRS
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;SBJV;PL;3
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;PL;3;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;SG;2;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IRR;PL;3;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PFV;SG;2;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PFV;SG;3;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IRR;SG;2;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IPFV;SG;3;PRS
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;PL;3;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IRR;SG;1;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;SBJV;PL;1+INCL
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;SBJV;SG;3
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IPFV;SG;2;PRS
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;SBJV;SG;1
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;SG;2;FUT
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PFV;SG;1;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PROG;SG;1;PST
n⁵ndí⁵ ʔ⁵hndíʔ⁵tzʔon³ V;PFV;PL;3;PST
n⁵ndo³ndɛ³⁴ V;IRR;PL;1+EXCL;FUT
n⁵ndo³ndɛ³⁴ V;SBJV;PL;1+INCL
n⁵ndo³ndɛ³⁴ V;PROG;PL;3;PST
n⁵ndo³ndɛ³⁴ V;PROG;SG;2;FUT
n⁵ndo³ndɛ³⁴ V;PFV;SG;1;PST
n⁵ndo³ndɛ³⁴ V;PROG;PL;1+INCL;PST
n⁵ndo³ndɛ³⁴ V;SBJV;SG;3
n⁵ndo³ndɛ³⁴ V;IRR;PL;1+INCL;FUT
n⁵ndo³ndɛ³⁴ V;PROG;SG;1;FUT
n⁵ndo³ndɛ³⁴ V;PFV;PL;1+INCL;PST
n⁵ndo³ndɛ³⁴ V;PROG;PL;1+INCL;FUT
n⁵ndo³ndɛ³⁴ V;IRR;SG;2;FUT
n⁵ndo³ndɛ³⁴ V;IRR;SG;1;FUT
n⁵ndo³ndɛ³⁴ V;SBJV;PL;3
n⁵ndo³ndɛ³⁴ V;PROG;SG;3;PST
n⁵ndo³ndɛ³⁴ V;IPFV;SG;2;PRS
n⁵ndo³ndɛ³⁴ V;IRR;PL;3;FUT
n⁵ndo³ndɛ³⁴ V;PFV;SG;2;PST
n⁵ndo³ndɛ³⁴ V;IPFV;PL;1+EXCL;PRS
n⁵ndo³ndɛ³⁴ V;PROG;SG;3;FUT
n⁵ndo³ndɛ³⁴ V;IPFV;SG;3;PRS
n⁵ndo³ndɛ³⁴ V;IPFV;PL;3;PRS
n⁵ndo³ndɛ³⁴ V;IRR;SG;3;FUT
n⁵ndo³ndɛ³⁴ V;PFV;PL;3;PST
n⁵ndo³ndɛ³⁴ V;SBJV;PL;1+EXCL
n⁵ndo³ndɛ³⁴ V;PFV;PL;1+EXCL;PST
n⁵ndo³ndɛ³⁴ V;PROG;PL;1+EXCL;PST
n⁵ndo³ndɛ³⁴ V;IPFV;PL;1+INCL;PRS
n⁵ndo³ndɛ³⁴ V;PROG;SG;1;PST
n⁵ndo³ndɛ³⁴ V;SBJV;SG;2
n⁵ndo³ndɛ³⁴ V;PROG;PL;3;FUT
n⁵ndo³ndɛ³⁴ V;SBJV;SG;1
n⁵ndo³ndɛ³⁴ V;IPFV;SG;1;PRS
n⁵ndo³ndɛ³⁴ V;PROG;PL;1+EXCL;FUT
n⁵ndo³ndɛ³⁴ V;PROG;SG;2;PST
n⁵ndo³ndɛ³⁴ V;PFV;SG;3;PST
n⁵ndui³⁵ V;IRR;PL;3;FUT
n⁵ndui³⁵ V;PFV;SG;3;PST
n⁵ndui³⁵ V;PROG;PL;3;FUT
n⁵ndui³⁵ V;PFV;SG;1;PST
n⁵ndui³⁵ V;IRR;PL;1+INCL;FUT
n⁵ndui³⁵ V;PFV;PL;1+EXCL;PST
n⁵ndui³⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndui³⁵ V;IRR;SG;2;FUT
n⁵ndui³⁵ V;IPFV;PL;3;PRS
n⁵ndui³⁵ V;SBJV;PL;3
n⁵ndui³⁵ V;PROG;SG;1;FUT
n⁵ndui³⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndui³⁵ V;PROG;SG;3;PST
n⁵ndui³⁵ V;SBJV;SG;2
n⁵ndui³⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndui³⁵ V;IRR;SG;3;FUT
n⁵ndui³⁵ V;SBJV;SG;1
n⁵ndui³⁵ V;IPFV;SG;1;PRS
n⁵ndui³⁵ V;PROG;PL;1+INCL;FUT
n⁵ndui³⁵ V;IPFV;SG;2;PRS
n⁵ndui³⁵ V;PROG;PL;3;PST
n⁵ndui³⁵ V;IRR;SG;1;FUT
n⁵ndui³⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndui³⁵ V;PFV;SG;2;PST
n⁵ndui³⁵ V;PROG;SG;3;FUT
n⁵ndui³⁵ V;PFV;PL;1+INCL;PST
n⁵ndui³⁵ V;SBJV;SG;3
n⁵ndui³⁵ V;SBJV;PL;1+INCL
n⁵ndui³⁵ V;PROG;PL;1+EXCL;PST
n⁵ndui³⁵ V;PROG;SG;2;FUT
n⁵ndui³⁵ V;IPFV;SG;3;PRS
n⁵ndui³⁵ V;PROG;PL;1+INCL;PST
n⁵ndui³⁵ V;SBJV;PL;1+EXCL
n⁵ndui³⁵ V;PROG;SG;2;PST
n⁵ndui³⁵ V;PFV;PL;3;PST
n⁵ndui³⁵ V;PROG;SG;1;PST
n⁵ndí⁵nkiáʔ⁵ V;PFV;PL;3;PST
n⁵ndí⁵nkiáʔ⁵ V;IRR;PL;3;FUT
n⁵ndí⁵nkiáʔ⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵nkiáʔ⁵ V;IRR;SG;1;FUT
n⁵ndí⁵nkiáʔ⁵ V;PROG;SG;1;FUT
n⁵ndí⁵nkiáʔ⁵ V;PFV;SG;3;PST
n⁵ndí⁵nkiáʔ⁵ V;SBJV;SG;1
n⁵ndí⁵nkiáʔ⁵ V;PROG;SG;1;PST
n⁵ndí⁵nkiáʔ⁵ V;IRR;SG;3;FUT
n⁵ndí⁵nkiáʔ⁵ V;IRR;SG;2;FUT
n⁵ndí⁵nkiáʔ⁵ V;SBJV;SG;2
n⁵ndí⁵nkiáʔ⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵nkiáʔ⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵nkiáʔ⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵nkiáʔ⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵nkiáʔ⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵nkiáʔ⁵ V;SBJV;PL;3
n⁵ndí⁵nkiáʔ⁵ V;SBJV;SG;3
n⁵ndí⁵nkiáʔ⁵ V;PROG;SG;2;PST
n⁵ndí⁵nkiáʔ⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵nkiáʔ⁵ V;PROG;PL;3;PST
n⁵ndí⁵nkiáʔ⁵ V;PROG;SG;3;PST
n⁵ndí⁵nkiáʔ⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵nkiáʔ⁵ V;PFV;SG;1;PST
n⁵ndí⁵nkiáʔ⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵nkiáʔ⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵nkiáʔ⁵ V;PROG;PL;3;FUT
n⁵ndí⁵nkiáʔ⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵nkiáʔ⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵nkiáʔ⁵ V;PROG;SG;3;FUT
n⁵ndí⁵nkiáʔ⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵nkiáʔ⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵nkiáʔ⁵ V;PFV;SG;2;PST
n⁵ndí⁵nkiáʔ⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵nkiáʔ⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵nkiáʔ⁵ V;PROG;SG;2;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;SBJV;SG;3
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IRR;SG;2;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IRR;SG;3;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PFV;SG;3;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;SBJV;PL;3
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PFV;SG;2;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PFV;SG;1;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;SG;1;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IRR;SG;1;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PFV;PL;3;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;SG;2;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;PL;3;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;SG;3;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;SG;3;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;SG;1;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IRR;PL;3;FUT
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;SBJV;SG;2
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;SBJV;SG;1
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;PL;3;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵bi³⁴ nthan³ʔndyó⁵ V;PROG;SG;2;PST
n⁵ndí⁵chio³⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵chio³⁵ V;SBJV;PL;3
n⁵ndí⁵chio³⁵ V;PROG;SG;3;FUT
n⁵ndí⁵chio³⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵chio³⁵ V;PROG;SG;3;PST
n⁵ndí⁵chio³⁵ V;SBJV;SG;1
n⁵ndí⁵chio³⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵chio³⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵chio³⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵chio³⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵chio³⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵chio³⁵ V;PFV;SG;3;PST
n⁵ndí⁵chio³⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵chio³⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵chio³⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵chio³⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵chio³⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵chio³⁵ V;IRR;SG;1;FUT
n⁵ndí⁵chio³⁵ V;PROG;SG;2;PST
n⁵ndí⁵chio³⁵ V;IRR;PL;3;FUT
n⁵ndí⁵chio³⁵ V;IRR;SG;2;FUT
n⁵ndí⁵chio³⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵chio³⁵ V;PROG;SG;1;FUT
n⁵ndí⁵chio³⁵ V;IRR;SG;3;FUT
n⁵ndí⁵chio³⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵chio³⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵chio³⁵ V;PFV;SG;2;PST
n⁵ndí⁵chio³⁵ V;PROG;PL;3;FUT
n⁵ndí⁵chio³⁵ V;PFV;PL;3;PST
n⁵ndí⁵chio³⁵ V;SBJV;SG;3
n⁵ndí⁵chio³⁵ V;PROG;SG;1;PST
n⁵ndí⁵chio³⁵ V;PFV;SG;1;PST
n⁵ndí⁵chio³⁵ V;PROG;SG;2;FUT
n⁵ndí⁵chio³⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵chio³⁵ V;SBJV;SG;2
n⁵ndí⁵chio³⁵ V;PROG;PL;3;PST
n⁵ndí⁵tha⁵³ V;IRR;SG;2;FUT
n⁵ndí⁵tha⁵³ V;SBJV;PL;3
n⁵ndí⁵tha⁵³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵tha⁵³ V;IPFV;PL;3;PRS
n⁵ndí⁵tha⁵³ V;IPFV;SG;2;PRS
n⁵ndí⁵tha⁵³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵tha⁵³ V;SBJV;SG;2
n⁵ndí⁵tha⁵³ V;PFV;PL;3;PST
n⁵ndí⁵tha⁵³ V;PROG;SG;2;PST
n⁵ndí⁵tha⁵³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵tha⁵³ V;PROG;SG;1;PST
n⁵ndí⁵tha⁵³ V;PROG;SG;3;PST
n⁵ndí⁵tha⁵³ V;PROG;SG;3;FUT
n⁵ndí⁵tha⁵³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵tha⁵³ V;SBJV;PL;1+EXCL
n⁵ndí⁵tha⁵³ V;IRR;SG;3;FUT
n⁵ndí⁵tha⁵³ V;IRR;SG;1;FUT
n⁵ndí⁵tha⁵³ V;PROG;PL;3;PST
n⁵ndí⁵tha⁵³ V;PFV;SG;1;PST
n⁵ndí⁵tha⁵³ V;PROG;PL;3;FUT
n⁵ndí⁵tha⁵³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵tha⁵³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵tha⁵³ V;IRR;PL;3;FUT
n⁵ndí⁵tha⁵³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵tha⁵³ V;SBJV;PL;1+INCL
n⁵ndí⁵tha⁵³ V;IPFV;SG;3;PRS
n⁵ndí⁵tha⁵³ V;PROG;SG;1;FUT
n⁵ndí⁵tha⁵³ V;IPFV;SG;1;PRS
n⁵ndí⁵tha⁵³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵tha⁵³ V;PROG;SG;2;FUT
n⁵ndí⁵tha⁵³ V;PFV;SG;3;PST
n⁵ndí⁵tha⁵³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵tha⁵³ V;PFV;SG;2;PST
n⁵ndí⁵tha⁵³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵tha⁵³ V;SBJV;SG;3
n⁵ndí⁵tha⁵³ V;SBJV;SG;1
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;SG;1;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;SBJV;PL;1+INCL
n⁵ndí⁵nké⁵ ndʔɔ³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;PL;3;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;SG;1;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;SG;3;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;SG;2;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;SBJV;SG;1
n⁵ndí⁵nké⁵ ndʔɔ³ V;PFV;SG;2;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;SBJV;PL;3
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;SG;2;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;IPFV;SG;3;PRS
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;SG;3;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;PFV;SG;1;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;SBJV;SG;3
n⁵ndí⁵nké⁵ ndʔɔ³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵nké⁵ ndʔɔ³ V;IPFV;PL;3;PRS
n⁵ndí⁵nké⁵ ndʔɔ³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;IPFV;SG;2;PRS
n⁵ndí⁵nké⁵ ndʔɔ³ V;SBJV;PL;1+EXCL
n⁵ndí⁵nké⁵ ndʔɔ³ V;IRR;SG;3;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;PFV;SG;3;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;IRR;SG;1;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;IPFV;SG;1;PRS
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;IRR;PL;3;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;IRR;SG;2;FUT
n⁵ndí⁵nké⁵ ndʔɔ³ V;SBJV;SG;2
n⁵ndí⁵nké⁵ ndʔɔ³ V;PFV;PL;3;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;PL;3;PST
n⁵ndí⁵nké⁵ ndʔɔ³ V;PROG;PL;1+EXCL;FUT
n⁵hndɛ³⁵ V;PFV;SG;1;PST
n⁵hndɛ³⁵ V;SBJV;PL;1+INCL
n⁵hndɛ³⁵ V;IPFV;PL;1+EXCL;PRS
n⁵hndɛ³⁵ V;PROG;PL;1+INCL;PST
n⁵hndɛ³⁵ V;PROG;PL;1+EXCL;PST
n⁵hndɛ³⁵ V;IPFV;PL;1+INCL;PRS
n⁵hndɛ³⁵ V;SBJV;SG;2
n⁵hndɛ³⁵ V;SBJV;PL;1+EXCL
n⁵hndɛ³⁵ V;PFV;PL;1+EXCL;PST
n⁵hndɛ³⁵ V;IRR;PL;3;FUT
n⁵hndɛ³⁵ V;IPFV;SG;1;PRS
n⁵hndɛ³⁵ V;IRR;PL;1+EXCL;FUT
n⁵hndɛ³⁵ V;PFV;SG;2;PST
n⁵hndɛ³⁵ V;IRR;PL;1+INCL;FUT
n⁵hndɛ³⁵ V;IRR;SG;1;FUT
n⁵hndɛ³⁵ V;IRR;SG;3;FUT
n⁵hndɛ³⁵ V;PFV;PL;1+INCL;PST
n⁵hndɛ³⁵ V;SBJV;PL;3
n⁵hndɛ³⁵ V;PROG;SG;3;FUT
n⁵hndɛ³⁵ V;PROG;SG;1;PST
n⁵hndɛ³⁵ V;PROG;SG;3;PST
n⁵hndɛ³⁵ V;PFV;SG;3;PST
n⁵hndɛ³⁵ V;IPFV;SG;2;PRS
n⁵hndɛ³⁵ V;PROG;SG;2;PST
n⁵hndɛ³⁵ V;PROG;SG;2;FUT
n⁵hndɛ³⁵ V;PROG;PL;1+EXCL;FUT
n⁵hndɛ³⁵ V;PROG;PL;1+INCL;FUT
n⁵hndɛ³⁵ V;IPFV;PL;3;PRS
n⁵hndɛ³⁵ V;IRR;SG;2;FUT
n⁵hndɛ³⁵ V;PROG;PL;3;PST
n⁵hndɛ³⁵ V;PFV;PL;3;PST
n⁵hndɛ³⁵ V;SBJV;SG;1
n⁵hndɛ³⁵ V;PROG;PL;3;FUT
n⁵hndɛ³⁵ V;PROG;SG;1;FUT
n⁵hndɛ³⁵ V;SBJV;SG;3
n⁵hndɛ³⁵ V;IPFV;SG;3;PRS
n⁵ndyui³⁵ V;IPFV;SG;1;PRS
n⁵ndyui³⁵ V;PFV;SG;3;PST
n⁵ndyui³⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndyui³⁵ V;PROG;SG;1;PST
n⁵ndyui³⁵ V;SBJV;PL;1+INCL
n⁵ndyui³⁵ V;IRR;SG;2;FUT
n⁵ndyui³⁵ V;PROG;PL;1+EXCL;PST
n⁵ndyui³⁵ V;SBJV;SG;2
n⁵ndyui³⁵ V;IRR;SG;3;FUT
n⁵ndyui³⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndyui³⁵ V;PROG;SG;2;FUT
n⁵ndyui³⁵ V;IPFV;SG;3;PRS
n⁵ndyui³⁵ V;PROG;SG;3;PST
n⁵ndyui³⁵ V;PROG;SG;3;FUT
n⁵ndyui³⁵ V;PFV;PL;3;PST
n⁵ndyui³⁵ V;PROG;SG;2;PST
n⁵ndyui³⁵ V;PFV;SG;1;PST
n⁵ndyui³⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndyui³⁵ V;SBJV;PL;1+EXCL
n⁵ndyui³⁵ V;PROG;PL;3;FUT
n⁵ndyui³⁵ V;PFV;PL;1+EXCL;PST
n⁵ndyui³⁵ V;IRR;PL;3;FUT
n⁵ndyui³⁵ V;PROG;SG;1;FUT
n⁵ndyui³⁵ V;SBJV;SG;3
n⁵ndyui³⁵ V;PFV;SG;2;PST
n⁵ndyui³⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndyui³⁵ V;IPFV;SG;2;PRS
n⁵ndyui³⁵ V;PFV;PL;1+INCL;PST
n⁵ndyui³⁵ V;IPFV;PL;3;PRS
n⁵ndyui³⁵ V;SBJV;SG;1
n⁵ndyui³⁵ V;IRR;PL;1+INCL;FUT
n⁵ndyui³⁵ V;PROG;PL;1+INCL;PST
n⁵ndyui³⁵ V;PROG;PL;3;PST
n⁵ndyui³⁵ V;PROG;PL;1+INCL;FUT
n⁵ndyui³⁵ V;IRR;SG;1;FUT
n⁵ndyui³⁵ V;SBJV;PL;3
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;SG;2;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IRR;PL;3;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IRR;SG;1;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;SBJV;SG;1
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;SBJV;PL;3
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;SG;2;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;SBJV;SG;2
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;SG;1;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;SBJV;SG;3
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PFV;SG;3;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PFV;PL;3;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PFV;SG;2;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;SG;3;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IRR;SG;2;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;SG;1;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;PL;3;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;SG;3;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IRR;SG;3;FUT
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PFV;SG;1;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;PROG;PL;3;PST
n⁵ndí⁵kíʔ⁵na³ ʔndyó⁵ V;SBJV;PL;1+INCL
n⁵ndyionʔ³⁵tzʔon³ V;SBJV;SG;2
n⁵ndyionʔ³⁵tzʔon³ V;PFV;PL;1+EXCL;PST
n⁵ndyionʔ³⁵tzʔon³ V;IRR;SG;2;FUT
n⁵ndyionʔ³⁵tzʔon³ V;IPFV;SG;2;PRS
n⁵ndyionʔ³⁵tzʔon³ V;IPFV;SG;1;PRS
n⁵ndyionʔ³⁵tzʔon³ V;IRR;PL;3;FUT
n⁵ndyionʔ³⁵tzʔon³ V;PROG;PL;1+EXCL;PST
n⁵ndyionʔ³⁵tzʔon³ V;PROG;PL;1+INCL;PST
n⁵ndyionʔ³⁵tzʔon³ V;IRR;SG;1;FUT
n⁵ndyionʔ³⁵tzʔon³ V;PROG;SG;2;FUT
n⁵ndyionʔ³⁵tzʔon³ V;PROG;SG;3;PST
n⁵ndyionʔ³⁵tzʔon³ V;SBJV;PL;3
n⁵ndyionʔ³⁵tzʔon³ V;PFV;SG;2;PST
n⁵ndyionʔ³⁵tzʔon³ V;IPFV;PL;1+INCL;PRS
n⁵ndyionʔ³⁵tzʔon³ V;IPFV;SG;3;PRS
n⁵ndyionʔ³⁵tzʔon³ V;IPFV;PL;3;PRS
n⁵ndyionʔ³⁵tzʔon³ V;PROG;PL;1+EXCL;FUT
n⁵ndyionʔ³⁵tzʔon³ V;SBJV;PL;1+INCL
n⁵ndyionʔ³⁵tzʔon³ V;PFV;SG;3;PST
n⁵ndyionʔ³⁵tzʔon³ V;SBJV;SG;3
n⁵ndyionʔ³⁵tzʔon³ V;PROG;SG;3;FUT
n⁵ndyionʔ³⁵tzʔon³ V;PFV;PL;3;PST
n⁵ndyionʔ³⁵tzʔon³ V;PROG;SG;1;FUT
n⁵ndyionʔ³⁵tzʔon³ V;PFV;PL;1+INCL;PST
n⁵ndyionʔ³⁵tzʔon³ V;PROG;PL;1+INCL;FUT
n⁵ndyionʔ³⁵tzʔon³ V;PROG;PL;3;FUT
n⁵ndyionʔ³⁵tzʔon³ V;PROG;PL;3;PST
n⁵ndyionʔ³⁵tzʔon³ V;IRR;SG;3;FUT
n⁵ndyionʔ³⁵tzʔon³ V;IPFV;PL;1+EXCL;PRS
n⁵ndyionʔ³⁵tzʔon³ V;SBJV;PL;1+EXCL
n⁵ndyionʔ³⁵tzʔon³ V;SBJV;SG;1
n⁵ndyionʔ³⁵tzʔon³ V;PROG;SG;1;PST
n⁵ndyionʔ³⁵tzʔon³ V;IRR;PL;1+EXCL;FUT
n⁵ndyionʔ³⁵tzʔon³ V;PROG;SG;2;PST
n⁵ndyionʔ³⁵tzʔon³ V;PFV;SG;1;PST
n⁵ndyionʔ³⁵tzʔon³ V;IRR;PL;1+INCL;FUT
n⁵ndyʔiù¹ V;PROG;SG;3;FUT
n⁵ndyʔiù¹ V;IRR;PL;3;FUT
n⁵ndyʔiù¹ V;IPFV;SG;1;PRS
n⁵ndyʔiù¹ V;IPFV;SG;2;PRS
n⁵ndyʔiù¹ V;SBJV;SG;1
n⁵ndyʔiù¹ V;PROG;SG;2;PST
n⁵ndyʔiù¹ V;SBJV;SG;3
n⁵ndyʔiù¹ V;PFV;PL;1+INCL;PST
n⁵ndyʔiù¹ V;PROG;SG;1;FUT
n⁵ndyʔiù¹ V;IRR;PL;1+INCL;FUT
n⁵ndyʔiù¹ V;PROG;PL;1+EXCL;PST
n⁵ndyʔiù¹ V;IPFV;PL;1+EXCL;PRS
n⁵ndyʔiù¹ V;IRR;SG;1;FUT
n⁵ndyʔiù¹ V;PROG;PL;1+EXCL;FUT
n⁵ndyʔiù¹ V;PROG;PL;3;FUT
n⁵ndyʔiù¹ V;PROG;SG;3;PST
n⁵ndyʔiù¹ V;PROG;SG;1;PST
n⁵ndyʔiù¹ V;IPFV;PL;1+INCL;PRS
n⁵ndyʔiù¹ V;PROG;PL;1+INCL;PST
n⁵ndyʔiù¹ V;IPFV;PL;3;PRS
n⁵ndyʔiù¹ V;PFV;SG;2;PST
n⁵ndyʔiù¹ V;SBJV;PL;1+INCL
n⁵ndyʔiù¹ V;PROG;PL;1+INCL;FUT
n⁵ndyʔiù¹ V;PROG;PL;3;PST
n⁵ndyʔiù¹ V;SBJV;PL;1+EXCL
n⁵ndyʔiù¹ V;PFV;SG;1;PST
n⁵ndyʔiù¹ V;SBJV;SG;2
n⁵ndyʔiù¹ V;IPFV;SG;3;PRS
n⁵ndyʔiù¹ V;PROG;SG;2;FUT
n⁵ndyʔiù¹ V;IRR;SG;3;FUT
n⁵ndyʔiù¹ V;IRR;PL;1+EXCL;FUT
n⁵ndyʔiù¹ V;IRR;SG;2;FUT
n⁵ndyʔiù¹ V;PFV;SG;3;PST
n⁵ndyʔiù¹ V;PFV;PL;1+EXCL;PST
n⁵ndyʔiù¹ V;SBJV;PL;3
n⁵ndyʔiù¹ V;PFV;PL;3;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;PL;3;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;SG;1;PST
n⁵ndí⁵na³nkoʔ³⁴ V;IRR;PL;3;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;IRR;SG;3;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;SBJV;PL;1+INCL
n⁵ndí⁵na³nkoʔ³⁴ V;IRR;SG;2;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;IPFV;SG;3;PRS
n⁵ndí⁵na³nkoʔ³⁴ V;SBJV;SG;2
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;SBJV;SG;3
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;SG;1;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;IPFV;SG;2;PRS
n⁵ndí⁵na³nkoʔ³⁴ V;PFV;SG;3;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;SG;2;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;PFV;PL;1+INCL;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;PL;1+INCL;PST
n⁵ndí⁵na³nkoʔ³⁴ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵na³nkoʔ³⁴ V;IPFV;SG;1;PRS
n⁵ndí⁵na³nkoʔ³⁴ V;PFV;SG;2;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PFV;SG;1;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;SG;2;PST
n⁵ndí⁵na³nkoʔ³⁴ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;SBJV;PL;1+EXCL
n⁵ndí⁵na³nkoʔ³⁴ V;SBJV;PL;3
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;PL;3;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;SG;3;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;IRR;SG;1;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;SBJV;SG;1
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵na³nkoʔ³⁴ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵na³nkoʔ³⁴ V;IPFV;PL;3;PRS
n⁵ndí⁵na³nkoʔ³⁴ V;PROG;SG;3;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵na³nkoʔ³⁴ V;PFV;PL;3;PST
n⁵ndí⁵kí⁵ V;PROG;SG;3;FUT
n⁵ndí⁵kí⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵kí⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵kí⁵ V;PROG;PL;3;FUT
n⁵ndí⁵kí⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵kí⁵ V;IRR;SG;1;FUT
n⁵ndí⁵kí⁵ V;SBJV;SG;1
n⁵ndí⁵kí⁵ V;IRR;PL;3;FUT
n⁵ndí⁵kí⁵ V;PFV;SG;2;PST
n⁵ndí⁵kí⁵ V;SBJV;PL;3
n⁵ndí⁵kí⁵ V;IRR;SG;2;FUT
n⁵ndí⁵kí⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵kí⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵kí⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵kí⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵kí⁵ V;PROG;SG;1;FUT
n⁵ndí⁵kí⁵ V;PFV;SG;3;PST
n⁵ndí⁵kí⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵kí⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵kí⁵ V;PROG;SG;3;PST
n⁵ndí⁵kí⁵ V;PFV;PL;3;PST
n⁵ndí⁵kí⁵ V;PROG;SG;2;FUT
n⁵ndí⁵kí⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵kí⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵kí⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵kí⁵ V;PROG;SG;1;PST
n⁵ndí⁵kí⁵ V;PROG;PL;3;PST
n⁵ndí⁵kí⁵ V;SBJV;SG;2
n⁵ndí⁵kí⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵kí⁵ V;PFV;SG;1;PST
n⁵ndí⁵kí⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵kí⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵kí⁵ V;SBJV;SG;3
n⁵ndí⁵kí⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵kí⁵ V;PROG;SG;2;PST
n⁵ndí⁵kí⁵ V;IRR;SG;3;FUT
n⁵ndí⁵hndɛ³ V;SBJV;PL;1+EXCL
n⁵ndí⁵hndɛ³ V;IPFV;SG;1;PRS
n⁵ndí⁵hndɛ³ V;PROG;SG;3;FUT
n⁵ndí⁵hndɛ³ V;IPFV;PL;3;PRS
n⁵ndí⁵hndɛ³ V;SBJV;SG;1
n⁵ndí⁵hndɛ³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵hndɛ³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵hndɛ³ V;SBJV;SG;3
n⁵ndí⁵hndɛ³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵hndɛ³ V;SBJV;PL;1+INCL
n⁵ndí⁵hndɛ³ V;PROG;SG;2;FUT
n⁵ndí⁵hndɛ³ V;IRR;SG;1;FUT
n⁵ndí⁵hndɛ³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵hndɛ³ V;PROG;PL;3;FUT
n⁵ndí⁵hndɛ³ V;PFV;SG;3;PST
n⁵ndí⁵hndɛ³ V;PROG;SG;1;PST
n⁵ndí⁵hndɛ³ V;PROG;PL;3;PST
n⁵ndí⁵hndɛ³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵hndɛ³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵hndɛ³ V;PROG;SG;2;PST
n⁵ndí⁵hndɛ³ V;IPFV;SG;3;PRS
n⁵ndí⁵hndɛ³ V;PFV;PL;3;PST
n⁵ndí⁵hndɛ³ V;IRR;PL;3;FUT
n⁵ndí⁵hndɛ³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵hndɛ³ V;SBJV;SG;2
n⁵ndí⁵hndɛ³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵hndɛ³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵hndɛ³ V;IPFV;SG;2;PRS
n⁵ndí⁵hndɛ³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵hndɛ³ V;PFV;SG;2;PST
n⁵ndí⁵hndɛ³ V;PROG;SG;3;PST
n⁵ndí⁵hndɛ³ V;PROG;SG;1;FUT
n⁵ndí⁵hndɛ³ V;IRR;SG;3;FUT
n⁵ndí⁵hndɛ³ V;SBJV;PL;3
n⁵ndí⁵hndɛ³ V;PFV;SG;1;PST
n⁵ndí⁵hndɛ³ V;IRR;SG;2;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;PL;3;PST
n⁵ndí⁵ten³⁴tzʔon³ V;SBJV;SG;1
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;SG;1;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;SG;3;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;SG;2;PST
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;SG;2;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ten³⁴tzʔon³ V;SBJV;PL;1+EXCL
n⁵ndí⁵ten³⁴tzʔon³ V;SBJV;SG;3
n⁵ndí⁵ten³⁴tzʔon³ V;PFV;SG;1;PST
n⁵ndí⁵ten³⁴tzʔon³ V;IPFV;PL;3;PRS
n⁵ndí⁵ten³⁴tzʔon³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;IRR;SG;2;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;SG;3;PST
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;SBJV;SG;2
n⁵ndí⁵ten³⁴tzʔon³ V;PFV;SG;2;PST
n⁵ndí⁵ten³⁴tzʔon³ V;IPFV;SG;2;PRS
n⁵ndí⁵ten³⁴tzʔon³ V;IRR;SG;1;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;IRR;SG;3;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;IPFV;SG;3;PRS
n⁵ndí⁵ten³⁴tzʔon³ V;SBJV;PL;1+INCL
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;SG;1;PST
n⁵ndí⁵ten³⁴tzʔon³ V;SBJV;PL;3
n⁵ndí⁵ten³⁴tzʔon³ V;IRR;PL;3;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;PL;3;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PFV;PL;3;PST
n⁵ndí⁵ten³⁴tzʔon³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ten³⁴tzʔon³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ten³⁴tzʔon³ V;IPFV;SG;1;PRS
n⁵ndí⁵ten³⁴tzʔon³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ten³⁴tzʔon³ V;PFV;SG;3;PST
n⁵ndí⁵ten³⁴tzʔon³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵hndyuá⁵ V;IRR;SG;2;FUT
n⁵ndí⁵hndyuá⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵hndyuá⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵hndyuá⁵ V;PROG;SG;2;FUT
n⁵ndí⁵hndyuá⁵ V;SBJV;SG;1
n⁵ndí⁵hndyuá⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵hndyuá⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵hndyuá⁵ V;PFV;SG;2;PST
n⁵ndí⁵hndyuá⁵ V;IRR;SG;3;FUT
n⁵ndí⁵hndyuá⁵ V;IRR;PL;3;FUT
n⁵ndí⁵hndyuá⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵hndyuá⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵hndyuá⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵hndyuá⁵ V;PROG;PL;3;PST
n⁵ndí⁵hndyuá⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵hndyuá⁵ V;SBJV;SG;3
n⁵ndí⁵hndyuá⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵hndyuá⁵ V;PROG;PL;3;FUT
n⁵ndí⁵hndyuá⁵ V;PROG;SG;2;PST
n⁵ndí⁵hndyuá⁵ V;PROG;SG;3;PST
n⁵ndí⁵hndyuá⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵hndyuá⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵hndyuá⁵ V;SBJV;PL;3
n⁵ndí⁵hndyuá⁵ V;IRR;SG;1;FUT
n⁵ndí⁵hndyuá⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵hndyuá⁵ V;PROG;SG;1;PST
n⁵ndí⁵hndyuá⁵ V;PFV;PL;3;PST
n⁵ndí⁵hndyuá⁵ V;PFV;SG;1;PST
n⁵ndí⁵hndyuá⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵hndyuá⁵ V;SBJV;SG;2
n⁵ndí⁵hndyuá⁵ V;PFV;SG;3;PST
n⁵ndí⁵hndyuá⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵hndyuá⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵hndyuá⁵ V;PROG;SG;1;FUT
n⁵ndí⁵hndyuá⁵ V;PROG;SG;3;FUT
n⁵ndí⁵hndyuá⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IRR;SG;3;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;SG;2;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IRR;PL;1+EXCL;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;SG;2;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IPFV;SG;1;PRS
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PFV;PL;1+EXCL;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;PL;1+EXCL;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;PL;1+EXCL;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IPFV;PL;3;PRS
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IRR;PL;3;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PFV;SG;3;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;SBJV;PL;1+EXCL
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IPFV;SG;3;PRS
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;PL;1+INCL;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;SBJV;PL;1+INCL
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IRR;SG;2;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IPFV;PL;1+INCL;PRS
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;PL;3;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PFV;SG;1;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;SBJV;PL;3
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;SG;1;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;SG;1;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;PL;1+INCL;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PFV;PL;3;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;SBJV;SG;2
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IRR;PL;1+INCL;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;PL;3;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;SBJV;SG;3
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IPFV;SG;2;PRS
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IPFV;PL;1+EXCL;PRS
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;IRR;SG;1;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PFV;PL;1+INCL;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PFV;SG;2;PST
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;SG;3;FUT
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;SBJV;SG;1
n⁵ndyion³ ndʔɔ³ cheʔ¹² V;PROG;SG;3;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;SG;2;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IRR;SG;1;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;SBJV;PL;3
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PFV;SG;1;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;SBJV;SG;3
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IRR;SG;2;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PFV;PL;3;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;SG;1;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;SG;3;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PFV;SG;2;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;SG;1;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;SG;3;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;PL;3;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;SBJV;SG;2
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PFV;SG;3;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IRR;PL;3;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;SBJV;SG;1
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;PL;3;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;IRR;SG;3;FUT
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ʔndáʔ⁵nchhi³⁵ V;PROG;SG;2;PST
n⁵ndí⁵ndyoʔ³⁴ V;IPFV;PL;3;PRS
n⁵ndí⁵ndyoʔ³⁴ V;PROG;SG;3;PST
n⁵ndí⁵ndyoʔ³⁴ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ndyoʔ³⁴ V;IPFV;SG;3;PRS
n⁵ndí⁵ndyoʔ³⁴ V;IPFV;SG;2;PRS
n⁵ndí⁵ndyoʔ³⁴ V;PROG;SG;3;FUT
n⁵ndí⁵ndyoʔ³⁴ V;SBJV;SG;2
n⁵ndí⁵ndyoʔ³⁴ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ndyoʔ³⁴ V;IPFV;SG;1;PRS
n⁵ndí⁵ndyoʔ³⁴ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ndyoʔ³⁴ V;SBJV;SG;3
n⁵ndí⁵ndyoʔ³⁴ V;SBJV;PL;3
n⁵ndí⁵ndyoʔ³⁴ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ndyoʔ³⁴ V;SBJV;PL;1+INCL
n⁵ndí⁵ndyoʔ³⁴ V;PROG;SG;1;PST
n⁵ndí⁵ndyoʔ³⁴ V;IRR;SG;1;FUT
n⁵ndí⁵ndyoʔ³⁴ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ndyoʔ³⁴ V;PFV;SG;3;PST
n⁵ndí⁵ndyoʔ³⁴ V;PROG;SG;1;FUT
n⁵ndí⁵ndyoʔ³⁴ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ndyoʔ³⁴ V;PFV;SG;1;PST
n⁵ndí⁵ndyoʔ³⁴ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ndyoʔ³⁴ V;IRR;SG;2;FUT
n⁵ndí⁵ndyoʔ³⁴ V;PROG;PL;3;PST
n⁵ndí⁵ndyoʔ³⁴ V;PFV;PL;3;PST
n⁵ndí⁵ndyoʔ³⁴ V;IRR;PL;3;FUT
n⁵ndí⁵ndyoʔ³⁴ V;SBJV;SG;1
n⁵ndí⁵ndyoʔ³⁴ V;PFV;SG;2;PST
n⁵ndí⁵ndyoʔ³⁴ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ndyoʔ³⁴ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ndyoʔ³⁴ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ndyoʔ³⁴ V;PROG;SG;2;FUT
n⁵ndí⁵ndyoʔ³⁴ V;PROG;SG;2;PST
n⁵ndí⁵ndyoʔ³⁴ V;PROG;PL;3;FUT
n⁵ndí⁵ndyoʔ³⁴ V;SBJV;PL;1+EXCL
n⁵ndí⁵ndyoʔ³⁴ V;IRR;SG;3;FUT
m⁵mèʔ¹ndàʔ¹ V;PROG;PL;1+INCL;PST
m⁵mèʔ¹ndàʔ¹ V;PFV;PL;3;PST
m⁵mèʔ¹ndàʔ¹ V;PROG;PL;1+INCL;FUT
m⁵mèʔ¹ndàʔ¹ V;IRR;SG;2;FUT
m⁵mèʔ¹ndàʔ¹ V;SBJV;PL;1+INCL
m⁵mèʔ¹ndàʔ¹ V;PROG;SG;2;PST
m⁵mèʔ¹ndàʔ¹ V;PROG;SG;3;FUT
m⁵mèʔ¹ndàʔ¹ V;SBJV;PL;3
m⁵mèʔ¹ndàʔ¹ V;IPFV;SG;3;PRS
m⁵mèʔ¹ndàʔ¹ V;PROG;SG;3;PST
m⁵mèʔ¹ndàʔ¹ V;PROG;PL;1+EXCL;PST
m⁵mèʔ¹ndàʔ¹ V;SBJV;PL;1+EXCL
m⁵mèʔ¹ndàʔ¹ V;PFV;SG;2;PST
m⁵mèʔ¹ndàʔ¹ V;PROG;PL;3;PST
m⁵mèʔ¹ndàʔ¹ V;IPFV;SG;2;PRS
m⁵mèʔ¹ndàʔ¹ V;PROG;PL;3;FUT
m⁵mèʔ¹ndàʔ¹ V;IRR;PL;3;FUT
m⁵mèʔ¹ndàʔ¹ V;IRR;PL;1+EXCL;FUT
m⁵mèʔ¹ndàʔ¹ V;SBJV;SG;3
m⁵mèʔ¹ndàʔ¹ V;SBJV;SG;2
m⁵mèʔ¹ndàʔ¹ V;IPFV;SG;1;PRS
m⁵mèʔ¹ndàʔ¹ V;PFV;PL;1+EXCL;PST
m⁵mèʔ¹ndàʔ¹ V;PROG;SG;1;PST
m⁵mèʔ¹ndàʔ¹ V;IPFV;PL;3;PRS
m⁵mèʔ¹ndàʔ¹ V;IPFV;PL;1+INCL;PRS
m⁵mèʔ¹ndàʔ¹ V;IPFV;PL;1+EXCL;PRS
m⁵mèʔ¹ndàʔ¹ V;PFV;SG;1;PST
m⁵mèʔ¹ndàʔ¹ V;SBJV;SG;1
m⁵mèʔ¹ndàʔ¹ V;IRR;PL;1+INCL;FUT
m⁵mèʔ¹ndàʔ¹ V;PFV;PL;1+INCL;PST
m⁵mèʔ¹ndàʔ¹ V;PFV;SG;3;PST
m⁵mèʔ¹ndàʔ¹ V;PROG;SG;2;FUT
m⁵mèʔ¹ndàʔ¹ V;PROG;PL;1+EXCL;FUT
m⁵mèʔ¹ndàʔ¹ V;PROG;SG;1;FUT
m⁵mèʔ¹ndàʔ¹ V;IRR;SG;1;FUT
m⁵mèʔ¹ndàʔ¹ V;IRR;SG;3;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IRR;PL;1+INCL;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PFV;SG;3;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IPFV;PL;1+EXCL;PRS
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IRR;SG;3;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PFV;SG;1;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PFV;PL;1+EXCL;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;SBJV;PL;3
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IRR;SG;1;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IPFV;PL;3;PRS
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PFV;SG;2;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IPFV;PL;1+INCL;PRS
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IPFV;SG;2;PRS
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;SBJV;SG;1
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;SG;1;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PFV;PL;3;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;SG;2;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;SG;3;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;PL;1+INCL;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IRR;PL;1+EXCL;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;SG;1;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;SG;2;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;SBJV;SG;2
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IRR;PL;3;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;SBJV;PL;1+EXCL
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;PL;3;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;SBJV;SG;3
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IPFV;SG;1;PRS
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;PL;1+EXCL;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;PL;3;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;PL;1+EXCL;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;SG;3;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IPFV;SG;3;PRS
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PROG;PL;1+INCL;PST
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;SBJV;PL;1+INCL
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;IRR;SG;2;FUT
n⁵ndyiaʔ³⁵ ʔá⁵ y๠V;PFV;PL;1+INCL;PST
n⁵ndí⁵xuè¹ V;IRR;SG;2;FUT
n⁵ndí⁵xuè¹ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵xuè¹ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵xuè¹ V;PROG;SG;2;FUT
n⁵ndí⁵xuè¹ V;PFV;PL;3;PST
n⁵ndí⁵xuè¹ V;IRR;SG;3;FUT
n⁵ndí⁵xuè¹ V;PROG;SG;3;FUT
n⁵ndí⁵xuè¹ V;PROG;PL;3;FUT
n⁵ndí⁵xuè¹ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵xuè¹ V;PROG;SG;2;PST
n⁵ndí⁵xuè¹ V;IPFV;SG;1;PRS
n⁵ndí⁵xuè¹ V;SBJV;SG;3
n⁵ndí⁵xuè¹ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵xuè¹ V;IRR;PL;3;FUT
n⁵ndí⁵xuè¹ V;SBJV;PL;1+INCL
n⁵ndí⁵xuè¹ V;IPFV;SG;2;PRS
n⁵ndí⁵xuè¹ V;IPFV;SG;3;PRS
n⁵ndí⁵xuè¹ V;PFV;PL;1+INCL;PST
n⁵ndí⁵xuè¹ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵xuè¹ V;SBJV;PL;1+EXCL
n⁵ndí⁵xuè¹ V;PROG;PL;1+INCL;PST
n⁵ndí⁵xuè¹ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵xuè¹ V;PFV;SG;3;PST
n⁵ndí⁵xuè¹ V;PROG;SG;3;PST
n⁵ndí⁵xuè¹ V;PFV;SG;1;PST
n⁵ndí⁵xuè¹ V;IRR;SG;1;FUT
n⁵ndí⁵xuè¹ V;SBJV;SG;2
n⁵ndí⁵xuè¹ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵xuè¹ V;PROG;SG;1;PST
n⁵ndí⁵xuè¹ V;PFV;SG;2;PST
n⁵ndí⁵xuè¹ V;PROG;PL;3;PST
n⁵ndí⁵xuè¹ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵xuè¹ V;SBJV;SG;1
n⁵ndí⁵xuè¹ V;PROG;SG;1;FUT
n⁵ndí⁵xuè¹ V;IPFV;PL;3;PRS
n⁵ndí⁵xuè¹ V;SBJV;PL;3
n⁵ndi³nkiʔ³ xken³ V;PFV;PL;3;PST
n⁵ndi³nkiʔ³ xken³ V;IPFV;PL;1+EXCL;PRS
n⁵ndi³nkiʔ³ xken³ V;SBJV;PL;1+EXCL
n⁵ndi³nkiʔ³ xken³ V;PROG;PL;1+EXCL;FUT
n⁵ndi³nkiʔ³ xken³ V;PROG;PL;1+EXCL;PST
n⁵ndi³nkiʔ³ xken³ V;SBJV;PL;1+INCL
n⁵ndi³nkiʔ³ xken³ V;IPFV;PL;3;PRS
n⁵ndi³nkiʔ³ xken³ V;IPFV;SG;3;PRS
n⁵ndi³nkiʔ³ xken³ V;SBJV;SG;2
n⁵ndi³nkiʔ³ xken³ V;SBJV;PL;3
n⁵ndi³nkiʔ³ xken³ V;IRR;SG;3;FUT
n⁵ndi³nkiʔ³ xken³ V;PROG;SG;1;PST
n⁵ndi³nkiʔ³ xken³ V;PFV;SG;2;PST
n⁵ndi³nkiʔ³ xken³ V;PFV;SG;1;PST
n⁵ndi³nkiʔ³ xken³ V;PROG;SG;3;PST
n⁵ndi³nkiʔ³ xken³ V;PFV;PL;1+INCL;PST
n⁵ndi³nkiʔ³ xken³ V;PROG;PL;3;PST
n⁵ndi³nkiʔ³ xken³ V;IPFV;SG;1;PRS
n⁵ndi³nkiʔ³ xken³ V;PROG;SG;2;FUT
n⁵ndi³nkiʔ³ xken³ V;SBJV;SG;1
n⁵ndi³nkiʔ³ xken³ V;IRR;SG;2;FUT
n⁵ndi³nkiʔ³ xken³ V;PROG;SG;3;FUT
n⁵ndi³nkiʔ³ xken³ V;SBJV;SG;3
n⁵ndi³nkiʔ³ xken³ V;IRR;SG;1;FUT
n⁵ndi³nkiʔ³ xken³ V;PROG;PL;1+INCL;FUT
n⁵ndi³nkiʔ³ xken³ V;IRR;PL;3;FUT
n⁵ndi³nkiʔ³ xken³ V;PROG;SG;1;FUT
n⁵ndi³nkiʔ³ xken³ V;IRR;PL;1+EXCL;FUT
n⁵ndi³nkiʔ³ xken³ V;PFV;SG;3;PST
n⁵ndi³nkiʔ³ xken³ V;PROG;PL;3;FUT
n⁵ndi³nkiʔ³ xken³ V;IPFV;PL;1+INCL;PRS
n⁵ndi³nkiʔ³ xken³ V;PFV;PL;1+EXCL;PST
n⁵ndi³nkiʔ³ xken³ V;IRR;PL;1+INCL;FUT
n⁵ndi³nkiʔ³ xken³ V;PROG;SG;2;PST
n⁵ndi³nkiʔ³ xken³ V;IPFV;SG;2;PRS
n⁵ndi³nkiʔ³ xken³ V;PROG;PL;1+INCL;PST
n⁵ndyiaʔ³⁵y๠V;IPFV;SG;2;PRS
n⁵ndyiaʔ³⁵y๠V;IPFV;PL;1+INCL;PRS
n⁵ndyiaʔ³⁵y๠V;SBJV;PL;1+EXCL
n⁵ndyiaʔ³⁵y๠V;PFV;SG;1;PST
n⁵ndyiaʔ³⁵y๠V;PROG;SG;1;FUT
n⁵ndyiaʔ³⁵y๠V;IRR;SG;2;FUT
n⁵ndyiaʔ³⁵y๠V;IPFV;PL;1+EXCL;PRS
n⁵ndyiaʔ³⁵y๠V;PROG;SG;3;PST
n⁵ndyiaʔ³⁵y๠V;IRR;PL;3;FUT
n⁵ndyiaʔ³⁵y๠V;PFV;PL;1+EXCL;PST
n⁵ndyiaʔ³⁵y๠V;PFV;PL;3;PST
n⁵ndyiaʔ³⁵y๠V;PROG;SG;3;FUT
n⁵ndyiaʔ³⁵y๠V;IRR;SG;3;FUT
n⁵ndyiaʔ³⁵y๠V;IRR;SG;1;FUT
n⁵ndyiaʔ³⁵y๠V;IPFV;SG;1;PRS
n⁵ndyiaʔ³⁵y๠V;PROG;PL;3;PST
n⁵ndyiaʔ³⁵y๠V;PROG;PL;3;FUT
n⁵ndyiaʔ³⁵y๠V;SBJV;SG;2
n⁵ndyiaʔ³⁵y๠V;PFV;SG;2;PST
n⁵ndyiaʔ³⁵y๠V;IRR;PL;1+EXCL;FUT
n⁵ndyiaʔ³⁵y๠V;PROG;SG;2;FUT
n⁵ndyiaʔ³⁵y๠V;PROG;PL;1+EXCL;PST
n⁵ndyiaʔ³⁵y๠V;SBJV;SG;3
n⁵ndyiaʔ³⁵y๠V;SBJV;SG;1
n⁵ndyiaʔ³⁵y๠V;SBJV;PL;1+INCL
n⁵ndyiaʔ³⁵y๠V;PFV;PL;1+INCL;PST
n⁵ndyiaʔ³⁵y๠V;PFV;SG;3;PST
n⁵ndyiaʔ³⁵y๠V;PROG;PL;1+INCL;FUT
n⁵ndyiaʔ³⁵y๠V;SBJV;PL;3
n⁵ndyiaʔ³⁵y๠V;PROG;PL;1+INCL;PST
n⁵ndyiaʔ³⁵y๠V;PROG;SG;2;PST
n⁵ndyiaʔ³⁵y๠V;IPFV;SG;3;PRS
n⁵ndyiaʔ³⁵y๠V;PROG;PL;1+EXCL;FUT
n⁵ndyiaʔ³⁵y๠V;IRR;PL;1+INCL;FUT
n⁵ndyiaʔ³⁵y๠V;PROG;SG;1;PST
n⁵ndyiaʔ³⁵y๠V;IPFV;PL;3;PRS
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;PL;3;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;SG;3;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;IPFV;SG;3;PRS
n⁵ndí⁵bìʔ¹tza³⁴ V;SBJV;PL;1+EXCL
n⁵ndí⁵bìʔ¹tza³⁴ V;PFV;SG;1;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;SBJV;PL;3
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;SG;2;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;SBJV;SG;2
n⁵ndí⁵bìʔ¹tza³⁴ V;IPFV;PL;3;PRS
n⁵ndí⁵bìʔ¹tza³⁴ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵bìʔ¹tza³⁴ V;PFV;PL;3;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;PFV;PL;1+INCL;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;SBJV;SG;3
n⁵ndí⁵bìʔ¹tza³⁴ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;PL;1+INCL;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;PL;3;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;SG;3;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;SG;1;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;IRR;SG;3;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;SBJV;SG;1
n⁵ndí⁵bìʔ¹tza³⁴ V;IPFV;SG;1;PRS
n⁵ndí⁵bìʔ¹tza³⁴ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;PFV;SG;2;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;IPFV;SG;2;PRS
n⁵ndí⁵bìʔ¹tza³⁴ V;PFV;SG;3;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;IRR;SG;1;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;SG;1;PST
n⁵ndí⁵bìʔ¹tza³⁴ V;IRR;SG;2;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;IRR;PL;3;FUT
n⁵ndí⁵bìʔ¹tza³⁴ V;SBJV;PL;1+INCL
n⁵ndí⁵bìʔ¹tza³⁴ V;PROG;SG;2;PST
n⁵nduèʔ¹ V;IRR;SG;3;FUT
n⁵nduèʔ¹ V;IPFV;SG;1;PRS
n⁵nduèʔ¹ V;IRR;SG;1;FUT
n⁵nduèʔ¹ V;PFV;PL;1+INCL;PST
n⁵nduèʔ¹ V;SBJV;PL;3
n⁵nduèʔ¹ V;PROG;PL;3;PST
n⁵nduèʔ¹ V;PROG;SG;2;FUT
n⁵nduèʔ¹ V;PROG;PL;1+EXCL;PST
n⁵nduèʔ¹ V;IPFV;PL;3;PRS
n⁵nduèʔ¹ V;PROG;PL;1+INCL;FUT
n⁵nduèʔ¹ V;PFV;PL;3;PST
n⁵nduèʔ¹ V;PFV;SG;1;PST
n⁵nduèʔ¹ V;PROG;SG;1;PST
n⁵nduèʔ¹ V;SBJV;SG;3
n⁵nduèʔ¹ V;PROG;PL;1+EXCL;FUT
n⁵nduèʔ¹ V;PFV;SG;3;PST
n⁵nduèʔ¹ V;SBJV;PL;1+EXCL
n⁵nduèʔ¹ V;PROG;SG;2;PST
n⁵nduèʔ¹ V;PROG;PL;3;FUT
n⁵nduèʔ¹ V;IRR;PL;3;FUT
n⁵nduèʔ¹ V;IPFV;PL;1+INCL;PRS
n⁵nduèʔ¹ V;PFV;PL;1+EXCL;PST
n⁵nduèʔ¹ V;IRR;PL;1+EXCL;FUT
n⁵nduèʔ¹ V;PROG;SG;1;FUT
n⁵nduèʔ¹ V;PFV;SG;2;PST
n⁵nduèʔ¹ V;IPFV;SG;2;PRS
n⁵nduèʔ¹ V;SBJV;SG;2
n⁵nduèʔ¹ V;PROG;SG;3;PST
n⁵nduèʔ¹ V;SBJV;SG;1
n⁵nduèʔ¹ V;IRR;PL;1+INCL;FUT
n⁵nduèʔ¹ V;IPFV;SG;3;PRS
n⁵nduèʔ¹ V;IRR;SG;2;FUT
n⁵nduèʔ¹ V;PROG;PL;1+INCL;PST
n⁵nduèʔ¹ V;PROG;SG;3;FUT
n⁵nduèʔ¹ V;SBJV;PL;1+INCL
n⁵nduèʔ¹ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵tyʔ๠V;PROG;PL;3;FUT
n⁵ndí⁵tyʔ๠V;IRR;PL;3;FUT
n⁵ndí⁵tyʔ๠V;PROG;SG;2;FUT
n⁵ndí⁵tyʔ๠V;PFV;SG;2;PST
n⁵ndí⁵tyʔ๠V;IPFV;PL;3;PRS
n⁵ndí⁵tyʔ๠V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵tyʔ๠V;PROG;SG;3;FUT
n⁵ndí⁵tyʔ๠V;PFV;PL;1+INCL;PST
n⁵ndí⁵tyʔ๠V;IRR;SG;3;FUT
n⁵ndí⁵tyʔ๠V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵tyʔ๠V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵tyʔ๠V;IPFV;SG;1;PRS
n⁵ndí⁵tyʔ๠V;PROG;PL;1+INCL;PST
n⁵ndí⁵tyʔ๠V;PROG;SG;2;PST
n⁵ndí⁵tyʔ๠V;PROG;PL;1+INCL;FUT
n⁵ndí⁵tyʔ๠V;SBJV;PL;1+EXCL
n⁵ndí⁵tyʔ๠V;PFV;PL;3;PST
n⁵ndí⁵tyʔ๠V;PFV;PL;1+EXCL;PST
n⁵ndí⁵tyʔ๠V;SBJV;PL;3
n⁵ndí⁵tyʔ๠V;IRR;SG;2;FUT
n⁵ndí⁵tyʔ๠V;IRR;SG;1;FUT
n⁵ndí⁵tyʔ๠V;SBJV;PL;1+INCL
n⁵ndí⁵tyʔ๠V;PROG;SG;1;FUT
n⁵ndí⁵tyʔ๠V;IPFV;SG;3;PRS
n⁵ndí⁵tyʔ๠V;IPFV;SG;2;PRS
n⁵ndí⁵tyʔ๠V;PROG;SG;1;PST
n⁵ndí⁵tyʔ๠V;SBJV;SG;1
n⁵ndí⁵tyʔ๠V;PROG;PL;1+EXCL;PST
n⁵ndí⁵tyʔ๠V;SBJV;SG;2
n⁵ndí⁵tyʔ๠V;PROG;PL;3;PST
n⁵ndí⁵tyʔ๠V;IRR;PL;1+INCL;FUT
n⁵ndí⁵tyʔ๠V;PROG;SG;3;PST
n⁵ndí⁵tyʔ๠V;PFV;SG;3;PST
n⁵ndí⁵tyʔ๠V;SBJV;SG;3
n⁵ndí⁵tyʔ๠V;PFV;SG;1;PST
n⁵ndí⁵tyʔ๠V;IPFV;PL;1+EXCL;PRS
n⁵ndyiaʔ³⁵nioʔ³⁴ V;SBJV;PL;1+INCL
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;PL;1+INCL;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IPFV;PL;1+INCL;PRS
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;PL;3;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IRR;SG;3;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;PL;1+INCL;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;SG;2;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PFV;SG;1;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;SBJV;SG;3
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IPFV;PL;1+EXCL;PRS
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IRR;PL;1+EXCL;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IRR;SG;2;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IPFV;SG;1;PRS
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IRR;PL;3;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IPFV;SG;2;PRS
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PFV;PL;1+INCL;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PFV;PL;3;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IPFV;SG;3;PRS
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;PL;3;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;SBJV;SG;1
n⁵ndyiaʔ³⁵nioʔ³⁴ V;SBJV;PL;3
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;SG;2;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;PL;1+EXCL;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PFV;SG;3;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;SBJV;PL;1+EXCL
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IRR;PL;1+INCL;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IPFV;PL;3;PRS
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PFV;PL;1+EXCL;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;PL;1+EXCL;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;SG;3;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;IRR;SG;1;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PFV;SG;2;PST
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;SG;3;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;SBJV;SG;2
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;SG;1;FUT
n⁵ndyiaʔ³⁵nioʔ³⁴ V;PROG;SG;1;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;PL;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PFV;SG;3;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;SG;1;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;SG;2;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;PL;3;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;SBJV;SG;2
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;SBJV;SG;1
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IRR;SG;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IRR;SG;1;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;SG;2;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;SBJV;PL;3
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PFV;PL;3;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IRR;PL;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;SG;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;SBJV;SG;3
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;SG;1;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;IRR;SG;2;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PROG;SG;3;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PFV;SG;2;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵hnó⁵ V;PFV;SG;1;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;PL;1+EXCL;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;IRR;PL;3;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;SBJV;SG;1
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;SG;1;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;IRR;SG;2;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;IPFV;PL;3;PRS
n⁵ndyio³ hñò¹tzʔon⁵³ V;IPFV;PL;1+INCL;PRS
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;SG;2;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;PFV;SG;1;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;PFV;PL;3;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;PFV;PL;1+EXCL;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;SBJV;SG;3
n⁵ndyio³ hñò¹tzʔon⁵³ V;IPFV;SG;3;PRS
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;PL;1+INCL;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;SBJV;PL;1+INCL
n⁵ndyio³ hñò¹tzʔon⁵³ V;SBJV;SG;2
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;PL;3;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;PL;3;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;SG;2;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;SG;3;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;PFV;PL;1+INCL;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;IRR;SG;1;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;IPFV;PL;1+EXCL;PRS
n⁵ndyio³ hñò¹tzʔon⁵³ V;IPFV;SG;2;PRS
n⁵ndyio³ hñò¹tzʔon⁵³ V;IRR;PL;1+INCL;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;SBJV;PL;1+EXCL
n⁵ndyio³ hñò¹tzʔon⁵³ V;IPFV;SG;1;PRS
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;SG;1;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;IRR;SG;3;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;SG;3;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;PL;1+EXCL;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;SBJV;PL;3
n⁵ndyio³ hñò¹tzʔon⁵³ V;IRR;PL;1+EXCL;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;PFV;SG;3;PST
n⁵ndyio³ hñò¹tzʔon⁵³ V;PROG;PL;1+INCL;FUT
n⁵ndyio³ hñò¹tzʔon⁵³ V;PFV;SG;2;PST
n⁵ndɛ³⁵ V;PROG;SG;3;FUT
n⁵ndɛ³⁵ V;PROG;PL;1+INCL;FUT
n⁵ndɛ³⁵ V;IRR;PL;1+INCL;FUT
n⁵ndɛ³⁵ V;PROG;PL;3;PST
n⁵ndɛ³⁵ V;PFV;PL;1+EXCL;PST
n⁵ndɛ³⁵ V;PROG;SG;2;FUT
n⁵ndɛ³⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndɛ³⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndɛ³⁵ V;PFV;SG;3;PST
n⁵ndɛ³⁵ V;PFV;PL;1+INCL;PST
n⁵ndɛ³⁵ V;SBJV;SG;1
n⁵ndɛ³⁵ V;PFV;SG;2;PST
n⁵ndɛ³⁵ V;IRR;SG;3;FUT
n⁵ndɛ³⁵ V;PROG;SG;1;FUT
n⁵ndɛ³⁵ V;SBJV;PL;1+EXCL
n⁵ndɛ³⁵ V;PROG;SG;3;PST
n⁵ndɛ³⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndɛ³⁵ V;PROG;PL;3;FUT
n⁵ndɛ³⁵ V;IPFV;SG;1;PRS
n⁵ndɛ³⁵ V;SBJV;PL;3
n⁵ndɛ³⁵ V;IRR;SG;1;FUT
n⁵ndɛ³⁵ V;PROG;PL;1+EXCL;PST
n⁵ndɛ³⁵ V;SBJV;SG;3
n⁵ndɛ³⁵ V;IPFV;SG;2;PRS
n⁵ndɛ³⁵ V;SBJV;SG;2
n⁵ndɛ³⁵ V;IPFV;SG;3;PRS
n⁵ndɛ³⁵ V;IRR;PL;3;FUT
n⁵ndɛ³⁵ V;PROG;SG;1;PST
n⁵ndɛ³⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndɛ³⁵ V;PROG;PL;1+INCL;PST
n⁵ndɛ³⁵ V;PROG;SG;2;PST
n⁵ndɛ³⁵ V;IRR;SG;2;FUT
n⁵ndɛ³⁵ V;IPFV;PL;3;PRS
n⁵ndɛ³⁵ V;SBJV;PL;1+INCL
n⁵ndɛ³⁵ V;PFV;SG;1;PST
n⁵ndɛ³⁵ V;PFV;PL;3;PST
n⁵ndí⁵kí⁵chì¹ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵kí⁵chì¹ V;PFV;PL;1+INCL;PST
n⁵ndí⁵kí⁵chì¹ V;PROG;SG;3;FUT
n⁵ndí⁵kí⁵chì¹ V;SBJV;PL;1+INCL
n⁵ndí⁵kí⁵chì¹ V;IPFV;SG;1;PRS
n⁵ndí⁵kí⁵chì¹ V;PFV;SG;2;PST
n⁵ndí⁵kí⁵chì¹ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵kí⁵chì¹ V;IRR;PL;3;FUT
n⁵ndí⁵kí⁵chì¹ V;SBJV;SG;1
n⁵ndí⁵kí⁵chì¹ V;IRR;SG;2;FUT
n⁵ndí⁵kí⁵chì¹ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵kí⁵chì¹ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵kí⁵chì¹ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵kí⁵chì¹ V;IPFV;SG;2;PRS
n⁵ndí⁵kí⁵chì¹ V;PROG;PL;3;PST
n⁵ndí⁵kí⁵chì¹ V;IPFV;PL;3;PRS
n⁵ndí⁵kí⁵chì¹ V;PROG;PL;1+INCL;PST
n⁵ndí⁵kí⁵chì¹ V;SBJV;PL;3
n⁵ndí⁵kí⁵chì¹ V;PFV;SG;1;PST
n⁵ndí⁵kí⁵chì¹ V;IPFV;SG;3;PRS
n⁵ndí⁵kí⁵chì¹ V;PROG;SG;2;FUT
n⁵ndí⁵kí⁵chì¹ V;PROG;SG;2;PST
n⁵ndí⁵kí⁵chì¹ V;IRR;SG;3;FUT
n⁵ndí⁵kí⁵chì¹ V;IRR;SG;1;FUT
n⁵ndí⁵kí⁵chì¹ V;SBJV;SG;2
n⁵ndí⁵kí⁵chì¹ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵kí⁵chì¹ V;SBJV;PL;1+EXCL
n⁵ndí⁵kí⁵chì¹ V;PROG;PL;3;FUT
n⁵ndí⁵kí⁵chì¹ V;SBJV;SG;3
n⁵ndí⁵kí⁵chì¹ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵kí⁵chì¹ V;PROG;SG;3;PST
n⁵ndí⁵kí⁵chì¹ V;PROG;SG;1;FUT
n⁵ndí⁵kí⁵chì¹ V;PFV;PL;3;PST
n⁵ndí⁵kí⁵chì¹ V;PROG;SG;1;PST
n⁵ndí⁵kí⁵chì¹ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵kí⁵chì¹ V;PFV;SG;3;PST
n⁵ndí⁵tzhɔ³⁴ V;SBJV;SG;2
n⁵ndí⁵tzhɔ³⁴ V;PROG;SG;1;PST
n⁵ndí⁵tzhɔ³⁴ V;IRR;SG;1;FUT
n⁵ndí⁵tzhɔ³⁴ V;SBJV;PL;1+INCL
n⁵ndí⁵tzhɔ³⁴ V;SBJV;PL;1+EXCL
n⁵ndí⁵tzhɔ³⁴ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵tzhɔ³⁴ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵tzhɔ³⁴ V;IRR;PL;3;FUT
n⁵ndí⁵tzhɔ³⁴ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵tzhɔ³⁴ V;IRR;SG;3;FUT
n⁵ndí⁵tzhɔ³⁴ V;PROG;SG;1;FUT
n⁵ndí⁵tzhɔ³⁴ V;PFV;PL;3;PST
n⁵ndí⁵tzhɔ³⁴ V;IRR;SG;2;FUT
n⁵ndí⁵tzhɔ³⁴ V;IPFV;SG;2;PRS
n⁵ndí⁵tzhɔ³⁴ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵tzhɔ³⁴ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵tzhɔ³⁴ V;PROG;SG;3;PST
n⁵ndí⁵tzhɔ³⁴ V;PROG;PL;1+INCL;PST
n⁵ndí⁵tzhɔ³⁴ V;PFV;SG;1;PST
n⁵ndí⁵tzhɔ³⁴ V;PROG;PL;3;PST
n⁵ndí⁵tzhɔ³⁴ V;PROG;SG;2;PST
n⁵ndí⁵tzhɔ³⁴ V;SBJV;SG;3
n⁵ndí⁵tzhɔ³⁴ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵tzhɔ³⁴ V;PROG;PL;3;FUT
n⁵ndí⁵tzhɔ³⁴ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵tzhɔ³⁴ V;IPFV;PL;3;PRS
n⁵ndí⁵tzhɔ³⁴ V;SBJV;PL;3
n⁵ndí⁵tzhɔ³⁴ V;PROG;SG;2;FUT
n⁵ndí⁵tzhɔ³⁴ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵tzhɔ³⁴ V;IPFV;SG;3;PRS
n⁵ndí⁵tzhɔ³⁴ V;IPFV;SG;1;PRS
n⁵ndí⁵tzhɔ³⁴ V;PROG;SG;3;FUT
n⁵ndí⁵tzhɔ³⁴ V;PFV;PL;1+INCL;PST
n⁵ndí⁵tzhɔ³⁴ V;SBJV;SG;1
n⁵ndí⁵tzhɔ³⁴ V;PFV;SG;2;PST
n⁵ndí⁵tzhɔ³⁴ V;PFV;SG;3;PST
n⁵ndí⁵kí⁵tzʔon³ V;IPFV;SG;2;PRS
n⁵ndí⁵kí⁵tzʔon³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵kí⁵tzʔon³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵kí⁵tzʔon³ V;PROG;SG;3;PST
n⁵ndí⁵kí⁵tzʔon³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵kí⁵tzʔon³ V;PROG;SG;3;FUT
n⁵ndí⁵kí⁵tzʔon³ V;IPFV;PL;3;PRS
n⁵ndí⁵kí⁵tzʔon³ V;SBJV;PL;1+EXCL
n⁵ndí⁵kí⁵tzʔon³ V;PROG;SG;2;PST
n⁵ndí⁵kí⁵tzʔon³ V;SBJV;PL;3
n⁵ndí⁵kí⁵tzʔon³ V;PROG;SG;1;PST
n⁵ndí⁵kí⁵tzʔon³ V;IRR;SG;1;FUT
n⁵ndí⁵kí⁵tzʔon³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵kí⁵tzʔon³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵kí⁵tzʔon³ V;PFV;SG;3;PST
n⁵ndí⁵kí⁵tzʔon³ V;PROG;PL;3;PST
n⁵ndí⁵kí⁵tzʔon³ V;PFV;SG;1;PST
n⁵ndí⁵kí⁵tzʔon³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵kí⁵tzʔon³ V;IPFV;SG;3;PRS
n⁵ndí⁵kí⁵tzʔon³ V;IRR;SG;2;FUT
n⁵ndí⁵kí⁵tzʔon³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵kí⁵tzʔon³ V;PFV;SG;2;PST
n⁵ndí⁵kí⁵tzʔon³ V;IRR;SG;3;FUT
n⁵ndí⁵kí⁵tzʔon³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵kí⁵tzʔon³ V;PROG;PL;3;FUT
n⁵ndí⁵kí⁵tzʔon³ V;PROG;SG;2;FUT
n⁵ndí⁵kí⁵tzʔon³ V;IRR;PL;3;FUT
n⁵ndí⁵kí⁵tzʔon³ V;PFV;PL;3;PST
n⁵ndí⁵kí⁵tzʔon³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵kí⁵tzʔon³ V;SBJV;PL;1+INCL
n⁵ndí⁵kí⁵tzʔon³ V;SBJV;SG;2
n⁵ndí⁵kí⁵tzʔon³ V;IPFV;SG;1;PRS
n⁵ndí⁵kí⁵tzʔon³ V;SBJV;SG;3
n⁵ndí⁵kí⁵tzʔon³ V;PROG;SG;1;FUT
n⁵ndí⁵kí⁵tzʔon³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵kí⁵tzʔon³ V;SBJV;SG;1
n⁵nduìʔ¹xʔon⁵³ V;IPFV;PL;1+INCL;PRS
n⁵nduìʔ¹xʔon⁵³ V;PROG;SG;2;FUT
n⁵nduìʔ¹xʔon⁵³ V;PFV;SG;1;PST
n⁵nduìʔ¹xʔon⁵³ V;PFV;SG;3;PST
n⁵nduìʔ¹xʔon⁵³ V;PROG;PL;3;FUT
n⁵nduìʔ¹xʔon⁵³ V;PROG;SG;1;FUT
n⁵nduìʔ¹xʔon⁵³ V;PROG;SG;3;PST
n⁵nduìʔ¹xʔon⁵³ V;IRR;PL;3;FUT
n⁵nduìʔ¹xʔon⁵³ V;PFV;SG;2;PST
n⁵nduìʔ¹xʔon⁵³ V;IPFV;SG;2;PRS
n⁵nduìʔ¹xʔon⁵³ V;PFV;PL;3;PST
n⁵nduìʔ¹xʔon⁵³ V;SBJV;SG;2
n⁵nduìʔ¹xʔon⁵³ V;PROG;PL;1+EXCL;FUT
n⁵nduìʔ¹xʔon⁵³ V;IRR;SG;3;FUT
n⁵nduìʔ¹xʔon⁵³ V;IRR;PL;1+EXCL;FUT
n⁵nduìʔ¹xʔon⁵³ V;PROG;PL;3;PST
n⁵nduìʔ¹xʔon⁵³ V;PROG;PL;1+EXCL;PST
n⁵nduìʔ¹xʔon⁵³ V;PROG;PL;1+INCL;PST
n⁵nduìʔ¹xʔon⁵³ V;PROG;SG;2;PST
n⁵nduìʔ¹xʔon⁵³ V;PFV;PL;1+EXCL;PST
n⁵nduìʔ¹xʔon⁵³ V;IRR;PL;1+INCL;FUT
n⁵nduìʔ¹xʔon⁵³ V;PROG;PL;1+INCL;FUT
n⁵nduìʔ¹xʔon⁵³ V;SBJV;PL;1+EXCL
n⁵nduìʔ¹xʔon⁵³ V;IRR;SG;2;FUT
n⁵nduìʔ¹xʔon⁵³ V;SBJV;PL;3
n⁵nduìʔ¹xʔon⁵³ V;IPFV;PL;3;PRS
n⁵nduìʔ¹xʔon⁵³ V;SBJV;PL;1+INCL
n⁵nduìʔ¹xʔon⁵³ V;SBJV;SG;3
n⁵nduìʔ¹xʔon⁵³ V;IPFV;PL;1+EXCL;PRS
n⁵nduìʔ¹xʔon⁵³ V;PROG;SG;1;PST
n⁵nduìʔ¹xʔon⁵³ V;IPFV;SG;1;PRS
n⁵nduìʔ¹xʔon⁵³ V;SBJV;SG;1
n⁵nduìʔ¹xʔon⁵³ V;IPFV;SG;3;PRS
n⁵nduìʔ¹xʔon⁵³ V;PROG;SG;3;FUT
n⁵nduìʔ¹xʔon⁵³ V;PFV;PL;1+INCL;PST
n⁵nduìʔ¹xʔon⁵³ V;IRR;SG;1;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IPFV;SG;1;PRS
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PFV;SG;3;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;PL;3;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IPFV;PL;3;PRS
n⁵ndí⁵tɛʔ⁵tzʔon³ V;SBJV;PL;1+EXCL
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;SG;1;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PFV;SG;2;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IPFV;SG;2;PRS
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IRR;SG;3;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PFV;SG;1;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;SG;3;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PFV;PL;3;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;SG;2;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;SBJV;SG;3
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵tɛʔ⁵tzʔon³ V;SBJV;PL;3
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IRR;SG;2;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IPFV;SG;3;PRS
n⁵ndí⁵tɛʔ⁵tzʔon³ V;SBJV;PL;1+INCL
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IRR;SG;1;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;PL;3;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;SG;1;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;SG;2;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;IRR;PL;3;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵tɛʔ⁵tzʔon³ V;SBJV;SG;1
n⁵ndí⁵tɛʔ⁵tzʔon³ V;PROG;SG;3;FUT
n⁵ndí⁵tɛʔ⁵tzʔon³ V;SBJV;SG;2
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;SG;1;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;SG;2;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;PFV;SG;2;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;SG;1;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;SBJV;PL;3
n⁵ndí⁵beʔ¹²tzʔon³ V;IPFV;SG;1;PRS
n⁵ndí⁵beʔ¹²tzʔon³ V;IRR;PL;3;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;IRR;SG;1;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;PFV;SG;3;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;PFV;SG;1;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;SBJV;SG;2
n⁵ndí⁵beʔ¹²tzʔon³ V;SBJV;PL;1+EXCL
n⁵ndí⁵beʔ¹²tzʔon³ V;SBJV;PL;1+INCL
n⁵ndí⁵beʔ¹²tzʔon³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵beʔ¹²tzʔon³ V;PFV;PL;3;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;SG;2;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;SBJV;SG;3
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;PL;3;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;IRR;SG;2;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;PL;3;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵beʔ¹²tzʔon³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;IPFV;PL;3;PRS
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;SG;3;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;SG;3;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;IPFV;SG;3;PRS
n⁵ndí⁵beʔ¹²tzʔon³ V;IRR;SG;3;FUT
n⁵ndí⁵beʔ¹²tzʔon³ V;IPFV;SG;2;PRS
n⁵ndí⁵beʔ¹²tzʔon³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵beʔ¹²tzʔon³ V;SBJV;SG;1
n⁵ndí⁵tzan¹²tzʔon³ V;PFV;SG;3;PST
n⁵ndí⁵tzan¹²tzʔon³ V;IRR;SG;3;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵tzan¹²tzʔon³ V;SBJV;SG;2
n⁵ndí⁵tzan¹²tzʔon³ V;IPFV;PL;3;PRS
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;SG;3;PST
n⁵ndí⁵tzan¹²tzʔon³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;SBJV;PL;3
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;PL;3;PST
n⁵ndí⁵tzan¹²tzʔon³ V;SBJV;PL;1+EXCL
n⁵ndí⁵tzan¹²tzʔon³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵tzan¹²tzʔon³ V;IPFV;SG;1;PRS
n⁵ndí⁵tzan¹²tzʔon³ V;SBJV;SG;3
n⁵ndí⁵tzan¹²tzʔon³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;SG;3;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;PFV;SG;1;PST
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;PL;3;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;SG;2;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;SBJV;SG;1
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;IRR;PL;3;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;SG;2;PST
n⁵ndí⁵tzan¹²tzʔon³ V;SBJV;PL;1+INCL
n⁵ndí⁵tzan¹²tzʔon³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;IPFV;SG;3;PRS
n⁵ndí⁵tzan¹²tzʔon³ V;IRR;SG;1;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;PFV;PL;3;PST
n⁵ndí⁵tzan¹²tzʔon³ V;IRR;SG;2;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;SG;1;FUT
n⁵ndí⁵tzan¹²tzʔon³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵tzan¹²tzʔon³ V;PFV;SG;2;PST
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;SG;1;PST
n⁵ndí⁵tzan¹²tzʔon³ V;IPFV;SG;2;PRS
n⁵ndí⁵tzan¹²tzʔon³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PFV;SG;3;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IRR;SG;3;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IPFV;SG;1;PRS
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;SG;2;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PFV;PL;3;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;SBJV;SG;3
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;SG;1;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PFV;SG;1;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵bìʔ¹nʔa⁵³ V;SBJV;SG;1
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;PL;3;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;SG;2;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IRR;SG;2;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;SBJV;PL;1+EXCL
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IPFV;SG;3;PRS
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IRR;SG;1;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;SG;1;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;PL;3;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IRR;PL;3;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IPFV;SG;2;PRS
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;SG;3;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;SBJV;SG;2
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PFV;SG;2;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;IPFV;PL;3;PRS
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;SBJV;PL;1+INCL
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵bìʔ¹nʔa⁵³ V;SBJV;PL;3
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵bìʔ¹nʔa⁵³ V;PROG;SG;3;PST
n⁵ndí⁵sʔ๠V;PROG;PL;3;PST
n⁵ndí⁵sʔ๠V;IRR;PL;1+INCL;FUT
n⁵ndí⁵sʔ๠V;SBJV;SG;3
n⁵ndí⁵sʔ๠V;IRR;SG;3;FUT
n⁵ndí⁵sʔ๠V;PROG;PL;3;FUT
n⁵ndí⁵sʔ๠V;IPFV;SG;3;PRS
n⁵ndí⁵sʔ๠V;PROG;PL;1+EXCL;PST
n⁵ndí⁵sʔ๠V;PROG;SG;3;FUT
n⁵ndí⁵sʔ๠V;IRR;SG;2;FUT
n⁵ndí⁵sʔ๠V;IPFV;PL;3;PRS
n⁵ndí⁵sʔ๠V;IPFV;SG;2;PRS
n⁵ndí⁵sʔ๠V;PFV;SG;2;PST
n⁵ndí⁵sʔ๠V;IPFV;SG;1;PRS
n⁵ndí⁵sʔ๠V;PFV;PL;3;PST
n⁵ndí⁵sʔ๠V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵sʔ๠V;PROG;SG;3;PST
n⁵ndí⁵sʔ๠V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵sʔ๠V;PROG;SG;2;FUT
n⁵ndí⁵sʔ๠V;PFV;PL;1+EXCL;PST
n⁵ndí⁵sʔ๠V;SBJV;SG;1
n⁵ndí⁵sʔ๠V;PROG;PL;1+INCL;PST
n⁵ndí⁵sʔ๠V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵sʔ๠V;PFV;SG;1;PST
n⁵ndí⁵sʔ๠V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵sʔ๠V;SBJV;PL;3
n⁵ndí⁵sʔ๠V;SBJV;PL;1+EXCL
n⁵ndí⁵sʔ๠V;SBJV;SG;2
n⁵ndí⁵sʔ๠V;IRR;SG;1;FUT
n⁵ndí⁵sʔ๠V;PROG;SG;2;PST
n⁵ndí⁵sʔ๠V;PFV;PL;1+INCL;PST
n⁵ndí⁵sʔ๠V;PFV;SG;3;PST
n⁵ndí⁵sʔ๠V;PROG;SG;1;FUT
n⁵ndí⁵sʔ๠V;PROG;SG;1;PST
n⁵ndí⁵sʔ๠V;PROG;PL;1+INCL;FUT
n⁵ndí⁵sʔ๠V;SBJV;PL;1+INCL
n⁵ndí⁵sʔ๠V;IRR;PL;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;SBJV;PL;1+EXCL
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IPFV;SG;2;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;SBJV;PL;3
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;SG;3;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;SBJV;SG;3
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;SG;1;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IRR;PL;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;PL;3;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;SBJV;SG;1
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IRR;SG;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;SG;2;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;SG;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PFV;SG;1;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;SBJV;SG;2
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;PL;3;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IRR;SG;1;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IPFV;SG;1;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;SBJV;PL;1+INCL
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IRR;SG;2;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PFV;SG;3;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PFV;SG;2;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;SG;2;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IPFV;PL;3;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PFV;PL;3;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IPFV;SG;3;PRS
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;PROG;SG;1;PST
n⁵ndí⁵ñèʔ¹ ki³tzí⁵nè¹ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵hnaʔ¹² V;IRR;SG;1;FUT
n⁵ndí⁵hnaʔ¹² V;IPFV;PL;3;PRS
n⁵ndí⁵hnaʔ¹² V;PROG;SG;2;PST
n⁵ndí⁵hnaʔ¹² V;IRR;SG;3;FUT
n⁵ndí⁵hnaʔ¹² V;SBJV;PL;1+INCL
n⁵ndí⁵hnaʔ¹² V;PROG;SG;2;FUT
n⁵ndí⁵hnaʔ¹² V;PFV;SG;2;PST
n⁵ndí⁵hnaʔ¹² V;PROG;SG;3;PST
n⁵ndí⁵hnaʔ¹² V;PFV;PL;1+EXCL;PST
n⁵ndí⁵hnaʔ¹² V;PROG;PL;3;PST
n⁵ndí⁵hnaʔ¹² V;IPFV;SG;2;PRS
n⁵ndí⁵hnaʔ¹² V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵hnaʔ¹² V;PROG;PL;1+EXCL;PST
n⁵ndí⁵hnaʔ¹² V;PROG;PL;1+INCL;FUT
n⁵ndí⁵hnaʔ¹² V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵hnaʔ¹² V;PROG;SG;1;PST
n⁵ndí⁵hnaʔ¹² V;PFV;SG;1;PST
n⁵ndí⁵hnaʔ¹² V;IRR;PL;3;FUT
n⁵ndí⁵hnaʔ¹² V;PFV;PL;1+INCL;PST
n⁵ndí⁵hnaʔ¹² V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵hnaʔ¹² V;IPFV;SG;3;PRS
n⁵ndí⁵hnaʔ¹² V;PROG;PL;3;FUT
n⁵ndí⁵hnaʔ¹² V;SBJV;PL;1+EXCL
n⁵ndí⁵hnaʔ¹² V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵hnaʔ¹² V;PROG;SG;1;FUT
n⁵ndí⁵hnaʔ¹² V;SBJV;SG;1
n⁵ndí⁵hnaʔ¹² V;PFV;PL;3;PST
n⁵ndí⁵hnaʔ¹² V;SBJV;SG;2
n⁵ndí⁵hnaʔ¹² V;PROG;SG;3;FUT
n⁵ndí⁵hnaʔ¹² V;SBJV;PL;3
n⁵ndí⁵hnaʔ¹² V;IPFV;SG;1;PRS
n⁵ndí⁵hnaʔ¹² V;SBJV;SG;3
n⁵ndí⁵hnaʔ¹² V;PROG;PL;1+INCL;PST
n⁵ndí⁵hnaʔ¹² V;IRR;SG;2;FUT
n⁵ndí⁵hnaʔ¹² V;IRR;PL;1+INCL;FUT
n⁵ndí⁵hnaʔ¹² V;PFV;SG;3;PST
n⁵ndoʔ³ V;IPFV;SG;1;PRS
n⁵ndoʔ³ V;IRR;SG;3;FUT
n⁵ndoʔ³ V;PROG;SG;1;PST
n⁵ndoʔ³ V;SBJV;PL;1+EXCL
n⁵ndoʔ³ V;PFV;SG;1;PST
n⁵ndoʔ³ V;PROG;SG;2;PST
n⁵ndoʔ³ V;IRR;PL;1+EXCL;FUT
n⁵ndoʔ³ V;SBJV;SG;3
n⁵ndoʔ³ V;PROG;PL;3;FUT
n⁵ndoʔ³ V;PFV;SG;2;PST
n⁵ndoʔ³ V;IRR;PL;1+INCL;FUT
n⁵ndoʔ³ V;PROG;PL;3;PST
n⁵ndoʔ³ V;SBJV;PL;1+INCL
n⁵ndoʔ³ V;IRR;SG;2;FUT
n⁵ndoʔ³ V;PFV;SG;3;PST
n⁵ndoʔ³ V;SBJV;PL;3
n⁵ndoʔ³ V;PFV;PL;1+EXCL;PST
n⁵ndoʔ³ V;PFV;PL;3;PST
n⁵ndoʔ³ V;PROG;SG;3;PST
n⁵ndoʔ³ V;IPFV;PL;3;PRS
n⁵ndoʔ³ V;PFV;PL;1+INCL;PST
n⁵ndoʔ³ V;PROG;PL;1+INCL;PST
n⁵ndoʔ³ V;IRR;PL;3;FUT
n⁵ndoʔ³ V;SBJV;SG;1
n⁵ndoʔ³ V;IPFV;PL;1+EXCL;PRS
n⁵ndoʔ³ V;IRR;SG;1;FUT
n⁵ndoʔ³ V;PROG;PL;1+INCL;FUT
n⁵ndoʔ³ V;SBJV;SG;2
n⁵ndoʔ³ V;PROG;PL;1+EXCL;FUT
n⁵ndoʔ³ V;PROG;SG;3;FUT
n⁵ndoʔ³ V;PROG;PL;1+EXCL;PST
n⁵ndoʔ³ V;IPFV;SG;3;PRS
n⁵ndoʔ³ V;PROG;SG;2;FUT
n⁵ndoʔ³ V;IPFV;SG;2;PRS
n⁵ndoʔ³ V;IPFV;PL;1+INCL;PRS
n⁵ndoʔ³ V;PROG;SG;1;FUT
n⁵ndí⁵kí⁵xʔen V;SBJV;PL;3
n⁵ndí⁵kí⁵xʔen V;IRR;PL;1+INCL;FUT
n⁵ndí⁵kí⁵xʔen V;IRR;PL;3;FUT
n⁵ndí⁵kí⁵xʔen V;PROG;SG;2;FUT
n⁵ndí⁵kí⁵xʔen V;PFV;PL;1+EXCL;PST
n⁵ndí⁵kí⁵xʔen V;IPFV;SG;1;PRS
n⁵ndí⁵kí⁵xʔen V;SBJV;SG;1
n⁵ndí⁵kí⁵xʔen V;IPFV;SG;2;PRS
n⁵ndí⁵kí⁵xʔen V;IPFV;PL;3;PRS
n⁵ndí⁵kí⁵xʔen V;SBJV;PL;1+INCL
n⁵ndí⁵kí⁵xʔen V;PROG;SG;2;PST
n⁵ndí⁵kí⁵xʔen V;PROG;SG;3;FUT
n⁵ndí⁵kí⁵xʔen V;SBJV;SG;3
n⁵ndí⁵kí⁵xʔen V;IRR;SG;3;FUT
n⁵ndí⁵kí⁵xʔen V;IRR;SG;2;FUT
n⁵ndí⁵kí⁵xʔen V;PFV;SG;2;PST
n⁵ndí⁵kí⁵xʔen V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵kí⁵xʔen V;IPFV;SG;3;PRS
n⁵ndí⁵kí⁵xʔen V;PROG;PL;1+INCL;PST
n⁵ndí⁵kí⁵xʔen V;PFV;SG;3;PST
n⁵ndí⁵kí⁵xʔen V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵kí⁵xʔen V;IRR;SG;1;FUT
n⁵ndí⁵kí⁵xʔen V;PROG;SG;1;FUT
n⁵ndí⁵kí⁵xʔen V;PROG;SG;1;PST
n⁵ndí⁵kí⁵xʔen V;PFV;PL;3;PST
n⁵ndí⁵kí⁵xʔen V;PROG;PL;3;PST
n⁵ndí⁵kí⁵xʔen V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵kí⁵xʔen V;PROG;SG;3;PST
n⁵ndí⁵kí⁵xʔen V;PFV;PL;1+INCL;PST
n⁵ndí⁵kí⁵xʔen V;SBJV;SG;2
n⁵ndí⁵kí⁵xʔen V;PROG;PL;3;FUT
n⁵ndí⁵kí⁵xʔen V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵kí⁵xʔen V;PFV;SG;1;PST
n⁵ndí⁵kí⁵xʔen V;PROG;PL;1+EXCL;PST
n⁵ndí⁵kí⁵xʔen V;PROG;PL;1+INCL;FUT
n⁵ndí⁵kí⁵xʔen V;SBJV;PL;1+EXCL
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;SBJV;SG;3
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;SBJV;SG;2
n⁵ndí⁵ñèʔ¹ ki³ta³ V;SBJV;PL;1+EXCL
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;SG;2;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PFV;SG;3;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;SG;3;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;PL;3;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;SG;1;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PFV;SG;2;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;SBJV;PL;1+INCL
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;SG;3;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IPFV;SG;3;PRS
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IPFV;SG;2;PRS
n⁵ndí⁵ñèʔ¹ ki³ta³ V;SBJV;SG;1
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IRR;PL;3;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;SG;2;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IRR;SG;3;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;SBJV;PL;3
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IRR;SG;2;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IPFV;SG;1;PRS
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;SG;1;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IPFV;PL;3;PRS
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PFV;SG;1;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PFV;PL;3;PST
n⁵ndí⁵ñèʔ¹ ki³ta³ V;IRR;SG;1;FUT
n⁵ndí⁵ñèʔ¹ ki³ta³ V;PROG;PL;3;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PFV;SG;1;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IPFV;SG;1;PRS
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;SBJV;SG;1
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PFV;SG;3;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IRR;SG;1;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;SG;2;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;SBJV;PL;1+INCL
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;SG;3;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IPFV;SG;3;PRS
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;SG;1;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PFV;PL;3;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;SBJV;PL;3
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PFV;SG;2;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;SBJV;SG;3
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;SG;1;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;PL;3;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;SG;2;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IRR;SG;3;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IPFV;SG;2;PRS
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IRR;PL;3;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IPFV;PL;3;PRS
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IRR;SG;2;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;SG;3;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;SBJV;SG;2
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;SBJV;PL;1+EXCL
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PROG;PL;3;FUT
n⁵ndí⁵ndyóʔ⁵ xtyoʔ³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ki³ndyaʔ³ V;PROG;SG;1;PST
n⁵ndí⁵ki³ndyaʔ³ V;SBJV;PL;3
n⁵ndí⁵ki³ndyaʔ³ V;PROG;SG;1;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PROG;PL;3;PST
n⁵ndí⁵ki³ndyaʔ³ V;PFV;SG;1;PST
n⁵ndí⁵ki³ndyaʔ³ V;IRR;SG;1;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PFV;PL;3;PST
n⁵ndí⁵ki³ndyaʔ³ V;IRR;PL;3;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PROG;SG;2;PST
n⁵ndí⁵ki³ndyaʔ³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ki³ndyaʔ³ V;SBJV;PL;1+INCL
n⁵ndí⁵ki³ndyaʔ³ V;IPFV;SG;1;PRS
n⁵ndí⁵ki³ndyaʔ³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ki³ndyaʔ³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PROG;SG;3;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PFV;SG;2;PST
n⁵ndí⁵ki³ndyaʔ³ V;SBJV;PL;1+EXCL
n⁵ndí⁵ki³ndyaʔ³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ki³ndyaʔ³ V;IPFV;SG;3;PRS
n⁵ndí⁵ki³ndyaʔ³ V;IPFV;PL;3;PRS
n⁵ndí⁵ki³ndyaʔ³ V;IRR;SG;3;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PROG;PL;3;FUT
n⁵ndí⁵ki³ndyaʔ³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ki³ndyaʔ³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ki³ndyaʔ³ V;PROG;SG;2;FUT
n⁵ndí⁵ki³ndyaʔ³ V;SBJV;SG;3
n⁵ndí⁵ki³ndyaʔ³ V;SBJV;SG;2
n⁵ndí⁵ki³ndyaʔ³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ki³ndyaʔ³ V;SBJV;SG;1
n⁵ndí⁵ki³ndyaʔ³ V;IRR;SG;2;FUT
n⁵ndí⁵ki³ndyaʔ³ V;IPFV;SG;2;PRS
n⁵ndí⁵ki³ndyaʔ³ V;PROG;SG;3;PST
n⁵ndí⁵ki³ndyaʔ³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ki³ndyaʔ³ V;PFV;SG;3;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;SG;3;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;PL;3;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IPFV;SG;3;PRS
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;SBJV;PL;1+EXCL
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PFV;SG;3;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PFV;SG;2;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;SG;1;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;SBJV;SG;1
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IRR;SG;3;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;SG;2;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;SBJV;SG;3
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;SG;2;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IPFV;SG;1;PRS
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;SBJV;PL;3
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;SG;3;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IPFV;SG;2;PRS
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PFV;PL;3;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PFV;SG;1;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IPFV;PL;3;PRS
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;SBJV;PL;1+INCL
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;SBJV;SG;2
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;PL;3;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IRR;SG;1;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;PROG;SG;1;PST
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IRR;PL;3;FUT
n⁵ndí⁵ndyiaʔ⁵³tzʔon³ V;IRR;SG;2;FUT
n⁵ndʔɛ¹ V;IPFV;SG;2;PRS
n⁵ndʔɛ¹ V;PROG;PL;1+EXCL;PST
n⁵ndʔɛ¹ V;PROG;PL;3;PST
n⁵ndʔɛ¹ V;PFV;SG;2;PST
n⁵ndʔɛ¹ V;PROG;SG;3;FUT
n⁵ndʔɛ¹ V;IRR;PL;3;FUT
n⁵ndʔɛ¹ V;PFV;SG;1;PST
n⁵ndʔɛ¹ V;PROG;SG;2;FUT
n⁵ndʔɛ¹ V;IPFV;PL;1+INCL;PRS
n⁵ndʔɛ¹ V;SBJV;PL;1+EXCL
n⁵ndʔɛ¹ V;IRR;SG;1;FUT
n⁵ndʔɛ¹ V;SBJV;SG;3
n⁵ndʔɛ¹ V;SBJV;SG;1
n⁵ndʔɛ¹ V;IPFV;SG;3;PRS
n⁵ndʔɛ¹ V;SBJV;PL;3
n⁵ndʔɛ¹ V;IPFV;SG;1;PRS
n⁵ndʔɛ¹ V;PROG;PL;1+INCL;PST
n⁵ndʔɛ¹ V;PFV;PL;1+EXCL;PST
n⁵ndʔɛ¹ V;PROG;PL;1+INCL;FUT
n⁵ndʔɛ¹ V;IPFV;PL;3;PRS
n⁵ndʔɛ¹ V;PFV;SG;3;PST
n⁵ndʔɛ¹ V;IRR;PL;1+INCL;FUT
n⁵ndʔɛ¹ V;SBJV;SG;2
n⁵ndʔɛ¹ V;IRR;SG;3;FUT
n⁵ndʔɛ¹ V;IRR;PL;1+EXCL;FUT
n⁵ndʔɛ¹ V;PFV;PL;1+INCL;PST
n⁵ndʔɛ¹ V;PROG;PL;1+EXCL;FUT
n⁵ndʔɛ¹ V;PROG;PL;3;FUT
n⁵ndʔɛ¹ V;PROG;SG;2;PST
n⁵ndʔɛ¹ V;PROG;SG;1;FUT
n⁵ndʔɛ¹ V;IPFV;PL;1+EXCL;PRS
n⁵ndʔɛ¹ V;PROG;SG;3;PST
n⁵ndʔɛ¹ V;PROG;SG;1;PST
n⁵ndʔɛ¹ V;PFV;PL;3;PST
n⁵ndʔɛ¹ V;IRR;SG;2;FUT
n⁵ndʔɛ¹ V;SBJV;PL;1+INCL
n⁵ndʔue³n⁵no³ V;PROG;SG;3;PST
n⁵ndʔue³n⁵no³ V;PROG;SG;1;PST
n⁵ndʔue³n⁵no³ V;IPFV;SG;2;PRS
n⁵ndʔue³n⁵no³ V;IPFV;SG;1;PRS
n⁵ndʔue³n⁵no³ V;IRR;PL;1+EXCL;FUT
n⁵ndʔue³n⁵no³ V;SBJV;PL;1+EXCL
n⁵ndʔue³n⁵no³ V;PROG;SG;1;FUT
n⁵ndʔue³n⁵no³ V;PROG;PL;3;FUT
n⁵ndʔue³n⁵no³ V;IRR;PL;3;FUT
n⁵ndʔue³n⁵no³ V;PROG;PL;1+EXCL;FUT
n⁵ndʔue³n⁵no³ V;SBJV;SG;1
n⁵ndʔue³n⁵no³ V;IRR;SG;3;FUT
n⁵ndʔue³n⁵no³ V;SBJV;SG;2
n⁵ndʔue³n⁵no³ V;IRR;SG;1;FUT
n⁵ndʔue³n⁵no³ V;PFV;PL;1+EXCL;PST
n⁵ndʔue³n⁵no³ V;IPFV;PL;1+INCL;PRS
n⁵ndʔue³n⁵no³ V;SBJV;SG;3
n⁵ndʔue³n⁵no³ V;IRR;SG;2;FUT
n⁵ndʔue³n⁵no³ V;IPFV;PL;3;PRS
n⁵ndʔue³n⁵no³ V;PROG;PL;1+EXCL;PST
n⁵ndʔue³n⁵no³ V;IPFV;PL;1+EXCL;PRS
n⁵ndʔue³n⁵no³ V;PFV;SG;3;PST
n⁵ndʔue³n⁵no³ V;SBJV;PL;1+INCL
n⁵ndʔue³n⁵no³ V;SBJV;PL;3
n⁵ndʔue³n⁵no³ V;PROG;SG;3;FUT
n⁵ndʔue³n⁵no³ V;IRR;PL;1+INCL;FUT
n⁵ndʔue³n⁵no³ V;PROG;SG;2;PST
n⁵ndʔue³n⁵no³ V;PROG;SG;2;FUT
n⁵ndʔue³n⁵no³ V;PFV;PL;1+INCL;PST
n⁵ndʔue³n⁵no³ V;IPFV;SG;3;PRS
n⁵ndʔue³n⁵no³ V;PFV;SG;1;PST
n⁵ndʔue³n⁵no³ V;PROG;PL;1+INCL;PST
n⁵ndʔue³n⁵no³ V;PROG;PL;1+INCL;FUT
n⁵ndʔue³n⁵no³ V;PROG;PL;3;PST
n⁵ndʔue³n⁵no³ V;PFV;SG;2;PST
n⁵ndʔue³n⁵no³ V;PFV;PL;3;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;IPFV;SG;2;PRS
n⁵ndí⁵hndaʔ⁵³ xken³ V;IPFV;PL;3;PRS
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;PFV;PL;3;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;PFV;SG;3;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;SG;1;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;IRR;SG;2;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;SBJV;SG;3
n⁵ndí⁵hndaʔ⁵³ xken³ V;IPFV;SG;1;PRS
n⁵ndí⁵hndaʔ⁵³ xken³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;PFV;SG;2;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵hndaʔ⁵³ xken³ V;IRR;PL;3;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;SBJV;PL;3
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;PL;3;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;PL;3;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;SG;3;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;SG;3;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;IPFV;SG;3;PRS
n⁵ndí⁵hndaʔ⁵³ xken³ V;IRR;SG;1;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;SBJV;SG;2
n⁵ndí⁵hndaʔ⁵³ xken³ V;SBJV;PL;1+EXCL
n⁵ndí⁵hndaʔ⁵³ xken³ V;IRR;SG;3;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;SBJV;PL;1+INCL
n⁵ndí⁵hndaʔ⁵³ xken³ V;SBJV;SG;1
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;SG;1;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵hndaʔ⁵³ xken³ V;PFV;SG;1;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;SG;2;PST
n⁵ndí⁵hndaʔ⁵³ xken³ V;PROG;SG;2;FUT
n⁵ndí⁵ ʔ⁵han³ V;IPFV;SG;3;PRS
n⁵ndí⁵ ʔ⁵han³ V;PROG;SG;1;FUT
n⁵ndí⁵ ʔ⁵han³ V;PROG;SG;3;FUT
n⁵ndí⁵ ʔ⁵han³ V;SBJV;PL;1+EXCL
n⁵ndí⁵ ʔ⁵han³ V;IRR;SG;1;FUT
n⁵ndí⁵ ʔ⁵han³ V;PROG;SG;1;PST
n⁵ndí⁵ ʔ⁵han³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ ʔ⁵han³ V;PFV;SG;1;PST
n⁵ndí⁵ ʔ⁵han³ V;IPFV;SG;1;PRS
n⁵ndí⁵ ʔ⁵han³ V;PFV;SG;3;PST
n⁵ndí⁵ ʔ⁵han³ V;PROG;SG;2;PST
n⁵ndí⁵ ʔ⁵han³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ ʔ⁵han³ V;IRR;PL;3;FUT
n⁵ndí⁵ ʔ⁵han³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ ʔ⁵han³ V;SBJV;PL;3
n⁵ndí⁵ ʔ⁵han³ V;IRR;SG;3;FUT
n⁵ndí⁵ ʔ⁵han³ V;IPFV;SG;2;PRS
n⁵ndí⁵ ʔ⁵han³ V;IRR;SG;2;FUT
n⁵ndí⁵ ʔ⁵han³ V;PROG;SG;2;FUT
n⁵ndí⁵ ʔ⁵han³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ ʔ⁵han³ V;SBJV;SG;1
n⁵ndí⁵ ʔ⁵han³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ ʔ⁵han³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ ʔ⁵han³ V;IPFV;PL;3;PRS
n⁵ndí⁵ ʔ⁵han³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ ʔ⁵han³ V;SBJV;SG;2
n⁵ndí⁵ ʔ⁵han³ V;PFV;SG;2;PST
n⁵ndí⁵ ʔ⁵han³ V;PFV;PL;3;PST
n⁵ndí⁵ ʔ⁵han³ V;PROG;SG;3;PST
n⁵ndí⁵ ʔ⁵han³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ ʔ⁵han³ V;PROG;PL;3;PST
n⁵ndí⁵ ʔ⁵han³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ ʔ⁵han³ V;SBJV;SG;3
n⁵ndí⁵ ʔ⁵han³ V;SBJV;PL;1+INCL
n⁵ndí⁵ ʔ⁵han³ V;PROG;PL;3;FUT
n⁵ndí⁵ ʔ⁵han³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵tzʔón⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵tzʔón⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵tzʔón⁵ V;PFV;SG;2;PST
n⁵ndí⁵tzʔón⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵tzʔón⁵ V;PROG;SG;2;FUT
n⁵ndí⁵tzʔón⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵tzʔón⁵ V;IRR;SG;2;FUT
n⁵ndí⁵tzʔón⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵tzʔón⁵ V;PROG;PL;3;FUT
n⁵ndí⁵tzʔón⁵ V;SBJV;SG;2
n⁵ndí⁵tzʔón⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵tzʔón⁵ V;IRR;SG;1;FUT
n⁵ndí⁵tzʔón⁵ V;SBJV;PL;3
n⁵ndí⁵tzʔón⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵tzʔón⁵ V;SBJV;SG;3
n⁵ndí⁵tzʔón⁵ V;SBJV;SG;1
n⁵ndí⁵tzʔón⁵ V;PROG;SG;2;PST
n⁵ndí⁵tzʔón⁵ V;PFV;SG;3;PST
n⁵ndí⁵tzʔón⁵ V;PFV;PL;3;PST
n⁵ndí⁵tzʔón⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵tzʔón⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵tzʔón⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵tzʔón⁵ V;PROG;SG;1;FUT
n⁵ndí⁵tzʔón⁵ V;PROG;PL;3;PST
n⁵ndí⁵tzʔón⁵ V;PROG;SG;3;PST
n⁵ndí⁵tzʔón⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵tzʔón⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵tzʔón⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵tzʔón⁵ V;PROG;SG;3;FUT
n⁵ndí⁵tzʔón⁵ V;PROG;SG;1;PST
n⁵ndí⁵tzʔón⁵ V;IRR;SG;3;FUT
n⁵ndí⁵tzʔón⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵tzʔón⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵tzʔón⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵tzʔón⁵ V;IRR;PL;3;FUT
n⁵ndí⁵tzʔón⁵ V;PFV;SG;1;PST
n⁵ndí⁵hndaʔ⁵³ V;SBJV;PL;1+INCL
n⁵ndí⁵hndaʔ⁵³ V;IPFV;SG;2;PRS
n⁵ndí⁵hndaʔ⁵³ V;PFV;SG;2;PST
n⁵ndí⁵hndaʔ⁵³ V;PROG;SG;1;FUT
n⁵ndí⁵hndaʔ⁵³ V;IPFV;PL;3;PRS
n⁵ndí⁵hndaʔ⁵³ V;IRR;SG;2;FUT
n⁵ndí⁵hndaʔ⁵³ V;PROG;PL;3;FUT
n⁵ndí⁵hndaʔ⁵³ V;PROG;SG;3;FUT
n⁵ndí⁵hndaʔ⁵³ V;PFV;SG;3;PST
n⁵ndí⁵hndaʔ⁵³ V;PROG;PL;3;PST
n⁵ndí⁵hndaʔ⁵³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵hndaʔ⁵³ V;SBJV;PL;3
n⁵ndí⁵hndaʔ⁵³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵hndaʔ⁵³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵hndaʔ⁵³ V;PROG;SG;2;FUT
n⁵ndí⁵hndaʔ⁵³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵hndaʔ⁵³ V;IPFV;SG;1;PRS
n⁵ndí⁵hndaʔ⁵³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵hndaʔ⁵³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵hndaʔ⁵³ V;PROG;SG;2;PST
n⁵ndí⁵hndaʔ⁵³ V;SBJV;SG;1
n⁵ndí⁵hndaʔ⁵³ V;PROG;SG;3;PST
n⁵ndí⁵hndaʔ⁵³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵hndaʔ⁵³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵hndaʔ⁵³ V;SBJV;SG;3
n⁵ndí⁵hndaʔ⁵³ V;SBJV;PL;1+EXCL
n⁵ndí⁵hndaʔ⁵³ V;IRR;SG;1;FUT
n⁵ndí⁵hndaʔ⁵³ V;PFV;PL;3;PST
n⁵ndí⁵hndaʔ⁵³ V;IRR;PL;3;FUT
n⁵ndí⁵hndaʔ⁵³ V;PROG;SG;1;PST
n⁵ndí⁵hndaʔ⁵³ V;SBJV;SG;2
n⁵ndí⁵hndaʔ⁵³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵hndaʔ⁵³ V;PFV;SG;1;PST
n⁵ndí⁵hndaʔ⁵³ V;IRR;SG;3;FUT
n⁵ndí⁵hndaʔ⁵³ V;IPFV;SG;3;PRS
n⁵ndí⁵hndaʔ⁵³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵hán⁵ V;PROG;SG;2;PST
n⁵ndí⁵hán⁵ V;IRR;PL;3;FUT
n⁵ndí⁵hán⁵ V;PROG;PL;1+INCL;PST
n⁵ndí⁵hán⁵ V;IPFV;SG;2;PRS
n⁵ndí⁵hán⁵ V;SBJV;PL;3
n⁵ndí⁵hán⁵ V;SBJV;PL;1+INCL
n⁵ndí⁵hán⁵ V;SBJV;SG;2
n⁵ndí⁵hán⁵ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵hán⁵ V;PFV;SG;3;PST
n⁵ndí⁵hán⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵hán⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵hán⁵ V;PFV;SG;1;PST
n⁵ndí⁵hán⁵ V;IRR;SG;3;FUT
n⁵ndí⁵hán⁵ V;IPFV;SG;3;PRS
n⁵ndí⁵hán⁵ V;PFV;SG;2;PST
n⁵ndí⁵hán⁵ V;SBJV;SG;1
n⁵ndí⁵hán⁵ V;PROG;PL;3;FUT
n⁵ndí⁵hán⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵hán⁵ V;PROG;SG;3;FUT
n⁵ndí⁵hán⁵ V;SBJV;SG;3
n⁵ndí⁵hán⁵ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵hán⁵ V;PFV;PL;1+INCL;PST
n⁵ndí⁵hán⁵ V;PROG;PL;3;PST
n⁵ndí⁵hán⁵ V;SBJV;PL;1+EXCL
n⁵ndí⁵hán⁵ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵hán⁵ V;PROG;SG;3;PST
n⁵ndí⁵hán⁵ V;PROG;SG;1;FUT
n⁵ndí⁵hán⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵hán⁵ V;PROG;SG;1;PST
n⁵ndí⁵hán⁵ V;PFV;PL;3;PST
n⁵ndí⁵hán⁵ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵hán⁵ V;IRR;SG;1;FUT
n⁵ndí⁵hán⁵ V;IPFV;PL;3;PRS
n⁵ndí⁵hán⁵ V;IPFV;SG;1;PRS
n⁵ndí⁵hán⁵ V;PROG;SG;2;FUT
n⁵ndí⁵hán⁵ V;IRR;SG;2;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;PL;3;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PFV;PL;1+EXCL;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;SBJV;PL;1+INCL
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IRR;SG;1;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PFV;PL;3;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IPFV;SG;2;PRS
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;SBJV;SG;2
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IPFV;SG;3;PRS
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;SG;1;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PFV;SG;3;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;PL;3;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;SG;3;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IPFV;PL;1+EXCL;PRS
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;PL;1+INCL;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;SBJV;PL;1+EXCL
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IRR;PL;1+INCL;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;PL;1+EXCL;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;SBJV;SG;1
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IRR;SG;3;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;SBJV;SG;3
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IPFV;SG;1;PRS
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PFV;SG;1;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IRR;PL;3;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;PL;1+EXCL;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PFV;SG;2;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IPFV;PL;3;PRS
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;SBJV;PL;3
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;SG;2;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IPFV;PL;1+INCL;PRS
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;IRR;SG;2;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;SG;2;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PFV;PL;1+INCL;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;SG;3;PST
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;PL;1+INCL;FUT
n⁵ndyion³ na³ ki³ndyaʔ³ nchhi³⁵ V;PROG;SG;1;PST
n⁵nda³hñʔo¹² V;SBJV;PL;1+EXCL
n⁵nda³hñʔo¹² V;PFV;SG;1;PST
n⁵nda³hñʔo¹² V;IRR;SG;1;FUT
n⁵nda³hñʔo¹² V;PROG;SG;3;FUT
n⁵nda³hñʔo¹² V;IRR;PL;3;FUT
n⁵nda³hñʔo¹² V;PROG;SG;1;PST
n⁵nda³hñʔo¹² V;IRR;SG;2;FUT
n⁵nda³hñʔo¹² V;PROG;PL;3;FUT
n⁵nda³hñʔo¹² V;PROG;SG;2;PST
n⁵nda³hñʔo¹² V;PFV;SG;2;PST
n⁵nda³hñʔo¹² V;PROG;SG;3;PST
n⁵nda³hñʔo¹² V;PROG;PL;1+EXCL;PST
n⁵nda³hñʔo¹² V;SBJV;SG;3
n⁵nda³hñʔo¹² V;IPFV;SG;3;PRS
n⁵nda³hñʔo¹² V;SBJV;SG;2
n⁵nda³hñʔo¹² V;IRR;PL;1+INCL;FUT
n⁵nda³hñʔo¹² V;PFV;PL;1+EXCL;PST
n⁵nda³hñʔo¹² V;IPFV;PL;3;PRS
n⁵nda³hñʔo¹² V;PROG;PL;3;PST
n⁵nda³hñʔo¹² V;SBJV;SG;1
n⁵nda³hñʔo¹² V;IRR;PL;1+EXCL;FUT
n⁵nda³hñʔo¹² V;IRR;SG;3;FUT
n⁵nda³hñʔo¹² V;SBJV;PL;1+INCL
n⁵nda³hñʔo¹² V;IPFV;PL;1+EXCL;PRS
n⁵nda³hñʔo¹² V;IPFV;PL;1+INCL;PRS
n⁵nda³hñʔo¹² V;PROG;SG;2;FUT
n⁵nda³hñʔo¹² V;IPFV;SG;1;PRS
n⁵nda³hñʔo¹² V;PFV;PL;1+INCL;PST
n⁵nda³hñʔo¹² V;IPFV;SG;2;PRS
n⁵nda³hñʔo¹² V;PROG;PL;1+INCL;FUT
n⁵nda³hñʔo¹² V;SBJV;PL;3
n⁵nda³hñʔo¹² V;PROG;PL;1+INCL;PST
n⁵nda³hñʔo¹² V;PFV;SG;3;PST
n⁵nda³hñʔo¹² V;PROG;PL;1+EXCL;FUT
n⁵nda³hñʔo¹² V;PFV;PL;3;PST
n⁵nda³hñʔo¹² V;PROG;SG;1;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PFV;SG;3;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;SBJV;SG;2
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;SG;2;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;SG;1;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PFV;SG;1;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IPFV;SG;2;PRS
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;PL;3;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PFV;PL;3;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PFV;PL;1+INCL;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;SG;3;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;PL;1+INCL;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;SG;3;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;PL;3;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IPFV;PL;3;PRS
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;SG;2;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IRR;SG;3;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PFV;SG;2;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IRR;PL;3;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;PROG;SG;1;PST
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;SBJV;SG;3
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;SBJV;PL;3
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IRR;SG;1;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IPFV;SG;3;PRS
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;SBJV;PL;1+EXCL
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IPFV;SG;1;PRS
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;SBJV;SG;1
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;IRR;SG;2;FUT
n⁵ndí⁵ ki³ndyaʔ³ nchhi⁵³ V;SBJV;PL;1+INCL
n⁵ndí⁵ kí⁵chi¹² V;IPFV;SG;3;PRS
n⁵ndí⁵ kí⁵chi¹² V;IPFV;SG;2;PRS
n⁵ndí⁵ kí⁵chi¹² V;IRR;PL;1+INCL;FUT
n⁵ndí⁵ kí⁵chi¹² V;PFV;PL;1+EXCL;PST
n⁵ndí⁵ kí⁵chi¹² V;PROG;SG;2;PST
n⁵ndí⁵ kí⁵chi¹² V;PFV;PL;3;PST
n⁵ndí⁵ kí⁵chi¹² V;PFV;PL;1+INCL;PST
n⁵ndí⁵ kí⁵chi¹² V;IPFV;SG;1;PRS
n⁵ndí⁵ kí⁵chi¹² V;IRR;PL;3;FUT
n⁵ndí⁵ kí⁵chi¹² V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵ kí⁵chi¹² V;IRR;SG;3;FUT
n⁵ndí⁵ kí⁵chi¹² V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵ kí⁵chi¹² V;PROG;SG;2;FUT
n⁵ndí⁵ kí⁵chi¹² V;PFV;SG;1;PST
n⁵ndí⁵ kí⁵chi¹² V;PFV;SG;2;PST
n⁵ndí⁵ kí⁵chi¹² V;SBJV;SG;2
n⁵ndí⁵ kí⁵chi¹² V;PROG;PL;3;FUT
n⁵ndí⁵ kí⁵chi¹² V;IRR;SG;1;FUT
n⁵ndí⁵ kí⁵chi¹² V;SBJV;PL;3
n⁵ndí⁵ kí⁵chi¹² V;SBJV;PL;1+EXCL
n⁵ndí⁵ kí⁵chi¹² V;PROG;PL;1+INCL;FUT
n⁵ndí⁵ kí⁵chi¹² V;PROG;SG;1;PST
n⁵ndí⁵ kí⁵chi¹² V;PROG;PL;1+EXCL;PST
n⁵ndí⁵ kí⁵chi¹² V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵ kí⁵chi¹² V;SBJV;PL;1+INCL
n⁵ndí⁵ kí⁵chi¹² V;IPFV;PL;3;PRS
n⁵ndí⁵ kí⁵chi¹² V;IRR;SG;2;FUT
n⁵ndí⁵ kí⁵chi¹² V;PROG;PL;1+INCL;PST
n⁵ndí⁵ kí⁵chi¹² V;PROG;PL;3;PST
n⁵ndí⁵ kí⁵chi¹² V;PFV;SG;3;PST
n⁵ndí⁵ kí⁵chi¹² V;SBJV;SG;3
n⁵ndí⁵ kí⁵chi¹² V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵ kí⁵chi¹² V;PROG;SG;1;FUT
n⁵ndí⁵ kí⁵chi¹² V;PROG;SG;3;FUT
n⁵ndí⁵ kí⁵chi¹² V;PROG;SG;3;PST
n⁵ndí⁵ kí⁵chi¹² V;SBJV;SG;1
n⁵ndí⁵hndoʔ³⁴ V;PROG;PL;1+EXCL;PST
n⁵ndí⁵hndoʔ³⁴ V;SBJV;SG;2
n⁵ndí⁵hndoʔ³⁴ V;SBJV;PL;1+INCL
n⁵ndí⁵hndoʔ³⁴ V;IRR;SG;2;FUT
n⁵ndí⁵hndoʔ³⁴ V;IPFV;SG;3;PRS
n⁵ndí⁵hndoʔ³⁴ V;PROG;PL;1+INCL;FUT
n⁵ndí⁵hndoʔ³⁴ V;IRR;SG;3;FUT
n⁵ndí⁵hndoʔ³⁴ V;PFV;SG;1;PST
n⁵ndí⁵hndoʔ³⁴ V;PROG;PL;3;FUT
n⁵ndí⁵hndoʔ³⁴ V;PFV;SG;2;PST
n⁵ndí⁵hndoʔ³⁴ V;PFV;SG;3;PST
n⁵ndí⁵hndoʔ³⁴ V;PROG;PL;1+EXCL;FUT
n⁵ndí⁵hndoʔ³⁴ V;SBJV;SG;3
n⁵ndí⁵hndoʔ³⁴ V;IPFV;PL;3;PRS
n⁵ndí⁵hndoʔ³⁴ V;IPFV;SG;2;PRS
n⁵ndí⁵hndoʔ³⁴ V;PFV;PL;1+INCL;PST
n⁵ndí⁵hndoʔ³⁴ V;PROG;SG;1;FUT
n⁵ndí⁵hndoʔ³⁴ V;IPFV;PL;1+EXCL;PRS
n⁵ndí⁵hndoʔ³⁴ V;PROG;PL;3;PST
n⁵ndí⁵hndoʔ³⁴ V;PROG;SG;3;FUT
n⁵ndí⁵hndoʔ³⁴ V;IRR;PL;1+INCL;FUT
n⁵ndí⁵hndoʔ³⁴ V;PFV;PL;3;PST
n⁵ndí⁵hndoʔ³⁴ V;PROG;SG;3;PST
n⁵ndí⁵hndoʔ³⁴ V;SBJV;PL;1+EXCL
n⁵ndí⁵hndoʔ³⁴ V;PROG;SG;1;PST
n⁵ndí⁵hndoʔ³⁴ V;IRR;PL;1+EXCL;FUT
n⁵ndí⁵hndoʔ³⁴ V;PFV;PL;1+EXCL;PST
n⁵ndí⁵hndoʔ³⁴ V;PROG;SG;2;PST
n⁵ndí⁵hndoʔ³⁴ V;PROG;SG;2;FUT
n⁵ndí⁵hndoʔ³⁴ V;PROG;PL;1+INCL;PST
n⁵ndí⁵hndoʔ³⁴ V;SBJV;PL;3
n⁵ndí⁵hndoʔ³⁴ V;IPFV;PL;1+INCL;PRS
n⁵ndí⁵hndoʔ³⁴ V;IRR;SG;1;FUT
n⁵ndí⁵hndoʔ³⁴ V;IRR;PL;3;FUT
n⁵ndí⁵hndoʔ³⁴ V;SBJV;SG;1
n⁵ndí⁵hndoʔ³⁴ V;IPFV;SG;1;PRS
m⁵ʔmé⁵ V;PROG;PL;1+EXCL;PST
m⁵ʔmé⁵ V;IPFV;SG;1;PRS
m⁵ʔmé⁵ V;IPFV;SG;3;PRS
m⁵ʔmé⁵ V;IRR;PL;3;FUT
m⁵ʔmé⁵ V;PFV;PL;1+INCL;PST
m⁵ʔmé⁵ V;PFV;SG;2;PST
m⁵ʔmé⁵ V;PROG;SG;3;FUT
m⁵ʔmé⁵ V;SBJV;SG;1
m⁵ʔmé⁵ V;PFV;PL;1+EXCL;PST
m⁵ʔmé⁵ V;IPFV;PL;3;PRS
m⁵ʔmé⁵ V;PROG;PL;1+EXCL;FUT
m⁵ʔmé⁵ V;SBJV;SG;3
m⁵ʔmé⁵ V;PROG;SG;2;FUT
m⁵ʔmé⁵ V;PROG;PL;3;PST
m⁵ʔmé⁵ V;IRR;PL;1+INCL;FUT
m⁵ʔmé⁵ V;PROG;SG;1;FUT
m⁵ʔmé⁵ V;PROG;PL;1+INCL;PST
m⁵ʔmé⁵ V;PROG;PL;1+INCL;FUT
m⁵ʔmé⁵ V;SBJV;PL;1+INCL
m⁵ʔmé⁵ V;IRR;SG;3;FUT
m⁵ʔmé⁵ V;SBJV;PL;1+EXCL
m⁵ʔmé⁵ V;PROG;PL;3;FUT
m⁵ʔmé⁵ V;IPFV;PL;1+INCL;PRS
m⁵ʔmé⁵ V;PFV;SG;1;PST
m⁵ʔmé⁵ V;PROG;SG;1;PST
m⁵ʔmé⁵ V;PFV;SG;3;PST
m⁵ʔmé⁵ V;IRR;SG;1;FUT
m⁵ʔmé⁵ V;IPFV;PL;1+EXCL;PRS
m⁵ʔmé⁵ V;PROG;SG;2;PST
m⁵ʔmé⁵ V;SBJV;SG;2
m⁵ʔmé⁵ V;PFV;PL;3;PST
m⁵ʔmé⁵ V;SBJV;PL;3
m⁵ʔmé⁵ V;PROG;SG;3;PST
m⁵ʔmé⁵ V;IRR;SG;2;FUT
m⁵ʔmé⁵ V;IPFV;SG;2;PRS
m⁵ʔmé⁵ V;IRR;PL;1+EXCL;FUT
n⁵ndyʔe³ V;PROG;SG;3;FUT
n⁵ndyʔe³ V;IRR;SG;1;FUT
n⁵ndyʔe³ V;PFV;SG;3;PST
n⁵ndyʔe³ V;PROG;PL;3;PST
n⁵ndyʔe³ V;PFV;PL;1+INCL;PST
n⁵ndyʔe³ V;IPFV;SG;1;PRS
n⁵ndyʔe³ V;PROG;SG;2;PST
n⁵ndyʔe³ V;SBJV;SG;2
n⁵ndyʔe³ V;PROG;SG;3;PST
n⁵ndyʔe³ V;PFV;SG;2;PST
n⁵ndyʔe³ V;PROG;PL;3;FUT
n⁵ndyʔe³ V;PROG;PL;1+INCL;PST
n⁵ndyʔe³ V;SBJV;SG;1
n⁵ndyʔe³ V;IRR;PL;1+EXCL;FUT
n⁵ndyʔe³ V;PROG;PL;1+INCL;FUT
n⁵ndyʔe³ V;SBJV;SG;3
n⁵ndyʔe³ V;SBJV;PL;1+INCL
n⁵ndyʔe³ V;PROG;PL;1+EXCL;FUT
n⁵ndyʔe³ V;IPFV;PL;1+EXCL;PRS
n⁵ndyʔe³ V;IRR;PL;3;FUT
n⁵ndyʔe³ V;IPFV;PL;1+INCL;PRS
n⁵ndyʔe³ V;PROG;SG;1;PST
n⁵ndyʔe³ V;SBJV;PL;1+EXCL
n⁵ndyʔe³ V;PFV;SG;1;PST
n⁵ndyʔe³ V;IPFV;PL;3;PRS
n⁵ndyʔe³ V;IRR;SG;2;FUT
n⁵ndyʔe³ V;IRR;SG;3;FUT
n⁵ndyʔe³ V;PROG;SG;2;FUT
n⁵ndyʔe³ V;SBJV;PL;3
n⁵ndyʔe³ V;IPFV;SG;3;PRS
n⁵ndyʔe³ V;PROG;SG;1;FUT
n⁵ndyʔe³ V;IRR;PL;1+INCL;FUT
n⁵ndyʔe³ V;PFV;PL;1+EXCL;PST
n⁵ndyʔe³ V;PROG;PL;1+EXCL;PST
n⁵ndyʔe³ V;PFV;PL;3;PST
n⁵ndyʔe³ V;IPFV;SG;2;PRS
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;SG;3;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IPFV;PL;1+INCL;PRS
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;SBJV;SG;1
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;SG;2;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;PL;3;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IRR;SG;2;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;SG;3;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;SBJV;PL;1+INCL
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;SBJV;SG;2
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;SBJV;PL;1+EXCL
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;SBJV;SG;3
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;PL;1+INCL;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;PL;1+EXCL;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;SBJV;PL;3
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IRR;PL;3;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;SG;1;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;PL;1+EXCL;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;PL;3;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IRR;PL;1+EXCL;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IRR;SG;3;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PFV;SG;1;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PFV;PL;1+INCL;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PFV;PL;3;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IPFV;SG;1;PRS
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;SG;2;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PFV;PL;1+EXCL;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PFV;SG;2;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IRR;PL;1+INCL;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IPFV;SG;2;PRS
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;SG;1;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IPFV;PL;1+EXCL;PRS
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IRR;SG;1;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PFV;SG;3;PST
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;PROG;PL;1+INCL;FUT
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IPFV;PL;3;PRS
n⁵nduiʔ³ ndá⁵thwènʔ¹ V;IPFV;SG;3;PRS
|
e1cdad04cb2f5d201c99cc99d8b16a62f5b209b6 | 048b7c76423fe27dee2e31a52bae93c95883614e | /macros/periodogram.sci | 33e15af7086d77955d0e82ded63afea87b226d6c | [] | no_license | vu2swz/FOSSEE-Signal-Processing-Toolbox | aa5f283d050be62418dddbf41552f197b9949c4c | d97a4b7e2f0f25fb5cd94bd90a3b822592179d1e | refs/heads/master | 2021-08-19T20:06:19.346872 | 2017-11-27T09:57:21 | 2017-11-27T09:57:21 | null | 0 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 505 | sci | periodogram.sci | function [d,n]=periodogram(a,b,c,d,e)
funcprot(0);
[nargout,nargin]=argn();
select nargin
case 1 then
[d,n]=callOctave('periodogram',a);
case 2 then
[d,n]=callOctave('periodogram',a,b);
case 3 then
[d,n]=callOctave('periodogram',a,b,c);
case 4 then
[d,n]=callOctave('periodogram',a,b,c,d);
case 5 then
[d,n]=callOctave('periodogram',a,b,c,d,e);
else
error("Incorrect no. of Input Arguments");
end
endfunction
|
b3621a546a226622025b5971439a69957bd4c87d | 449d555969bfd7befe906877abab098c6e63a0e8 | /3411/CH10/EX2.5.u2/Ex2_5_u2.sce | 7e6d6b207145d26c8aade847cacfb70fbee6ef95 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 742 | sce | Ex2_5_u2.sce | //Example 2_5_u2
clc();
clear;
//To calculate the no of states for conduction electrons and the average energy interval
n=9.11*10^-31 //units in Kg
E=5*1.6*10^-19 //units in J
v=10^-6 //units in meter^3
h=6.67*10^-34 //units in m^2 kg s^-1
NE=(8*sqrt(2)*%pi*n^1.5*E^0.5*v)/h^3 //units in J^-1
no=NE*0.01*1.6*10^-19 //units in J
printf("Available number of energy states is ")
disp(no)
interval=0.01/no //units in eV
printf("Average energy interval is")
disp(interval)
printf("eV")
//Given in text book available no of energy states is 1.52*10^20 but correct answer is 1.490D+20 and for average energy interval is 7*10^-23 eV but correct answer is 6.709D-23 eV
|
6888acf244874f793341acb4bd905db05a37f832 | 449d555969bfd7befe906877abab098c6e63a0e8 | /1376/CH3/EX3.1/3_1.sci | 528d7892215018d63422d64f505705ad793ec2c5 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 329 | sci | 3_1.sci | // 3.1
clc;
disp('For spring controlled Tc is proportional to theta')
theta=90*(3/5)^2;
printf("Deflection for spring controlled instrument=%.2f degree",theta)
disp('For gravity controlled Tc is proportional to sin(theta)')
theta=asind((3/5)^2);
printf("\nDeflection for gravity controlled instrument=%.2f degree",theta)
|
2b456182477b845e7ec81da1b75b706d6d73e63a | 449d555969bfd7befe906877abab098c6e63a0e8 | /2420/CH7/EX7.9/7_9.sce | 1b244f5bbde746c755261dc5d38447d6b3c38828 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 336 | sce | 7_9.sce | clc
clear
//Initialization of variables
pow=1000 //kw
ms=16000 //lb/hr
P=200 //psia
T=540 //F
//calculations
disp("From mollier charts,")
h1=1290 //Btu/hr
h2=940 //Btu/hr
dh=h1-h2
rate=3413/dh
act=ms/pow
//results
printf("Ideal steam rate = %.2f lb per kw hr",rate)
printf("\n Actual steam rate = %d lb per kw hr",act)
|
ddd12cf46dfe0469e0582ca2ea9ecfe1d7adbefb | 717ddeb7e700373742c617a95e25a2376565112c | /1448/CH8/EX8.1.i/I8_1.sce | f17b708407db6013bb4845617fee2562786c976d | [] | no_license | appucrossroads/Scilab-TBC-Uploads | b7ce9a8665d6253926fa8cc0989cda3c0db8e63d | 1d1c6f68fe7afb15ea12fd38492ec171491f8ce7 | refs/heads/master | 2021-01-22T04:15:15.512674 | 2017-09-19T11:51:56 | 2017-09-19T11:51:56 | 92,444,732 | 0 | 0 | null | 2017-05-25T21:09:20 | 2017-05-25T21:09:19 | null | UTF-8 | Scilab | false | false | 232 | sce | I8_1.sce | clc
//Initialization of variables
ph1=6.37
ph2=10.25
ph3=7.21
ph4=12.67
//calculations
pH1=0.5*(ph1+ph2)
pH2=0.5*(ph3+ph4)
//results
printf("Equilibrium pH in case 1 = ",pH1)
printf("\n Equilibrium pH in case 2 = ",pH2)
|
e4a7a80985dec38a0ed47fc03c15a2484cb69b04 | 8217f7986187902617ad1bf89cb789618a90dd0a | /browsable_source/2.5/Unix-Windows/scilab-2.5/examples/mex-examples/fortran/test.sce | 918a3130aeb9b3492baee459e1551a5e71cf2fc3 | [
"LicenseRef-scancode-public-domain",
"LicenseRef-scancode-warranty-disclaimer"
] | permissive | clg55/Scilab-Workbench | 4ebc01d2daea5026ad07fbfc53e16d4b29179502 | 9f8fd29c7f2a98100fa9aed8b58f6768d24a1875 | refs/heads/master | 2023-05-31T04:06:22.931111 | 2022-09-13T14:41:51 | 2022-09-13T14:41:51 | 258,270,193 | 0 | 1 | null | null | null | null | UTF-8 | Scilab | false | false | 57 | sce | test.sce | exec startup.sce
[p,q,r,s,t]=fmexfunction2([1;2],[3,4])
|
92b6fbe38f72e9112bb3d8f74acef710656ee9cf | 449d555969bfd7befe906877abab098c6e63a0e8 | /3875/CH9/EX9.3/Ex9_3.sce | ec8796bf93fe93a537d4904f2863c58626543817 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 274 | sce | Ex9_3.sce | clc;
clear;
n1=1.48 //core refractive index
delta=0.05 //fractional refractive index
//calculation
NA=n1*sqrt(2*delta) //numerical aperture
i_a=asind(NA)
mprintf("\nThe numerical aperture is = %1.3f\n",NA)
mprintf("The acceptance angle is = %2.1f degree.",i_a)
|
0f4613d9701bff5652de8db6398ec331f2efdac1 | 8217f7986187902617ad1bf89cb789618a90dd0a | /browsable_source/2.3.1/Unix-Windows/scilab-2.3/Win95-util/DllSci/tdll.sci | 8f2ae4bf4d8735d9797d0a35e70102388b5b9f55 | [
"MIT",
"LicenseRef-scancode-warranty-disclaimer",
"LicenseRef-scancode-public-domain"
] | permissive | clg55/Scilab-Workbench | 4ebc01d2daea5026ad07fbfc53e16d4b29179502 | 9f8fd29c7f2a98100fa9aed8b58f6768d24a1875 | refs/heads/master | 2023-05-31T04:06:22.931111 | 2022-09-13T14:41:51 | 2022-09-13T14:41:51 | 258,270,193 | 0 | 1 | null | null | null | null | UTF-8 | Scilab | false | false | 95 | sci | tdll.sci |
host("make");
link('libtdll.dll",'doit','c');
[a,b]=fort('doit',1,1,'d',2,2,'d','sort',1,2);
|
486c4ce20e605ce38de02f52ec3a246450b96998 | be72b348d2bbd0cd916ee42daf3151ca8d3d6fc5 | /Fourier-Transform-in-Image-Formation/grating.sce | 1787c631c939d5a7a90d1527bc19d57f67fd9d98 | [] | no_license | albertyumol/Image-Processing-on-Scilab | f9b859b35cd4279abaa79aef65598425a7ef37c9 | 33032c819026222dc75b8364b81012986a5e46ab | refs/heads/master | 2020-04-26T15:40:55.463187 | 2019-12-06T16:25:15 | 2019-12-06T16:25:15 | 173,654,065 | 3 | 0 | null | null | null | null | UTF-8 | Scilab | false | false | 346 | sce | grating.sce | //Grating along x direction
nx = 128; ny = 128;
x = linspace(-10,10,nx);
y = linspace(-10,10,ny);
[X,Y] = ndgrid(x,y);
A = squarewave(Y);
//a = %pi/4
//r = [cos(a) -sin(a);
// sin(a) cos(a)];
//A = A*r;
f = scf(0);
grayplot(x,y,A);
imwrite(A,'C:\Users\csrc-lab03\Desktop\Activity5\grating.jpg');
f.color_map = graycolormap(32);
|
855bcc6da0b355ed4af9493979314f709091dcc5 | 449d555969bfd7befe906877abab098c6e63a0e8 | /69/CH3/EX3.1/3_1.sce | 1150f198dcc91ac37ee5df50e8708d355e67d554 | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 396 | sce | 3_1.sce | clear; clc; close;
//part a
Ie = 3*10^(-3);
Vcb = 10;
Ic = Ie;
disp(Ic,'Ic (A):');
//part b
Vcb = 2;
Ie = 3*10^(-3);
Ic = Ie;
disp(Ic,'No effect of changing Vcb & Ic remains same, Ic(A) is : ');
//part c
Ic = 4*10^(-3);
Vcb = 20;
Ie = Ic;
Vbe = 0.74;
disp(Vbe,'Vbe(volts) is :');
//part d
Ic = 4*10^(-3);
Ie = Ic;
Vbe = 0.7;
disp(Vbe,'Vbe(volts) in this case is : ');
|
b6cedc5320487ded98333eca90fb77568e68745e | 449d555969bfd7befe906877abab098c6e63a0e8 | /2276/CH7/EX7.8/chapter7_ex8.sce | c00c5862c8fe7ec2843a249b29bd6b1e608a671e | [] | no_license | FOSSEE/Scilab-TBC-Uploads | 948e5d1126d46bdd2f89a44c54ba62b0f0a1f5e1 | 7bc77cb1ed33745c720952c92b3b2747c5cbf2df | refs/heads/master | 2020-04-09T02:43:26.499817 | 2018-02-03T05:31:52 | 2018-02-03T05:31:52 | 37,975,407 | 3 | 12 | null | null | null | null | UTF-8 | Scilab | false | false | 899 | sce | chapter7_ex8.sce | clc
clear
//input
d=125;//power taken by an industrial load in kilowatts
pf=0.6;//power factor
v=415;//supply voltage in volts
f=50;//supply frequency in hertz
//calculations
phii=acos(pf);//initial phase angle in radians
kVAo=d/pf;//original kVA
kvaro=d*tan(phii);//original kvar
//for 0.9power factor
phif=acos(0.9);//phase angle in radians
kvarf=d*tan(phif);//final kvar
kvarc=kvaro-kvarf;//capacitor kvar
c1=(kvarc*(10^3)*(10^6))/(v*v*2*%pi*f);//capacitance in microfarad
kVAf=d/0.9;//final kVA
kVAr=kVAo-kVAf;//reduction in kVA
//for unity power factor
kvarC=kvaro;//capacitor kvar
c2=(kvarC*(10^3)*(10^6))/(v*v*2*%pi*f);//capacitance in microfarad
kVAF=d;//final kVA
kVAR=kVAo-kVAF;//reduction in kVA
//output
mprintf('the required values of capacitance are %3.0f uF and %3.0f uF and the respective savings in kVA are %3.1f kVA and %3.1f kVA',c1,c2,kVAr,kVAR )
|
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