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|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
f71bc756274d32895978d0740797afba7bdbec8e
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/491/CH12/EX12.7/12_7.sce
|
87db6c2a134fb535489b7d59cd5bcf92947db876
|
[] |
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
| 777
|
sce
|
12_7.sce
|
Ix = 29.29e06; // Moment of inertia of crosssection about x-axis
Iy = 5.667e06; // Moment of inertia of crosssection about y-axis
Ixy = -9.336e06; // Moment of inertia of crosssection
tp1 = (atand(-(2*Ixy)/(Ix-Iy)))/2 ; // Angle definig a Principle axix
tp2 = 90 + tp1 // ""
disp("degree",tp1,"The Principle axis is inclined at an angle")
disp("degree",tp2,"Second angle of inclination of Principle axis is")
Ix1 = (Ix+Iy)/2 + ((Ix-Iy)/2)*cosd(tp1) - Ixy*sind(tp1) ; // Principle Moment of inertia corresponding to tp1
Ix2 = (Ix+Iy)/2 + ((Ix-Iy)/2)*cosd(tp2) - Ixy*sind(tp2) ; // Principle Moment of inertia corresponding to tp2
disp("mm^4",Ix1,"Principle Moment of inertia corresponding to tp1")
disp("mm^4",Ix2,"Principle Moment of inertia corresponding to tp2")
|
5344a1994bbadf403947de90e5691326d8cfeca7
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/647/CH5/EX5.17/Example5_17.sce
|
c22cdc24314caa2e97db60dd69229ac1538d2d06
|
[] |
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
|
Example5_17.sce
|
clear;
clc;
// Example: 5.17
// Page: 170
printf("Example: 5.17 - Page: 170\n\n");
// Solution
//*****Data*****//
deff('[y] = Cp(T)','y = 7.25 + 2.28*10^(-3)*T');
T1 = 273 + 137;// [K]
T2 = 273 + 877;// [K]
//************//
deltaS = integrate('Cp(T)/T','T',T1,T2);// [cal/K]
printf("Change in Entropy is %.3f cal/K",deltaS);
|
b129c8c98e6beecd05a6be2a55049d0e2d62a45c
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1883/CH5/EX5.7.7/Example5_21.sce
|
214c2daf7beb2b06d0e78220c093001ce6421aa1
|
[] |
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
| 693
|
sce
|
Example5_21.sce
|
//Chapter-5,Example5_7_7,pg 5-29
//By Heisenberg's uncertainty principle
//(delta_E*delta_t)>=h/(4*%pi)
//therefore (h*c*delta_wavelength*delta_t/wavelength^2) >= h/(4*%pi)
wavelength=546*10^-9 //wavelength of spectral line
c=3*10^8 //velocity of light in air
delta_wavelength=10^-14 //width of spectral line
delta_t=wavelength^2/(4*%pi*c*delta_wavelength)
printf("\nThe time spent by an atom in the excited state \n")
disp(delta_t)
printf("sec\n")
|
0e771eb3cf2c85ea6ff3f087fc6fe0295718c8f9
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1979/CH11/EX11.5/Ex11_5.sce
|
938a93d334fa65b122e09c423077b622de72cfad
|
[] |
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
| 710
|
sce
|
Ex11_5.sce
|
//chapter-11 page 505 example 11.5
//==============================================================================
clc;
clear;
//For a military radar
Pt=2500000;//power output in W
f=5*10^9;//frequency of radar in H
c=3*10^8;//Velocity of light in m/sec
D=5;//antenna diameter in m
B=1.6*10^6;//receiver bandwidth in Hz
s=1;//radar cross sectional area in sq m
NF=12;//noise figure in dB
//CALCULATION
w=c/f;//wavelength in m
F=10^(NF/10);//noise figure
Rmax=(48*((Pt*s*D^4)/(B*(F-1)*w^2))^(1/4));//Maximum detection range in km
//OUTPUT
mprintf('\nMaximum detection range of a radar is Rmax=%3.0f km',Rmax);
//=========================END OF PROGRAM===============================
|
c3170dd75daa7eb2ed4ebc6e1dbaf18043ff995c
|
b7c000944f3bdb1516cb63cc765742ab020019eb
|
/diffImplicitborder.sce
|
f6b0509a9867c3d7e6aff5754997c556f03a7131
|
[] |
no_license
|
arngucci/TP2
|
42411f06cce1b079fe9e8738716864638385376e
|
7dc248be305ccc420b57224cbe33766e96ef4353
|
refs/heads/master
| 2023-01-19T06:06:47.517276
| 2020-11-19T09:14:49
| 2020-11-19T09:14:49
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 628
|
sce
|
diffImplicitborder.sce
|
L=100;
Ttot=50;
dx=1;
dt=0.1;
D=6;
T=round(Ttot/dt);
//initial gaussian spatial distribution
x0=L/2;
d=5;
A=10;
x=1:L;
init=A*exp(-(x-x0).^2/(2*d^2));
U=zeros(L,T);
U(:,1)=init';
F=D*dt/dx^2;
//Numerical simulation of the diffusion process (implicit Euler method)
//Building the diffusion matrix
A=zeros(L,L);
A(1,1:2)=[1+F -F];
A(L,(L-1):L)=[-F 1+F];
for i=2:(L-1)
A(i,i-1)=-F;
A(i,i)=1+2*F;
A(i,i+1)=-F;
end
iA=inv(A);
for n=1:T-1
b=U(:,n);
U(:,n+1)=iA*b;
end
figure
set(gca(),"auto_clear","off");
tgraph=1:(T/10-1):T;
for i=1:11
plot((1:L)',U(:,tgraph(i)))
end
set(gca(),"auto_clear","on");
|
38dfc634db9e6e039d41fcde30e6d9eea25b61f3
|
b80969c9d72c732b0153d0de2b8fd28dc10d8a16
|
/Biologie/Site/sauvegarde/28.07.2016/www/Documents/simulation/initation_scilab/ex18.sci
|
5ee4960c0e141b98e7f6c3de565c3b59df3f1101
|
[] |
no_license
|
adamdepossylux/stem_cells
|
6a2596a0734e3604b570cfdaa1e6cb798d13d7b7
|
e1ffdf24a223fea3a3606a0bd262067edc81f5b9
|
refs/heads/master
| 2020-04-01T17:26:21.772875
| 2017-05-10T15:15:09
| 2017-05-10T15:15:09
| 61,795,551
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 145
|
sci
|
ex18.sci
|
x=linspace(-2,2,101)
plot2d(x,-x.^2)
plot2d(x,exp(-x.^2),4)
plot2d(x,-x.^2,-3)
plot2d(x,exp(-x.^2),5)
legend('x','exp(-x^2)')
title('exp(-x^2)')
|
78fa62a93faee85036709cf54131b6d0463d6aa0
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1583/CH3/EX3.9/NNID_Ex_3_9.sce
|
336dc8c5eebe255ba9a77f372f6c6da86f04d2a4
|
[] |
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
| 580
|
sce
|
NNID_Ex_3_9.sce
|
clc
//Chapter 3:Network noise and intermodulation distortion
//example 3.8 page no 84
//given
NF=4//noise figure in dB
B=3*10^3//bandwidth
Rs=50//sourse resistance
k=1.38*10^-23//Boltzmmans constant
T=290//tempreture
NFa=20//antenna noise figure
NFr=10//receiver noise figure
Fa=10^(NFa/10)//antenna noise factor
Fr=10^(NFr/10)//receiver noise factor
S_N=10//output signal to noise ratio
Si_W=(S_N)*(Fa+Fr-1)*k*T*B//available input power in Watts
Ei=sqrt(Si_W*4*Rs)//minimum detectable signal
mprintf('the minimum detectable signal is %f uV',round(Ei*1e6*10)/10)
|
d8fcd8eeedd384bd59689a42100c011f99dd364c
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/564/CH9/EX9.1/9_1.sce
|
1ddde273fb71207f33561485cf6a336e4b0ddda0
|
[] |
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
| 635
|
sce
|
9_1.sce
|
pathname=get_absolute_file_path('9_1.sce')
filename=pathname+filesep()+'9_1data.sci'
exec(filename)
alpha= atan(((1+ t*d/(2*Af))/(1+ t*b/As))^0.25);//α
Ft=(W*z/d)+(W/(2*tan(alpha)));//FT
printf("\nFT: %f N",Ft);
Mmax= (W*tan(alpha)*b^2)/(12*d);
Smax= (Mmax/ESM)+(Ft/Af);//σ max
printf("\nMaximum Stress in Flange: %f N/mm^2",Smax);
P=(W*b*tan(alpha))/d;
if(b<1.5*d) then//le
Le=d/((4-(2*b/d))^0.5);
else
Le=d;
end
Pcr= ((%pi^2)*E*I)/(Le^2);
printf("\nPcr: %f KN",Pcr);
printf("\nP: %f KN",P);
if(P<Pcr) then
printf("\nstiffener will not buckle")
else
printf("\nstiffener will buckle")
end
|
fb0d385d7ab027a12754cf12c63b885d24400e16
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2240/CH4/EX3.1/EX3_1.sce
|
89178d9188e93afc99e7672efa9839724969febc
|
[] |
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
| 356
|
sce
|
EX3_1.sce
|
// Grob's Basic Electronics 11e
// Chapter No. 03
// Example No. 3_1
clc; clear;
// A heater with the resistance of 8 Ohms is connected across the 120-V power line. How much is current I?
// Given data
V = 120; // Voltage of Power line=120 Volts
R = 8; // Heater Resistance=8 Ohms
I = V/R;
disp (I,'The Current I in Amps')
|
a1232fe460d021079b709185d97e2744e14a9740
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3487/CH4/EX4.1/Ex4_1.sce
|
915af16c8324f476401149878f93d041b5a64020
|
[] |
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
| 415
|
sce
|
Ex4_1.sce
|
//Chapter 4,Example 4.1 Page 144
clc
clear
//Determine the voltge when S=2 cm
S = 0.2 // cm
Vb = 24.22*S+6.08*sqrt(S)
printf (" Vb when S = 2 cm is %f kV \n ",Vb)
//Determine the voltge when S=1.5 cm
S = 1.5 // cm
Vb = 24.22*S+6.08*sqrt(S)
printf (" Vb when S = 1.5 is %f kV \n ",Vb)
b = 75
t = 35
D = (3.92*b)/(273+t)
printf (" Air density correction factor= %f \n ",D)
//Answer may vary due to round off error
|
9d649484aac409b247afadb7760c868ab57fd5b0
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1475/CH6/EX6.15/Example_6_15.sce
|
098ed9abe480f22bfcc6a3a3e8f73688e81802c6
|
[] |
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
| 881
|
sce
|
Example_6_15.sce
|
// Example 6.15 Compute the trend by the method of moving averages
clc;
clear;
Year=[1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 ];
Val=[54 40.5 47.0 48.5 42.9 42.1 36.6 42.7 45.7 45.1 37.8];
MV1=0;
MV2=0;
MV10=0;
MV11=0;
MV3=Val(1)+Val(2)+Val(3)+Val(4);
MV4=Val(2)+Val(3)+Val(4)+Val(5);
MV5=Val(3)+Val(4)+Val(5)+Val(6);
MV6=Val(4)+Val(5)+Val(6)+Val(7);
MV7=Val(5)+Val(6)+Val(7)+Val(8);
MV8=Val(6)+Val(7)+Val(8)+Val(9);
MV9=Val(7)+Val(8)+Val(9)+Val(10);
MV10=Val(8)+Val(9)+Val(10)+Val(11);
MVT=[MV1 MV2 MV3 MV4 MV5 MV6 MV7 MV8 MV9 MV10 MV11];
T1=0;
T2=0;
T10=0;
T11=0;
T3=MV3+MV4;
T4=MV4+MV5;
T5=MV5+MV6;
T6=MV6+MV7;
T7=MV7+MV8;
T8=MV8+MV9;
T9=MV9+MV10;
T=[T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11];
MA=T./8;
disp(MA,"4 year Moving Average",T,"2 year Moving Average Total",MVT,"4 year Moving Average Total",Val,"Values =",Year,"Years are ");
|
374ab06af014987857489b26e350963f24d0e53e
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1301/CH4/EX4.7/ex4_7.sce
|
c33970ffd1d14a9b7e0bfdd7318633b015ec2cfc
|
[] |
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
| 590
|
sce
|
ex4_7.sce
|
clc;
g=9.8; //gravitaional constant in metre/sec
r=0.5; //radius in metre
m=1; //mass in kg
v=5; //velocity in metre/sec
F=(m*v*v)/r; //calculationg centripetal force in Newton
w=m*g; //calculating weight in Newton
T=F-w; //calculating Tension in string at top position in Newton
disp(T,"Tension in the string at the top position in Newton = "); //displaying result
T=F+w; //calculating Tension at bottom of string in Newton.
disp(T,"Tension in the string at the bottom position in Newton = "); // displaying Tension at bottom of string in Newton.
|
f956ac543f9d4caf68c6f562f84c06e47b543968
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2606/CH4/EX4.16/ex4_16.sce
|
035107bbd87e05aaa4f9e12b17a564e3fc10e690
|
[] |
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
| 385
|
sce
|
ex4_16.sce
|
//Page Number: 4.18
//Example 4.15
clc;
//Given
//x(t)=10cos(wct+3sinwmt)
//Comparing with standard equation of fm
B=3;
fm=1D+3; //hz
fb=2*(B+1)*fm;
//B is inversaly proportional to fm
//(a)fm is doubled
Ba=B/2;
fma=2*fm;;
fba=2*(Ba+1)*fma;
disp(fba,"fb with 2fm: ");
//(b)fm is one halved
Bb=2*B;
fmb=fm/2;
fbb=2*(Bb+1)*fmb;
disp(fbb,"fb with 0.5fm: ");
|
9966f8f9d3d8476a3af44db50ee81a783f994ae3
|
52cff1a2ef2292f8b9acf18dcfe1d4b0df75c558
|
/LAB 8/60002190043_SCILAB 8 (1).sce
|
4751c1d30fa1bb9e6205d188ec1563b50641205f
|
[] |
no_license
|
Hetankshi/SCILAB
|
692a3abc71e6686f40745d69a66e4511db244491
|
424d4cc3459bb535e2f6793249f6a583374820ad
|
refs/heads/main
| 2023-01-16T05:39:22.830875
| 2020-11-25T12:23:14
| 2020-11-25T12:23:14
| 315,916,735
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 247
|
sce
|
60002190043_SCILAB 8 (1).sce
|
//plot the values of sin2x+sin3x+sin4x+sin5x+...
//vary x from 0 to 2pi i.e vary x from 0 to 6.28 take intervals as 0.01
x=0:0.001:6.28
y=sin (2*x)
plot2d3 (y)
figure;
y=sin (3*x)
plot2d3 (y)
figure;
y=sin (4*x)
plot2d3 (y)
figure;
|
c85efa4e44bc8b87891e8724b049f6cacec3c313
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1073/CH3/EX3.33/3_33.sce
|
9735551d9202ea11f1020159c4767fecfdf727af
|
[] |
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
| 518
|
sce
|
3_33.sce
|
clc;
clear;
//Example 3.33
k=0.03406 //[W/(m/K)]
Beta=2.47*10^-3 //K^-1
Npr=0.687 //Prandtl number
v=26.54*10^-6 //m^2/s
g=9.81 //[m/s^2]
Tw=523 //[K]
T_inf=288 //[K]
dT=Tw-T_inf //[K]
D=0.3048 //[m]
Ngr=(g*Beta*dT*(D^3))/(v^2) //Grashof number
Nra=Ngr*Npr
//For Nra less than 10^9,we have for horizontal cylinder
Nnu=0.53*(Nra^(1.0/4.0)) //Nusselt number
h=Nnu*k/D //[W/sq m.K]
Q_by_l=h*%pi*D*dT; //W/m
printf("Heat loss of heat transfer per meter lengh is %f W/m",Q_by_l);
|
185e19e6da6b0dfbc90f2913e8e0f68b49c0edf3
|
99b4e2e61348ee847a78faf6eee6d345fde36028
|
/Toolbox Test/strips/strips7.sce
|
3f342c1e14ae054179682a48bbf5abc24163aa36
|
[] |
no_license
|
deecube/fosseetesting
|
ce66f691121021fa2f3474497397cded9d57658c
|
e353f1c03b0c0ef43abf44873e5e477b6adb6c7e
|
refs/heads/master
| 2021-01-20T11:34:43.535019
| 2016-09-27T05:12:48
| 2016-09-27T05:12:48
| 59,456,386
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 276
|
sce
|
strips7.sce
|
//too many i/p args are passed to the function
scale=2;
fs = 1000;t = 0:1/fs:2;
//x = vco(sin(2*pi*t),[10 490],fs);
strips(x,0.25,fs,scale,1);
//output
// !--error 58
//Wrong number of input arguments.at line 6 of exec file called by :
//OW!!/strips7.sce', -1
//
|
3e21f0003597e0af2c3b1b9dadf15da170145b06
|
584105ff5b87869494a42f632079668e4c3f82de
|
/Help-files/convertPointsToHomogeneous.sci~
|
80f177825123955e439df66da9ba70ecfc619677
|
[] |
no_license
|
kevgeo/FOSSEE-Computer-Vision
|
0ceb1aafb800580498ea7d79982003714d88fb48
|
9ca5ceae56d11d81a178a9dafddc809238e412ba
|
refs/heads/master
| 2021-01-17T21:11:31.309967
| 2016-08-01T14:45:40
| 2016-08-01T14:45:40
| 63,127,286
| 6
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 623
|
convertPointsToHomogeneous.sci~
|
// Converts the points from Euclidean to homogeneous type or space.
//
// Calling Sequence
// pts_homogenous = convertPointsToHomogeneous(pts_euclidean);
//
// Parameters
// pts_euclidean : vector of N points in Euclidean space
//
// Description
// The function converts vector of N points in Euclidean space to a vector of N+1 dimensional points in homogenous space.
//
// Examples
// //N dimensional points in Euclidean space
// pts_euclidean = [20 12 11 40 34 14];
// //Getting N+1 dimensional points in homogenous space
// pts_homogenous = convertPointsToHomogeneous(pts_euclidean);
//
// Author
// Kevin George
//
|
|
f058d523dd170d073b0496dfcf344a99b1e56a9b
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/650/CH8/EX8.4/4.sce
|
d31cc4e3936c8d98c74e7810e5e9a2840f78d2d1
|
[] |
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
| 438
|
sce
|
4.sce
|
clc
rho=867; // kg/m^3
Q=12/3600; // m^3/s
u=7.5*10^(-4); // Ns/m^2
L=200; // m
H=10; // m
g=9.81; // m/s^2
d=(H*2*g/(4*0.079*(4*rho*Q/%pi/u)^(-1/4)*L*(4*Q/%pi)^2))^(-4/19);
disp("Internal diameter of the pipeline =")
disp(d)
disp("m")
Re=4*rho*Q/%pi/d/u;
disp("Re =")
disp(Re)
disp("The value of Reynolds number lies between 4000 and 10^5, confirming the validity of using the Blasius equation for smooth-walled pipes")
|
41aae324cea6288ba59df50a627ace4d3f18b330
|
99b4e2e61348ee847a78faf6eee6d345fde36028
|
/Toolbox Test/stmcb/stmcb1.sce
|
864c41dd7f49076d9b4e5c7bbf245d71a807e332
|
[] |
no_license
|
deecube/fosseetesting
|
ce66f691121021fa2f3474497397cded9d57658c
|
e353f1c03b0c0ef43abf44873e5e477b6adb6c7e
|
refs/heads/master
| 2021-01-20T11:34:43.535019
| 2016-09-27T05:12:48
| 2016-09-27T05:12:48
| 59,456,386
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 512
|
sce
|
stmcb1.sce
|
h=[0.000340537652720128
0.00326215824060921
0.0148577582806899
0.0432245731900713
0.0910890792168420
0.149260671713139
0.198484121887318
0.219008839463434
0.200744867213037
0.147879438719692];
[b,a]=stmcb(h,4,4);
disp(b);
disp(a);
//output
//
// column 1 to 4
//
// 0.0003405 0.0019918 0.0047235 0.0055189
//
// column 5
//
// 0.0030455
//
//
// column 1 to 4
//
// 1. - 3.7282406 5.9347319 - 4.8245702
//
// column 5
//
// 1.7318821
//
|
7fb31cdea4de5f406fd5b5ee8eb43389c30a5caf
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/998/CH29/EX29.11/Ex11.sce
|
3570865eb71090ef1a20c5c21dedf08cb56a48f4
|
[] |
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
| 279
|
sce
|
Ex11.sce
|
//Ex:11
clc;
clear;
close;
eirp=21;//Eirp in db
g_r=50.5;//Receiving antenna gain in db
y=2.727*10^(-2);//Wavelength in m
h=4*10^7;//Height in m
p_l=20*log(4*%pi*h/y)/log(10);//Path loss in db
p_r=eirp+g_r-p_l;//received power in db
printf("Received power =%f db",p_r);
|
42ca9d49f4e84f9535e75aee9c65ff55803c2343
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/608/CH44/EX44.14/44_14.sce
|
4a0ca40e9fc6bbe1f665208bcf5005da9e055e5b
|
[] |
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
| 622
|
sce
|
44_14.sce
|
//Problem 44.14: A long transmission line has a characteristic impedance of 500 - j40 ohm and is terminated in an impedance of (a) 500 + j40 ohm and (b) 600 + j20 ohm. Determine the magnitude of the reflection coefficient in each case.
//initializing the variables:
Zo = 500 - %i*40; // in ohm
ZR1 = 500 + %i*40; // in ohm
ZR2 = 600 + %i*20; // in ohm
//calculation:
//reflection coefficient
p1 = (Zo - ZR1)/(Zo + ZR1)
p2 = (Zo - ZR2)/(Zo + ZR2)
p1mag = (real(p1)^2 + imag(p1)^2)^0.5
p2mag = (real(p2)^2 + imag(p2)^2)^0.5
printf("\n\n Result \n\n")
printf("\n reflection coefficient (a)%.3f and (b)%.3f",p1mag, p2mag)
|
d92b59457931aa42f1b287fa8942c66403238cea
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2207/CH6/EX6.5.3/ex_6_5_3.sce
|
4b305859bd53fdc909f3b14ab15e3e87e20e4230
|
[] |
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
| 457
|
sce
|
ex_6_5_3.sce
|
//Example 6.5.3: Duty Cycle,Average Load voltage and RMS Load Voltage
clc;
clear;
close;
format('v',6)
//given data
V=200;// in volts
T_on=500*10^-6;
f=1*10^3;// in Hz
D=T_on*f;
disp("part (a)")
disp("duty cycle is "+string(D)+" or "+string(D*100)+"%")
disp("part (b)")
VL_dc=D*V;
disp(VL_dc,"Average Load Voltage,(volts) = ")
disp("part (c)")
VL_rms=sqrt(D)*V;
disp(VL_rms,"RMS Load Voltage,VL_rms(volts) = ")
//part c answer is calculated wrong in book
|
063ac9eb9b3a98a155f35352cd4ffbf5ece8bfa2
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3542/CH5/EX5.7/Ex5_7.sce
|
bd254cc3015b1563e9189ac60cfbc2fc11b07b20
|
[] |
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
| 1,104
|
sce
|
Ex5_7.sce
|
// Example no 5.7
// To compute the positive-going lvel crossing rate and maximum velocity of mobile
// Page no. 224
clc;
clear all;
// Given data
rho=1; // Value of normalized level of fading amplitude to rms amplitude
fm=20; // Maximum Doppler frequency in Hz
fc=900*10^6; // Carrier frequency in Hz
c=3*10^8; // Speed of ligth in air in m/s
// The positive-going level crossing rate
NR=sqrt(2*%pi)*fm*rho*exp(-rho^2); // Number of zero level crossings per second
lambda=c/fc; // Carrier wavelength
// The maximum velocity of mobile
v=fm*lambda; // Maximum velocity of mobile in m/s
v=v*(18/5); // Maximum velocity of mobile in km/hr
// Displaying the result in command window
printf('\n The positive-going level crossing rate = %0.2f crossings per second',NR);
printf('\n The maximum velocity of mobile = %0.0f Km/Hr',v);
|
0f848ef805d79aadb7318b7be32f5caed16f9751
|
bacd6919260d728f4316702bbe1edf811810bede
|
/legacy/33/console/Untitled3.sce
|
829b2590771da85a4e4e915bbea45d1a210db977
|
[] |
no_license
|
vopl/sp
|
332d8c2ff536fc5d8772ff2f3fbeca9b50c47641
|
a4313f4d7af47cc3132d7546947d4d668c7e487e
|
refs/heads/master
| 2020-04-16T02:09:36.036424
| 2016-10-05T18:08:30
| 2016-10-05T18:08:30
| 65,293,458
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 51,871
|
sce
|
Untitled3.sce
|
arr = [
1.10861
1.21569
1.3216
1.42662
1.53105
1.63489
1.73843
1.84168
1.94434
2.047
2.14937
2.25144
2.35351
2.45528
2.55676
2.65854
2.76002
2.8612
2.96239
3.06357
3.16476
3.26594
3.36683
3.46772
3.56861
3.6695
3.77039
3.87099
3.97188
4.07247
4.17306
4.27366
4.37425
4.47485
4.57545
4.67604
4.77634
4.87694
4.97724
5.07783
5.17813
5.27872
5.37902
5.47932
5.57963
5.68022
5.78052
5.88082
5.98112
6.092124872
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12.33985466
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22.42431709
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22.62600638
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390.2073052
390.3081505
390.4089959
390.5098412
390.6106866
390.7115319
390.8123773
390.9132226
391.014068
391.1149133
391.2157587
391.316604
391.4174494
391.5182947
391.6191401
391.7199854
391.8208308
391.9216761
392.0225215
392.1233668
392.2242122
392.3250575
392.4259029
392.5267482
392.6275936
392.7284389
392.8292843
392.9301296
393.030975
393.1318204
393.2326657
393.3335111
393.4343564
393.5352018
393.6360471
393.7368925
393.8377378
393.9385832
394.0394285
394.1402739
394.2411192
394.3419646
394.4428099
394.5436553
394.6445006
394.745346
394.8461913
394.9470367
395.047882
395.1487274
395.2495727
395.3504181
395.4512634
395.5521088
395.6529541
395.7537995
395.8546448
395.9554902
396.0563355
396.1571809
396.2580262
396.3588716
396.4597169
396.5605623
396.6614076
396.762253
396.8630983
396.9639437
397.064789
397.1656344
397.2664797
397.3673251
397.4681704
397.5690158
397.6698611
397.7707065
397.8715518
397.9723972
398.0732425
398.1740879
398.2749332
398.3757786
398.4766239
398.5774693
398.6783146
398.77916
398.8800053
398.9808507
399.081696
399.1825414
399.2833867
399.3842321
399.4850774
399.5859228
399.6867681
399.7876135
399.8884588
399.9893042
400.0901495
400.1909949
400.2918402
400.3926856
400.4935309
400.5943763
400.6952216
400.796067
400.8969123
400.9977577
401.098603
401.1994484
401.3002937
401.4011391
401.5019844
401.6028298
401.7036751
401.8045205
401.9053658
402.0062112
402.1070565
402.2079019
402.3087473
402.4095926
402.510438
402.6112833
402.7121287
402.812974
402.9138194
403.0146647
403.1155101
403.2163554
403.3172008
403.4180461
403.5188915
403.6197368
403.7205822
403.8214275
403.9222729
404.0231182
404.1239636
404.2248089
404.3256543
404.4264996
404.527345
404.6281903
404.7290357
404.829881
404.9307264
405.0315717
405.1324171
405.2332624
405.3341078
405.4349531
405.5357985
405.6366438
405.7374892
405.8383345
405.9391799
406.0400252
406.1408706
406.2417159
406.3425613
406.4434066
406.544252
406.6450973
];
function y=pp(x)
y = 1;
for i=1:40;//size(arr,1) do
y = y .* (1-(x-1)/(arr(i)-1));
end;
endfunction;
x = 0.9999:0.01:5;
clf;
y = pp(x);
plot(x, y.^0.1 .*sign(y));
|
6cc56f7a2f18f1fcd69ee97f24b17532e8d5293a
|
e0124ace5e8cdd9581e74c4e29f58b56f7f97611
|
/3913/CH6/EX6.3/Ex6_3.sce
|
cd626a52ec6de0dccea2c772f7c5eaf89faeec5d
|
[] |
no_license
|
psinalkar1988/Scilab-TBC-Uploads-1
|
159b750ddf97aad1119598b124c8ea6508966e40
|
ae4c2ff8cbc3acc5033a9904425bc362472e09a3
|
refs/heads/master
| 2021-09-25T22:44:08.781062
| 2018-10-26T06:57:45
| 2018-10-26T06:57:45
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 560
|
sce
|
Ex6_3.sce
|
//Chapter 6 : Linear Mappings
//Example 6.15
//Scilab 6.0.1
//Windows 10
clear;
clc;
f100_1=(1/2)*(1)+(1/2)*(0)-(1/2)*(2)
f100_2=(1/2)*(2)+(1/2)*(0)-(1/2)*(1)
mprintf("f(1,0,0)=(%f,%f)",f100_1,f100_2)
f010_1=(1/2)*(1)+(1/2)*(2)
f010_2=(1/2)*(2)+(1/2)*(1)
mprintf("\n f(0,1,0)=(%f,%f)",f010_1,f010_2)
f001_1=-(1/2)*(1)+(1/2)*(2)
f001_2=-(1/2)*(2)+(1/2)*(1)
mprintf("\n f(0,0,1)=(%f,%f)",f001_1,f001_2)
mprintf("\n f(x,y,z)=x(%f,%f)+y(%f,%f)+z(%f,%f)",f100_1,f100_2,f010_1,f010_2,f001_1,f001_2)
mprintf("\n =((1/2)(-x+3y+z),(1/2)(x+3y-z))")
|
0a713b6f66ea98439dc40fdd1e4cdfc40d03d3d7
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1820/CH4/EX4.9/Example4_9.sce
|
c30e58801b7f870cf34fc6e13c2ff6004daed1b8
|
[] |
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
| 979
|
sce
|
Example4_9.sce
|
// ELECTRIC POWER TRANSMISSION SYSTEM ENGINEERING ANALYSIS AND DESIGN
// TURAN GONEN
// CRC PRESS
// SECOND EDITION
// CHAPTER : 4 : OVERHEAD POWER TRANSMISSION
// EXAMPLE : 4.9 :
clear ; clc ; close ; // Clear the work space and console
// GIVEN DATA
L = 2.60 * 10^-3 ; // Inductance of line in H/mi
R = 0.1858 ; // Resistance of line in Ω/mi
C = 0.012 * 10^-6 ; // Capacitance in F/mi
kV = 138 ; // Transmission line voltage in kV
Z_c1 = 469.60085 // Characteristic impedance of line in Ω . Obtained from example 4.6
// CALCULATIONS
Z_c = sqrt(L/C) ; // Approximate value of surge Impedance of line in ohm
SIL = kV^2/Z_c ; // Approximate Surge impedance loading in MW
SIL1 = kV^2/Z_c1 ; // Exact value of SIL in MW
// DISPLAY RESULTS
disp("EXAMPLE : 4.9 : SOLUTION :-") ;
printf("\n Approximate value of SIL of transmission line , SIL_app = %.3f MW\n",SIL) ;
printf("\n Exact value of SIL of transmission line , SIL_exact = %.3f MW\n",SIL1) ;
|
c0d56485893167c7b2445b572fafb9793ca81d4d
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/746/DEPENDENCIES/3_03.sci
|
c2fd3768594c98f61ca496eaf70836728779cca9
|
[] |
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
| 304
|
sci
|
3_03.sci
|
//Acceleration due to gravity(in ft/sec^2):
g=32.2;
//Specific gravity of mercury:
SGm=13.6;
//Specific gravity of oil:
SGo=0.88;
//Specific gravity of water:
SGw=1;
//Density of water(in slug/ft^3):
d=1.94;
//Heights of liquid in various tubes(in inches):
d1=10;
d2=3;
d3=4;
d4=5;
d5=8;
|
eb4d6f291d204e422667bf1960b6cf3339191ed1
|
460900277dde2407f14200e223c77c7d2acbfe7e
|
/msgflow/TestClientBarFiles/IB10NODE_default.tst
|
4afe2f19e89a783c83dc96926b354b485a0fa576
|
[
"MIT"
] |
permissive
|
itnelo/ibm-websphere-messageflow-example
|
bc5b39b874bdca401aa752d11472780966e93191
|
75881de63df54e42c3d348b89b86939cba78415c
|
refs/heads/master
| 2020-04-01T16:24:12.654779
| 2015-12-24T07:29:33
| 2015-12-24T07:29:33
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 229
|
tst
|
IB10NODE_default.tst
|
***************************************************
* Run the following command to create the queues *
* runmqsc <queue manager name> <IB10NODE_default.tst *
***************************************************
DEFINE QL('LQ2')
|
ba89356d784e424038cbbc069228d33c46799771
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/462/CH3/EX3.4.b/ex_3_4_b.sce
|
8aa864703708206a3a672789aeb0c8ba9457777d
|
[] |
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
| 280
|
sce
|
ex_3_4_b.sce
|
//example 3.4(b)//
clc
//clears the screen//
clear
//clears the command window//
disp('when V(i)=0V, the JFET is operating at point B, where I(D)=3.8mA and V(o)=1V')
disp('this corresponds to the switch in ON stage')
//the answers have been taken directly from the figure//
|
1356d5131279aa08452c0e7ae18078a803822815
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/98/CH17/EX17.4/example17_4.sce
|
eda2400e0a04495fcfe3e0447fc388cc923b9a02
|
[] |
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
| 689
|
sce
|
example17_4.sce
|
//Chapter 17
//Example 17_4
//Page 405
clear;clc;
kva=[10000 10000 5000];
x=[12 12 18];
kva_tr=5000;
x_tr=5;
base=input("Enter base kva: ");
for i=1:3;
per_x(i)= x(i)*base/kva(i);
printf("%% x(%i) = %.0f \n\n", i, per_x(i));
end
per_xt=x_tr*base/kva_tr;
printf("%% Xt = %.0f \n\n", per_xt);
tx1=1/(1/per_x(1)+1/per_x(2)+1/per_x(3));
fmva1=base*100/tx1*1/1000;
tx2=tx1+per_xt;
fmva2=base*100/tx2*1/1000;
printf("(i) Total percentage reactance from generator to fault F1 = %.2f %% \n\n", tx1);
printf(" Fault MVA = %.2f \n\n", fmva1);
printf("(ii) Total percentage reactance from generator to fault to F2 = %.2f %% \n\n", tx2);
printf(" Fault MVA = %.2f \n\n", fmva2);
|
2d7b45ead7bb11ec457e9dfdbc3d0d371a15ebe2
|
b29e9715ab76b6f89609c32edd36f81a0dcf6a39
|
/ketpic2escifiles6/Hatchdata.sci
|
236287efad319578efc6faaf2c24dd6d2d0244a8
|
[] |
no_license
|
ketpic/ketcindy-scilab-support
|
e1646488aa840f86c198818ea518c24a66b71f81
|
3df21192d25809ce980cd036a5ef9f97b53aa918
|
refs/heads/master
| 2021-05-11T11:40:49.725978
| 2018-01-16T14:02:21
| 2018-01-16T14:02:21
| 117,643,554
| 1
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 3,178
|
sci
|
Hatchdata.sci
|
// 08.05.21
// 09.10.05
// 09.12.25
// 10.01.20
// 10.02.01
// 10.11.04 ( debugged 83 )
function ShaLs=Hatchdata(varargin)
global XMIN XMAX YMIN YMAX MilliIn;
ShaL=[];
Nargs=length(varargin);
Kakudo=45;
Kankaku=0.125*1000/2.54/MilliIn;
Tmp=Doscaling([XMIN,YMIN]);
Xmn=Tmp(1); Ymn=Tmp(2);
Tmp=Doscaling([XMAX,YMAX]);
Xmx=Tmp(1); Ymx=Tmp(2);
for N=Nargs:-1:1
Tmp=varargin(N);
if Mixtype(Tmp)~=1
break
end
end
if N<Nargs
Kakudo=varargin(N+1);
if N==Nargs-2
Kankaku=0.125*varargin(Nargs);
end
end
NaitenL=varargin(1);
if Mixtype(NaitenL)==1
NaitenL=list(NaitenL);
end
Ns=2;
StartP=Op(1,NaitenL);
if type(StartP)==10
StartP=[(Xmn+Xmx)/2,(Ymn+Ymx)/2];
end
if Mixtype(varargin(2))==1
StartP=varargin(2);
StartP=Doscaling(StartP);
Ns=3;
end
Tmp=list();
for I=Ns:N
Tmp1=list(varargin(I));
Tmp=Mixjoin(Tmp,Tmp1);
end
Bdy=Kyoukai(Tmp);
Bdys=list();
for I=1:length(Bdy)
Tmp1=Bdy(I);
Tmp2=Doscaling(Tmp1);
Bdys=Mixjoin(Bdys,list(Tmp2));
end;
Bdy=Bdys;
PtnL=list();
for I=1:length(NaitenL)
Tmp=Op(I,NaitenL);
if type(Tmp)==1
Tmp1=Naigai(Tmp,Bdy);
PtnL=Mixjoin(PtnL,list(Tmp1));
else
if type(Tmp)~=10
disp('Type Error');
return
end
Ptn=[];
for J=1:length(Tmp)
if Op(J,Tmp)=='i'
Ptn=[Ptn,1];
else
Ptn=[Ptn,0];
end
end
PtnL=Mixjoin(PtnL,list(Ptn));
end
end
Call=length(Bdy);
Ptn=zeros(1,Call);
if Member(Ptn,PtnL)
Wn=Doscaling(Framedata());
Bdy=Mixjoin(Bdy,list(Wn));
Tmp=list();
for I=1:length(PtnL)
Tmp1=[Op(I,PtnL),1];
Tmp=Mixjoin(Tmp,Tmp1); // 10.11.04
end
PtnL=Tmp;
end
V=[cos(Kakudo*%pi/180),sin(Kakudo*%pi/180)];
Vm=[-sin(Kakudo*%pi/180),cos(Kakudo*%pi/180)];
Tmp=Op(1,NaitenL);
if type(Tmp)==1 & size(Tmp,2)==2
Tmp=Doscaling(Tmp);
Delta=Tmp-StartP;
K=Trunc((Delta(1)*Vm(1)+Delta(2)*Vm(2))/Kankaku);
PA=StartP+K*Kankaku*Vm;
Sha=Makeshasen(PtnL,PA,V,Bdy);
I=1;
while length(Sha)~=0
for J=1:length(Sha)
ShaL=Mixadd(ShaL,Sha(J));
end;
Sha=Makeshasen(PtnL,PA+I*Kankaku*Vm,V,Bdy);
I=I+1;
end
Sha=Makeshasen(PtnL,PA-Kankaku*Vm,V,Bdy);
I=2;
while length(Sha)~=0
for J=1:length(Sha)
ShaL=Mixjoin(ShaL,list(Sha(J)));
end;
Sha=Makeshasen(PtnL,PA-I*Kankaku*Vm,V,Bdy);
I=I+1;
end
else
Delta=[Xmn,Ymn]-StartP;
K1=Trunc((Delta(1)*Vm(1)+Delta(2)*Vm(2))/Kankaku);
Delta=[Xmx,Ymn]-StartP;
K2=Trunc((Delta(1)*Vm(1)+Delta(2)*Vm(2))/Kankaku);
Delta=[Xmx,Ymx]-StartP;
K3=Trunc((Delta(1)*Vm(1)+Delta(2)*Vm(2))/Kankaku);
Delta=[Xmn,Ymx]-StartP;
K4=Trunc((Delta(1)*Vm(1)+Delta(2)*Vm(2))/Kankaku);
IM=max(K1,K2,K3,K4);
Im=min(K1,K2,K3,K4);
for I=Im:IM
Sha=Makeshasen(PtnL,StartP+I*Kankaku*Vm,V,Bdy);
for J=1:length(Sha)
ShaL=Mixjoin(ShaL,list(Sha(J)));
end
end
end
ShaLs=list();
for I=1:length(ShaL)
Tmp=ShaL(I);
Tmp1=Unscaling(Tmp);
ShaLs=Mixjoin(ShaLs,list(Tmp1));
end;
endfunction;
|
d08c0b50ea21c97e75485a5a6f1c5b6776fb684e
|
a5f0fbcba032f945a9ee629716f6487647cafd5f
|
/Development/Algorithms/Affinity propagation/Affinity.sci
|
c658e47b9b51372205decb3f1e2da0fe528dee75
|
[] |
no_license
|
SoumitraAgarwal/Scilab-gsoc
|
692c00e3fb7a5faf65082e6c23765620f4ecdf35
|
678e8f80c8a03ef0b9f4c1173bdda7f3e16d716f
|
refs/heads/master
| 2021-04-15T17:55:48.334164
| 2018-08-07T13:43:26
| 2018-08-07T13:43:26
| 126,500,126
| 1
| 1
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 1,863
|
sci
|
Affinity.sci
|
// Macro for affinity -- Scilab
// Subroutine to get distance between two points
function dist = getDistance(point1, point2)
n1 = length(point1)
dist = 0
for i = 1:n1
dist = dist + (point1(i)-point2(i))^2;
end
dist = sqrt(dist);
endfunction
// Function to return flags for category of each data point
function flags = affinityCluster(x, centres, iterations)
points = length(x(:, 1))
affinity = [];
for i = 1:points
rowAffinity = [];
for j = 1:points
rowAffinity = [rowAffinity, -1*(getDistance(x(j, :), x(i, :))^2)];
end
affinity = [affinity; rowAffinity];
end
medianVal = median(affinity)
for i = 1:points
affinity(i, i) = medianVal;
end
responsibility = zeros(points, points)
availability = zeros(points, points)
for p = 1:iterations
for i = 1:points
for j = 1:points
columnList = 1:points
columnList(j) = %nan
columnList = columnList(~isnan(columnList))
responsibility(i,j) = affinity(i,j) - max(real(affinity(:, [columnList]) + availability(:, [columnList])));
end
end
for i = 1:points
for j = 1:points
maxMat = []
for k = 1:points
if(k~=i && k~=j)
maxMat = [maxMat, max(real([0, responsibility(k, j)]))]
end
end
if(i ~= j)
availability(i, j) = min(real([0, responsibility(j,j) + sum(maxMat)]))
else
availability(i, j) = sum(maxMat);
end
end
end
disp('Iteration complete ' + string(p))
end
resultMat = availability + responsibility;
result = diag(availability + responsibility)
sortedResults = gsort(result)
indices = find(result >= sortedResults(centres))
flags = []
for i = 1:points
bestindex = 1;
bestVal = resultMat(i, indices(1))
for j = 1:centres
if(bestVal < resultMat(i, indices(j)))
bestVal = resultMat(i, indices(j));
bestindex = j;
end
end
flags = [flags, bestindex];
end
endfunction
|
fe079f4d55304cc97aa0f9a519bafc79e53674c9
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/497/CH11/EX11.3/Chap11_Ex3.sce
|
d972b9fd30891b26582ca6b34664319d7f0464ca
|
[] |
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
| 2,115
|
sce
|
Chap11_Ex3.sce
|
//Kunii D., Levenspiel O., 1991. Fluidization Engineering(II Edition). Butterworth-Heinemann, MA, pp 491
//Chapter-11, Example 3, Page 273
//Title: Fitting Reported Heat Transfer Data with the Bubbling Bed Model
//==========================================================================================================
clear
clc
//INPUT
rhos=1.3;//Density of solids in g/cc
phis=0.806;//Sphericity of solids
gammab=0.001;//Ratio of volume of dispersed solids to that of bubble phase
rhog=1.18E-3;//Density of air in g/cc
Pr=0.69;//Prandtl number
myu=1.8E-4;//Viscosity of gas in g/cm s
Cpg=1.00;//Specific heat capacity of gas in J/g K
ephsilonmf=0.45;//Void fraction at minimum fluidization condition
kg=2.61E-4;//Thermal concuctivity of gas in W/cm k
dp=0.036;//Particle size in cm
umf=6.5;//Velocity at minimum fluidization condition in cm/s
ut=150;//Terminal velocity in cm/s
db=0.4;//Equilibrium bubble size in cm
etah=1;//Efficiency of heat transfer
uo=[10;20;30;40;50];//Superficial gas velocity in cm/s
g=980;//Acceleration due to gravity in square cm/s^2
//CALCULATION
Nustar=2+[((dp*ut*rhog)/myu)^0.5*Pr^(1/3)];//Nusselt no. from Eqn.(25)
Hbc=4.5*(umf*rhog*Cpg/db)+5.85*((kg*rhog*Cpg)^0.5*g^0.25/db^(5/4));//Total heat interchange across the bubble-cloud boundary from Eqn.(32)
ubr=0.711*(g*db)^0.5;//Rise velocity of the bubble from Eqn.(6.7)
n=length(uo);
i=1;
while i<=n
x(i)=(uo(i)-umf)/(ubr*(1-ephsilonmf));//The term delta/(1-epshilonf) after simplification
Nubed(i)=x(i)*[gammab*Nustar*etah+(phis*dp^2/(6*kg))*Hbc];//Nusselt no. from Eqn.(36)
Rep(i)=(dp*uo(i)*rhog)/myu;//Reynolds of the particle
i=i+1;
end
//OUTPUT
printf('\nThe desired result is the relationship between Nubed and Rep which is in the form of a straight line y=mx+c');
printf('\nRep');
printf('\t\tNubed');
i=1;
while i<=n
printf('\n%f',Rep(i));
printf('\t%f',Nubed(i));
i=i+1;
end
plot(Rep,Nubed);
xlabel("Rep");
ylabel("Nubed");
//====================================END OF PROGRAM ======================================================
|
c06ed07af311dc400bef47ea82893ba20f0f4279
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3772/CH5/EX5.13/Ex5_13.sce
|
69d2eb537044dcea0a065e16c0fb144c7588eb92
|
[] |
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
| 1,110
|
sce
|
Ex5_13.sce
|
// Problem 5.13,Page no.135
clc;clear;
close;
d=10 //cm //distance between joists
t=2 //cm //thickness of steel plate
d_2=20 //cm //depth of beam
sigma_t=8.5 //N/mm**2 //stress in timber
E_s=2*10**5 //N/mm**2 //Modulus of elasticity of steel
E_t=10**4 //N/mm**2 ////Modulus of elasticity of timber
L=5 //cm //span of beam
//calculation
sigma=10*15**-1*sigma_t //stress in timber at distance of 10 cm from XX (N/mm**2)
dell=sigma*E_t**-1 //strain in timber at 10 cm from XX (N/mm**2)
sigma_s=dell*E_s //N/mm**2 //Max stress
//For Timber
Z_w=1*6**-1*10*30**2*2 //cm**3 //section modulus of timber
M_w=sigma_t*100*Z_w //moment of resistance of timber (N-cm)
//For steel
Z_s=1*6**-1*2*20**2 //cm**3 //section modulus of steel
M_s=sigma_s*Z_s*100 //moment of resistance of steel (N-cm)
M=(M_w+M_s)*10**-5 //total moment of resistance(N-cm)
//M=w*L**2*8**-1 //N*cm //Max bending moment
w=8*M*(L**2)**-1 //kN/m //Max uniform distributed Load
//Result kN/m
printf("Moment of resistance is %.3f N-cm",M)
printf("\n Max uniform distributed Load = %.3f kN/m",w)
// answer in the textbook is not accurate.
|
5312734865d483be552188023b9200176fe57903
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/32/CH12/EX12.11/12_11.sce
|
4986e9cd6c0b8cde6566a31e779100022522ba58
|
[] |
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
| 950
|
sce
|
12_11.sce
|
//pathname=get_absolute_file_path('12.11.sce')
//filename=pathname+filesep()+'12.11-data.sci'
//exec(filename)
//Pressure at which steam is supplied(in kPa):
p1=1.4*10^3
//Pressure at exhaust(in kPa):
p4=25
//Expansion ratio:
r=8
//Rpm of engine:
N=240
//Bore diameter(in m):
d=0.60
//Stroke length(in m):
L=0.60
//Diagram factor:
d1=0.8
//Area of cylinder(in m^2):
A=%pi*d^2/4
//Hypothetical mep(in kPa):
mep=p1/r*(1+log(r))-p4
//Actual mep(in kPa):
mepa=mep*d1
//Indicated power(in kW):
IP=mepa*L*A*N/60*2
//Work done in HP cylinder(in kJ):
W=mepa*A*L/2
//Volume at state 1(in m^3):
V1=%pi*d^2*L/(4*8)
//Volume at state 2(in m^3):
V2=2.71^(W/(p1*V1))*V1
//Diameter of HP cylinder(in m):
D=sqrt(V2*4/(L*%pi))
//Intermediate pressure(in kPa):
p2=p1*V1/V2
printf("\n RESULT \n")
printf("\nIndicated power = %f kW",IP)
printf("\nDiameter of HP cylinder = %f cm",D*100)
printf("\nIntermediate pressure = %f kPa",p2)
|
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
|
0711878bcb5fa22b5d16b3e75672b571942d031c
|
6e257f133dd8984b578f3c9fd3f269eabc0750be
|
/ScilabFromTheoryToPractice/CreatingPlots/testnofacette.sce
|
a45027ffd42a407edc282178b6015ca4ce0eebe5
|
[] |
no_license
|
markusmorawitz77/Scilab
|
902ef1b9f356dd38ea2dbadc892fe50d32b44bd0
|
7c98963a7d80915f66a3231a2235010e879049aa
|
refs/heads/master
| 2021-01-19T23:53:52.068010
| 2017-04-22T12:39:21
| 2017-04-22T12:39:21
| 89,051,705
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 138
|
sce
|
testnofacette.sce
|
function z=plan(x,y)
z=x-y
endfunction
// evaluate over a grid
x=[0:2],y=x,z=feval(x,y,plan)'
// display the surface
clf;surf(x,y,z)
|
3cbf1db5a8992e64a0ac563340f53933171c7484
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1823/CH6/EX6.8/SolEx6_8.sce
|
9b21d82554b7b8607f357a301c28c992561e6562
|
[] |
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
| 217
|
sce
|
SolEx6_8.sce
|
//Determine the voltage gain Av
//Example 6.8 page no 179
clear
clc
vl=1.1528 //output voltage
vi=0.250 //input voltage
Av=-(vl/vi) //voltage gain
printf("\n The value of Av=%0.3f " ,Av)
|
2bd4622c6a0440513ed798aa06de50e8c71988f4
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2873/CH5/EX5.4/Ex5_4.sce
|
d12f35701d1a47c2606aeb9798e9998c5f4bedad
|
[] |
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
| 977
|
sce
|
Ex5_4.sce
|
// Display mode
mode(0);
// Display warning for floating point exception
ieee(1);
clear;
clc;
disp("Engineering Thermodynamics by Onkar Singh Chapter 5 Example 4")
T1=(150+273.15);//temperature of copper block in K
T2=(25+273.15);//temperature of sea water in K
m=1;//mass of copper block in kg
C=0.393;//heat capacity of copper in KJ/kg K
disp("entropy change in universe(deltaS_universe)=deltaS_block+deltaS_water")
disp("where deltaS_block=m*C*log(T2/T1)")
disp("here hot block is put into sea water,so block shall cool down upto sea water at 25 degree celcius as sea may be treated as sink")
disp("therefore deltaS_block=m*C*log(T2/T1)in KJ/K")
deltaS_block=m*C*log(T2/T1)
disp("heat loss by block =heat gained by water(Q)in KJ")
disp("Q=-m*C*(T1-T2)")
Q=-m*C*(T1-T2)
disp("therefore deltaS_water=-Q/T2 in KJ/K")
deltaS_water=-Q/T2
disp("thus deltaS_universe=(deltaS_block+deltaS_water)*1000 in J/K")
deltaS_universe=(deltaS_block+deltaS_water)*1000
|
f12267611dfd7429bdf5df661c5faa7a7f4af394
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/147/CH8/EX8.5/Example8_5.sce
|
1b1697072787e679af2e99766157b189f593b917
|
[] |
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
|
Example8_5.sce
|
close();
clear;
clc;
Ibq = 40*10^(-6); //A
Vbb = 6; //V
Vbeq = 0.7; //for Si transistor
//By KVL around the base-emitter
//Vbb = Ibq*Rb + Vbeq;
Rb = (Vbb-Vbeq)/Ibq; //ohm
mprintf("Rb = %0.1f k ohm",Rb/1000);
|
80a33df8326674e638a5f05250fd9de20d0d4a91
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/443/CH8/EX8.1/8_1.sce
|
31f0a9111d4a28c926c2019a90beedbe6b9486a3
|
[] |
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
| 978
|
sce
|
8_1.sce
|
pathname=get_absolute_file_path('8_1.sce')
filename=pathname+filesep()+'8_1_data.sci'
exec(filename)
//Pressure at outlet(in bar)
p2=(1-(C2/Vc)^2/(2*Cp*T1))^(y/(y-1))*p1
//Volume at inlet(in m^3/kg)
v1=(R*T1)/(p1*10^5)*1000
//Volume at outlet(in m^3/kg)
v2=v1*(p1/p2)^(1/y)
//Throat area(in cm^2)
A2=(ma*v2)/(C2*60)*10^4
//Outlet diameter(in cm)
d2=sqrt((A2*4)/%pi)
//Change in air pressure(in bar)
dpa=p1-p2
//change in fuel pressure(in bar)
dpf=pd*dpa
//Area of orifice(in cm^2)
Af=(mf*10^4)/(60*Cf*sqrt(2*Pf*1000*dpf*10^5))
//Diameter of orifice(in mm^2)
df=sqrt((Af*4)/%pi)
printf("\n\nRESULTS\n\n")
printf("\nPressure at outlet:%f\n",p2)
printf("\nVolume at inlet:%f\n",v1)
printf("\nVolume at outlet:%f\n",v2)
printf("\nThroat area:%f\n",A2)
printf("\nOutlet diameter:%f\n",d2)
printf("\nChange in air pressure:%f\n",dpa)
printf("\nChange in fuel pressure:%f\n",dpf)
printf("\nArea of orifice:%f\n",Af)
printf("\nDiameter of orifice:%f\n",df)
|
be956f70bb5db1c1dcfaa7eedbe27f28e27dc6c7
|
ac1f8441b0319b4a391cd5a959bd3bb7988edfa7
|
/data/news2015/news2015/EnTa/enta11.tst
|
5ddfc1f121216e6fefe4d0d0fbf606e1c61d261a
|
[
"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
| 7,959
|
tst
|
enta11.tst
|
colista
vajeer
ayachit
haisiyat
aakaankshaa
satyanaaraayan
cancer
antarah
ghulam
malay
abdus
urdhvareshe
shanpak
vishraant
volkswagen
tanmay
kabuliwala
adrian
gihlan
muballigh
pushpa
geneva
raymond
nasr
snowboarding
radi
tatkar
marenda
fletcher
amadis
tegetthoff
maithili
prabuddha
junoon
tanpura
dominick
geodesic
suparna
orthopaedics
bilva
gharonda
aruni
awaargi
amalatas
simak
orion
kalaa
naqi
sidbi
mangalaa
shirina
jera
newby
deependra
adway
wilderness
palamu
banas
umran
helsinki
chandrakumar
richmond
adimurti
mandakini
maruti
wesley
kenton
ur
pemgirikar
jibran
adity
bhaumik
daksha
slalom
electrosteel
pritilata
nandurkar
ligurian
charan
ujagar
achaleshvara
panikarn
rolta
gosper
july
sidhdheshvaree
cleo
prithviraj
arkasut
mahati
bhoomika
phyliss
durafe
ranger
christopher
sevaaram
un_manaa
iyaas
chamba
zulfaqar
himaanee
melia
gazala
bobby
malawi
khirwadkar
pathway
muhajir
nayak
durrah
wilhelmina
chittaranjan
raamateke
kohima
hashmat
jerrell
raksha
angag
sharat
bagha
agharr
mahasamund
gurdayal
sumatra
riverside
drafts
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hamnah
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adharm
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target
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aayushmati
|
f0c4120a3214d6b61adf70001458a2a26e12d7ed
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3511/CH5/EX5.15/Ex5_15.sce
|
9dd175c7541172f6af65e34338a5b0a6af3b21ff
|
[] |
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
| 1,426
|
sce
|
Ex5_15.sce
|
clc;
p1=1; // Pressure at state 1 in bar
T1=300; // Temperature at state 1 in kelvin
p4=5; // Pressure at state 4 in bar
T5=1250; // Temperature at state 5 in kelvin
Cp=1.005; // Specific heat at constant pressure in kJ/kg K
r=1.4; // Specific heat ratio
rp=p4/p1; // pressure ratio
p2=sqrt (rp); // Because of perfect intercooling
c1=p2^((r-1)/r);
T2=T1*c1; // Temperature at state 2
T4=T2; T3=T1;
Wc1=Cp*(T2-T1); // Work of compressor 1
Wc=2*Wc1; // net work of compressor
WT1=Wc;
T6=T5-(WT1/Cp); // Temperature at state 6
p5_p6=(T5/T6)^(r/(r-1)); // Pressure ratio
p6=rp/p5_p6; // Pressure at state 6
p7=p1; T7=T5;p8=p6;
T8=T7*(p7/p8)^((r-1)/r); // Temperature in state 8
WT2=Cp*(T7-T8); // Turbine 2 work
q=Cp*(T5-T4)+Cp*(T7-T6); // Heat supplied
eff=WT2/q; // Efficiency of the cycle
// With regenerator
T9=T8;
q_withregen=Cp*((T5-T9)+(T7-T6)); // Heat supplied with regenerator
eff_withregen=WT2/q_withregen; // Efficiency of the cycle with regenerator
I_eff=(eff_withregen-eff)/eff_withregen; // Percentage improvement in efficiency
disp ("%",eff*100,"Efficiency of the cycle = ","kJ/kg",q,"Heat supplied = ","kJ/kg",WT2,"Work of turbine = ","(i). Without regenerator ");
disp ("%",eff_withregen*100,"Efficiency of the cycle = ","kJ/kg (roundoff error)",q_withregen,"Heat supplied = ","(ii). With regenerator" );
disp ("%",I_eff*100,"Percentage improvement in efficiency = ");
|
f9e863c0cb4675a3b1a36e3f7eafd57cab563bf0
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1583/CH10/EX10.11/FS_Ex_10_11.sce
|
ca82b98a1570a5033ae6d58cbffb1f939b734998
|
[] |
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
| 357
|
sce
|
FS_Ex_10_11.sce
|
clc
//Chapter 10:Frequency Synthesizers
//Example 10.11 page no 446
disp('A signal sideband power is -140dB/Hz ')
N=5*10^6//frequency of reference oscillator
M=5*10^3//count
No=-140+10*log10((N/M)^2)//the output noise power due to the reference oscillator
mprintf('The single sideband noise power at a frequency offset of 0.5KHz is %d dB/Hz ',No)
|
b60fca5fd70c5cfd8ae48b74024b8d66a48c8170
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1322/CH8/EX8.5/65ex1.sce
|
5720264866ebf79b85143315fa28befe75ad2909
|
[] |
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
|
65ex1.sce
|
//ex1
clear;
clc;
close;
x=poly(0,'x');
//sum of first no.(i.e., x) and 3 times the second no.(i.e., y) is 53 =>x+3*y=53
y=(53-x)/3;
//difference between 4 times the first and twice the 2nd is 2 => 4x-2y=2
y=(4*x-2)/2;
printf("the solution is : \n");
for x=1:100
if((53-x)/3==(4*x-2)/2)
mprintf("x=%i",x)
break
end
end
//"substitute the x value in any one of the above equations"
y=(53-x)/3;mprintf("y=%i",y)
|
a2febcf822a984f6a0a72cef03c3f62554ac4281
|
8ea401b354e99fe129b2961e8ee6f780dedb12bd
|
/macros/dataframe.sci
|
389ce661171541e754a57cc38d6a83b671e0e179
|
[
"BSD-2-Clause"
] |
permissive
|
adityadhinavahi/SciPandas
|
91340ca30e7b4a0d76102a6622c97733a28923eb
|
b78b7571652acf527f877d9f1ce18115f327fa18
|
refs/heads/master
| 2022-12-20T04:04:35.984747
| 2020-08-19T16:10:51
| 2020-08-19T16:10:51
| 288,765,541
| 0
| 1
| null | 2020-08-19T15:35:04
| 2020-08-19T15:14:46
|
Python
|
UTF-8
|
Scilab
| false
| false
| 658
|
sci
|
dataframe.sci
|
function [df] = DataFrame()
// Calls and initializes DataFrame function
//
// Syntax
// df = DataFrame()
//
// Parameters
//df: DataFrame input
//
// Description
//Two-dimensional, size-mutable, potentially heterogeneous tabular data.Data structure also contains labeled axes (rows and columns). Arithmetic operations align on both row and column labels. Can be thought of as a dict-like container for Series objects. The primary pandas data structure.
// Examples
// //Constructing DataFrame from a dictionary.
//df = pd_f.DataFrame("+df_str+")
// Authors
// Aditya Dhinavahi
// Sundeep Akella
endfunction
|
7e4832d48b9c8931d46cf39f167622c12d289be0
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2510/CH17/EX17.4/Ex17_4.sce
|
87c3206d3a34d0cc0c93be24246bab330133aadb
|
[] |
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
| 587
|
sce
|
Ex17_4.sce
|
//Variable declaration:
L = 3.0*0.0254 //Height of fin (m)
t = 1.0*0.0254 //Thickness of fin (m)
h = 15.0 //Heat transfer coefficient (W/m^2.K)
k = 300.0 //Thermal conductivity (W/m.K)
//Calculation:
Lc = L + t/2.0 //Corrected height of fin (m)
Ap = Lc*t //Profile area of fin (m^2)
x = sqrt((Lc**3*h)/(k*Ap)) //x-coordinate of figure 17.3
//From figure 17.3:
nf = 98.0 //Fin efficiency
//Result:
printf("The fin efficiency is : %f %%",nf)
|
48a56cc1894e187a599a529df4ca233a74cbe6e6
|
b84a4a40dbd2d8bea5236b6ce15dfba9b560bd5a
|
/NaiveGauss_SALVEDIA.sce
|
deb5afb076360fcb7f1cc0ab8ce040b38953f0f3
|
[] |
no_license
|
ronzohan/SciLab
|
f8cf060d8d7be63b7520fc97f5f2db9d5f576bd6
|
bccd05f1f2a0cf56f1de25d466f496a2ba436b79
|
refs/heads/master
| 2021-01-10T21:40:00.810683
| 2014-10-01T13:23:07
| 2014-10-01T13:23:07
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 1,823
|
sce
|
NaiveGauss_SALVEDIA.sce
|
function gauss(coefficient_m,constant_m)
is_square = isSquareMatrix(coefficient_m);
if is_square == 0 then
printf("Not a square matrix");
return;
end
is_compatible = isCompatible(coefficient_m,constant_m)
if is_compatible == 0 then
printf("Incompatible matrices size");
return;
end
mtrx_size = size(coefficient_m);
n = mtrx_size(1,1);
constant_size = size(constant_m);
L=eye(n,n);
M=coefficient_m;
C = constant_m;
disp("Augmented Matrix");
disp([M C])
//forward elimination
for k=1:n-1
for i = k+1:n
pivot = M(i,k)/M(k,k);
for j = k+1:n
M(i,k) = 0
M(i,j) = M(i,j)-(pivot*M(k,j));
end
//for constant_m
C(i) = C(i) - (pivot * C(k));
end
end
disp([M C],"Upper Triangular Matrix");
//back substitution
for i=n:-1:1
x(i) = C(i)/M(i,i);
for j=1:n-1
C(j) = C(j) - (x(i) *M(j,i))
end
end
disp("Solution Matrix")
disp(x)
endfunction
//checks if the matrix is a square matrix
function is_square = isSquareMatrix(input_matrix)
m = size(input_matrix)
if m(1) == m(2) then
is_square = 1
else
is_square = 0
end
endfunction
//checks if the input matrices are dimensionally compatible
function is_compatible = isCompatible(coefficient_m,constant_m)
coefficient_dim = size(coefficient_m);//dimensions of the matrices
constant_dim = size(constant_m);
if coefficient_dim(2) == constant_dim(1) then
is_compatible = 1;
else
is_compatible = 0;
end
endfunction
//SAMPLE
//matA = [25 5 1; 64 8 1; 144 12 1]
//matB = [106.8; 177.2; 279.2]
//gauss(matA,matB)
|
fed6095451baa8173bb7b3e5d6b70306777eaf21
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/587/CH3/EX3.10/example3_10.sce
|
c9e4cda750493d4de21ac8df20a8bf81c026fdb4
|
[] |
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
| 500
|
sce
|
example3_10.sce
|
clear;
clc;
//Example3.10[Maximum Power dissipation of a Transistor]
//Given:-
T_ambient=25;//Ambient temperature[degree Celcius]
T_case=85;//Maximum temperature of the case[degree Celcius]
R_case_ambient=20;//Resistance for convection b/w case and ambient [degree Celcius/W]
//Solution:-
Q_=(T_case-T_ambient)/R_case_ambient;//[W]
disp("W",Q_,"The given power transistor should not be operated at power levels above")
disp("if is its case temperature is not to exceed 85 degree Celcius")
|
7c6123e6d682aee034f5213c096e75bada24490b
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2873/CH2/EX2.3/Ex2_3.sce
|
58113497ebdc4bdd442bfd9c3933b990799099ad
|
[] |
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
| 1,232
|
sce
|
Ex2_3.sce
|
// Display mode
mode(0);
// Display warning for floating point exception
ieee(1);
clear;
clc;
disp("Engineering Thermodynamics by Onkar Singh,Chapter 2,Example 3")
disp("emf equation")
disp("E=(0.003*t)-((5*10^-7)*t^2))+(0.5*10^-3)")
disp("using emf equation at ice point,E_0 in volts")
t=0;//ice point temperature in degree celcius
disp("E_0=(0.003*t)-((5*10^-7)*t^2)+(0.5*10^-3)")
E_0=(0.003*t)-((5*10^-7)*t^2)+(0.5*10^-3)
disp("using emf equation at steam point,E_100 in volts")
t=100;//steam point temperature in degree celcius
disp("E_100=(0.003*t)-((5*10^-7)*t^2)+(0.5*10^-3)")
E_100=(0.003*t)-((5*10^-7)*t^2)+(0.5*10^-3)
disp("now emf at 30 degree celcius using emf equation(E_30)in volts")
t=30;//temperature of substance in degree celcius
E_30=(0.003*t)-((5*10^-7)*t^2)+(0.5*10^-3)
disp("now the temperature(T) shown by this thermometer")
disp("T=((E_30-E_0)/(E_100-E_0))*(T_100-T_0) in degree celcius")
T_100=100;//steam point temperature in degree celcius
T_0=0;//ice point temperature in degree celcius
T=((E_30-E_0)/(E_100-E_0))*(T_100-T_0)
disp("NOTE=>In this question,values of emf at 100 and 30 degree celcius is calculated wrong in book so it is corrected above so the answers may vary.")
|
64957eec965bc872c7894d9af33bb0a9436d62d2
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1835/CH10/EX10.6/Ex10_6.sce
|
1015c4b0866361922225a519762cd36d2732c604
|
[] |
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
| 988
|
sce
|
Ex10_6.sce
|
//CHAPTER 10 ILLUSRTATION 6 PAGE NO 272
//TITLE:Brakes and Dynamometers
clc
clear
//===========================================================================================
//INPUT DATA
d=0.5;//Drum diamter in m
U=0.3;//Coefficient of friction
q=250;//Angle of contact in degree
P=750;//Force in N
a=0.1;//Band width in m
b=0.8;//Distance in m
ft=(70*10^6);//Tensile stress in Pa
f=(60*10^6);//Stress in Pa
b1=0.1;//Distance in m
T=exp(U*(q*(3.14/180)));//Tensions ratio
T2=(P*b*10)/(T+1);//Tension in N
T1=(T*T2);//Tension in N
TB=(T1-T2)*(d/2);//Torque in N.m
t=(max(T1,T2)/(ft*a))*1000;//Thickness in mm
M=(P*b);//bending moment at fulcrum in Nm
X=(M/((1/6)*f));//Value of th^2
//t varies from 10mm to 15 mm. Taking t=15mm,
h=sqrt(X/(0.015))*1000;//Section of the lever in m
printf('Torque required is %3.2f N.m \nThickness necessary to limit the tensile stress to 70 MPa is %3.3f mm \n Section of the lever taking stress to 60 MPa is %3.1f mm',TB,t,h)
|
c208fc1c86799f4d36fbfff8c1688d4ca77068ba
|
7b27ad20f976a60e46bd40584a1463c76e9d3801
|
/volatilite_implicite.sci
|
cd84061ad8a4ddc0e12ef6b69d58f9ccbe187942
|
[] |
no_license
|
AmineKheldouni/MOPSI-Project
|
a7c898472f333f41f9b9f2058b35af123d652153
|
51f08c467564b5e395d8fcd449d8aed945e5de94
|
refs/heads/master
| 2021-01-13T15:35:26.688067
| 2017-02-17T09:06:01
| 2017-02-17T09:06:01
| 76,885,914
| 1
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 1,432
|
sci
|
volatilite_implicite.sci
|
exec('/home/amine/Documents/2A/Projet MOPSI/MOPSI-Project/sousjacent.sci', -1)
Call_market = 20;
function [Y]=f(t,T,K,r,sigma,x)
Y = prix_call(t,T,K,r,sigma,x)-Call_market;
endfunction
function [Y]= vega(t,T,r,K,sigma,x)
Y = x*sqrt(T)*dN(d1(t,T,K,r,sigma,x))
endfunction
function [Y]=volimpl(t,T,K,r,sgm,x)
a1 = 0.001;
a2 = sgm;
tmp = (a1+a2)/2;
i = 0;
while i<300 then
if f(t,T,K,r,a1,x)*f(t,T,K,r,tmp,x) > 0 then
a1 = tmp;
else
a2 = tmp;
end
tmp = (a1+a2)/2;
i = i+1;
end
Y = tmp;
endfunction
vi =volimpl(0,T,K(100),r,1,10);
disp(vi);
n = prod(size(K));
function [sigmaC]=bsimpvol(option,S,K,r,T,sigma0);
function [Y]=difference(s);
d1=-((log(K/S)-(r+1/2*s^2)*T)/(s*sqrt(T)));
d2=-((log(K/S)-(r-1/2*s^2)*T)/(s*sqrt(T)));
Y=segno*S*cdfnor('PQ',segno*d1,0,1)-segno*K*exp(-r*T)*cdfnor('PQ',segno*d2,0,1)-option;
endfunction
segno=1;
[sigmaC,d,inf]=fsolve(sigma0,difference);
endfunction
pas = 100;
m = zeros(1,M+1);
tt = zeros(1, pas);
for i=1:M+1
m(1,i) = K(i)/S0;
end
for i=1:pas
tt(1,i) = i*T/pas;
end
sg_imp = zeros(pas,M+1);
for i=1:pas
for j=1:M+1
sg_imp(i,j) = bsimpvol(Call_market,S0,K(j),r,tt(1,i),0.2)
end
end
//cmap=hotcolormap(40);
//f=gcf();//figure courante
//f.color_map=cmap;
plot3d(tt,m,sg_imp);
xtitle('Nappe de volatilité implicite','Maturité T', 'Moneyness K/S0','volatilité implicite')
//plot(m,sg_imp(1,:));
|
3f0046e53c855c1c8bacdb7acdd2c9e2801de48d
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/800/CH2/EX2.4/2_4.sce
|
29f1110819a5f25dcd67daf83566b74650cc7a6f
|
[] |
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
| 190
|
sce
|
2_4.sce
|
//clear//
clc
clear
exec("2.4data.sci");
VCSTR = FA0*X(7)*(1/-rAat);
VPFR = FA0*inttrap(X,p)
disp("VCSTR =")
disp(VCSTR)
disp("dm^3")
disp("VPFR =")
disp(VPFR)
disp ("dm^3")
|
a241b83248b03a522b211a0ce745a52e887f89c9
|
36c5f94ce0d09d8d1cc8d0f9d79ecccaa78036bd
|
/closefast.sce
|
f8f2e95a0e5e6611068a52ac5567b1872662e493
|
[] |
no_license
|
Ahmad6543/Scenarios
|
cef76bf19d46e86249a6099c01928e4e33db5f20
|
6a4563d241e61a62020f76796762df5ae8817cc8
|
refs/heads/master
| 2023-03-18T23:30:49.653812
| 2020-09-23T06:26:05
| 2020-09-23T06:26:05
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 24,413
|
sce
|
closefast.sce
|
Name=closefast
PlayerCharacters=ow-heavysurgerifle
BotCharacters=ow-rotation.rot
IsChallenge=true
Timelimit=60.0
PlayerProfile=ow-heavysurgerifle
AddedBots=ow-rotation.rot
PlayerMaxLives=0
BotMaxLives=0
PlayerTeam=2
BotTeams=1
MapName=boxernobounds.map
MapScale=2.0
BlockProjectilePredictors=true
BlockCheats=true
InvinciblePlayer=true
InvincibleBots=false
Timescale=1.0
BlockHealthbars=false
TimeRefilledByKill=0.0
ScoreToWin=1000.0
ScorePerDamage=3.0
ScorePerKill=0.0
ScorePerMidairDirect=0.0
ScorePerAnyDirect=0.0
ScorePerTime=0.0
ScoreLossPerDamageTaken=0.0
ScoreLossPerDeath=0.0
ScoreLossPerMidairDirected=0.0
ScoreLossPerAnyDirected=0.0
ScoreMultAccuracy=false
ScoreMultDamageEfficiency=false
ScoreMultKillEfficiency=false
GameTag=Reflex, Quake
WeaponHeroTag=Lightning Gun, LG
DifficultyTag=3
AuthorsTag=KovaaK
BlockHitMarkers=false
BlockHitSounds=false
BlockMissSounds=true
BlockFCT=false
Description=Low pressure hitscan tracking against a hard to hit target.
GameVersion=1.0.8.0
ScorePerDistance=0.0
MBSEnable=true
MBSTime1=0.25
MBSTime2=0.5
MBSTime3=0.75
MBSTime1Mult=1.0
MBSTime2Mult=2.0
MBSTime3Mult=3.0
MBSFBInstead=false
MBSRequireEnemyAlive=false
[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=ow-fast
DodgeProfileNames=Close Very Short Strafes
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=ow-lawbringer
SeeThroughWalls=false
NoDodging=false
NoAiming=false
[Bot Profile]
Name=Bot Profile
DodgeProfileNames=ADAD
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=ow-lawbringer
SeeThroughWalls=false
NoDodging=false
NoAiming=false
[Bot Profile]
Name=Bot Profile2
DodgeProfileNames=Long Strafes
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=ow-lawbringer
SeeThroughWalls=false
NoDodging=false
NoAiming=false
[Bot Rotation Profile]
Name=ow-rotation
ProfileNames=ow-fast;Bot Profile;Bot Profile2
ProfileWeights=1.0;1.0;1.0
Randomized=true
[Character Profile]
Name=ow-heavysurgerifle
MaxHealth=120.0
WeaponProfileNames=Heavy Surge Rifle;;;;;;;
MinRespawnDelay=1.0
MaxRespawnDelay=5.0
StepUpHeight=58.333332
CrouchHeightModifier=0.7
CrouchAnimationSpeed=2.0
CameraOffset=X=0.000 Y=0.000 Z=0.000
HeadshotOnly=false
DamageKnockbackFactor=4.0
MovementType=Base
MaxSpeed=641.666687
MaxCrouchSpeed=350.0
Acceleration=16041.666992
AirAcceleration=0.0
Friction=0.0
BrakingFrictionFactor=0.0
JumpVelocity=700.0
Gravity=2.625
AirControl=0.12
CanCrouch=true
CanPogoJump=false
CanCrouchInAir=false
CanJumpFromCrouch=true
EnemyBodyColor=X=1.000 Y=1.000 Z=1.000
EnemyHeadColor=X=1.000 Y=1.000 Z=1.000
TeamBodyColor=X=1.000 Y=1.000 Z=1.000
TeamHeadColor=X=1.000 Y=1.000 Z=1.000
BlockSelfDamage=false
InvinciblePlayer=false
InvincibleBots=false
BlockTeamDamage=false
AirJumpCount=0
AirJumpVelocity=0.0
MainBBType=Cylindrical
MainBBHeight=170.334137
MainBBRadius=32.238731
MainBBHasHead=true
MainBBHeadRadius=15.748805
MainBBHeadOffset=-5.249601
MainBBHide=false
ProjBBType=Cylindrical
ProjBBHeight=170.334137
ProjBBRadius=40.298412
ProjBBHasHead=true
ProjBBHeadRadius=19.686007
ProjBBHeadOffset=-5.249601
ProjBBHide=true
HasJetpack=false
JetpackActivationDelay=0.0
JetpackFullFuelTime=0.0
JetpackFuelIncPerSec=0.1
JetpackFuelRegensInAir=false
JetpackThrust=0.1
JetpackMaxZVelocity=600.0
JetpackAirControlWithThrust=0.0
AbilityProfileNames=Run.abilsprint;;;Punch.abilmelee
HideWeapon=false
AerialFriction=0.0
StrafeSpeedMult=1.0
BackSpeedMult=0.9
RespawnInvulnTime=0.0
BlockedSpawnRadius=0.0
BlockSpawnFOV=0.0
BlockSpawnDistance=0.0
RespawnAnimationDuration=0.5
AllowBufferedJumps=false
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=0.000 Z=150.000
BrakingDeceleration=10500.0
VerticalSpawnOffset=0.0
SpawnXOffset=0.0
SpawnYOffset=0.0
InvertBlockedSpawn=false
[Character Profile]
Name=ow-lawbringer
MaxHealth=200.0
WeaponProfileNames=;;;;;;;
MinRespawnDelay=0.1
MaxRespawnDelay=1.0
StepUpHeight=58.333332
CrouchHeightModifier=0.7
CrouchAnimationSpeed=2.0
CameraOffset=X=0.000 Y=0.000 Z=0.000
HeadshotOnly=false
DamageKnockbackFactor=4.0
MovementType=Base
MaxSpeed=641.666687
MaxCrouchSpeed=350.0
Acceleration=16041.666992
AirAcceleration=0.0
Friction=0.0
BrakingFrictionFactor=0.0
JumpVelocity=700.0
Gravity=2.625
AirControl=0.12
CanCrouch=true
CanPogoJump=false
CanCrouchInAir=false
CanJumpFromCrouch=true
EnemyBodyColor=X=1.000 Y=1.000 Z=1.000
EnemyHeadColor=X=1.000 Y=1.000 Z=1.000
TeamBodyColor=X=1.000 Y=1.000 Z=1.000
TeamHeadColor=X=1.000 Y=1.000 Z=1.000
BlockSelfDamage=false
InvinciblePlayer=false
InvincibleBots=false
BlockTeamDamage=false
AirJumpCount=0
AirJumpVelocity=0.0
MainBBType=Cylindrical
MainBBHeight=153.140213
MainBBRadius=36.388447
MainBBHasHead=true
MainBBHeadRadius=18.789669
MainBBHeadOffset=-6.263223
MainBBHide=false
ProjBBType=Cylindrical
ProjBBHeight=153.140213
ProjBBRadius=45.485558
ProjBBHasHead=true
ProjBBHeadRadius=23.487087
ProjBBHeadOffset=-6.263223
ProjBBHide=true
HasJetpack=false
JetpackActivationDelay=0.0
JetpackFullFuelTime=0.0
JetpackFuelIncPerSec=0.1
JetpackFuelRegensInAir=false
JetpackThrust=0.1
JetpackMaxZVelocity=600.0
JetpackAirControlWithThrust=0.0
AbilityProfileNames=;;;
HideWeapon=false
AerialFriction=0.0
StrafeSpeedMult=1.0
BackSpeedMult=0.9
RespawnInvulnTime=0.0
BlockedSpawnRadius=0.0
BlockSpawnFOV=0.0
BlockSpawnDistance=0.0
RespawnAnimationDuration=0.0
AllowBufferedJumps=false
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=0.000 Z=150.000
BrakingDeceleration=10500.0
VerticalSpawnOffset=0.0
SpawnXOffset=0.0
SpawnYOffset=0.0
InvertBlockedSpawn=false
[Dodge Profile]
Name=Close Very Short Strafes
MaxTargetDistance=400.0
MinTargetDistance=0.0
ToggleLeftRight=true
ToggleForwardBack=false
MinLRTimeChange=0.1
MaxLRTimeChange=0.2
MinFBTimeChange=0.2
MaxFBTimeChange=0.5
DamageReactionChangesDirection=false
DamageReactionChanceToIgnore=0.5
DamageReactionMinimumDelay=0.125
DamageReactionMaximumDelay=0.25
DamageReactionCooldown=1.0
DamageReactionThreshold=50.0
DamageReactionResetTimer=0.5
JumpFrequency=0.0
CrouchInAirFrequency=0.0
CrouchOnGroundFrequency=0.0
TargetStrafeOverride=Ignore
TargetStrafeMinDelay=0.125
TargetStrafeMaxDelay=0.25
MinProfileChangeTime=0.5
MaxProfileChangeTime=0.9
MinCrouchTime=0.3
MaxCrouchTime=0.6
MinJumpTime=0.3
MaxJumpTime=0.6
LeftStrafeTimeMult=1.0
RightStrafeTimeMult=1.0
StrafeSwapMinPause=0.0
StrafeSwapMaxPause=0.0
BlockedMovementPercent=0.5
BlockedMovementReactionMin=0.125
BlockedMovementReactionMax=0.2
[Dodge Profile]
Name=ADAD
MaxTargetDistance=2500.0
MinTargetDistance=750.0
ToggleLeftRight=true
ToggleForwardBack=false
MinLRTimeChange=0.2
MaxLRTimeChange=0.5
MinFBTimeChange=0.2
MaxFBTimeChange=0.5
DamageReactionChangesDirection=false
DamageReactionChanceToIgnore=0.5
DamageReactionMinimumDelay=0.125
DamageReactionMaximumDelay=0.25
DamageReactionCooldown=1.0
DamageReactionThreshold=0.0
DamageReactionResetTimer=0.1
JumpFrequency=0.0
CrouchInAirFrequency=0.0
CrouchOnGroundFrequency=0.2
TargetStrafeOverride=Ignore
TargetStrafeMinDelay=0.125
TargetStrafeMaxDelay=0.16
MinProfileChangeTime=0.0
MaxProfileChangeTime=0.0
MinCrouchTime=0.1
MaxCrouchTime=0.2
MinJumpTime=0.3
MaxJumpTime=0.6
LeftStrafeTimeMult=1.0
RightStrafeTimeMult=1.0
StrafeSwapMinPause=0.0
StrafeSwapMaxPause=0.0
BlockedMovementPercent=0.5
BlockedMovementReactionMin=0.125
BlockedMovementReactionMax=0.2
[Dodge Profile]
Name=Long Strafes
MaxTargetDistance=2500.0
MinTargetDistance=750.0
ToggleLeftRight=true
ToggleForwardBack=false
MinLRTimeChange=0.5
MaxLRTimeChange=1.5
MinFBTimeChange=0.2
MaxFBTimeChange=0.5
DamageReactionChangesDirection=true
DamageReactionChanceToIgnore=0.5
DamageReactionMinimumDelay=0.125
DamageReactionMaximumDelay=0.25
DamageReactionCooldown=1.0
DamageReactionThreshold=50.0
DamageReactionResetTimer=0.5
JumpFrequency=0.2
CrouchInAirFrequency=0.0
CrouchOnGroundFrequency=0.0
TargetStrafeOverride=Ignore
TargetStrafeMinDelay=0.125
TargetStrafeMaxDelay=0.25
MinProfileChangeTime=0.0
MaxProfileChangeTime=0.0
MinCrouchTime=0.3
MaxCrouchTime=0.6
MinJumpTime=0.3
MaxJumpTime=0.6
LeftStrafeTimeMult=1.0
RightStrafeTimeMult=1.0
StrafeSwapMinPause=0.0
StrafeSwapMaxPause=0.0
BlockedMovementPercent=0.5
BlockedMovementReactionMin=0.125
BlockedMovementReactionMax=0.2
[Weapon Profile]
Name=Heavy Surge Rifle
Type=Hitscan
ShotsPerClick=1
DamagePerShot=20.0
KnockbackFactor=0.1
TimeBetweenShots=0.11265
Pierces=false
Category=FullyAuto
BurstShotCount=1
TimeBetweenBursts=0.1
ChargeStartDamage=0.0
ChargeStartVelocity=X=0.100 Y=0.000 Z=0.000
ChargeTimeToAutoRelease=0.1
ChargeTimeToCap=0.1
ChargeMoveSpeedModifier=1.0
MuzzleVelocityMin=X=0.100 Y=0.000 Z=0.000
MuzzleVelocityMax=X=0.100 Y=0.000 Z=0.000
InheritOwnerVelocity=0.0
OriginOffset=X=0.000 Y=0.000 Z=0.000
MaxTravelTime=10.0
MaxHitscanRange=999999.0
GravityScale=0.0
HeadshotCapable=true
HeadshotMultiplier=2.0
MagazineMax=25
AmmoPerShot=1
ReloadTimeFromEmpty=1.660547
ReloadTimeFromPartial=1.660547
DamageFalloffStartDistance=3500.0
DamageFalloffStopDistance=5833.333496
DamageAtMaxRange=10.0
DelayBeforeShot=0.0
HitscanVisualEffect=None
ProjectileGraphic=Ball
VisualLifetime=0.1
WallParticleEffect=None
HitParticleEffect=None
BounceOffWorld=false
BounceFactor=0.0
BounceCount=0
HomingProjectileAcceleration=0.0
ProjectileEnemyHitRadius=1.0
CanAimDownSight=false
ADSZoomDelay=0.0
ADSZoomSensFactor=0.379403
ADSMoveFactor=1.0
ADSStartDelay=0.0
ShootSoundCooldown=0.08
HitSoundCooldown=0.08
HitscanVisualOffset=X=0.000 Y=0.000 Z=-50.000
ADSBlocksShooting=true
ShootingBlocksADS=false
KnockbackFactorAir=0.1
RecoilNegatable=true
DecalType=1
DecalSize=7.875
DelayAfterShooting=0.0
BeamTracksCrosshair=false
AlsoShoot=
ADSShoot=
StunDuration=0.0
CircularSpread=false
SpreadStationaryVelocity=0.0
PassiveCharging=false
BurstFullyAuto=true
FlatKnockbackHorizontal=0.0
FlatKnockbackVertical=0.0
HitscanRadius=0.0
HitscanVisualRadius=3.15
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=true
AimPunchAmount=0.0
AimPunchResetTime=0.05
AimPunchCooldown=0.5
AimPunchHeadshotOnly=false
AimPunchCosmeticOnly=true
MinimumDecelVelocity=0.0
PSRManualNegation=false
PSRAutoReset=true
AimPunchUpTime=0.05
AmmoReloadedOnKill=25
CancelReloadOnKill=true
FlatKnockbackHorizontalMin=0.0
FlatKnockbackVerticalMin=0.0
ADSScope=No Scope
ADSFOVOverride=51.0
ADSFOVScale=Overwatch
ADSAllowUserOverrideFOV=false
IsBurstWeapon=false
ForceFirstPersonInADS=true
ZoomBlockedInAir=true
ADSCameraOffsetX=0.0
ADSCameraOffsetY=0.0
ADSCameraOffsetZ=0.0
QuickSwitchTime=0.1
Explosive=false
Radius=0.1
DamageAtCenter=0.0
DamageAtEdge=0.0
SelfDamageMultiplier=0.0
ExplodesOnContactWithEnemy=false
DelayAfterEnemyContact=0.0
ExplodesOnContactWithWorld=false
DelayAfterWorldContact=0.0
ExplodesOnNextAttack=false
DelayAfterSpawn=0.0
BlockedByWorld=false
SpreadSSA=0.0,0.1,0.0,0.0
SpreadSCA=0.0,0.1,0.0,0.0
SpreadMSA=0.0,0.1,0.0,0.0
SpreadMCA=0.0,0.1,0.0,0.0
SpreadSSH=0.0,0.1,0.0,0.0
SpreadSCH=0.0,0.1,0.0,0.0
SpreadMSH=0.0,0.1,0.0,0.0
SpreadMCH=0.0,0.1,0.0,0.0
MaxRecoilUp=0.0
MinRecoilUp=0.0
MinRecoilHoriz=0.0
MaxRecoilHoriz=0.0
FirstShotRecoilMult=1.0
RecoilAutoReset=true
TimeToRecoilPeak=0.1
TimeToRecoilReset=0.1
AAMode=2
AAPreferClosestPlayer=false
AAAlpha=1.0
AAMaxSpeed=1.5
AADeadZone=0.0
AAFOV=75.0
AANeedsLOS=true
TrackHorizontal=true
TrackVertical=true
AABlocksMouse=true
AAOffTimer=0.0
AABackOnTimer=0.0
TriggerBotEnabled=true
TriggerBotDelay=0.01
TriggerBotFOV=0.1
StickyLock=false
HeadLock=true
VerticalOffset=0.0
DisableLockOnKill=false
UsePerShotRecoil=false
PSRLoopStartIndex=0
PSRViewRecoilTracking=0.45
PSRCapUp=9.0
PSRCapRight=4.0
PSRCapLeft=4.0
PSRTimeToPeak=0.095
PSRResetDegreesPerSec=40.0
UsePerBulletSpread=false
PBS0=0.0,0.0
[Melee Ability Profile]
Name=Punch
MaxCharges=1.0
ChargeTimer=0.25
ChargesRefundedOnKill=0.0
DelayAfterUse=1.0
FullyAuto=false
AbilityDuration=0.1
HurtboxRadius=229.485748
HurtboxDamage=30.0
HurtboxGroundKnockbackFactor=4.0
HurtboxAirKnockbackFactor=4.0
BlockAttackTimer=0.5
AbilityBlockedWhenAttacking=false
AmmoPerShot=0
FlatKnockbackHorizontal=0.0
FlatKnockbackVertical=0.0
FlatKnockbackHorizontalMin=0.0
FlatKnockbackVerticalMin=0.0
AIUseInCombat=false
AIUseOutOfCombat=false
AIUseOnGround=false
AIUseInAir=false
AIReuseTimer=1.0
AIMinSelfHealth=0.0
AIMaxSelfHealth=100.0
AIMinTargHealth=0.0
AIMaxTargHealth=100.0
AIMinTargDist=0.0
AIMaxTargDist=2000.0
AIMaxTargFOV=15.0
AIDamageReaction=false
AIDamageReactionIgnoreChance=0.0
AIDamageReactionMinDelay=0.125
AIDamageReactionMaxDelay=0.25
AIDamageReactionCooldown=1.0
AIDamageReactionThreshold=0.0
AIDamageReactionResetTimer=0.1
[Sprint Ability Profile]
Name=Run
MaxCharges=1.0
ChargeTimer=0.1
ChargesRefundedOnKill=0.0
DelayAfterUse=0.1
FullyAuto=false
AbilityDuration=0.0
BlockAttackWhileSprinting=true
AbilityBlockedWhenAttacking=false
SpeedModifier=1.3
45DegreeSprint=true
90DegreeSprint=false
135DegreeSprint=false
180DegreeSprint=false
TapToSprint=true
Block45DegreesWhenSprinting=false
AIUseInCombat=false
AIUseOutOfCombat=false
AIUseOnGround=false
AIUseInAir=false
AIReuseTimer=1.0
AIMinSelfHealth=0.0
AIMaxSelfHealth=100.0
AIMinTargHealth=0.0
AIMaxTargHealth=100.0
AIMinTargDist=0.0
AIMaxTargDist=2000.0
AIMaxTargFOV=15.0
AIDamageReaction=false
AIDamageReactionIgnoreChance=0.0
AIDamageReactionMinDelay=0.125
AIDamageReactionMaxDelay=0.25
AIDamageReactionCooldown=1.0
AIDamageReactionThreshold=0.0
AIDamageReactionResetTimer=0.1
[Map Data]
reflex map version 8
global
entity
type WorldSpawn
String32 targetGameOverCamera end
UInt8 playersMin 1
UInt8 playersMax 16
brush
vertices
-576.000000 0.000000 256.000000
448.000000 0.000000 256.000000
448.000000 0.000000 -768.000000
-576.000000 0.000000 -768.000000
-576.000000 -16.000000 256.000000
448.000000 -16.000000 256.000000
448.000000 -16.000000 -768.000000
-576.000000 -16.000000 -768.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000
brush
vertices
-576.000000 272.000000 -768.000000
448.000000 272.000000 -768.000000
448.000000 272.000000 -784.000000
-576.000000 272.000000 -784.000000
-576.000000 0.000000 -768.000000
448.000000 0.000000 -768.000000
448.000000 0.000000 -784.000000
-576.000000 0.000000 -784.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000
brush
vertices
-576.000000 272.000000 272.000000
448.000000 272.000000 272.000000
448.000000 272.000000 256.000000
-576.000000 272.000000 256.000000
-576.000000 0.000000 272.000000
448.000000 0.000000 272.000000
448.000000 0.000000 256.000000
-576.000000 0.000000 256.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000
brush
vertices
448.000000 272.000000 256.000000
464.000000 272.000000 256.000000
464.000000 272.000000 -768.000000
448.000000 272.000000 -768.000000
448.000000 0.000000 256.000000
464.000000 0.000000 256.000000
464.000000 0.000000 -768.000000
448.000000 0.000000 -768.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000
brush
vertices
-592.000000 272.000000 256.000000
-576.000000 272.000000 256.000000
-576.000000 272.000000 -768.000000
-592.000000 272.000000 -768.000000
-592.000000 0.000000 256.000000
-576.000000 0.000000 256.000000
-576.000000 0.000000 -768.000000
-592.000000 0.000000 -768.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000
brush
vertices
-592.000000 704.000000 256.000000
-576.000000 704.000000 256.000000
-576.000000 704.000000 -768.000000
-592.000000 704.000000 -768.000000
-592.000000 272.000000 256.000000
-576.000000 272.000000 256.000000
-576.000000 272.000000 -768.000000
-592.000000 272.000000 -768.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000 internal/editor/textures/editor_clip
brush
vertices
448.000000 704.000000 256.000000
464.000000 704.000000 256.000000
464.000000 704.000000 -768.000000
448.000000 704.000000 -768.000000
448.000000 272.000000 256.000000
464.000000 272.000000 256.000000
464.000000 272.000000 -768.000000
448.000000 272.000000 -768.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000 internal/editor/textures/editor_clip
brush
vertices
-576.000000 704.000000 -768.000000
448.000000 704.000000 -768.000000
448.000000 704.000000 -784.000000
-576.000000 704.000000 -784.000000
-576.000000 272.000000 -768.000000
448.000000 272.000000 -768.000000
448.000000 272.000000 -784.000000
-576.000000 272.000000 -784.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000 internal/editor/textures/editor_clip
brush
vertices
-576.000000 704.000000 272.000000
448.000000 704.000000 272.000000
448.000000 704.000000 256.000000
-576.000000 704.000000 256.000000
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448.000000 272.000000 272.000000
448.000000 272.000000 256.000000
-576.000000 272.000000 256.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000 internal/editor/textures/editor_clip
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0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000 internal/editor/textures/editor_clip
brush
vertices
-576.000000 720.000000 256.000000
448.000000 720.000000 256.000000
448.000000 720.000000 -768.000000
-576.000000 720.000000 -768.000000
-576.000000 704.000000 256.000000
448.000000 704.000000 256.000000
448.000000 704.000000 -768.000000
-576.000000 704.000000 -768.000000
faces
0.000000 0.000000 1.000000 1.000000 0.000000 0 1 2 3 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 6 5 4 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 2 1 5 6 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 0 3 7 4 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 3 2 6 7 0x00000000 internal/editor/textures/editor_clip
0.000000 0.000000 1.000000 1.000000 0.000000 1 0 4 5 0x00000000 internal/editor/textures/editor_clip
entity
type PlayerSpawn
Vector3 position -64.000000 0.000000 -736.000000
Bool8 teamA 0
entity
type CameraPath
UInt32 entityIdAttachedTo 5
UInt8 posLerp 2
UInt8 angleLerp 2
entity
type Effect
Vector3 position 0.000000 256.000000 0.000000
String64 effectName internal/misc/reflectionprobe
entity
type Target
Vector3 position 352.000000 256.000000 224.000000
Vector3 angles -135.000000 30.000000 0.000000
String32 name end
entity
type PlayerSpawn
Vector3 position -64.000000 0.000000 224.000000
Vector3 angles 180.000000 0.000000 0.000000
Bool8 teamA 0
entity
type PlayerSpawn
Vector3 position 416.000000 0.000000 -256.000000
Vector3 angles 270.000000 0.000000 0.000000
Bool8 teamA 0
entity
type PlayerSpawn
Vector3 position -544.000000 0.000000 -256.000000
Vector3 angles 90.000000 0.000000 0.000000
Bool8 teamA 0
entity
type PlayerSpawn
Vector3 position -64.000000 0.000000 -256.000000
Vector3 angles 90.000000 0.000000 0.000000
Bool8 teamB 0
|
625c29e1bf65bc2a962f5e215c422eda4389fe84
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/503/CH8/EX8.14/ch8_14.sci
|
e28b01d8c126cfd5e6af76dc36ae5649521e056f
|
[] |
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
| 836
|
sci
|
ch8_14.sci
|
//to calculate armature current, pf ,power angle, power , shaft torques,kVar
clc;
j=sqrt(-1);
P=8000;
Prot=500;
Pmg=P+Prot;
Pein=Pmg;
Ef=750/sqrt(3);
Vt=231;
Xs=16;
dl=asind(Xs*(Pein/3)/(Ef*Vt));
Eff=Ef*complex(cosd(-dl),sind(-dl));
Ia=(Vt-Eff)/(j*Xs);
disp(abs(Ia),'armature current(A)');
disp(cosd(atand(imag(Ia)/real(Ia))),'pf');
f=50;
p=4;
n_s=120*f/p;
w_s=2*%pi*n_s/60;
T=Pein/w_s;disp(T,'torque developed(Nm)');
T_s=P/w_s;disp(T_s,'shaft torques(Nm)');
Ef=600/sqrt(3);
Ia=(Vt-Ef)/(j*Xs);
rr=3*Vt*Ia/1000;
disp(rr,'kVar rating');
c=(abs(Ia)/Vt)/(2*%pi*f);
disp(-c,'capicator rating(F)');
Ef=300/sqrt(3);
Ia=(Vt-Ef)/(j*Xs);
rr=3*Vt*Ia/1000;
disp(-rr,'kVar rating');
L=(Vt/abs(rr))/(2*%pi*f);
disp(L,'inductor rating(H)');
Ia=j*2000/Vt;
Ef=Vt-j*Ia*Xs;
disp(abs(Ef)*sqrt(3),'excitation(V)');
|
fe3d2fb5952161cf8a64b80621998b705818dee0
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/506/CH13/EX13.4.a/Example13_4a.sce
|
fcfd14de3ebfc6cba4dd5b04e53f31c7b468cd44
|
[] |
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
| 407
|
sce
|
Example13_4a.sce
|
clear;
clc;
//Caption: To find gain and resistance of Voltage Shunt Feedback
//Given Values
Rc=4;//in K
r=40;//in K
Rs=10;//in K
hie=1.1;//in K
hfe=50;
hre=0;
hoe=0;
//Required Formulae
rc=(Rc*r)/(Rc+r);
R=(Rs*r)/(Rs+r);
Rm=-(hfe*rc*R)/(R+hie);
disp('K',Rm,'Rm=');
B=-1/r;//in mA/V
D=1+(B*Rm);
Rmf=Rm/D;
//Avf = Vo/Vs = Vo/(Is*Rs) = Rmf/Rs
Avf=Rmf/Rs;
disp(Avf,'Avf=');
//End
|
b5b9a63d2e65b8a2bdc283b46e9291e7115439f8
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2294/CH8/EX8.29/EX8_29.sce
|
35ac651ad3dfb576cf3f3d0f83d61fc4f20b368e
|
[] |
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
|
EX8_29.sce
|
//Find dft of the following sequence
//Example 8.29.1
clc;
n=-10:10;
for i=1:length(n)
if n(i)==0 then
x(i)=1;
else
x(i)=0;
end
end
y=fft(x,-1);
disp(y,'The dft of the sequence is:');
//Find dft of the following sequence
//Example 8.29.2
clc;
n=-10:10;n0=2;
for i=1:length(n)
if n(i)==n0 then
x(i)=1;
else
x(i)=0;
end
end
y=fft(x,-1);
disp(y,'The dft of the sequence is:');
//Find dft of the following sequence
//Example 8.29.3
clc;
n=-10:10;a=2;
for i=1:length(n)
x(i)=a^n(i);
end
y=fft(x,-1);
disp(y,'The dft of the sequence is:');
|
5f74f39bde71debc8ab509c7b050f7ee7ff24607
|
d01bf962afff16bc1ce292c49da5923ebbe59775
|
/Maths/Scilab/Finance-LMRS.sce
|
f6f8d5119fc11db83b0d58ca3f84889c341d423e
|
[] |
no_license
|
fredkerdraon/Reference-research
|
71d0af22f84605ed0c53907acd6b248400c47388
|
1f48fdfebbe766bbd268b4f1853ab98162f57425
|
refs/heads/master
| 2023-05-05T12:18:18.655367
| 2020-02-08T22:08:15
| 2020-02-08T22:08:15
| 71,020,179
| 0
| 0
| null | 2023-04-19T18:37:49
| 2016-10-15T23:49:14
|
POV-Ray SDL
|
UTF-8
|
Scilab
| false
| false
| 4,223
|
sce
|
Finance-LMRS.sce
|
function V0=crr_put_europ(r,sigma,T,K,S0,M)
// version naïve avec tableau !
dt=T/M
beta=.5*(exp(-r*dt)+exp((r+sigma^2)*dt))
u=beta+sqrt((beta^2-1))
d=1/u
p=(exp(r*dt)-d)/(u-d)
MS=zeros(M+1,M)
MV=zeros(M+1,M)
for i=1:M
for j=0:i
MS(j+1,i)=S0*u^j*d^(i-j)
end
end
for j=0:M
MV(j+1,M)=max(K-MS(j+1,M),0)
end
for i=M-1:-1:1
for j=0:i
MV(j+1,i)=exp(-r*dt)*(p*MV(j+2,i+1)+(1-p)*MV(j+1,i+1))
end
end
V0=exp(-r*dt)*(p*MV(2,1)+(1-p)*MV(1,1))
endfunction
function V0=crr_put_europ2(r,sigma,T,K,S0,M)
// version sans tableau
// encore optimisable en utilisant produit matriciel
// de Scilab
dt=T/M
beta=.5*(exp(-r*dt)+exp((r+sigma^2)*dt))
u=beta+sqrt((beta^2-1))
d=1/u
p=(exp(r*dt)-d)/(u-d)
MV=zeros(M+1,1)
a=exp(-r*dt)
for j=0:M
MV(j+1,1)=max(K-S0*u^j*d^(M-j),0)
end
for i=M-1:-1:1 // boucles imbriquées !!
for j=0:i
MV(j+1,1)=a*(p*MV(j+2,1)+(1-p)*MV(j+1,1))
end
end
V0=a*(p*MV(2,1)+(1-p)*MV(1,1))
endfunction
function V0=crr_put_europ3(r,sigma,T,K,S0,M)
// version sans tableau
// 2nde optimisation
dt=T/M
beta=.5*(exp(-r*dt)+exp((r+sigma^2)*dt))
u=beta+sqrt((beta^2-1))
d=1/u
p=(exp(r*dt)-d)/(u-d)
MV=zeros(M+1,1)
a=exp(-r*dt)
for j=0:M
MV(j+1,1)=max(K-S0*u^j*d^(M-j),0)
end
for i=M-1:-1:1 // 1 seule boucle
MV(1:i+1)=a*(p*MV(2:i+2,1)+(1-p)*MV(1:i+1,1))
// vectorisation Scilab : le top !
end
V0=a*(p*MV(2,1)+(1-p)*MV(1,1))
endfunction
function V0=crr_calldiv_europ3(r,sigma,dd,T,K,S0,M)
// version sans tableau
// 2nde optimisation
dt=T/M
beta=.5*(exp(-(r-dd)*dt)+exp((r-dd+sigma^2)*dt))
u=beta+sqrt((beta^2-1))
d=1/u
p=(exp((r-dd)*dt)-d)/(u-d)
MV=zeros(M+1,1)
a=exp(-(r)*dt)
for j=0:M
MV(j+1,1)=max(S0*u^j*d^(M-j)-K,0)
end
for i=M-1:-1:1 // 1 seule boucle
MV(1:i+1)=a*(p*MV(2:i+2,1)+(1-p)*MV(1:i+1,1))
// vectorisation Scilab : le top !
end
V0=a*(p*MV(2,1)+(1-p)*MV(1,1))
endfunction
function V0=crr_put_amer(r,sigma,T,K,S0,M)
// version sans tableau
// plus difficilement optimisable
// en utilisant produit matriciel
dt=T/M
beta=.5*(exp(-r*dt)+exp((r+sigma^2)*dt))
u=beta+sqrt((beta^2-1))
d=1/u
p=(exp(r*dt)-d)/(u-d)
MV=zeros(M+1,1)
a=exp(-r*dt)
for j=0:M
MV(j+1,1)=max(K-S0*u^j*d^(M-j),0)
end
for i=M-1:-1:1 // boucles imbriquées !!
for j=0:i
MV(j+1,1)=max(max(K-S0*u^j*d^(i-j),0),a*(p*MV(j+2,1)+(1-p)*MV(j+1,1)))
end
end
V0=max(max(K-S0),a*(p*MV(2,1)+(1-p)*MV(1,1)))
endfunction
function V0=crr_call_amer(r,sigma,T,K,S0,M)
// version sans tableau
// plus difficilement optimisable
// en utilisant produit matriciel
dt=T/M
beta=.5*(exp(-r*dt)+exp((r+sigma^2)*dt))
u=beta+sqrt((beta^2-1))
d=1/u
p=(exp(r*dt)-d)/(u-d)
MV=zeros(M+1,1)
a=exp(-r*dt)
for j=0:M
MV(j+1,1)=max(S0*u^j*d^(M-j)-K,0)
end
for i=M-1:-1:1 // boucles imbriquées !!
for j=0:i
MV(j+1,1)=max(max(S0*u^j*d^(i-j)-K,0),a*(p*MV(j+2,1)+(1-p)*MV(j+1,1)))
end
end
V0=max(max(S0-K),a*(p*MV(2,1)+(1-p)*MV(1,1)))
endfunction
function V0=crr_calldiv_amer(r,sigma,dd,T,K,S0,M)
// version sans tableau
// plus difficilement optimisable
// en utilisant produit matriciel
dt=T/M
beta=.5*(exp(-(r-dd)*dt)+exp((r-dd+sigma^2)*dt))
u=beta+sqrt((beta^2-1))
d=1/u
p=(exp((r-dd)*dt)-d)/(u-d)
MV=zeros(M+1,1)
a=exp(-r*dt)
for j=0:M
MV(j+1,1)=max(S0*u^j*d^(M-j)-K,0)
end
for i=M-1:-1:1 // boucles imbriquées !!
for j=0:i
MV(j+1,1)=max(max(S0*u^j*d^(i-j)-K,0),a*(p*MV(j+2,1)+(1-p)*MV(j+1,1)))
end
end
V0=max(max(S0-K),a*(p*MV(2,1)+(1-p)*MV(1,1)))
endfunction
function V=callbs_formule(S,K,T,r,sig,dd)
d1=(log(S/K)+(r-dd+sig^2/2)*T)/(sig*T^.5)
d2=d1-sig*T^.5
D1=cdfnor("PQ",d1,0,1)
D2=cdfnor("PQ",d2,0,1)
V=S*exp(-dd*T)*D1-K*exp(-T*r)*D2
endfunction
function V=putbs_formule(S,K,T,r,sig)
d1=(log(S/K)+(r+sig^2/2)*T)/(sig*T^.5)
d2=d1-sig*T^.5
D1=cdfnor("PQ",-d1,0,1)
D2=cdfnor("PQ",-d2,0,1)
V=-S*D2+K*exp(-T*r)*D1
endfunction
xpt=linspace(1,30,20);
K=10
r=.25
sigma=.6
T=1
dd=.2
M=1024
VAM=[]
VEU=[]
for i=1:length(xpt)
VAM=[VAM, callbs_formule(xpt(i),K,T,r,sigma,dd)];
VEU=[VEU, crr_calldiv_amer(r,sigma,dd,T,K,xpt(i),M)];
end
|
4b3d6a002750c4dfda9a9dd11150845a1519fea8
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1026/CH10/EX10.10/Example10_10.sce
|
d2e524de9cd26d67c0b49afad667c8378c24e5e5
|
[] |
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
|
Example10_10.sce
|
//chapter10,Example10_10,pg 275
//F=mg=qE
E=250
R=10^-8
rho=10^3//density
m=(4/3)*%pi*(R^3)*rho//m=volume*density
W=m*9.8//weight of drop(mg)
q=W/E
printf("charge on water drop\n")
disp(q)
|
93cbb46b96d570a12ff37f594885c760d99c3449
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1898/CH13/EX13.7/Ex13_7.sce
|
2ee337dac68af5420f1adfac559df503e1ad6aa9
|
[] |
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
|
Ex13_7.sce
|
clear all; clc;
disp("Scilab Code Ex 13.7 : ")
//Given:
d = 30; //mm
r = d/2;
L = 600; //mm
sigma_pl = 150;//MPa
//Calculations:
I = (%pi/4)*(r^4);
A = %pi*r^2;
r_gyr = sqrt(I/A);
K = 1;
sl_ratio = (K*L)/(r_gyr);
flag1 = 0;
//Assuming the critical stress is elastic:
E = 150/0.001;
sigma_cr1 = (%pi^2*E)/(sl_ratio^2); //Pcr = (%pi^2*EI)/(l^2)
if(sigma_cr1 > sigma_pl)
Et = (270 - 150)/(0.002 - 0.001);
sigma_cr2 = (%pi^2*Et)/(sl_ratio^2); //Pcr = (%pi^2*EI)/(l^2)
if(sigma_cr2>150 & sigma_cr2<270)
Pcr = sigma_cr2*A;
Pcr = Pcr/1000; //in kN
printf('\n\nThe critical load when used as a pin supported column = %1.0fkN',Pcr);
end
end
|
a939adbee9d53ff72bafff7a6ba330a5fbacbc23
|
4058f38b392324aa5099819881f3c7d7219a174f
|
/3 bit Shift Register/SIPO_using_74HC595/SIPO_using_74HC595_consecutive_inputs/Method 2/cmd_shift_out_.sci
|
3649eb6bda37fd97e671717aba62e6ad1249a79f
|
[] |
no_license
|
anupma-s/Scilab-Xcos-Arduino-Digital-Circuits
|
612a033422bf14e2e58bcdce371f15cafb30224f
|
2b4bf8e8f155d20a5eda2feb31c5523a51569d73
|
refs/heads/master
| 2021-01-20T17:20:13.073180
| 2016-07-04T15:25:07
| 2016-07-04T15:25:07
| 62,569,455
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 417
|
sci
|
cmd_shift_out_.sci
|
function[]= cmd_shift_out_(dataPin,clockPin,inPin)
disp ("Give serial input: ")
sleep(250)
cmd_digital_out(1,dataPin,cmd_digital_in(1,inPin))//if inPin is HIGH i.e. if input is given, write HIGH on Serial In Pin of IC
disp("Serial input stored: ")
cmd_digital_out(1,clockPin,1)
cmd_digital_out(1,clockPin,0)
sleep(150)
endfunction
|
8fe078a4252c500d38681170194da7d97645bba7
|
67a252961f6616fc6db89eb11c1c83abf4d41468
|
/CS4110Design4/CS16B032RAM4K.tst
|
95b37a4f348ad20486618d6aa94d3e03eeed0c2a
|
[] |
no_license
|
ramyavelaga9/CS4110
|
5a45497cd7ef28d4472a57a257dad8e5f4a3d17b
|
4a3cd82916820e4f7a4930a0efce14def8268dfc
|
refs/heads/master
| 2020-07-17T23:41:12.196500
| 2019-11-20T04:24:32
| 2019-11-20T04:24:32
| 203,223,619
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 1,981
|
tst
|
CS16B032RAM4K.tst
|
load CS16B032RAM4K.hdl,
output-file CS16B032RAM4K.out,
compare-to CS16B032RAM4K.cmp,
output-list time%S1.4.1 in%D1.6.1 load%B2.1.2 address%D2.5.2 out%D1.6.1;
set in 16994,
set load 0,
set address 3755,
tick,
output;
tock,
output;
set in 11171,
set load 1,
set address 2707,
tick,
output;
tock,
output;
set in 12034,
set load 1,
set address 3285,
tick,
output;
tock,
output;
set in 1239,
set load 1,
set address 3107,
tick,
output;
tock,
output;
set in 20297,
set load 0,
set address 3425,
tick,
output;
tock,
output;
set in 11360,
set load 1,
set address 1559,
tick,
output;
tock,
output;
set in 789,
set load 0,
set address 3439,
tick,
output;
tock,
output;
set in -11712,
set load 0,
set address 2308,
tick,
output;
tock,
output;
set in 12567,
set load 1,
set address 616,
tick,
output;
tock,
output;
set in 18189,
set load 1,
set address 2678,
tick,
output;
tock,
output;
set in 3213,
set load 0,
set address 1950,
tick,
output;
tock,
output;
set in -15079,
set load 1,
set address 1824,
tick,
output;
tock,
output;
set in 18207,
set load 1,
set address 2859,
tick,
output;
tock,
output;
set in -949,
set load 0,
set address 3461,
tick,
output;
tock,
output;
set in -4493,
set load 0,
set address 1611,
tick,
output;
tock,
output;
set in -3252,
set load 0,
set address 929,
tick,
output;
tock,
output;
set in 3342,
set load 0,
set address 1412,
tick,
output;
tock,
output;
set in -21234,
set load 1,
set address 3058,
tick,
output;
tock,
output;
set in -13741,
set load 0,
set address 1614,
tick,
output;
tock,
output;
set in -14773,
set load 0,
set address 2303,
tick,
output;
tock,
output;
set in -11409,
set load 0,
set address 2508,
tick,
output;
tock,
output;
set in 13548,
set load 1,
set address 1753,
tick,
output;
tock,
output;
set in 20825,
set load 1,
set address 2627,
tick,
output;
tock,
output;
set in -1018,
set load 0,
set address 2685,
tick,
output;
tock,
output;
set in 20824,
set load 0,
set address 2590,
tick,
output;
tock,
output;
|
327fe2d937ebc9832b114f0d653283f06862689b
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1448/CH9/EX9.1.i/I9_1.sce
|
b6f2025b75a7cbf16cce2714339c0243652630cd
|
[] |
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
| 165
|
sce
|
I9_1.sce
|
clc
//Initialization of variables
Gr=-10^5 //kJ/mol
v=1
F=9.6485*10^4 //C/mol
//calculations
E=-Gr/(v*F)
//results
printf("potential of the cell = %d V",E)
|
0c34de224f9624dbaeeaccfa7725547e61bf4155
|
bc0270610663ade53f4307ff9e8f1ecc1637bc16
|
/SynthesizeTest.sce
|
a674604768971dbbbcee5810742d3b5593b6ae58
|
[] |
no_license
|
kani-m/SoundSynthesize
|
8f3e05928a8600e843a60feee218510b3a72452e
|
b4d317c487d1afe81d02257d01e49919a769678c
|
refs/heads/master
| 2016-09-10T16:26:04.203819
| 2015-01-13T07:14:07
| 2015-01-13T07:14:07
| 29,176,889
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 1,654
|
sce
|
SynthesizeTest.sce
|
clear;
clf()
function [out]=H(s)
// Butterworth filter with 2 degree
out = 1 ./ (s.^2+1.4142*s+1);
// Butterworth filter with 5 degree
// out = 1 ./ (s.^5+3.24*s.^4+5.24*s.^3+5.24*s.^2+3.24*s+1);
endfunction
n = 8192*2
sf = 44100;
Source = zeros(1,n);
Formant = zeros(1,n);
//V = [800 1300 2500 3500 4500]; // Vowwl for [a]
//V = [250 2100 3100 3500 4500]; // Vowel for [i]
//V = [250 1400 2200 3500 4500]; // Vowel for [u]
//V = [450 1900 2400 3500 4500]; // Voewl for [e]
V = [450 900 2600 3500 4500]; // Vowel for [o]
// Gain = 20*log10(Signal) [dB]
// As max(Signal) = 9.45,
// if Ratio = (Peaks(Signal)/Max(Signal) = [1.0 0.275 0.041 0.025 0.008]),
// then Gain ~~ [19 8 -8 -12 -22].
//
// Max of H(s) of this program may be 1.0,
// so we use Ratio*10.0*abs(H(s)) = Strong*abs(H(s))
Strong = [10.0 2.75 0.41 0.25 0.08];
bw_for = 180; //bandwidth for formant
bf = 150; // base_frequency
for i = bf:bf:n/2
t = i/bf;
if t <= 100 then
Source(1,i) = 10-0.1*t;
end
end
//Source(1) = 10000 + 100.0*rand();
//for i=1:n
// Source(i) = Source(i) + 10.0*rand(1.0);
//end
f = 1:1:n;
omega = 2 * %pi .* f;
s = %i*omega;
for iter = 1:5
omega_low = omega(V(iter)-bw_for);
omega_high = omega(V(iter)+bw_for);
omega_0 = sqrt(omega_low*omega_high);
omega_b = omega_high - omega_low;
Formant = Formant + Strong(iter)*abs(H((s.^2+omega_0^2) ./ (s.*omega_b)));
end
Spectrum = Source .* Formant;
for i = 1:n/2
Spectrum(1,n-i+1) = Spectrum(1,i)
end
//plot(Source);
//plot(Formant);
//plot(20*log10(Formant));
plot(Spectrum);
//graph = gca();
//graph.data_bounds = [0 0; 5000 1.0];
snd = ifft(Spectrum);
playsnd(snd*100, sf);
|
466ebf5ffe994162004204ddc3b8fa2ba54873fe
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/683/CH11/EX11.6/RJ_6.sce
|
9f47f80d4e7d3a75e3a37afa8057407129e4c582
|
[] |
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
| 263
|
sce
|
RJ_6.sce
|
// sum 11-6
clc;
clear;
P=12*10^3;
Tmax=100;
n=6;
e=50+50+(5/2);
T=P*e;
Td=P/n;
ra=125;
k=T/((2*125^2)+(2*75^2)+(2*25^2));
Tr=(k*ra)+Td;
A=Tr/Tmax;
d=sqrt(A*4/%pi);
d=12;
// printing data in scilab o/p window
printf(" d is %0.0f mm ",d);
|
ce882fde1c0a68a21ed0e095dd3440109d131f59
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2582/CH1/EX1.9/Ex1_9.sce
|
1d0512a7c7c8cf00ff6f33ed7dc6d8aa167c1a1e
|
[] |
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
| 141
|
sce
|
Ex1_9.sce
|
//Ex 1.9
clc;
clear;
close;
format('v',5);
Beta=20;//unitless
IObyIREF=1/(1+2/Beta);//Current gain
disp(IObyIREF,"Current gain : ");
|
240dccec775e9c2881c92283331da98f581bf802
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/167/CH7/EX7.14/ex14.sce
|
df5f0cf3861b8cf5a1bd78b80b6c8b7e63fd2c0b
|
[] |
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
| 1,097
|
sce
|
ex14.sce
|
//ques14
//Isentropic Efficiency of a Steam Turbine
clear
clc
//state 1
P1=3;//pressure in MPa
T1=400;//temperature in C
//from table
h1=3231.7;//enthalpy of heat in kJ/kg
s1=6.9235;//enropy in kJ/kg.k
//state 2a
P2a=50;//pressure in kPa
T2a=100;//temp in C
h2a=2682.4;//enthalpy of heat in kJ/kg
//state 2s
P2s=50;//pressure in kPa
s2s=6.9235;//s2s=s1 entropy remains same
//from table
sf=1.0912;//entropy of fluid state in kJ/kg.k
sg=7.5931;//entropy of vapor in kJ.kg.k
//at end,steam exists as a saturated mixture since sf<s2s<sg
hf=340.54;//enthalpy of heat of fluid state in kJ/kg
hfg=2304.7;//enthalpy difference of vapor and liquid state in kJ/kg
x2s=(s2s-sf)/(sg-sf);//x factor
h2s=hf+x2s*(hfg);//enthalpy of heat in kJ/kg
//using the equation 7-61 in book we get
n=(h1-h2a)/(h1-h2s);
printf('(a) Isentropic efficiency = %.1f percent \n',n*100);
Wout=2000//output power in kJ/s
ms=Wout/(h1-h2a);//mass flow rate in kg/s
printf(' (b) The mass flow rate of steam = %.2f kg/s ',ms);//through this turbine from the energy balance for steady-flow systems
|
c6d422e2fef89a6a03e8a1eecdc5d67b07516480
|
ee0e6c3f6c8b066bda30a45fb7b3820dd5a2911d
|
/PCB/PCB/vbreport/work/VBPCBP.TST
|
4b2bb2e83b6d2689d64098a3a164756c443e1637
|
[] |
no_license
|
le-roux/Makahiya
|
30723ee1190ce015822d0d48cccb2e0992e90669
|
5e62d17ef47d0e4a421cb7858f5c3fb7d63881fe
|
refs/heads/master
| 2021-01-01T20:14:25.686284
| 2017-02-10T07:39:40
| 2017-02-10T07:39:40
| 98,795,127
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 16,440
|
tst
|
VBPCBP.TST
|
CellID CellName CompType MountType Verified NoPins GlueX GlueY AssemblyX AssemblyY Height TimeStamp History Description
1 AMW006 IC_OTHER SURFACE NO 48 0.000 0.000 0.000 0.000 0.000 12/03/2015 17:20 Cell modified: Mar 12, 2015 @ 04:34 PM by ROSE@BI-WIN7
2 B3U_3000P GENERAL SURFACE NO 2 0.000 0.000 0.000 0.000 4.500 27/03/2010 19:09 Cell modified: Mar 27, 2010 @ 07:09 PM by Alexis@LUTIN2
3 RN42 IC_OTHER MIXED NO 36 0.000 0.000 0.000 0.000 2.400 23/10/2016 22:35 Cell modified: Oct 23, 2016 @ 10:35 PM by root@WIN10
4 AMP7-188275-4 CONNECTOR MIXED NO 4 0.000 0.000 0.000 0.000 7.000 05/04/2012 23:56 Cell modified: Apr 05, 2012 @ 11:56 PM by Alexis@LUTIN2
5 AMP7-188275-8 CONNECTOR MIXED NO 8 0.000 0.000 0.000 0.000 7.000 30/03/2011 02:22 Cell modified: Mar 30, 2011 @ 02:22 AM by Alexis@LUTIN2
6 BAR03P2.54/W1.27 CONNECTOR THROUGH NO 3 0.000 0.000 0.000 0.000 10.000 25/02/2003 12:54 Cell modified: Feb 25, 2003 @ 12:54 PM by alexis@LUTIN
7 BAR03P2.54/W2.54 CONNECTOR THROUGH NO 3 0.000 0.000 0.000 0.000 10.000 25/02/2003 12:55 Cell modified: Feb 25, 2003 @ 12:55 PM by alexis@LUTIN
8 DC_JACK CONNECTOR THROUGH NO 3 0.000 0.000 0.000 0.000 11.000 10/10/2003 14:27 Cell modified: Oct 10, 2003 @ 02:27 PM by alexis@LUTIN
9 FTSH-105-01-L-DV CONNECTOR SURFACE NO 10 0.000 0.000 0.000 0.000 5.600 21/03/2014 19:36 Cell modified: Mar 21, 2014 @ 07:36 PM by Alexis@BI-WIN7
10 LUMBERG-1503-02 CONNECTOR MIXED NO 4 0.000 0.000 0.000 0.000 11.000 21/10/2007 21:42 Cell modified: Oct 21, 2007 @ 09:42 PM by Alexis@LUTIN2
11 U.FL-R-SMT01 CONNECTOR MIXED NO 3 0.000 0.000 0.000 0.000 1.250 14/03/2015 17:01 Cell modified: Mar 14, 2015 @ 05:01 PM by ROSE@BI-WIN7
12 C0603 DISCRETE_CHIP SURFACE NO 2 0.000 0.000 0.000 0.000 0.870 21/11/2001 17:30 Cell modified: Nov 21, 2001 @ 05:30 PM by phde@PHDE1
13 C0805 DISCRETE_CHIP SURFACE NO 2 0.000 0.000 0.000 0.000 1.350 21/11/2001 17:32 Cell modified: Nov 21, 2001 @ 05:32 PM by phde@PHDE1
14 C1210 DISCRETE_CHIP SURFACE NO 2 0.000 0.000 0.000 0.000 1.800 25/02/2003 13:01 Cell modified: Feb 25, 2003 @ 01:01 PM by alexis@LUTIN
15 L0805 DISCRETE_CHIP SURFACE NO 2 0.000 0.000 0.000 0.000 1.450 25/02/2003 13:05 Cell modified: Feb 25, 2003 @ 01:05 PM by alexis@LUTIN
16 L080510 DISCRETE_CHIP SURFACE NO 2 0.000 0.000 0.000 0.000 0.900 01/09/2016 23:29 Cell modified: Sep 01, 2016 @ 11:29 PM by root@WIN10
17 PAD_3x2 CONNECTOR SURFACE NO 1 0.000 0.000 0.000 0.000 0.000 28/03/2013 20:23 Cell modified: Mar 28, 2013 @ 08:23 PM by Alexis@BI-WIN7 Connecteur de test 3x2mm
18 R0603 DISCRETE_CHIP SURFACE NO 2 0.000 0.000 0.000 0.000 0.870 21/11/2001 19:14 Cell modified: Nov 21, 2001 @ 07:14 PM by phde@PHDE1
19 R2010W DISCRETE_CHIP SURFACE NO 2 0.000 0.000 0.000 0.000 0.750 23/03/2014 22:27 Cell modified: Mar 23, 2014 @ 10:27 PM by Alexis@LUTIN2
20 R2512 DISCRETE_CHIP SURFACE NO 2 0.000 0.000 0.000 0.000 0.550 21/11/2001 19:19 Cell modified: Nov 21, 2001 @ 07:19 PM by phde@PHDE1
21 SM49US DISCRETE_OTHER SURFACE NO 2 0.000 0.000 0.000 0.000 4.000 25/02/2003 13:08 Cell modified: Feb 25, 2003 @ 01:08 PM by alexis@LUTIN
22 SOT23 DISCRETE_CHIP SURFACE NO 3 0.000 0.000 0.000 0.000 1.100 08/10/2016 23:56 Cell modified: Oct 08, 2016 @ 11:56 PM by root@WIN10
23 SOT223 DISCRETE_CHIP SURFACE NO 4 0.000 0.000 0.000 0.000 1.800 21/11/2001 18:26 Cell modified: Nov 21, 2001 @ 06:26 PM by phde@PHDE1
24 LQFP064_050_1215_1215_160 IC_PLCC SURFACE NO 64 0.000 0.000 0.000 0.000 1.600 28/03/2010 18:37 Cell modified: Mar 28, 2010 @ 06:37 PM by Alexis@LUTIN2
25 QFN16E_050_400_400_81 IC_FLIPCHIP SURFACE NO 17 0.000 0.000 0.000 0.000 0.800 24/10/2016 00:27 Cell modified: Oct 24, 2016 @ 12:27 AM by root@WIN10
26 MS10_050_30_30_110 IC_SOIC SURFACE NO 10 0.000 0.000 0.000 0.000 1.100 25/03/2014 00:14 Cell modified: Mar 25, 2014 @ 12:14 AM by Alexis@LUTIN2
27 (_VB_DRILL_DRAWING_)THRU GENERAL SURFACE YES 0 0.000 0.000 0.000 0.000 0.000 05/01/2017 07:03 No History Found Drill Chart
28 (_VB_DRILL_SYMBOLS_)THRU GENERAL SURFACE YES 0 0.000 0.000 0.000 0.000 0.000 05/01/2017 07:03 No History Found Drill Symbols
29 DXF_SVG battery GENERAL SURFACE NO 0 0.000 0.000 0.000 0.000 0.000 01/09/2016 21:16 Cell created: Sep 01, 2016 @ 09:16 PM by WIN10:root
|
0636f85fbc58772362f7c3225d64be7b0ca2961d
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3769/CH3/EX3.22/Ex3_22.sce
|
f118f6805d63fbbe360ec8839ecb85e9918401b8
|
[] |
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
| 157
|
sce
|
Ex3_22.sce
|
clear
//Given
q=8.85*10**-6
e=8.85*10**-12
//Calculation
a=q/e
b=a/6.0
//Result
printf("\n Electric flux through each face is %0.2f Nm**2C-1",b*10**-5)
|
aae38885e9554560313b4fedf92add85fac624a7
|
e0124ace5e8cdd9581e74c4e29f58b56f7f97611
|
/3913/CH12/EX12.3/Ex12_3.sce
|
86e160b29c0a45616bfd40e2a81cbed3b817ad4b
|
[] |
no_license
|
psinalkar1988/Scilab-TBC-Uploads-1
|
159b750ddf97aad1119598b124c8ea6508966e40
|
ae4c2ff8cbc3acc5033a9904425bc362472e09a3
|
refs/heads/master
| 2021-09-25T22:44:08.781062
| 2018-10-26T06:57:45
| 2018-10-26T06:57:45
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 280
|
sce
|
Ex12_3.sce
|
//Chapter 12 : Solutions to the Exercises
//Scilab 6.0.1
//Windows 10
clear;
clc;
//Solution for 1.3
//matrix whose entries are given by
//xij = (-1)^i-j
A=[1 -1 1;-1 1 -1;1 -1 1];
mprintf('matrix whose entries are given by ')
mprintf('\nxij = (-1)^i-j')
disp(A)
|
468410b38212a085ba6cd5be7cd6a6717405727c
|
01ecab2f6eeeff384acae2c4861aa9ad1b3f6861
|
/sci2blif/sci2blif_added_blocks/Hyst_diff.sce
|
d3152a4d9fd76cdeb3c1411a8774016602c92a1d
|
[] |
no_license
|
jhasler/rasp30
|
9a7c2431d56c879a18b50c2d43e487d413ceccb0
|
3612de44eaa10babd7298d2e0a7cddf4a4b761f6
|
refs/heads/master
| 2023-05-25T08:21:31.003675
| 2023-05-11T16:19:59
| 2023-05-11T16:19:59
| 62,917,238
| 3
| 3
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 558
|
sce
|
Hyst_diff.sce
|
//**************************** Hyst_diff **********************************
if (blk_name.entries(bl) == "Hyst_diff") then
mputl("#Hyst_diff",fd_w);
for ss=1:scs_m.objs(bl).model.ipar(1)
Hyst_diff_str= '.subckt Hyst_diff'+' in[0]=net'+string(blk(blk_objs(bl),2))+'_'+string(ss)+' out[0]=net'+string(blk(blk_objs(bl),2+numofip))+'_'+string(ss)+' #Hyst_diff_ls =0'+'&Hyst_diff_ota1_ibias ='+string(sprintf('%e',scs_m.objs(bl).model.rpar(scs_m.objs(bl).model.ipar(1)*(1-1)+ss)))
mputl(Hyst_diff_str,fd_w);
mputl("",fd_w);
end
end
|
ba5edd1353baaa54b6e869cabc23debb114ed204
|
4d05c7f7559264f205dc6abda9e49aca7d7057ac
|
/Nand2Tetris/07_vm_parser_I/custom overflow test/overflow.tst
|
f3cc635f5b8a2e31dc9b16440b04eaa8beaa37b6
|
[] |
no_license
|
daniellevin233/Python_projects
|
22cc1a4a194d0b5253d06f9596d21f07bc5e44fb
|
7f9eba191d0ad656b0b55421f2054efa2a1177cf
|
refs/heads/master
| 2023-01-14T05:29:33.591746
| 2020-11-20T13:36:40
| 2020-11-20T13:36:40
| 298,377,620
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 633
|
tst
|
overflow.tst
|
load overflow.asm,
output-file overflow.out,
compare-to overflow.cmp,
output-list RAM[256]%D1.6.1
RAM[257]%D1.6.1 RAM[258]%D1.6.1 RAM[259]%D1.6.1
RAM[260]%D1.6.1 RAM[261]%D1.6.1 RAM[262]%D1.6.1
RAM[263]%D1.6.1 RAM[264]%D1.6.1 RAM[265]%D1.6.1
RAM[266]%D1.6.1 RAM[267]%D1.6.1 RAM[268]%D1.6.1
RAM[269]%D1.6.1 RAM[270]%D1.6.1 RAM[271]%D1.6.1
RAM[272]%D1.6.1 RAM[273]%D1.6.1 RAM[274]%D1.6.1;
set RAM[0] 256, // initializes the stack pointer
repeat 1500 { // enough cycles to complete the execution
ticktock;
}
// Output the outputs of all lt, gt, eq combinations with overflow possibilities
output;
|
3296f007f32b5f742999f9a8403fe50646872f1e
|
226851ab7bb8a3e1137e72fd154d4aa6939229f1
|
/60002190048_SS SCILAB_2B(CORRELATION).sce
|
0f65d1b1b8a6924d880a272e0fb20b23e9e04449
|
[] |
no_license
|
Ishitaa48/SS-Practicals-EXTC-1-E13-60002190048
|
637a855701ef0a07675e519cf002fa4742a571e7
|
183baae9ad66d093ba13d41a01f1d61751ef8036
|
refs/heads/main
| 2023-01-18T22:39:05.696201
| 2020-11-25T11:52:15
| 2020-11-25T11:52:15
| 315,921,545
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 252
|
sce
|
60002190048_SS SCILAB_2B(CORRELATION).sce
|
clc;
clear all;
close;
x1=[1,3,7,-2,5];
x2=[2,-1,0,3];
z=xcorr(x1,x2);
disp(z,"This is the required correlation");
l=length(z);
t=0:l-1;
plot2d3(t,z);
xlabel("n");
ylabel("Amplitude");
title("Correlation: y(n)=x1(n)*x2(-n)");
figure;
|
4d115f69332fa48305e6724cbb5bfea3528b8d32
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1319/CH8/EX8.11/8_11.sce
|
92abc95456f4ab6e21b1b488fb674620b2779cdf
|
[] |
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
|
8_11.sce
|
// Determine the shaft power of 6 pole Induction Motor
clc;
clear;
f=50;
p=6;
rf=120/60; // Rotor Frequency
T=150; // Full Load torque
s=rf/f;
Ns=120*f/p;
Nr=Ns*(1-s);
Ps=2*%pi*Nr*T/60; // Shaft power
printf('The shaft power of the motor = %g kW \n',Ps/1000)
|
97b73cf7b103022d3771f21039bc54ae4f5ae337
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3886/CH12/EX12.6/12_6.sce
|
bf95837332904800b17c7ce126ec9c4404905ea7
|
[] |
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
| 486
|
sce
|
12_6.sce
|
//Distance covered
//refer fig.12.9
//Let the particle start from A and come to halt at E
//Let initial velocity be u m/sec
//consider motion between A and B
//u+a=10
//consider motion between A and C
//70=7*u+7*a
//solving
a=-10/17.5 //m/sec^2
u=10-(a) //m/sec
//Let distance AD be s1
s1=10.571*10+(-0.571*10^2)/2 //m
//Distance covered in the interval 7 sec to 10 sec
CD=77.16-60 //m
//Let AE=s
s=(10.571^2)/(2*0.571) //m
printf("\nCD=%.2f m\ns=%.2f m",CD,s)
|
990d36dcf8c185fd84c7e9a68e1ddebe486aa027
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/605/CH4/EX4.4/4_4.sce
|
1263d5e7da6f6b4a17a34bb7e47f9895eedf36ff
|
[] |
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
| 124
|
sce
|
4_4.sce
|
Q=[0:0.01:2*%pi]
q=[0:0.01:%pi]
k=integrate('60*%pi/sin(Q)*cos(%pi/2*cos(Q))^2','Q',0,%pi/2)
printf("\nk=%.2f W",4*k*%pi)
|
4a8353a054c8e88ccbb4f4a9912505ebaf6369ec
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3774/CH3/EX3.10/Ex3_10.sce
|
a9d5db7fae1db39ca4bdb5cd00bcc2513fe0fba8
|
[] |
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
| 831
|
sce
|
Ex3_10.sce
|
// exa 3.10 Pg 71
clc;clear;close;
// Given Data
d=4;// cm
M=15000;// N.cm
Syt=20000;// N/cm.sq.
printf('\n (i) Maximum Principal Stress Theory-')
z=%pi*d**3/32;// cm.cube.
sigma_b=M/z;// N/cm.sq.
T=poly(0,'T')
tau=16*T/(%pi*d**3);// N/cm.sq.
//sigma1=(1/2)*(sigma_b+sqrt(sigma_b**2+4*tau**2)) // Maximum principal stress
//sigma1=(sigma_b/2+sqrt(sigma_b**2/4+tau**2)) // on solving
//tau=sqrt((sigma1-sigma_b/2)**2-sigma_b**2/4)
sigma1=Syt;// N/cm.sq.
T=sqrt((sigma1-sigma_b/2)**2-sigma_b**2/4)*(%pi*d**3)/16;// N.cm.
printf('\n Maximum value of torque, T = %.f N.cm.',T)
printf('\n (ii) Maximum Shear Stress Theory')
tau_d=0.5*Syt;// N.cm.
//Te=sqrt(M**2+T**2)=(%pi/16)*d**3*tau_d
T=sqrt(((%pi/16)*d**3*tau_d)**2-M**2);// N.cm.
printf('\n Maximum value of torque, T = %.f N.cm.',T)
// Answer in the textbook is not accurate.
|
4d0cc470a5bb98f94f096aed998cc9ab047b6976
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/821/CH5/EX5.57/5_57.sce
|
e130c96f7d31bbcecec51803bc8dc5a2f388250a
|
[] |
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
| 572
|
sce
|
5_57.sce
|
T0=373;//temperature in kelvin//
Kb=0.52;//value of Kb in deg per mol//
T1=373.208;//temperature in kelvin//
W2=3.40;//weight of BaCl2 in grams//
W1=100;//weight of water boils in grams//
dTb=T1-T0;//change in temperature//
Mobs=(Kb*1000*W2)/(dTb*W1);//Molecular weight of BaCl2 observed in grams//
printf('Molecular weight of BaCl2 observed=Mobs=%fgrams',Mobs);
Mthr=208.4;//Theoritical Molecular weight of BaCl2 in grams//
i=Mthr/Mobs;
a=0.5*(i-1);//apparent degree of dissociation of BaCl2//
printf('\nApparent degree of dissociation of BaCl2=a=%f',a);
|
39e28b33307990a5b637ce6c5b1c83a196290268
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/764/CH4/EX4.7.b/solution4_7.sce
|
a67b1f7bb9327eee22c60df78bdfbe0991b7ce10
|
[] |
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
| 1,189
|
sce
|
solution4_7.sce
|
//Obtain path of solution file
path = get_absolute_file_path('solution4_7.sce')
//Obtain path of data file
datapath = path + filesep() + 'data4_7.sci'
//Clear all
clc
//Execute the data file
exec(datapath)
//Calculate permissible tensile stress sigmat (N/mm2)
sigmat = Syt/fs
//Assume the wudth of the cross-section to be 1mm t
t = 1
//Calculate direct compressive stress sigmac (N/mm2)
sigmac = P/(t * (ratio * t))
//Calculate maximum bending moment Mb (N-mm)
Mb = P * l
//Calculate y
y = 1.5 * t
//Calculate the second moment of area I (mm4)
I = (t * ((ratio * t)^3))/12
//Calculate tensile bending stress at the lower fibre sigmab(N/mm2)
sigmab = (Mb * y)/I
//Finding the real value of width t (mm)
//On superimposing the stress values, a cubic equation in t is obtained
a = 0
b = (sigmac/sigmat)
c = (-1 * (sigmab/sigmat))
//Define polynomial
p = [1,a,b,c]
//Calculate roots of this polynomial
r = roots(p)
real_part = real(r)
for i = 1:1:3
if(real_part(i)>0)
t = real_part(i)
break
end
end
//Print results
printf('\nValue of t = %f mm\n',t)
printf('\nArea of cross-section = (%f x %f) mm2\n',t,(ratio * t))
|
a5601f57dba629518cab0360a32652ec35e19da6
|
c90039f74887835096a93884110d643c4823e530
|
/doc/oficial/dados para treinamento RNA/RNA_ANALISE_TECNICA/RNA_ANALISE_TECNICA.sce
|
11b9acabfb613983da00bc3c1d3c7435ab242538
|
[] |
no_license
|
igorlima/CellInvest
|
da991366b329b5d8021e9b949d7b726023489ec8
|
c5411247e504b8a8d0ad77d32d41bbd2aee39930
|
refs/heads/master
| 2020-04-06T03:40:05.614164
| 2012-10-23T12:58:20
| 2012-10-23T12:58:20
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 1,528
|
sce
|
RNA_ANALISE_TECNICA.sce
|
path_rna_analise_tec = get_absolute_file_path('RNA_ANALISE_TECNICA.sce');
exec( path_rna_analise_tec+"\_util.sce" );
exec( path_rna_analise_tec+"\_carregar_rede_de_treinamento.sce" );
exec( path_rna_analise_tec+"\_arquivo.sce" );
exec( path_rna_analise_tec+"\_dados.sce" );
exec( path_rna_analise_tec+"\Indicador\RNA_INDICADOR.sce" );
//rna_analise_tecnica( 'BBAS3', 52.11600, 0.00000, -138.22420, 239.700000, 377.924200, 15375314249 )
function saida_da_rna = rna_analise_tecnica( nome_do_ativo, ifr, estocastico, hist, macdLine, macdSinal, obv )
ativo = getDados( nome_do_ativo, MAXIMO_LINHA_ARQUIVO );
ifr = ifr/100;
estocastico = estocastico/100;
hist = normalizar( [ativo(:,3); hist ] );
hist = hist( length(hist) );
alphaHist = convert_to_alpha( [ativo(:,3); hist] );
alphaHist = alphaHist( length(alphaHist) );
macdLine = normalizar( [ativo(:,4); macdLine] );
macdLine = macdLine( length(macdLine) );
alphaMacdLine = convert_to_alpha( [ativo(:,4); macdLine] );
alphaMacdLine = alphaMacdLine( length(alphaMacdLine) );
macdSinal = normalizar( [ativo(:,5); macdSinal] );
macdSinal = macdSinal( length(macdSinal) );
alphaMacdSinal = convert_to_alpha( [ativo(:,5); macdSinal] );
alphaMacdSinal = alphaMacdSinal( length(alphaMacdSinal) );
alphaObv = convert_to_alpha( [ativo(:,6); obv] );
alphaObv = alphaObv( length(alphaObv) );
saida_da_rna = rna_indicador( ifr, estocastico, hist, alphaHist, macdLine, alphaMacdLine, macdSinal, alphaMacdSinal, alphaObv )
endfunction
|
40fb98de12a3b01cf1a6457c42dc6717e297f372
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/839/CH27/EX27.5/Example_27_5.sce
|
07942177eb134271d9791667a59c5878f17b19da
|
[] |
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
| 992
|
sce
|
Example_27_5.sce
|
//clear//
clear;
clc;
//Example 27.5
//Let: A = MgSO4; B = MgSO4.7H2O; C = H2O
//Given
xA = 0.31;
T = 86; //[F]
Tb = 2; //[F]
vbys = 0.15;
//PB =
rho_cr = 105; //[lb/ft^3]
rho_ml = 82.5; //[lb/ft^3]
//Solution
//Basis:
F = 10000; //[lb/h]
//From Fig 27.13 and Fig 27.4
crbyml = vbys*rho_cr/((1-vbys)*rho_ml);
ml_prod = F/crbyml; //[lb/h]
magma_prod = F+ml_prod //[lb/h]
xA_avg = (crbyml*0.488+0.285)/1.224;
//The enthalpy of the magam
Hmag = (crbyml*(-149)+(-43))/1.224; //[Btu/lb]
//These are the concenrations of the point e. The point for the feed must
//lie on the straight line ae.
//The enthalpy of the feed
Hf = -21; //[Btu/lb]
//Temperature of the feed
Tf = 130; //[F]
//By COG principle, the evaporation rate
evap_rate = magma_prod*(Hf-Hmag)/(1098-Hf); //[lb/h]
Total_feed = magma_prod+evap_rate; //[lb/h]
disp('F',Tf,'Temperature of the feed is');
disp('lb/h',Total_feed,'Total feed rate');
disp('lb/h',evap_rate,'Total evaporation rate');
|
a7ab3e07a1628563edf316d451f9f3cb78b25f22
|
089894a36ef33cb3d0f697541716c9b6cd8dcc43
|
/NLP_Project/test/tweet/bow/bow.1_14.tst
|
3b991c0a81709f138c6765a2ba68bcc6940e016c
|
[] |
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
| 28,445
|
tst
|
bow.1_14.tst
|
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1 12:0.017857142857142856 20:0.15384615384615385 24:1.0 35:0.09090909090909091 56:0.037037037037037035 67:0.25 69:0.5 75:0.2 79:0.045454545454545456 139:0.5 148:0.07142857142857142 191:0.6666666666666666 192:0.5 252:0.3333333333333333 266:0.5 487:1.0 506:2.0 530:0.5 712:0.3333333333333333 854:1.0 915:1.0 1095:0.5 1155:1.0 1184:1.0 1422:1.0 1761:1.0 1969:1.0 2278:1.0 2833:1.0 4562:1.0 4563:1.0
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1 11:0.2 24:1.0 35:0.09090909090909091 41:0.2857142857142857 67:0.75 75:0.1 85:0.5 87:1.0 96:1.0 113:1.0 128:1.0 141:1.0 415:0.08333333333333333 499:1.0 508:1.0 773:1.0 1025:1.0 1572:1.0 2112:1.0 2217:1.0 2446:1.0
1 12:0.017857142857142856 20:0.07692307692307693 27:0.034482758620689655 67:0.5 70:0.09090909090909091 77:0.25 109:0.5 124:0.14285714285714285 303:1.0 305:0.3333333333333333 322:1.0 369:0.5 375:1.0 692:1.0 765:1.0 799:1.0 810:1.0 871:1.0 2074:1.0 3991:1.0 5418:1.0
1 12:0.03571428571428571 47:0.5 67:0.5 72:1.0 75:0.1 140:0.5 166:0.16666666666666666 197:0.030303030303030304 226:0.25 291:1.0 376:1.0 599:1.0 1435:1.0 1701:1.0 1900:1.0 3395:1.0
1 3:1.0 12:0.05357142857142857 13:0.2 20:0.07692307692307693 29:1.0 36:0.1 47:0.5 53:0.5 67:0.25 77:0.25 79:0.045454545454545456 98:1.0 108:0.3333333333333333 115:0.3333333333333333 337:1.0 374:1.0 441:1.0 513:1.0 748:0.5 824:1.0 870:1.0 958:0.3333333333333333 1026:1.0 1238:1.0 1388:1.0 1999:1.0 4521:1.0
1 12:0.017857142857142856 15:1.0 53:0.5 63:1.0 67:0.25 75:0.1 82:0.125 96:1.0 136:1.0 250:1.0 305:0.3333333333333333 430:1.0 688:0.5 1432:1.0
1 3:2.0 12:0.08928571428571429 13:0.2 18:0.6 20:0.07692307692307693 27:0.034482758620689655 58:0.25 63:1.0 67:0.25 75:0.1 79:0.09090909090909091 84:0.3333333333333333 94:1.0 139:1.0 145:1.0 176:0.3333333333333333 243:1.0 285:1.0 494:2.0 502:1.0 506:1.0 535:1.0 559:1.0 601:1.0 703:1.0 732:1.0 766:1.0 931:1.0 998:1.0 1149:1.0 1582:1.0 1625:1.0 4642:1.0 6265:1.0
1 3:1.0 11:0.4 12:0.017857142857142856 18:0.4 20:0.07692307692307693 35:0.09090909090909091 41:0.14285714285714285 58:0.25 67:0.25 70:0.18181818181818182 85:0.5 93:0.5 98:1.0 106:1.0 113:1.0 115:1.0 122:0.14285714285714285 177:0.5 214:0.3333333333333333 374:1.0 454:1.0 494:1.0 543:0.25 621:1.0 691:1.0 707:1.0 739:0.5 767:1.0 873:1.0 966:1.0 1573:1.0 4217:1.0 4321:1.0
1 1:0.14285714285714285 75:0.1 77:0.25 96:1.0 104:0.1 191:0.3333333333333333 194:1.0 502:1.0
1 11:0.4 12:0.017857142857142856 18:0.4 41:0.2857142857142857 56:0.037037037037037035 70:0.18181818181818182 75:0.2 98:2.0 113:0.5 115:0.3333333333333333 191:0.3333333333333333 197:0.030303030303030304 214:0.3333333333333333 296:0.2 326:1.0 568:0.07142857142857142 771:1.0 813:1.0 975:1.0 1564:1.0 1746:1.0 2054:1.0 2669:1.0 3659:1.0 4859:1.0 5404:1.0
1 6:1.0 11:0.2 18:0.4 20:0.07692307692307693 35:0.09090909090909091 67:0.5 75:0.1 110:1.0 162:1.0 209:0.2 362:1.0 398:0.3333333333333333 653:1.0 895:1.0 1122:1.0 1778:1.0 2171:1.0 5982:1.0
1 3:1.0 18:0.2 24:1.0 113:0.5 194:1.0 299:1.0 398:0.3333333333333333 540:1.0 871:1.0 1095:0.5 1111:1.0 1182:0.5 1556:1.0 1754:1.0
1 1:0.14285714285714285 18:0.2 24:1.0 67:0.25 79:0.045454545454545456 82:0.125 85:0.5 109:0.5 177:0.25 542:0.3333333333333333 560:1.0 758:0.25 784:1.0 1550:1.0 2203:1.0 3180:0.5
1 12:0.03571428571428571 13:0.2 18:0.2 20:0.3076923076923077 24:2.0 35:0.09090909090909091 41:0.14285714285714285 52:0.5 64:0.5 67:0.75 75:0.1 85:0.5 91:1.0 93:0.5 96:1.0 98:1.0 104:0.1 154:1.0 164:1.0 209:0.2 331:0.3333333333333333 455:1.0 506:2.0 535:1.0 684:1.0 758:0.125 779:1.0 898:1.0 966:1.0 1063:1.0 1182:0.5 1184:1.0 1282:1.0 1488:1.0 1508:1.0 2638:1.0 2833:1.0 3223:1.0 5746:1.0
|
5455de7d21e9f6c0197abf623828a8fe6b373f75
|
99b4e2e61348ee847a78faf6eee6d345fde36028
|
/Toolbox Test/latcfilt/latcfilt2.sce
|
f179ae0beb60fdd27990fcee033d137b90b1ad03
|
[] |
no_license
|
deecube/fosseetesting
|
ce66f691121021fa2f3474497397cded9d57658c
|
e353f1c03b0c0ef43abf44873e5e477b6adb6c7e
|
refs/heads/master
| 2021-01-20T11:34:43.535019
| 2016-09-27T05:12:48
| 2016-09-27T05:12:48
| 59,456,386
| 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 503
|
sce
|
latcfilt2.sce
|
//i/p arg x is empty
k=[0.2 0.3 0.4 1];
x=[];
[f,g] = latcfilt(k,x);
disp(f);
disp(g);
//output
//--error 10000
//dimension mis-match between k and v
//at line 46 of function latcfilt called by :
//[f,g] = latcfilt(k,x);
//at line 4 of exec file called by :
//lt/latcfilt2.sce', -1
//corresponding MATLAB o/p
//Error using latcfiltmex
//Ladder filter coefficients (V) must be a double precision 2-D
//array.
//
//Error in latcfilt (line 69)
// [F,G,Zf] = latcfiltmex(varargin{:});
|
682cf1230496596ff6bc80a0aeb3a996c0b206de
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1628/CH4/EX4.3/Ex4_3.sce
|
e616a95493e2f99e6bf1e7aa39894a5dfaee9cc9
|
[] |
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
| 983
|
sce
|
Ex4_3.sce
|
// Example 4.3
// From the diagram 4.5
// Using super position theorem
// 4-A current source is active
i=4/{1+(2+3)}; // Current
R=3; // Rsistance of 3 Ohms
V4=i*R; // Voltage across 3 Ohms resistance in Case-1
// 5-A current source is active
i5=5; // 5-A current source
V5=(-i5)*{1/[1+(2+3)]*3}; // Voltage across 3 Ohms resistance in Case-2
// 6-V voltage source is active
i6=6; // 6-A current source
V6=i6*{3/[1+(2+3)]}; // Voltage across 3 Ohms resistance in Case-3
V=V4+V5+V6; // Voltage across 3 Ohms resistance
disp(' Voltage across 3 Ohms resistance is = '+string(V)+' Volt');
// p 106 4.3
|
17f9a8bc0c39b09c9bbece1903b82021dd1a0b18
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2657/CH14/EX14.1/Ex14_1.sce
|
2b0b839161bddf02b690b9dc2746ab3ba5c79e50
|
[] |
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
| 822
|
sce
|
Ex14_1.sce
|
//Calculation of saving in fuel
clc,clear
//Given:
bp=80 //Brake power in kW
eta_m=80 //Mechanical efficiency in percent
bsfc=258 //Brake specific fuel consumption in gm/kWh
Reduction=3.7 //Reduction in friction power in kW
//Solution:
ip1=bp*100/eta_m //Initial indicated power in kW
fp1=ip1-bp //Initial friction power in kW
fp2=fp1-Reduction //Final friction power in kW
ip2=bp+fp2 //Final indicated power in kW
eta_m2=bp/ip2 //Final mechanical efficiency
bsfc2=bsfc*(eta_m/(100*eta_m2)) //Final brake specific fuel consumption in gm/kWh
Saving=bp*(bsfc-bsfc2)/1000 //Saving in fuel in kg/hr
//Results:
printf("\n (a)The new mechanical efficiency, eta_m = %.3f",eta_m2)
printf("\n (b)The new bsfc = %.1f gm/kWh",bsfc2)
printf("\n (c)The saving in fuel per hour = %.2f kg/hr\n\n",Saving)
//Answers in the book are wrong
|
127f48db9b0777438135d188387de01367301775
|
f542bc49c4d04b47d19c88e7c89d5db60922e34e
|
/PresentationFiles_Subjects/CONT/KP85YLZ/ATWM1_Working_Memory_MEG_KP85YLZ_Session1/ATWM1_Working_Memory_MEG_Nonsalient_Uncued_Run1.sce
|
281ba20bf7991f1e77ad7a2c7e58de201967e3ef
|
[] |
no_license
|
atwm1/Presentation
|
65c674180f731f050aad33beefffb9ba0caa6688
|
9732a004ca091b184b670c56c55f538ff6600c08
|
refs/heads/master
| 2020-04-15T14:04:41.900640
| 2020-02-14T16:10:11
| 2020-02-14T16:10:11
| 56,771,016
| 0
| 1
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 48,615
|
sce
|
ATWM1_Working_Memory_MEG_Nonsalient_Uncued_Run1.sce
|
# ATWM1 MEG Experiment
scenario = "ATWM1_Working_Memory_MEG_salient_cued_run1";
#scenario_type = fMRI; # Fuer Scanner
#scenario_type = fMRI_emulation; # Zum Testen
scenario_type = trials; # for MEG
#scan_period = 2000; # TR
#pulses_per_scan = 1;
#pulse_code = 1;
pulse_width=6;
default_monitor_sounds = false;
active_buttons = 2;
response_matching = simple_matching;
button_codes = 10, 20;
default_font_size = 36;
default_font = "Arial";
default_background_color = 0 ,0 ,0 ;
write_codes=true; # for MEG only
begin;
#Picture definitions
box { height = 382; width = 382; color = 0, 0, 0;} frame1;
box { height = 369; width = 369; color = 255, 255, 255;} frame2;
box { height = 30; width = 4; color = 0, 0, 0;} fix1;
box { height = 4; width = 30; color = 0, 0, 0;} fix2;
box { height = 30; width = 4; color = 255, 0, 0;} fix3;
box { height = 4; width = 30; color = 255, 0, 0;} fix4;
box { height = 369; width = 369; color = 42, 42, 42;} background;
TEMPLATE "StimuliDeclaration.tem" {};
trial {
sound sound_incorrect;
time = 0;
duration = 1;
} wrong;
trial {
sound sound_correct;
time = 0;
duration = 1;
} right;
trial {
sound sound_no_response;
time = 0;
duration = 1;
} miss;
# Start of experiment (MEG only) - sync with CTF software
trial {
picture {
box frame1; x=0; y=0;
box frame2; x=0; y=0;
box background; x=0; y=0;
bitmap fixation_cross_black; x=0; y=0;
} expStart;
time = 0;
duration = 1000;
code = "ExpStart";
port_code = 80;
};
# baselinePre (at the beginning of the session)
trial {
picture {
box frame1; x=0; y=0;
box frame2; x=0; y=0;
box background; x=0; y=0;
bitmap fixation_cross_black; x=0; y=0;
}default;
time = 0;
duration = 10000;
#mri_pulse = 1;
code = "BaselinePre";
port_code = 91;
};
TEMPLATE "ATWM1_Working_Memory_MEG.tem" {
trigger_encoding trigger_retrieval cue_time preparation_time encoding_time single_stimulus_presentation_time delay_time retrieval_time intertrial_interval alerting_cross stim_enc1 stim_enc2 stim_enc3 stim_enc4 stim_enc_alt1 stim_enc_alt2 stim_enc_alt3 stim_enc_alt4 trial_code stim_retr1 stim_retr2 stim_retr3 stim_retr4 stim_cue1 stim_cue2 stim_cue3 stim_cue4 fixationcross_cued retr_code the_target_button posX1 posY1 posX2 posY2 posX3 posY3 posX4 posY4;
44 62 292 292 399 125 1842 2992 2042 fixation_cross gabor_068 gabor_011 gabor_143 gabor_032 gabor_068 gabor_011_alt gabor_143 gabor_032_alt "1_1_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1850_3000_2050_gabor_patch_orientation_068_011_143_032_target_position_1_3_retrieval_position_3" gabor_circ gabor_circ gabor_143_framed gabor_circ blank blank blank blank fixation_cross_white "1_1_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_143_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1942 2992 1992 fixation_cross gabor_075 gabor_108 gabor_127 gabor_050 gabor_075 gabor_108 gabor_127_alt gabor_050_alt "1_2_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1950_3000_2000_gabor_patch_orientation_075_108_127_050_target_position_1_2_retrieval_position_2" gabor_circ gabor_158_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_2_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_158_retrieval_position_2" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1892 2992 1892 fixation_cross gabor_074 gabor_129 gabor_098 gabor_180 gabor_074_alt gabor_129 gabor_098_alt gabor_180 "1_3_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1900_3000_1900_gabor_patch_orientation_074_129_098_180_target_position_2_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_180_framed blank blank blank blank fixation_cross_white "1_3_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_180_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1892 2992 2592 fixation_cross gabor_053 gabor_068 gabor_141 gabor_035 gabor_053 gabor_068_alt gabor_141 gabor_035_alt "1_4_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1900_3000_2600_gabor_patch_orientation_053_068_141_035_target_position_1_3_retrieval_position_3" gabor_circ gabor_circ gabor_091_framed gabor_circ blank blank blank blank fixation_cross_white "1_4_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_091_retrieval_position_3" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1792 2992 2542 fixation_cross gabor_113 gabor_072 gabor_139 gabor_007 gabor_113_alt gabor_072_alt gabor_139 gabor_007 "1_5_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1800_3000_2550_gabor_patch_orientation_113_072_139_007_target_position_3_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_053_framed blank blank blank blank fixation_cross_white "1_5_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_053_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2242 2992 2392 fixation_cross gabor_085 gabor_174 gabor_014 gabor_126 gabor_085_alt gabor_174 gabor_014_alt gabor_126 "1_6_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2250_3000_2400_gabor_patch_orientation_085_174_014_126_target_position_2_4_retrieval_position_2" gabor_circ gabor_174_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_6_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_174_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2092 2992 1892 fixation_cross gabor_173 gabor_054 gabor_094 gabor_110 gabor_173 gabor_054_alt gabor_094 gabor_110_alt "1_7_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2100_3000_1900_gabor_patch_orientation_173_054_094_110_target_position_1_3_retrieval_position_1" gabor_035_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_7_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_035_retrieval_position_1" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 64 292 292 399 125 2192 2992 2292 fixation_cross gabor_079 gabor_011 gabor_140 gabor_100 gabor_079 gabor_011_alt gabor_140_alt gabor_100 "1_8_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_300_300_399_2200_3000_2300_gabor_patch_orientation_079_011_140_100_target_position_1_4_retrieval_position_2" gabor_circ gabor_011_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_8_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_retrieval_patch_orientation_011_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2192 2992 2442 fixation_cross gabor_142 gabor_086 gabor_170 gabor_125 gabor_142_alt gabor_086 gabor_170 gabor_125_alt "1_9_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2200_3000_2450_gabor_patch_orientation_142_086_170_125_target_position_2_3_retrieval_position_3" gabor_circ gabor_circ gabor_170_framed gabor_circ blank blank blank blank fixation_cross_white "1_9_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_170_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2092 2992 2292 fixation_cross gabor_003 gabor_155 gabor_087 gabor_069 gabor_003_alt gabor_155 gabor_087_alt gabor_069 "1_10_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2100_3000_2300_gabor_patch_orientation_003_155_087_069_target_position_2_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_019_framed blank blank blank blank fixation_cross_white "1_10_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_019_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1792 2992 2042 fixation_cross gabor_045 gabor_015 gabor_175 gabor_030 gabor_045 gabor_015_alt gabor_175_alt gabor_030 "1_11_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1800_3000_2050_gabor_patch_orientation_045_015_175_030_target_position_1_4_retrieval_position_1" gabor_093_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_11_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_093_retrieval_position_1" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1992 2992 2092 fixation_cross gabor_106 gabor_065 gabor_176 gabor_041 gabor_106_alt gabor_065_alt gabor_176 gabor_041 "1_12_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2000_3000_2100_gabor_patch_orientation_106_065_176_041_target_position_3_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_088_framed blank blank blank blank fixation_cross_white "1_12_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_088_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 64 292 292 399 125 2142 2992 2192 fixation_cross gabor_017 gabor_093 gabor_048 gabor_065 gabor_017 gabor_093_alt gabor_048 gabor_065_alt "1_13_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_300_300_399_2150_3000_2200_gabor_patch_orientation_017_093_048_065_target_position_1_3_retrieval_position_2" gabor_circ gabor_093_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_13_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_retrieval_patch_orientation_093_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2192 2992 2492 fixation_cross gabor_116 gabor_005 gabor_152 gabor_027 gabor_116_alt gabor_005_alt gabor_152 gabor_027 "1_14_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2200_3000_2500_gabor_patch_orientation_116_005_152_027_target_position_3_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_073_framed blank blank blank blank fixation_cross_white "1_14_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_073_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2092 2992 2492 fixation_cross gabor_112 gabor_053 gabor_001 gabor_089 gabor_112 gabor_053_alt gabor_001_alt gabor_089 "1_15_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2100_3000_2500_gabor_patch_orientation_112_053_001_089_target_position_1_4_retrieval_position_1" gabor_112_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_15_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_112_retrieval_position_1" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1992 2992 1942 fixation_cross gabor_014 gabor_180 gabor_034 gabor_148 gabor_014_alt gabor_180 gabor_034_alt gabor_148 "1_16_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2000_3000_1950_gabor_patch_orientation_014_180_034_148_target_position_2_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_148_framed blank blank blank blank fixation_cross_white "1_16_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_148_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 64 292 292 399 125 1742 2992 2592 fixation_cross gabor_095 gabor_056 gabor_165 gabor_076 gabor_095_alt gabor_056 gabor_165_alt gabor_076 "1_17_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_300_300_399_1750_3000_2600_gabor_patch_orientation_095_056_165_076_target_position_2_4_retrieval_position_3" gabor_circ gabor_circ gabor_165_framed gabor_circ blank blank blank blank fixation_cross_white "1_17_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_retrieval_patch_orientation_165_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2092 2992 2242 fixation_cross gabor_128 gabor_099 gabor_071 gabor_160 gabor_128_alt gabor_099_alt gabor_071 gabor_160 "1_18_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2100_3000_2250_gabor_patch_orientation_128_099_071_160_target_position_3_4_retrieval_position_3" gabor_circ gabor_circ gabor_021_framed gabor_circ blank blank blank blank fixation_cross_white "1_18_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_021_retrieval_position_3" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 63 292 292 399 125 2142 2992 2292 fixation_cross gabor_160 gabor_078 gabor_048 gabor_100 gabor_160_alt gabor_078 gabor_048 gabor_100_alt "1_19_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_300_300_399_2150_3000_2300_gabor_patch_orientation_160_078_048_100_target_position_2_3_retrieval_position_1" gabor_024_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_19_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_retrieval_patch_orientation_024_retrieval_position_1" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1892 2992 2042 fixation_cross gabor_091 gabor_110 gabor_076 gabor_166 gabor_091_alt gabor_110_alt gabor_076 gabor_166 "1_20_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1900_3000_2050_gabor_patch_orientation_091_110_076_166_target_position_3_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_026_framed blank blank blank blank fixation_cross_white "1_20_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_026_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1892 2992 1992 fixation_cross gabor_014 gabor_126 gabor_151 gabor_102 gabor_014_alt gabor_126 gabor_151 gabor_102_alt "1_21_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1900_3000_2000_gabor_patch_orientation_014_126_151_102_target_position_2_3_retrieval_position_2" gabor_circ gabor_126_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_21_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_126_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1992 2992 1992 fixation_cross gabor_104 gabor_173 gabor_020 gabor_084 gabor_104 gabor_173 gabor_020_alt gabor_084_alt "1_22_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2000_3000_2000_gabor_patch_orientation_104_173_020_084_target_position_1_2_retrieval_position_2" gabor_circ gabor_037_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_22_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_037_retrieval_position_2" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1842 2992 2142 fixation_cross gabor_065 gabor_045 gabor_154 gabor_090 gabor_065 gabor_045_alt gabor_154_alt gabor_090 "1_23_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1850_3000_2150_gabor_patch_orientation_065_045_154_090_target_position_1_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_090_framed blank blank blank blank fixation_cross_white "1_23_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_090_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 64 292 292 399 125 1842 2992 1892 fixation_cross gabor_089 gabor_116 gabor_055 gabor_171 gabor_089 gabor_116 gabor_055_alt gabor_171_alt "1_24_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_300_300_399_1850_3000_1900_gabor_patch_orientation_089_116_055_171_target_position_1_2_retrieval_position_3" gabor_circ gabor_circ gabor_055_framed gabor_circ blank blank blank blank fixation_cross_white "1_24_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_retrieval_patch_orientation_055_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1742 2992 2342 fixation_cross gabor_019 gabor_104 gabor_125 gabor_050 gabor_019 gabor_104_alt gabor_125 gabor_050_alt "1_25_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1750_3000_2350_gabor_patch_orientation_019_104_125_050_target_position_1_3_retrieval_position_3" gabor_circ gabor_circ gabor_079_framed gabor_circ blank blank blank blank fixation_cross_white "1_25_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_079_retrieval_position_3" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1742 2992 2392 fixation_cross gabor_029 gabor_009 gabor_093 gabor_063 gabor_029 gabor_009 gabor_093_alt gabor_063_alt "1_26_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1750_3000_2400_gabor_patch_orientation_029_009_093_063_target_position_1_2_retrieval_position_1" gabor_169_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_26_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_169_retrieval_position_1" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2042 2992 2292 fixation_cross gabor_045 gabor_179 gabor_016 gabor_123 gabor_045_alt gabor_179_alt gabor_016 gabor_123 "1_27_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2050_3000_2300_gabor_patch_orientation_045_179_016_123_target_position_3_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_123_framed blank blank blank blank fixation_cross_white "1_27_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_123_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2142 2992 2542 fixation_cross gabor_012 gabor_119 gabor_102 gabor_084 gabor_012 gabor_119_alt gabor_102_alt gabor_084 "1_28_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2150_3000_2550_gabor_patch_orientation_012_119_102_084_target_position_1_4_retrieval_position_1" gabor_012_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_28_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_012_retrieval_position_1" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2142 2992 1892 fixation_cross gabor_066 gabor_099 gabor_011 gabor_120 gabor_066 gabor_099 gabor_011_alt gabor_120_alt "1_29_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2150_3000_1900_gabor_patch_orientation_066_099_011_120_target_position_1_2_retrieval_position_2" gabor_circ gabor_149_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_29_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_149_retrieval_position_2" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1792 2992 2042 fixation_cross gabor_069 gabor_102 gabor_050 gabor_085 gabor_069_alt gabor_102_alt gabor_050 gabor_085 "1_30_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1800_3000_2050_gabor_patch_orientation_069_102_050_085_target_position_3_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_132_framed blank blank blank blank fixation_cross_white "1_30_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_132_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 64 292 292 399 125 2092 2992 2242 fixation_cross gabor_134 gabor_025 gabor_112 gabor_052 gabor_134 gabor_025_alt gabor_112_alt gabor_052 "1_31_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_300_300_399_2100_3000_2250_gabor_patch_orientation_134_025_112_052_target_position_1_4_retrieval_position_3" gabor_circ gabor_circ gabor_112_framed gabor_circ blank blank blank blank fixation_cross_white "1_31_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_retrieval_patch_orientation_112_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1792 2992 2192 fixation_cross gabor_019 gabor_162 gabor_052 gabor_140 gabor_019 gabor_162_alt gabor_052 gabor_140_alt "1_32_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1800_3000_2200_gabor_patch_orientation_019_162_052_140_target_position_1_3_retrieval_position_3" gabor_circ gabor_circ gabor_003_framed gabor_circ blank blank blank blank fixation_cross_white "1_32_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_003_retrieval_position_3" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2192 2992 2092 fixation_cross gabor_165 gabor_041 gabor_124 gabor_075 gabor_165_alt gabor_041 gabor_124_alt gabor_075 "1_33_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2200_3000_2100_gabor_patch_orientation_165_041_124_075_target_position_2_4_retrieval_position_2" gabor_circ gabor_041_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_33_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_041_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 64 292 292 399 125 2242 2992 2542 fixation_cross gabor_048 gabor_106 gabor_032 gabor_087 gabor_048_alt gabor_106_alt gabor_032 gabor_087 "1_34_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_300_300_399_2250_3000_2550_gabor_patch_orientation_048_106_032_087_target_position_3_4_retrieval_position_2" gabor_circ gabor_106_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_34_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_retrieval_patch_orientation_106_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2242 2992 2442 fixation_cross gabor_009 gabor_134 gabor_085 gabor_068 gabor_009 gabor_134_alt gabor_085_alt gabor_068 "1_35_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2250_3000_2450_gabor_patch_orientation_009_134_085_068_target_position_1_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_116_framed blank blank blank blank fixation_cross_white "1_35_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_116_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1742 2992 2242 fixation_cross gabor_159 gabor_003 gabor_020 gabor_140 gabor_159_alt gabor_003_alt gabor_020 gabor_140 "1_36_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1750_3000_2250_gabor_patch_orientation_159_003_020_140_target_position_3_4_retrieval_position_3" gabor_circ gabor_circ gabor_020_framed gabor_circ blank blank blank blank fixation_cross_white "1_36_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_020_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1742 2992 2592 fixation_cross gabor_030 gabor_173 gabor_101 gabor_056 gabor_030_alt gabor_173 gabor_101_alt gabor_056 "1_37_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1750_3000_2600_gabor_patch_orientation_030_173_101_056_target_position_2_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_056_framed blank blank blank blank fixation_cross_white "1_37_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_056_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1942 2992 2092 fixation_cross gabor_012 gabor_119 gabor_082 gabor_148 gabor_012 gabor_119_alt gabor_082 gabor_148_alt "1_38_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1950_3000_2100_gabor_patch_orientation_012_119_082_148_target_position_1_3_retrieval_position_3" gabor_circ gabor_circ gabor_037_framed gabor_circ blank blank blank blank fixation_cross_white "1_38_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_037_retrieval_position_3" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1942 2992 2442 fixation_cross gabor_031 gabor_006 gabor_169 gabor_086 gabor_031_alt gabor_006 gabor_169_alt gabor_086 "1_39_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1950_3000_2450_gabor_patch_orientation_031_006_169_086_target_position_2_4_retrieval_position_2" gabor_circ gabor_053_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_39_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_053_retrieval_position_2" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 63 292 292 399 125 2242 2992 2142 fixation_cross gabor_004 gabor_161 gabor_077 gabor_030 gabor_004_alt gabor_161_alt gabor_077 gabor_030 "1_40_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_300_300_399_2250_3000_2150_gabor_patch_orientation_004_161_077_030_target_position_3_4_retrieval_position_2" gabor_circ gabor_112_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_40_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_retrieval_patch_orientation_112_retrieval_position_2" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2042 2992 2192 fixation_cross gabor_123 gabor_056 gabor_012 gabor_138 gabor_123_alt gabor_056_alt gabor_012 gabor_138 "1_41_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2050_3000_2200_gabor_patch_orientation_123_056_012_138_target_position_3_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_089_framed blank blank blank blank fixation_cross_white "1_41_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_089_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1842 2992 2142 fixation_cross gabor_170 gabor_080 gabor_037 gabor_102 gabor_170 gabor_080 gabor_037_alt gabor_102_alt "1_42_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1850_3000_2150_gabor_patch_orientation_170_080_037_102_target_position_1_2_retrieval_position_2" gabor_circ gabor_080_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_42_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_080_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2092 2992 2092 fixation_cross gabor_104 gabor_147 gabor_177 gabor_066 gabor_104_alt gabor_147 gabor_177_alt gabor_066 "1_43_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2100_3000_2100_gabor_patch_orientation_104_147_177_066_target_position_2_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_021_framed blank blank blank blank fixation_cross_white "1_43_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_021_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1992 2992 2492 fixation_cross gabor_007 gabor_069 gabor_174 gabor_154 gabor_007_alt gabor_069 gabor_174_alt gabor_154 "1_44_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2000_3000_2500_gabor_patch_orientation_007_069_174_154_target_position_2_4_retrieval_position_2" gabor_circ gabor_119_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_44_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_119_retrieval_position_2" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 63 292 292 399 125 2042 2992 2542 fixation_cross gabor_145 gabor_113 gabor_056 gabor_039 gabor_145 gabor_113_alt gabor_056 gabor_039_alt "1_45_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_300_300_399_2050_3000_2550_gabor_patch_orientation_145_113_056_039_target_position_1_3_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_174_framed blank blank blank blank fixation_cross_white "1_45_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_retrieval_patch_orientation_174_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1942 2992 2442 fixation_cross gabor_097 gabor_052 gabor_114 gabor_138 gabor_097_alt gabor_052_alt gabor_114 gabor_138 "1_46_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1950_3000_2450_gabor_patch_orientation_097_052_114_138_target_position_3_4_retrieval_position_3" gabor_circ gabor_circ gabor_114_framed gabor_circ blank blank blank blank fixation_cross_white "1_46_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_114_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1842 2992 2242 fixation_cross gabor_095 gabor_022 gabor_065 gabor_129 gabor_095 gabor_022_alt gabor_065_alt gabor_129 "1_47_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1850_3000_2250_gabor_patch_orientation_095_022_065_129_target_position_1_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_129_framed blank blank blank blank fixation_cross_white "1_47_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_129_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1942 2992 1942 fixation_cross gabor_014 gabor_046 gabor_151 gabor_171 gabor_014_alt gabor_046 gabor_151 gabor_171_alt "1_48_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1950_3000_1950_gabor_patch_orientation_014_046_151_171_target_position_2_3_retrieval_position_3" gabor_circ gabor_circ gabor_103_framed gabor_circ blank blank blank blank fixation_cross_white "1_48_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_103_retrieval_position_3" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1892 2992 2342 fixation_cross gabor_044 gabor_026 gabor_003 gabor_133 gabor_044 gabor_026_alt gabor_003_alt gabor_133 "1_49_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1900_3000_2350_gabor_patch_orientation_044_026_003_133_target_position_1_4_retrieval_position_1" gabor_089_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_49_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_089_retrieval_position_1" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1792 2992 2342 fixation_cross gabor_119 gabor_029 gabor_098 gabor_083 gabor_119_alt gabor_029 gabor_098 gabor_083_alt "1_50_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1800_3000_2350_gabor_patch_orientation_119_029_098_083_target_position_2_3_retrieval_position_2" gabor_circ gabor_168_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_50_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_168_retrieval_position_2" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1742 2992 1942 fixation_cross gabor_019 gabor_131 gabor_154 gabor_175 gabor_019 gabor_131 gabor_154_alt gabor_175_alt "1_51_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1750_3000_1950_gabor_patch_orientation_019_131_154_175_target_position_1_2_retrieval_position_1" gabor_019_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_51_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_019_retrieval_position_1" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 64 292 292 399 125 1892 2992 1992 fixation_cross gabor_006 gabor_174 gabor_067 gabor_150 gabor_006 gabor_174_alt gabor_067_alt gabor_150 "1_52_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_300_300_399_1900_3000_2000_gabor_patch_orientation_006_174_067_150_target_position_1_4_retrieval_position_2" gabor_circ gabor_174_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_52_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_UncuedRetriev_retrieval_patch_orientation_174_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2042 2992 2292 fixation_cross gabor_066 gabor_139 gabor_121 gabor_083 gabor_066 gabor_139_alt gabor_121_alt gabor_083 "1_53_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2050_3000_2300_gabor_patch_orientation_066_139_121_083_target_position_1_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_083_framed blank blank blank blank fixation_cross_white "1_53_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_083_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 63 292 292 399 125 1942 2992 2492 fixation_cross gabor_172 gabor_132 gabor_094 gabor_027 gabor_172_alt gabor_132 gabor_094_alt gabor_027 "1_54_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_300_300_399_1950_3000_2500_gabor_patch_orientation_172_132_094_027_target_position_2_4_retrieval_position_3" gabor_circ gabor_circ gabor_046_framed gabor_circ blank blank blank blank fixation_cross_white "1_54_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_retrieval_patch_orientation_046_retrieval_position_3" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2142 2992 2342 fixation_cross gabor_106 gabor_016 gabor_064 gabor_125 gabor_106_alt gabor_016 gabor_064_alt gabor_125 "1_55_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2150_3000_2350_gabor_patch_orientation_106_016_064_125_target_position_2_4_retrieval_position_2" gabor_circ gabor_016_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_55_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_016_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2042 2992 2192 fixation_cross gabor_135 gabor_178 gabor_021 gabor_158 gabor_135 gabor_178_alt gabor_021_alt gabor_158 "1_56_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2050_3000_2200_gabor_patch_orientation_135_178_021_158_target_position_1_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_110_framed blank blank blank blank fixation_cross_white "1_56_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_110_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1742 2992 1892 fixation_cross gabor_166 gabor_084 gabor_105 gabor_035 gabor_166 gabor_084_alt gabor_105 gabor_035_alt "1_57_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1750_3000_1900_gabor_patch_orientation_166_084_105_035_target_position_1_3_retrieval_position_1" gabor_166_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_57_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_166_retrieval_position_1" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 2242 2992 2342 fixation_cross gabor_001 gabor_159 gabor_041 gabor_123 gabor_001_alt gabor_159 gabor_041_alt gabor_123 "1_58_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_2250_3000_2350_gabor_patch_orientation_001_159_041_123_target_position_2_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_075_framed blank blank blank blank fixation_cross_white "1_58_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_075_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1792 2992 2242 fixation_cross gabor_179 gabor_043 gabor_067 gabor_007 gabor_179 gabor_043_alt gabor_067 gabor_007_alt "1_59_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1800_3000_2250_gabor_patch_orientation_179_043_067_007_target_position_1_3_retrieval_position_3" gabor_circ gabor_circ gabor_067_framed gabor_circ blank blank blank blank fixation_cross_white "1_59_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_067_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1992 2992 2142 fixation_cross gabor_080 gabor_138 gabor_101 gabor_048 gabor_080 gabor_138 gabor_101_alt gabor_048_alt "1_60_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2000_3000_2150_gabor_patch_orientation_080_138_101_048_target_position_1_2_retrieval_position_1" gabor_080_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_60_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_080_retrieval_position_1" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1992 2992 2392 fixation_cross gabor_024 gabor_083 gabor_102 gabor_045 gabor_024_alt gabor_083_alt gabor_102 gabor_045 "1_61_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2000_3000_2400_gabor_patch_orientation_024_083_102_045_target_position_3_4_retrieval_position_3" gabor_circ gabor_circ gabor_102_framed gabor_circ blank blank blank blank fixation_cross_white "1_61_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_102_retrieval_position_3" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2042 2992 2192 fixation_cross gabor_091 gabor_113 gabor_024 gabor_074 gabor_091_alt gabor_113 gabor_024_alt gabor_074 "1_62_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2050_3000_2200_gabor_patch_orientation_091_113_024_074_target_position_2_4_retrieval_position_2" gabor_circ gabor_113_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_62_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_113_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 63 292 292 399 125 1842 2992 2392 fixation_cross gabor_097 gabor_156 gabor_030 gabor_070 gabor_097_alt gabor_156 gabor_030 gabor_070_alt "1_63_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_300_300_399_1850_3000_2400_gabor_patch_orientation_097_156_030_070_target_position_2_3_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_116_framed blank blank blank blank fixation_cross_white "1_63_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_retrieval_patch_orientation_116_retrieval_position_4" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2242 2992 2042 fixation_cross gabor_028 gabor_099 gabor_062 gabor_145 gabor_028_alt gabor_099 gabor_062_alt gabor_145 "1_64_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2250_3000_2050_gabor_patch_orientation_028_099_062_145_target_position_2_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_145_framed blank blank blank blank fixation_cross_white "1_64_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_145_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 61 292 292 399 125 1892 2992 1942 fixation_cross gabor_157 gabor_180 gabor_070 gabor_091 gabor_157 gabor_180_alt gabor_070_alt gabor_091 "1_65_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_300_300_399_1900_3000_1950_gabor_patch_orientation_157_180_070_091_target_position_1_4_retrieval_position_1" gabor_111_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_65_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_CuedRetrieval_retrieval_patch_orientation_111_retrieval_position_1" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 2142 2992 2092 fixation_cross gabor_141 gabor_029 gabor_177 gabor_110 gabor_141_alt gabor_029 gabor_177_alt gabor_110 "1_66_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_2150_3000_2100_gabor_patch_orientation_141_029_177_110_target_position_2_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_110_framed blank blank blank blank fixation_cross_white "1_66_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_110_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 63 292 292 399 125 2192 2992 2592 fixation_cross gabor_005 gabor_086 gabor_116 gabor_059 gabor_005 gabor_086_alt gabor_116 gabor_059_alt "1_67_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_300_300_399_2200_3000_2600_gabor_patch_orientation_005_086_116_059_target_position_1_3_retrieval_position_2" gabor_circ gabor_038_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_67_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_retrieval_patch_orientation_038_retrieval_position_2" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1842 2992 1992 fixation_cross gabor_047 gabor_113 gabor_180 gabor_095 gabor_047 gabor_113 gabor_180_alt gabor_095_alt "1_68_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1850_3000_2000_gabor_patch_orientation_047_113_180_095_target_position_1_2_retrieval_position_2" gabor_circ gabor_113_framed gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_68_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_113_retrieval_position_2" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 63 292 292 399 125 2192 2992 2142 fixation_cross gabor_016 gabor_152 gabor_125 gabor_087 gabor_016_alt gabor_152 gabor_125_alt gabor_087 "1_69_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_300_300_399_2200_3000_2150_gabor_patch_orientation_016_152_125_087_target_position_2_4_retrieval_position_1" gabor_063_framed gabor_circ gabor_circ gabor_circ blank blank blank blank fixation_cross_white "1_69_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_DoChange_UncuedRetriev_retrieval_patch_orientation_063_retrieval_position_1" 1 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
44 62 292 292 399 125 1792 2992 1942 fixation_cross gabor_160 gabor_053 gabor_135 gabor_077 gabor_160 gabor_053_alt gabor_135_alt gabor_077 "1_70_Encoding_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_300_300_399_1800_3000_1950_gabor_patch_orientation_160_053_135_077_target_position_1_4_retrieval_position_4" gabor_circ gabor_circ gabor_circ gabor_077_framed blank blank blank blank fixation_cross_white "1_70_Retrieval_Working_Memory_MEG_P1_RL_Nonsalient_NoChange_CuedRetrieval_retrieval_patch_orientation_077_retrieval_position_4" 2 58.69 58.69 -58.69 58.69 -58.69 -58.69 58.69 -58.69;
};
# baselinePost (at the end of the session)
trial {
picture {
box frame1; x=0; y=0;
box frame2; x=0; y=0;
box background; x=0; y=0;
bitmap fixation_cross_black; x=0; y=0;
};
time = 0;
duration = 5000;
code = "BaselinePost";
port_code = 92;
};
|
d50c20eacad1a33e63c2781df214b25f18966dff
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2354/CH10/EX10.6/10_6.sce
|
b6dfde00b678e5869660148755cddc636b0370e3
|
[] |
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
| 389
|
sce
|
10_6.sce
|
//example 10.6
clc; funcprot(0);
// Initialization of Variable
omega1=0.002;
omega2=0.0094;
ma1dot=180.0;
ma2dot=497.0;
omega3=(omega1*ma1dot+omega2*ma2dot)/(ma1dot+ma2dot);
disp(omega3,"relative humidity");
k1=10;//(ha+whv)1
k2=47.8;//(ha+whv)2
k3=(ma1dot*k1+ma2dot*k2)/(ma1dot+ma2dot)
disp(k3,"(ha+whv)3 in kJ/kg");
disp(19,"temperature by inspection in degreeC")
clear()
|
794a7050dd71944bdc42ba3d6f2ac80ad11765c3
|
f891f5aed2e66371488173c2b9c4e8f977a9f64a
|
/UL 1741 SA/Tests/SS/SS.tst
|
6afb45124a1f2a0932f1a58db7bdf246deb9f0b1
|
[] |
no_license
|
jakedm/svp_directories
|
d9b85c41b45a3ded7572f9f730e8d1efc8515099
|
19272f8784baabf83e197778768933aef015432c
|
refs/heads/master
| 2021-01-18T18:08:29.224016
| 2017-01-16T20:09:35
| 2017-01-16T20:09:35
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 1,178
|
tst
|
SS.tst
|
<scriptConfig name="SS" script="SoftStart">
<params>
<param name="invt.pretest_delay" type="int">0</param>
<param name="ss.RRss_min" type="float">2.0</param>
<param name="ss.MSARR" type="float">2.5</param>
<param name="ss.t_dwell" type="float">3.0</param>
<param name="comm.slave_id" type="int">5</param>
<param name="invt.verification_delay" type="int">5</param>
<param name="invt.posttest_delay" type="int">10</param>
<param name="ss.RRss_max" type="float">100.0</param>
<param name="ss.Irated" type="float">100.0</param>
<param name="comm.baudrate" type="int">9600</param>
<param name="comm.ifc_name" type="string">COM7</param>
<param name="gridsim.auto_config" type="string">Disabled</param>
<param name="datatrig.dsm_method" type="string">Disabled - Data from EUT</param>
<param name="datatrig.trigger_method" type="string">Disabled - Data from EUT</param>
<param name="pvsim.mode" type="string">Manual</param>
<param name="gridsim.mode" type="string">Manual</param>
<param name="comm.parity" type="string">N</param>
<param name="comm.ifc_type" type="string">RTU</param>
</params>
</scriptConfig>
|
2e3ceb58880b38ec7ca505c77484a1699b2c2778
|
f2068f2734a1b9080ea2db4455a5fc3581ab0a1c
|
/plus-tau-general.sci
|
90521eaf5b5e721471a12de5771a295103142f3f
|
[] |
no_license
|
NnataKha/Conflict-models-with-attractive-interaction
|
5a9bc20603f05cfefa5283db453bc377ff68ff15
|
afc53eff31d1d16134b76fde0b51698abc4a9c67
|
refs/heads/master
| 2020-03-16T18:48:14.182188
| 2018-05-10T11:17:25
| 2018-05-10T11:17:25
| null | 0
| 0
| null | null | null | null |
UTF-8
|
Scilab
| false
| false
| 1,315
|
sci
|
plus-tau-general.sci
|
clear;
// function that determines p_i
function y=fun1(x)
y=sin(4*x*%pi)+1;
endfunction
// function that determines r_i
function y=fun2(x)
y=cos(4*x*%pi)+1;
endfunction
cp=intg(0,1,fun1);
cr=intg(0,1,fun2);
function y=fun11(x)
y=fun1(x)/cp;
endfunction
function y=fun21(x)
y=fun2(x)/cr;
endfunction
d=0.01;//the length of the intervals of partitioning at the graphic drawn with dash line
//set B_mu
B_mu0=0.0/d;
B_mu1=0.7/d;
//set B_nu
B_nu0=0.3/d;
B_nu1=1/d;
m=1+1/d;
x=0;
for i=1:m
p(i)=fun11(x);
r(i)=fun21(x);
T(i)=x;
x=x+d;
end
p1=p;
r1=r;
alpha=0.5;
be=0.5;
//set tau
for i=1:m
if (i>=B_mu0 & i<=B_mu1)|(i>=B_nu0 & i<=B_nu1) then
tau(i)=alpha*p(i)+be*r(i)
else tau(i)=0;
end
end
ctau=sum(tau.*d);
tau1=tau./ctau;
p_v(1,:)=p';
N=100;// number of steps (graphic drawn with dash line)
for k=1:N
Theta = sum(sqrt(p.*r)*d);
for i=1:m
if (i>=B_mu0 & i<=B_mu1)|(i>=B_nu0 & i<=B_nu1) then
tau(i)=alpha*p(i)+be*r(i)
else tau(i)=0;
end
end
W = sum(tau.*d);
z = 1+W+Theta;
p = (p.*(1+Theta)+tau)./z;
r = (r.*(1+Theta)+tau)./z;
//p_v(k+1,:)=r';
end
plot(T,p,'g');
plot(T,p1,'g--');
plot(T,r1,'r--');
plot(T,r,'r');
|
d192c6ad66155c22b005d6fdb5b19f09ea0853c1
|
8217f7986187902617ad1bf89cb789618a90dd0a
|
/browsable_source/1.1/Unix/scilab-1.1/man/Man-Part1/robust/dhnorm.sci
|
dadfad52e36d16aace1c7b68215d09d77debaf5c
|
[
"LicenseRef-scancode-public-domain",
"LicenseRef-scancode-warranty-disclaimer",
"LicenseRef-scancode-unknown-license-reference"
] |
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
| 663
|
sci
|
dhnorm.sci
|
.TH h_norm 1 "April 1993" "Scilab Group" "Scilab Function"
.so man1/sci.an
.SH NAME
dhnorm- discrete H-infinity norm
.SH CALLING SEQUENCE
.nf
[hinfnorm]=dhnorm(sl,[tol],[normax])
.fi
.SH PARAMETERS
.TP 10
sl
: the state space system (\fVsyslin\fR list) (discrete-time)
.TP
tol
: tolerance in bisection step, default value \fV0.01\fR
.TP
normax
: upper bound for the norm , default value is \fV1000\fR
.TP
hinfnorm
: the discrete infinity norm of \fVSl\fR
.SH DESCRIPTION
produces the discrete-time infinity norm of a state-space system
(the maximum over all frequencies on the unit circle of the maximum singular value).
.SH SEE ALSO
H_norm, linfn
|
f27deb40335431dfcd4d5f8efd26dedc089458d8
|
089894a36ef33cb3d0f697541716c9b6cd8dcc43
|
/NLP_Project/test/blog/bow/bow.1_10.tst
|
e2b678c63b0991d4a688ca40ef3f2a56832fbcc4
|
[] |
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
| 3,591
|
tst
|
bow.1_10.tst
|
1 10:0.3333333333333333 19:0.05555555555555555 30:0.2 66:0.5 149:1.0 203:1.0
1 4:0.1 11:1.0 49:0.125 249:0.1111111111111111 345:1.0 1455:1.0
1 3:1.0 13:0.5 14:0.06060606060606061 17:0.02631578947368421 28:1.0 30:0.2 84:0.25 187:1.0 298:1.0 883:1.0
1 4:0.1 6:1.0 10:0.3333333333333333 14:0.06060606060606061 17:0.05263157894736842 25:0.5 74:0.3333333333333333 84:0.25 665:1.0 721:1.0
1 4:0.1 84:0.25 150:1.0 156:1.0 542:1.0 955:1.0
1 6:1.0 13:0.5 14:0.030303030303030304 19:0.05555555555555555
1 6:1.0 10:0.3333333333333333 13:0.5 14:0.030303030303030304 17:0.05263157894736842 19:0.05555555555555555 49:0.125 68:1.0 69:0.6666666666666666 137:1.0 181:0.3333333333333333 517:1.0
1 14:0.030303030303030304 17:0.05263157894736842 25:0.5 30:0.2 72:1.0 121:0.125 404:1.0 469:1.0 475:1.0 698:1.0
1 13:0.5 19:0.1111111111111111 20:1.0 55:0.5 74:0.6666666666666666 159:0.2 160:0.3333333333333333
1 13:0.5 14:0.030303030303030304 17:0.02631578947368421 30:0.2 69:0.3333333333333333 121:0.125 149:1.0 160:0.6666666666666666 183:0.25 226:1.0 249:0.1111111111111111 286:1.0 556:1.0 611:1.0 1538:1.0
1 4:0.1 6:1.0 10:0.3333333333333333 14:0.030303030303030304 54:0.5 84:0.25 86:1.0 93:1.0 569:1.0 663:1.0
1 25:0.5 396:1.0 494:0.5 1369:1.0
1 25:0.5 30:0.2 84:0.25 148:1.0 286:1.0 326:1.0 409:1.0
1 3:1.0 6:1.0 13:0.5 14:0.09090909090909091 25:0.5 28:1.0 29:1.0 42:0.3333333333333333 43:0.3333333333333333 56:0.25 60:1.0 181:0.3333333333333333 207:0.1 214:2.0 236:0.3333333333333333 237:1.0 409:1.0 480:0.3333333333333333 556:1.0 581:0.3333333333333333 794:1.0 920:1.0
1 54:0.5 69:0.3333333333333333 236:0.3333333333333333 448:1.0 556:1.0 652:1.0
1 4:0.1 14:0.030303030303030304 54:0.5 64:1.0 171:0.25 598:1.0
1 4:0.1 14:0.030303030303030304 19:0.05555555555555555 25:0.5 69:0.3333333333333333 542:1.0 851:1.0
1 349:0.3333333333333333
1 10:0.3333333333333333 13:0.5 25:0.5 69:0.3333333333333333 70:0.25 193:0.5
1 25:0.5 30:0.2 64:1.0 67:1.0 70:0.25 183:0.25 1184:1.0 1349:1.0 1373:1.0
1 279:0.5
1 14:0.030303030303030304 69:0.3333333333333333
1 6:1.0 14:0.030303030303030304 30:0.2 1129:1.0
1 4:0.1 19:0.05555555555555555 25:0.5 66:0.5 679:1.0
1 10:0.3333333333333333 19:0.05555555555555555 25:0.5 66:0.5 199:0.125 237:1.0 394:1.0 1210:1.0
1 19:0.05555555555555555 69:0.3333333333333333 84:0.25 121:0.125 189:0.5 249:0.1111111111111111 355:1.0 489:1.0 511:1.0 1359:1.0 1503:1.0
1 3:1.0 6:1.0 14:0.06060606060606061 17:0.05263157894736842 19:0.1111111111111111 20:1.0 21:1.0 74:0.3333333333333333 91:1.0 181:0.3333333333333333 226:1.0 249:0.1111111111111111 274:1.0 602:1.0 705:1.0 856:1.0 911:1.0
1 17:0.05263157894736842 19:0.05555555555555555 837:1.0 842:1.0
1 6:1.0 14:0.030303030303030304 17:0.05263157894736842 69:0.6666666666666666 381:1.0 486:1.0 611:1.0 837:1.0
1 14:0.030303030303030304 17:0.02631578947368421 20:1.0 30:0.2 184:0.5 250:1.0 349:0.3333333333333333 625:1.0 924:1.0 965:1.0
1 3:1.0 4:0.2 349:0.3333333333333333
1 6:1.0 14:0.06060606060606061 17:0.02631578947368421 30:0.2 133:1.0 226:1.0 377:1.0 465:1.0
1 25:0.5 167:1.0 901:1.0
1 6:1.0 13:1.0 14:0.09090909090909091 17:0.05263157894736842 19:0.05555555555555555 49:0.125 74:0.3333333333333333 84:0.25 256:1.0 442:1.0 553:1.0 837:1.0 1553:1.0
1 17:0.02631578947368421 20:1.0 25:0.5 147:1.0 171:0.5 284:1.0 828:1.0
1 13:0.5 127:1.0 249:0.1111111111111111 441:1.0
1 14:0.030303030303030304 17:0.02631578947368421 475:1.0 883:1.0
1 4:0.1 13:0.5 202:0.14285714285714285
1 19:0.05555555555555555 20:1.0 21:1.0 43:0.3333333333333333
1 3:1.0 14:0.06060606060606061 17:0.02631578947368421 25:1.0 28:1.0 84:0.25 298:1.0 326:1.0 462:1.0 716:1.0
|
708d5c163b609353e3288a971c6361612269206f
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1364/CH9/EX9.3.1/9_3_1.sce
|
8675e87f9a6b13681b881bb6930c72b9a0b73990
|
[] |
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
| 181
|
sce
|
9_3_1.sce
|
clc
//initialisation of variables
va= 0.2
r= 1/1.25
r1= 1/50
P= 20 //atm
v= 400 //m.p.h
//CALCULATIONS
Um= v*va/(P*r*r1)
//RESULTS
printf (' Speed of air= %.f m.p.h',Um)
|
0b79d6b0ca4371f1c393136dada447bf3d4c36c9
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/581/CH5/EX5.9/Example5_9.sce
|
10eca133993e6e00c0e587188d25a7053da53daa
|
[] |
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
| 320
|
sce
|
Example5_9.sce
|
clear;
clc;
printf("\t Example 5.9\n");
r=3; // radius ratio of one-quarter section of cylinder
S=%pi/(2*log(r)); // shape factor
printf("\t shape factor is : %.2f \n the quarter cylinder will be pictured for the radius ratio of 3, but for the different sizes.in both the cases it will be 1.43",S);
//end
|
b6428504ac4ef9a0fcb2c1485dce79995b3f375a
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/548/CH6/EX6.9/6_09.sce
|
b5388a5ed033dfc0df68d64822687d673749991b
|
[] |
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
| 479
|
sce
|
6_09.sce
|
pathname=get_absolute_file_path('6_09.sce')
filename=pathname+filesep()+'6_09data.sci'
exec(filename)
V1=sqrt(2*Wl*cos(a)/(D1*Cl));disp(V1,"V1=","V1=sqrt(2*Wl*cos(a)/(D1*Cl))","For altitude 3048 meter:")
V2=sqrt(2*Wl*cos(a)/(D2*Cl));disp(V2,"V2=","V2=sqrt(2*Wl*cos(a)/(D2*Cl))","For altitude 609.6 meter:")
printf("\Answer:\n")
printf("\Velocity at equilibrium glide angle at 3048 m: %f m/s\n",V1)
printf("\n\Velocity at equilibrium glide angle at 609.6 m: %f m/s\n\n",V2)
|
5dd1deded1a3d0c9e42ea733d8c1468e45e5bee0
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1439/CH18/EX18.5/18_5.sce
|
de57686f91a0ceb4d31bf3f961e2cfbb7fb4ca26
|
[] |
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
| 258
|
sce
|
18_5.sce
|
clc
//initialisation of variables
m= 1.008 //gms
m1= 36.98 //gms
N= 6*10^23 //molecules
r= 1.275*10^-8 //cm
//CALCULATIONS
u= m*m1/(N*(m+m1))
I= u*r^2
//RESULTS
printf (' reduced mass = %.2e g',u)
printf (' \n moment of inertia = %.2e g cm^2',I)
|
1b649c5ab14c0bd048c04ce129a97790296e9c4e
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3733/CH32/EX32.16A/Ex32_16A.sce
|
639c0aa8b1139a7a25313986dd7588bfb0492f37
|
[] |
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
| 493
|
sce
|
Ex32_16A.sce
|
// Example 32_16A
clc;funcprot(0);
//Given data
P=1000;// Plant capacity in MW
P_1=1000;// MW
t_1=2;// hours
P_2=500;// MW
t_2=6;// hours
n=60;// Number of days plant should shut down annualy
// Calculation
E_d=((P_1*t_1))+((P_2*t_2));//The amount of energy generated per day in Mwh/day
N=365-n;// No. of days (the plant is working)
E_y=E_d*N;//The amount of energy generated per year in Mwh
L_f=E_y/(P*(N*24));// Annual load factor
printf('\n Annual load factor=%0.3f',L_f);
|
262643731595953352cb87c2dff6e9c71147373c
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/2837/CH12/EX12.1/Ex12_1.sce
|
94cee61fdc2f51e1f918198c1a6f43c8116e646c
|
[] |
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
| 355
|
sce
|
Ex12_1.sce
|
clc
clear
//Initialization of variables
km1=0.62
km2=0.16
km3=0.4
l1=8 //in
l2=4 //in
l3=4 //in
Tf=1600 //F
Tc=100 //F
//calculations
Rw=l1/12/km1 +l2/12/km2 +l3/12/km3
Rb=l1/12/km1
Ti=Tf-Rb/Rw *(Tf-Tc)
//results
printf("Interface temperature = %.1f F",Ti)
disp("The answers might differ a bit from textbook due to rounding off error.")
|
45f321dffa17d7aa9f04a2c7761561634a9db4ee
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1787/CH2/EX2.3/Exa2_3.sce
|
c1be6dad5a1b73cb928472ef44fe08d0272db599
|
[] |
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
| 221
|
sce
|
Exa2_3.sce
|
//Exa 2.3
clc;
clear;
close;
//given data
n=10^24;//electrons/m^3
e=1.6*10^-19;//constant
v=1.5*10^-2;//in m/s
A=1;//in cm^2
A=1*10^-4;//in m^2
I=e*n*v*A;//in Ampere
disp(I,"Magnitude of current in Ampere : ");
|
5be60668696f769d19a930cddd0b115e37d80928
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/1583/CH2/EX2.8/SSA_Ex_2_8.sce
|
e9f698e68f1b247c122f3a6ccf16bd7d0239fede
|
[] |
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
| 480
|
sce
|
SSA_Ex_2_8.sce
|
clc
//Chapter 2:Small Signal Amplifiers
//example 2.8 page no 42
//given
disp('Assuming Vi (input voltage)=1')
V1=(5+10^6)/(5+2*10^6)//voltage on the positive terminal
V2=10^6/(5+2*10^6)//the voltage on the inverting terminal
ed=V1-V2//differential voltage
ec=(V1+V2)/2//common-mode voltage
Ad=2*10^3//differentail gain
Ac=2*10^-3//common mode gain (here 20% of differentail gain)
Vo=Ad*ed+Ac*ec//actual amplifier output
mprintf('the voltage gain is %3.2e Volts',Vo)
|
c6075d86f66616c250e0af9e2d15770e2387d15f
|
449d555969bfd7befe906877abab098c6e63a0e8
|
/3507/CH23/EX23.6/Ex23_6.sce
|
9b7f3c6d994d467242821a6a1c1eeb1b31140e6b
|
[] |
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
| 491
|
sce
|
Ex23_6.sce
|
//chapter23
//example23.6
//page515
Vm=240 // V
v=180 // V
// figure given is for understanding purpose only. It is not required to solve the example
// SCR remains off till it reaches 180 V i.e. forward breakdown voltage
// since v=Vm*sin(theta), we get
theta=asin(v/Vm) // firing angle in terms of degrees
// since theta=314*t, we get
t=theta/314 // seconds
printf("off duration of SCR = %.3f ms \n",t*1000) //multiply t by 1000 to display time in milliseconds
|
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