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Biomni/experiments/bioagent_bench/runs/scale_250_rerun_sharded10_20260523_130637/comparative-genomics_20260523_130651/prokka_KBS0714_v3/KBS0714.log

@@ -0,0 +1,139 @@
+[14:00:28] This is prokka 1.15.6
+[14:00:28] Written by Torsten Seemann <torsten.seemann@gmail.com>
+[14:00:28] Homepage is https://github.com/tseemann/prokka
+[14:00:28] Local time is Sat May 23 14:00:28 2026
+[14:00:28] You are root
+[14:00:28] Operating system is linux
+[14:00:28] You have BioPerl 1.7.8
+[14:00:28] System has 128 cores.
+[14:00:28] Will use maximum of 4 cores.
+[14:00:28] Annotating as >>> Bacteria <<<
+[14:00:28] Generating locus_tag from '/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna' contents.
+[14:00:28] Setting --locustag MOLHKGIG from MD5 6851402062f9a6db2d633ff9bc46b2f3
+[14:00:28] Creating new output folder: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_250_rerun_sharded10_20260523_130637/comparative-genomics_20260523_130651/prokka_KBS0714_v3
+[14:00:28] Running: mkdir -p \/225040511\/project\/Biomni\/experiments\/bioagent_bench\/runs\/scale_250_rerun_sharded10_20260523_130637\/comparative\-genomics_20260523_130651\/prokka_KBS0714_v3
+[14:00:28] Using filename prefix: KBS0714.XXX
+[14:00:28] Setting HMMER_NCPU=1
+[14:00:28] Writing log to: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_250_rerun_sharded10_20260523_130637/comparative-genomics_20260523_130651/prokka_KBS0714_v3/KBS0714.log
+[14:00:28] Command: /225040511/miniconda3/envs/biomni_e1/bin/prokka --outdir /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_250_rerun_sharded10_20260523_130637/comparative-genomics_20260523_130651/prokka_KBS0714_v3 --prefix KBS0714 --genus Micrococcus --strain KBS0714 --force --cpus 4 /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna
+[14:00:28] Looking for 'aragorn' - found /225040511/miniconda3/envs/biomni_e1/bin/aragorn
+[14:00:29] Determined aragorn version is v1.2 from 'ARAGORN v1.2.41 Dean Laslett'
+[14:00:29] Looking for 'barrnap' - found /225040511/miniconda3/envs/biomni_e1/bin/barrnap
+[14:00:29] Determined barrnap version is v0.9 from 'barrnap 0.9'
+[14:00:29] Looking for 'blastp' - found /225040511/miniconda3/envs/biomni_e1/bin/blastp
+[14:00:31] Determined blastp version is v2.17 from 'blastp: 2.17.0+'
+[14:00:31] Looking for 'cmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/cmpress
+[14:00:31] Determined cmpress version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[14:00:31] Looking for 'cmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/cmscan
+[14:00:32] Determined cmscan version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[14:00:32] Looking for 'egrep' - found /usr/bin/egrep
+[14:00:32] Looking for 'find' - found /usr/bin/find
+[14:00:32] Looking for 'grep' - found /usr/bin/grep
+[14:00:32] Looking for 'hmmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmpress
+[14:00:32] Determined hmmpress version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[14:00:32] Looking for 'hmmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmscan
+[14:00:32] Determined hmmscan version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[14:00:32] Looking for 'java' - found /225040511/miniconda3/envs/biomni_e1/bin/java
+[14:00:32] Looking for 'makeblastdb' - found /225040511/miniconda3/envs/biomni_e1/bin/makeblastdb
+[14:00:33] Determined makeblastdb version is v2.17 from 'makeblastdb: 2.17.0+'
+[14:00:33] Looking for 'minced' - found /225040511/miniconda3/envs/biomni_e1/bin/minced
+[14:00:36] Determined minced version is v4.2 from 'minced 0.4.2'
+[14:00:36] Looking for 'parallel' - found /225040511/miniconda3/envs/biomni_e1/bin/parallel
+[14:00:38] Determined parallel version is 20260422 from 'GNU parallel 20260422'
+[14:00:38] Looking for 'prodigal' - found /225040511/miniconda3/envs/biomni_e1/bin/prodigal
+[14:00:39] Determined prodigal version is v2.6 from 'Prodigal V2.6.3: February, 2016'
+[14:00:39] Looking for 'prokka-genbank_to_fasta_db' - found /225040511/miniconda3/envs/biomni_e1/bin/prokka-genbank_to_fasta_db
+[14:00:39] Looking for 'sed' - found /225040511/miniconda3/envs/biomni_e1/bin/sed
+[14:00:39] Looking for 'tbl2asn' - found /225040511/miniconda3/envs/biomni_e1/bin/tbl2asn
+[14:00:40] Determined tbl2asn version is v25.7 from 'tbl2asn 25.7   arguments:'
+[14:00:40] Using genetic code table 11.
+[14:00:40] Loading and checking input file: /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna
+[14:00:41] Wrote 1 contigs totalling 2522703 bp.
+[14:00:41] Predicting tRNAs and tmRNAs
+[14:00:41] Running: aragorn -l -gc11  -w \/225040511\/project\/Biomni\/experiments\/bioagent_bench\/runs\/scale_250_rerun_sharded10_20260523_130637\/comparative\-genomics_20260523_130651\/prokka_KBS0714_v3\/KBS0714\.fna
+[14:01:09] 1 tRNA-Ile [11095,11169] 35 (gat)
+[14:01:09] 2 tRNA-Ala [11400,11474] 34 (tgc)
+[14:01:09] 3 tRNA-Leu [28649,28734] 35 (cag)
+[14:01:09] 4 tRNA-Lys [124259,124332] 34 (ttt)
+[14:01:09] 5 tRNA-Glu [137770,137843] 35 (ttc)
+[14:01:09] 6 tRNA-Asp [137959,138033] 35 (gtc)
+[14:01:09] 7 tRNA-Phe [138105,138180] 34 (gaa)
+[14:01:09] 8 tRNA-Ser [245784,245870] 35 (gga)
+[14:01:09] 9 tRNA-Ser c[315614,315704] 35 (cga)
+[14:01:09] 10 tRNA-Arg c[318941,319015] 35 (acg)
+[14:01:09] 11 tRNA-Ser c[330464,330553] 35 (gct)
+[14:01:09] 12 tRNA-Ser c[339160,339248] 35 (tga)
+[14:01:09] 13 tRNA-Thr c[340979,341054] 35 (cgt)
+[14:01:09] 14 tRNA-Pro [368575,368651] 35 (cgg)
+[14:01:09] 15 tRNA-Thr [381544,381620] 35 (tgt)
+[14:01:09] 16 tRNA-Val [383938,384013] 35 (cac)
+[14:01:09] 17 tRNA-Arg c[400154,400229] 35 (cct)
+[14:01:09] 18 tRNA-Leu [499685,499760] 35 (taa)
+[14:01:09] 19 tRNA-Gln [546090,546163] 33 (ttg)
+[14:01:09] 20 tRNA-Ala [608522,608619] 36 (ggc)
+[14:01:09] 21 tRNA-Asn [643583,643655] 33 (gtt)
+[14:01:09] 22 tRNA-Met [705763,705837] 35 (cat)
+[14:01:09] 23 tmRNA [812896,813265] 96,134 AESKRTDFALAA*
+[14:01:09] 24 tRNA-Arg c[846154,846227] 34 (ccg)
+[14:01:09] 25 tRNA-Leu c[900527,900608] 35 (tag)
+[14:01:09] 26 tRNA-Lys c[901247,901324] 35 (ctt)
+[14:01:09] 27 tRNA-Gln [931597,931669] 34 (ctg)
+[14:01:09] 28 tRNA-Glu [931724,931797] 35 (ctc)
+[14:01:09] 29 tRNA-Glu [931926,932000] 35 (ctc)
+[14:01:09] 30 tRNA-Val [1010731,1010806] 35 (tac)
+[14:01:09] 31 tRNA-His c[1034437,1034512] 34 (gtg)
+[14:01:09] 32 tRNA-Arg c[1041690,1041765] 35 (tct)
+[14:01:09] 33 tRNA-Ala c[1053998,1054087] 31 (cgc)
+[14:01:09] 34 tRNA-Gly c[1055246,1055318] 33 (tcc)
+[14:01:09] 35 tRNA-Pro [1056384,1056458] 35 (tgg)
+[14:01:09] 36 tRNA-Ala [1094883,1094958] 34 (ggc)
+[14:01:09] 37 tRNA-Ala [1096345,1096421] 35 (ggc)
+[14:01:09] 38 tRNA-Gly c[1138144,1138219] 35 (gcc)
+[14:01:09] 39 tRNA-Val c[1138247,1138319] 33 (gac)
+[14:01:09] 40 tRNA-Cys c[1138377,1138448] 33 (gca)
+[14:01:09] 41 tRNA-Gly c[1138466,1138540] 35 (gcc)
+[14:01:09] 42 tRNA-Leu [1177274,1177357] 35 (caa)
+[14:01:09] 43 tRNA-Leu c[1264464,1264549] 35 (gag)
+[14:01:09] 44 tRNA-Ile [1353125,1353219] 35 (gat)
+[14:01:09] 45 tRNA-Pro c[1535472,1535548] 35 (ggg)
+[14:01:09] 46 tmRNA* [1638170,1638576] 272,316 ASAARTCRPPAWWA*
+[14:01:09] 47 tRNA-Met c[1658678,1658752] 35 (cat)
+[14:01:09] 48 tRNA-Trp c[1893471,1893544] 34 (cca)
+[14:01:09] 49 tRNA-Met c[1911202,1911276] 35 (cat)
+[14:01:09] 50 tRNA-Thr c[1911336,1911408] 33 (ggt)
+[14:01:09] 51 tRNA-Tyr c[1922631,1922714] 35 (gta)
+[14:01:09] 52 tRNA-Arg c[1944250,1944342] 37 (cct)
+[14:01:09] 53 tRNA-Gly [2062710,2062783] 33 (ccc)
+[14:01:09] 54 tRNA-Ala c[2158546,2158619] 34 (cgc)
+[14:01:09] Found 54 tRNAs
+[14:01:09] Predicting Ribosomal RNAs
+[14:01:09] Running Barrnap with 4 threads
+[14:01:21] 1 NZ_CP042169.1 362528 16S ribosomal RNA
+[14:01:21] 2 NZ_CP042169.1 364492 23S ribosomal RNA
+[14:01:21] 3 NZ_CP042169.1 367774 5S ribosomal RNA
+[14:01:21] 4 NZ_CP042169.1 1562474 5S ribosomal RNA
+[14:01:21] 5 NZ_CP042169.1 1562781 23S ribosomal RNA
+[14:01:21] 6 NZ_CP042169.1 1566309 16S ribosomal RNA
+[14:01:21] Found 6 rRNAs
+[14:01:21] Skipping ncRNA search, enable with --rfam if desired.
+[14:01:21] Total of 58 tRNA + rRNA features
+[14:01:21] Searching for CRISPR repeats
+[14:01:29] CRISPR1 NZ_CP042169.1 2422827 with 8 spacers
+[14:01:29] CRISPR2 NZ_CP042169.1 2427487 with 11 spacers
+[14:01:29] Found 2 CRISPRs
+[14:01:29] Predicting coding sequences
+[14:01:29] Contigs total 2522703 bp, so using single mode
+[14:01:29] Running: prodigal -i \/225040511\/project\/Biomni\/experiments\/bioagent_bench\/runs\/scale_250_rerun_sharded10_20260523_130637\/comparative\-genomics_20260523_130651\/prokka_KBS0714_v3\/KBS0714\.fna -c -m -g 11 -p single -f sco -q
+[14:02:14] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:606702..609095 on + strand
+[14:02:14] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:643616..643948 on - strand
+[14:02:17] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1053740..1054213 on + strand
+[14:02:19] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1352703..1354082 on - strand
+[14:02:22] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1943376..1944674 on - strand
+[14:02:26] Found 2252 CDS
+[14:02:26] Connecting features back to sequences
+[14:02:27] Not using genus-specific database. Try --usegenus to enable it.
+[14:02:27] Annotating CDS, please be patient.
+[14:02:27] Will use 4 CPUs for similarity searching.
+[14:02:30] There are still 2252 unannotated CDS left (started with 2252)
+[14:02:30] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS with 4 CPUs
+[14:02:30] Running: cat \/225040511\/project\/Biomni\/experiments\/bioagent_bench\/runs\/scale_250_rerun_sharded10_20260523_130637\/comparative\-genomics_20260523_130651\/prokka_KBS0714_v3\/KBS0714\.IS\.tmp\.1182559\.faa | parallel --gnu --plain -j 4 --block 96516 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Biomni\/experiments\/bioagent_bench\/runs\/scale_250_rerun_sharded10_20260523_130637\/comparative\-genomics_20260523_130651\/prokka_KBS0714_v3\/KBS0714\.IS\.tmp\.1182559\.blast 2> /dev/null

Biomni/experiments/bioagent_bench/runs/scale_250_rerun_sharded10_20260523_130637/comparative-genomics_20260523_130651/proteomes/AS2_nt.njs

@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "AS2_nt",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_005280335.1_ASM528033v1_genomic.fna",
+  "number-of-letters": 2848891,
+  "number-of-sequences": 1,
+  "last-updated": "2026-05-23T14:16:00",
+  "number-of-volumes": 1,
+  "bytes-total": 749458,
+  "bytes-to-cache": 712432,
+  "files": [
+    "AS2_nt.ndb",
+    "AS2_nt.nhr",
+    "AS2_nt.nin",
+    "AS2_nt.not",
+    "AS2_nt.nsq",
+    "AS2_nt.ntf",
+    "AS2_nt.nto"
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_250_rerun_sharded10_20260523_130637/comparative-genomics_20260523_130651/proteomes/KBS0714_nt.njs

@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "KBS0714_nt",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna",
+  "number-of-letters": 2522703,
+  "number-of-sequences": 1,
+  "last-updated": "2026-05-23T14:12:00",
+  "number-of-volumes": 1,
+  "bytes-total": 667905,
+  "bytes-to-cache": 630885,
+  "files": [
+    "KBS0714_nt.ndb",
+    "KBS0714_nt.nhr",
+    "KBS0714_nt.nin",
+    "KBS0714_nt.not",
+    "KBS0714_nt.nsq",
+    "KBS0714_nt.ntf",
+    "KBS0714_nt.nto"
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_250_rerun_sharded10_20260523_130637/comparative-genomics_20260523_130651/proteomes/KD337-16_nt.njs

@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "KD337-16_nt",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_020097155.1_ASM2009715v1_genomic.fna",
+  "number-of-letters": 2648900,
+  "number-of-sequences": 1,
+  "last-updated": "2026-05-23T14:18:00",
+  "number-of-volumes": 1,
+  "bytes-total": 699456,
+  "bytes-to-cache": 662435,
+  "files": [
+    "KD337-16_nt.ndb",
+    "KD337-16_nt.nhr",
+    "KD337-16_nt.nin",
+    "KD337-16_nt.not",
+    "KD337-16_nt.nsq",
+    "KD337-16_nt.ntf",
+    "KD337-16_nt.nto"
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_250_rerun_sharded10_20260523_130637/comparative-genomics_20260523_130651/proteomes/SA211_nt.njs

@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "SA211_nt",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_003691675.1_ASM369167v1_genomic.fna",
+  "number-of-letters": 2483045,
+  "number-of-sequences": 1,
+  "last-updated": "2026-05-23T14:14:00",
+  "number-of-volumes": 1,
+  "bytes-total": 657999,
+  "bytes-to-cache": 620971,
+  "files": [
+    "SA211_nt.ndb",
+    "SA211_nt.nhr",
+    "SA211_nt.nin",
+    "SA211_nt.not",
+    "SA211_nt.nsq",
+    "SA211_nt.ntf",
+    "SA211_nt.nto"
+  ]
+}