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Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/agent_runtime/biomni_data/runtime_mcp_configs/runtime_mcp_20260520_140957_333268.yaml

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+mcp_servers:
+  prokka:
+    enabled: true
+    description: 'Installs packages: prokka. Copies scripts: prokka_server.py. Default
+      command: ["python", "/app/prokka_server.py"] | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_prokka/app/prokka_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_prokka/app/prokka_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_prokka/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_prokka/app/prokka_server.py
+    packages:
+    - prokka
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/prokka.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/bin:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: prokka_uniprot_to_fasta_db
+      description: Tool bound for operation protein_identification
+      inputSchema:
+        properties: {}
+        required: []

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.log

@@ -0,0 +1,403 @@
+[14:12:48] This is prokka 1.15.6
+[14:12:48] Written by Torsten Seemann <torsten.seemann@gmail.com>
+[14:12:48] Homepage is https://github.com/tseemann/prokka
+[14:12:48] Local time is Wed May 20 14:12:48 2026
+[14:12:48] You are root
+[14:12:48] Operating system is linux
+[14:12:48] You have BioPerl 1.7.8
+[14:12:48] System has 104 cores.
+[14:12:48] Will use maximum of 4 cores.
+[14:12:48] Annotating as >>> Bacteria <<<
+[14:12:48] Generating locus_tag from '/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna' contents.
+[14:12:48] Setting --locustag MOLHKGIG from MD5 6851402062f9a6db2d633ff9bc46b2f3
+[14:12:48] Creating new output folder: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic
+[14:12:48] Running: mkdir -p \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic
+[14:12:48] Using filename prefix: ASM200830v4_genomic.XXX
+[14:12:48] Setting HMMER_NCPU=1
+[14:12:48] Writing log to: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.log
+[14:12:48] Command: /225040511/miniconda3/envs/biomni_e1/bin/prokka --outdir /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic --prefix ASM200830v4_genomic --genus Micrococcus --force --quiet --cpus 4 /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna
+[14:12:48] Looking for 'aragorn' - found /225040511/miniconda3/envs/biomni_e1/bin/aragorn
+[14:12:48] Determined aragorn version is v1.2 from 'ARAGORN v1.2.41 Dean Laslett'
+[14:12:48] Looking for 'barrnap' - found /225040511/miniconda3/envs/biomni_e1/bin/barrnap
+[14:12:48] Determined barrnap version is v0.9 from 'barrnap 0.9'
+[14:12:48] Looking for 'blastp' - found /225040511/miniconda3/envs/biomni_e1/bin/blastp
+[14:12:50] Determined blastp version is v2.17 from 'blastp: 2.17.0+'
+[14:12:50] Looking for 'cmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/cmpress
+[14:12:50] Determined cmpress version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[14:12:50] Looking for 'cmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/cmscan
+[14:12:50] Determined cmscan version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[14:12:50] Looking for 'egrep' - found /usr/bin/egrep
+[14:12:50] Looking for 'find' - found /usr/bin/find
+[14:12:50] Looking for 'grep' - found /usr/bin/grep
+[14:12:50] Looking for 'hmmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmpress
+[14:12:50] Determined hmmpress version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[14:12:50] Looking for 'hmmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmscan
+[14:12:50] Determined hmmscan version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[14:12:50] Looking for 'java' - found /225040511/miniconda3/envs/biomni_e1/bin/java
+[14:12:50] Looking for 'makeblastdb' - found /225040511/miniconda3/envs/biomni_e1/bin/makeblastdb
+[14:12:50] Determined makeblastdb version is v2.17 from 'makeblastdb: 2.17.0+'
+[14:12:50] Looking for 'minced' - found /225040511/miniconda3/envs/biomni_e1/bin/minced
+[14:12:50] Determined minced version is v4.2 from 'minced 0.4.2'
+[14:12:50] Looking for 'parallel' - found /225040511/miniconda3/envs/biomni_e1/bin/parallel
+[14:12:51] Determined parallel version is 20260422 from 'GNU parallel 20260422'
+[14:12:51] Looking for 'prodigal' - found /225040511/miniconda3/envs/biomni_e1/bin/prodigal
+[14:12:51] Determined prodigal version is v2.6 from 'Prodigal V2.6.3: February, 2016'
+[14:12:51] Looking for 'prokka-genbank_to_fasta_db' - found /225040511/miniconda3/envs/biomni_e1/bin/prokka-genbank_to_fasta_db
+[14:12:51] Looking for 'sed' - found /225040511/miniconda3/envs/biomni_e1/bin/sed
+[14:12:51] Looking for 'tbl2asn' - found /225040511/miniconda3/envs/biomni_e1/bin/tbl2asn
+[14:12:51] Determined tbl2asn version is v25.7 from 'tbl2asn 25.7   arguments:'
+[14:12:51] Using genetic code table 11.
+[14:12:51] Loading and checking input file: /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna
+[14:12:51] Wrote 1 contigs totalling 2522703 bp.
+[14:12:51] Predicting tRNAs and tmRNAs
+[14:12:51] Running: aragorn -l -gc11  -w \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.fna
+[14:12:54] 1 tRNA-Ile [11095,11169] 35 (gat)
+[14:12:54] 2 tRNA-Ala [11400,11474] 34 (tgc)
+[14:12:54] 3 tRNA-Leu [28649,28734] 35 (cag)
+[14:12:54] 4 tRNA-Lys [124259,124332] 34 (ttt)
+[14:12:54] 5 tRNA-Glu [137770,137843] 35 (ttc)
+[14:12:54] 6 tRNA-Asp [137959,138033] 35 (gtc)
+[14:12:54] 7 tRNA-Phe [138105,138180] 34 (gaa)
+[14:12:54] 8 tRNA-Ser [245784,245870] 35 (gga)
+[14:12:54] 9 tRNA-Ser c[315614,315704] 35 (cga)
+[14:12:54] 10 tRNA-Arg c[318941,319015] 35 (acg)
+[14:12:54] 11 tRNA-Ser c[330464,330553] 35 (gct)
+[14:12:54] 12 tRNA-Ser c[339160,339248] 35 (tga)
+[14:12:54] 13 tRNA-Thr c[340979,341054] 35 (cgt)
+[14:12:54] 14 tRNA-Pro [368575,368651] 35 (cgg)
+[14:12:54] 15 tRNA-Thr [381544,381620] 35 (tgt)
+[14:12:54] 16 tRNA-Val [383938,384013] 35 (cac)
+[14:12:54] 17 tRNA-Arg c[400154,400229] 35 (cct)
+[14:12:54] 18 tRNA-Leu [499685,499760] 35 (taa)
+[14:12:54] 19 tRNA-Gln [546090,546163] 33 (ttg)
+[14:12:54] 20 tRNA-Ala [608522,608619] 36 (ggc)
+[14:12:54] 21 tRNA-Asn [643583,643655] 33 (gtt)
+[14:12:54] 22 tRNA-Met [705763,705837] 35 (cat)
+[14:12:54] 23 tmRNA [812896,813265] 96,134 AESKRTDFALAA*
+[14:12:54] 24 tRNA-Arg c[846154,846227] 34 (ccg)
+[14:12:54] 25 tRNA-Leu c[900527,900608] 35 (tag)
+[14:12:54] 26 tRNA-Lys c[901247,901324] 35 (ctt)
+[14:12:54] 27 tRNA-Gln [931597,931669] 34 (ctg)
+[14:12:54] 28 tRNA-Glu [931724,931797] 35 (ctc)
+[14:12:54] 29 tRNA-Glu [931926,932000] 35 (ctc)
+[14:12:54] 30 tRNA-Val [1010731,1010806] 35 (tac)
+[14:12:54] 31 tRNA-His c[1034437,1034512] 34 (gtg)
+[14:12:54] 32 tRNA-Arg c[1041690,1041765] 35 (tct)
+[14:12:54] 33 tRNA-Ala c[1053998,1054087] 31 (cgc)
+[14:12:54] 34 tRNA-Gly c[1055246,1055318] 33 (tcc)
+[14:12:54] 35 tRNA-Pro [1056384,1056458] 35 (tgg)
+[14:12:54] 36 tRNA-Ala [1094883,1094958] 34 (ggc)
+[14:12:54] 37 tRNA-Ala [1096345,1096421] 35 (ggc)
+[14:12:54] 38 tRNA-Gly c[1138144,1138219] 35 (gcc)
+[14:12:54] 39 tRNA-Val c[1138247,1138319] 33 (gac)
+[14:12:54] 40 tRNA-Cys c[1138377,1138448] 33 (gca)
+[14:12:54] 41 tRNA-Gly c[1138466,1138540] 35 (gcc)
+[14:12:54] 42 tRNA-Leu [1177274,1177357] 35 (caa)
+[14:12:54] 43 tRNA-Leu c[1264464,1264549] 35 (gag)
+[14:12:54] 44 tRNA-Ile [1353125,1353219] 35 (gat)
+[14:12:54] 45 tRNA-Pro c[1535472,1535548] 35 (ggg)
+[14:12:54] 46 tmRNA* [1638170,1638576] 272,316 ASAARTCRPPAWWA*
+[14:12:54] 47 tRNA-Met c[1658678,1658752] 35 (cat)
+[14:12:54] 48 tRNA-Trp c[1893471,1893544] 34 (cca)
+[14:12:54] 49 tRNA-Met c[1911202,1911276] 35 (cat)
+[14:12:54] 50 tRNA-Thr c[1911336,1911408] 33 (ggt)
+[14:12:54] 51 tRNA-Tyr c[1922631,1922714] 35 (gta)
+[14:12:54] 52 tRNA-Arg c[1944250,1944342] 37 (cct)
+[14:12:54] 53 tRNA-Gly [2062710,2062783] 33 (ccc)
+[14:12:54] 54 tRNA-Ala c[2158546,2158619] 34 (cgc)
+[14:12:54] Found 54 tRNAs
+[14:12:54] Predicting Ribosomal RNAs
+[14:12:54] Running Barrnap with 4 threads
+[14:12:55] 1 NZ_CP042169.1 362528 16S ribosomal RNA
+[14:12:55] 2 NZ_CP042169.1 364492 23S ribosomal RNA
+[14:12:55] 3 NZ_CP042169.1 367774 5S ribosomal RNA
+[14:12:55] 4 NZ_CP042169.1 1562474 5S ribosomal RNA
+[14:12:55] 5 NZ_CP042169.1 1562781 23S ribosomal RNA
+[14:12:55] 6 NZ_CP042169.1 1566309 16S ribosomal RNA
+[14:12:55] Found 6 rRNAs
+[14:12:55] Skipping ncRNA search, enable with --rfam if desired.
+[14:12:55] Total of 58 tRNA + rRNA features
+[14:12:55] Searching for CRISPR repeats
+[14:12:56] CRISPR1 NZ_CP042169.1 2422827 with 8 spacers
+[14:12:56] CRISPR2 NZ_CP042169.1 2427487 with 11 spacers
+[14:12:56] Found 2 CRISPRs
+[14:12:56] Predicting coding sequences
+[14:12:56] Contigs total 2522703 bp, so using single mode
+[14:12:56] Running: prodigal -i \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.fna -c -m -g 11 -p single -f sco -q
+[14:13:16] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:606702..609095 on + strand
+[14:13:16] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:643616..643948 on - strand
+[14:13:16] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1053740..1054213 on + strand
+[14:13:16] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1352703..1354082 on - strand
+[14:13:17] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1943376..1944674 on - strand
+[14:13:17] Found 2252 CDS
+[14:13:17] Connecting features back to sequences
+[14:13:17] Not using genus-specific database. Try --usegenus to enable it.
+[14:13:17] Annotating CDS, please be patient.
+[14:13:17] Will use 4 CPUs for similarity searching.
+[14:13:18] There are still 2252 unannotated CDS left (started with 2252)
+[14:13:18] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS with 4 CPUs
+[14:13:18] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.IS\.tmp\.348397\.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\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.IS\.tmp\.348397\.blast 2> /dev/null
+[14:13:33] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.IS.tmp.348397.faa
+[14:13:33] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.IS.tmp.348397.blast
+[14:13:34] There are still 2199 unannotated CDS left (started with 2252)
+[14:13:34] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR with 4 CPUs
+[14:13:34] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.AMR\.tmp\.348397\.faa | parallel --gnu --plain -j 4 --block 94459 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.AMR\.tmp\.348397\.blast 2> /dev/null
+[14:13:56] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.AMR.tmp.348397.faa
+[14:13:56] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.AMR.tmp.348397.blast
+[14:13:57] There are still 2196 unannotated CDS left (started with 2252)
+[14:13:57] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot with 4 CPUs
+[14:13:57] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.sprot\.tmp\.348397\.faa | parallel --gnu --plain -j 4 --block 94110 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.sprot\.tmp\.348397\.blast 2> /dev/null
+[14:15:06] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
+[14:15:06] Modify product: Probable cation-transporting ATPase G => putative cation-transporting ATPase G
+[14:15:06] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[14:15:06] Modify product: Aldo-keto reductase MSMEG_2408/MSMEI_2347 => Aldo-keto reductase/MSMEI_2347
+[14:15:07] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA
+[14:15:07] Modify product: Uncharacterized methyltransferase Rv3342 => putative methyltransferase
+[14:15:07] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
+[14:15:07] Modify product: Probable acetyl-CoA acetyltransferase => putative acetyl-CoA acetyltransferase
+[14:15:07] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit A => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit A
+[14:15:07] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B
+[14:15:07] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[14:15:07] Modify product: Uncharacterized protein Rv1841c => putative protein
+[14:15:07] Modify product: Uncharacterized HIT-like protein Rv0759c => putative HIT-like protein
+[14:15:07] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ
+[14:15:07] Modify product: Uncharacterized protein Rv1324 => putative protein
+[14:15:07] Modify product: Uncharacterized protein Rv1339 => putative protein
+[14:15:07] Modify product: Probable malate:quinone oxidoreductase => putative malate:quinone oxidoreductase
+[14:15:07] Modify product: Putative peroxiredoxin Rv2521 => Putative peroxiredoxin
+[14:15:07] Modify product: Protein Rv2993c => Protein
+[14:15:07] Modify product: RNA/DNA methyltransferase Rv2966c => RNA/DNA methyltransferase
+[14:15:07] Modify product: Probable N-succinyldiaminopimelate aminotransferase DapC => putative N-succinyldiaminopimelate aminotransferase DapC
+[14:15:07] Modify product: Uncharacterized protein Rv2926c => putative protein
+[14:15:07] Modify product: Uncharacterized protein Rv2901c => putative protein
+[14:15:07] Modify product: Uncharacterized protein Rv2242 => putative protein
+[14:15:07] Modify product: Uncharacterized protein Rv2239c => putative protein
+[14:15:07] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 
+[14:15:07] Modify product: Alpha-(1->6)-mannopyranosyltransferase Rv1459c => Alpha-(1->6)-mannopyranosyltransferase
+[14:15:07] Modify product: Thioredoxin-like reductase Rv2466c => Thioredoxin-like reductase
+[14:15:07] Modify product: Uncharacterized oxidoreductase Rv0484c => putative oxidoreductase
+[14:15:07] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase
+[14:15:07] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ
+[14:15:07] Modify product: Uncharacterized SufE-like protein Rv3284 => putative SufE-like protein
+[14:15:07] Modify product: Putative methyltransferase Rv1407 => Putative methyltransferase
+[14:15:07] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB 
+[14:15:07] Modify product: Uncharacterized protein Rv1841c => putative protein
+[14:15:07] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[14:15:07] Modify product: Uncharacterized membrane protein Rv2723 => putative membrane protein
+[14:15:07] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase
+[14:15:07] Modify product: Nucleotide-binding protein Rv1421 => Nucleotide-binding protein
+[14:15:07] Modify product: Probable cell division protein WhiA => putative cell division protein WhiA
+[14:15:07] Modify product: Iron-sulfur cluster assembly SufBD family protein SA0778 => Iron-sulfur cluster assembly SufBD family protein
+[14:15:07] Modify product: Iron-sulfur cluster assembly SufBD family protein Rv1462 => Iron-sulfur cluster assembly SufBD family protein
+[14:15:07] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[14:15:07] Modify product: Uncharacterized SURF1-like protein Rv2235 => putative SURF1-like protein
+[14:15:07] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA
+[14:15:07] Modify product: Uncharacterized protein Rv1276c => putative protein
+[14:15:07] Modify product: Phosphate-specific transport system accessory protein PhoU homolog 2 => Phosphate-specific transport system accessory protein PhoU 
+[14:15:07] Modify product: Uncharacterized tRNA/rRNA methyltransferase Rv3579c => putative tRNA/rRNA methyltransferase
+[14:15:07] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[14:15:07] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[14:15:07] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
+[14:15:07] Modify product: Probable hydrolase sll0100 => putative hydrolase
+[14:15:07] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR
+[14:15:07] Modify product: Uncharacterized protein YihR => putative protein YihR
+[14:15:07] Modify product: Putative transport protein Rv0205 => Putative transport protein
+[14:15:07] Modify product: Uncharacterized metal-dependent hydrolase TatD => putative metal-dependent hydrolase TatD
+[14:15:07] Modify product: Probable phosphomannomutase => putative phosphomannomutase
+[14:15:07] Modify product: pH-sensitive adenylate cyclase Rv1264 => pH-sensitive adenylate cyclase
+[14:15:07] Modify product: Protein Rv0786c => Protein
+[14:15:07] Modify product: UPF0312 protein SA2479 => hypothetical protein
+[14:15:07] Modify product: Type I restriction enzyme BthVORF4518P methylase subunit => Type I restriction enzymeP methylase subunit
+[14:15:07] Modify product: Probable glycerophosphodiester phosphodiesterase 2 => putative glycerophosphodiester phosphodiesterase 2
+[14:15:07] Modify product: Putative low molecular weight protein-tyrosine-phosphatase slr0328 => Putative low molecular weight protein-tyrosine-phosphatase
+[14:15:07] Modify product: Putative 2-hydroxyacid dehydrogenase SA2098 => Putative 2-hydroxyacid dehydrogenase
+[14:15:07] Modify product: Probable glycerophosphodiester phosphodiesterase 1 => putative glycerophosphodiester phosphodiesterase 1
+[14:15:07] Modify product: UPF0045 protein Rv1898 => hypothetical protein
+[14:15:07] Modify product: Universal stress protein MT2698 => Universal stress protein
+[14:15:07] Modify product: Probable inactive lipase Rv1592c => putative inactive lipase
+[14:15:07] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB 
+[14:15:07] Modify product: Acetyl- and succinyl-CoA transferase Rv0802c => Acetyl- and succinyl-CoA transferase
+[14:15:07] Modify product: Uncharacterized protein Rv2895c => putative protein
+[14:15:07] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[14:15:07] Modify product: Probable malonic semialdehyde reductase RutE => putative malonic semialdehyde reductase RutE
+[14:15:07] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[14:15:07] Modify product: Probable 3-hydroxyisobutyrate dehydrogenase => putative 3-hydroxyisobutyrate dehydrogenase
+[14:15:07] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
+[14:15:07] Modify product: Probable glycine dehydrogenase (decarboxylating) => putative glycine dehydrogenase (decarboxylating)
+[14:15:07] Modify product: Uncharacterized HTH-type transcriptional regulator Rv0472c => putative HTH-type transcriptional regulator
+[14:15:07] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase
+[14:15:07] Modify product: Probable helicase HelY => putative helicase HelY
+[14:15:07] Modify product: Uncharacterized protein Rv1488 => putative protein
+[14:15:07] Modify product: Probable cytochrome c oxidase polypeptide 4 => putative cytochrome c oxidase polypeptide 4
+[14:15:07] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1
+[14:15:07] Modify product: Protein Rv2204c => Protein
+[14:15:07] Modify product: Uncharacterized protein Rv2206 => putative protein
+[14:15:07] Modify product: UPF0053 protein Rv2366c => hypothetical protein
+[14:15:07] Modify product: Probable DNA polymerase III subunit delta => putative DNA polymerase III subunit delta
+[14:15:07] Modify product: DegV domain-containing protein SA1258 => DegV domain-containing protein
+[14:15:07] Modify product: Probable replication restart protein PriA => putative replication restart protein PriA
+[14:15:07] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein
+[14:15:07] Modify product: Uncharacterized transporter Rv1999c => putative transporter
+[14:15:07] Modify product: Uncharacterized protein MSMEG_2731/MSMEI_2664 => putative protein/MSMEI_2664
+[14:15:07] Modify product: Probable transcriptional regulatory protein Rv2603c => putative transcriptional regulatory protein
+[14:15:07] Modify product: Uncharacterized protein YdhK => putative protein YdhK
+[14:15:07] Modify product: Probable cytosol aminopeptidase => putative cytosol aminopeptidase
+[14:15:07] Modify product: Uncharacterized RNA pseudouridine synthase Rv1540 => putative RNA pseudouridine synthase
+[14:15:07] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW
+[14:15:07] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1830 => putative HTH-type transcriptional regulator
+[14:15:07] Modify product: Uncharacterized protein Rv1829 => putative protein
+[14:15:07] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1828 => putative HTH-type transcriptional regulator
+[14:15:07] Modify product: Uncharacterized protein Rv1708 => putative protein
+[14:15:07] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
+[14:15:07] Modify product: UPF0182 protein MSMEG_1959/MSMEI_1915 => hypothetical protein
+[14:15:07] Modify product: Uncharacterized protein YlbL => putative protein YlbL
+[14:15:08] Modify product: Probable O-methyltransferase Rv1220c => putative O-methyltransferase
+[14:15:08] Modify product: Probable aminotransferase Rv1178 => putative aminotransferase
+[14:15:08] Modify product: Uncharacterized lipoprotein Rv2585c => putative lipoprotein
+[14:15:08] Modify product: Probable bacterial non-heme ferritin => putative bacterial non-heme ferritin
+[14:15:08] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating]
+[14:15:08] Modify product: Protein Rv2133c => Protein
+[14:15:08] Modify product: Uncharacterized protein YdhK => putative protein YdhK
+[14:15:08] Modify product: Macro domain-containing protein PG1779 => Macro domain-containing protein
+[14:15:08] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564
+[14:15:08] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[14:15:08] Modify product: Uncharacterized protein Rv3421c => putative protein
+[14:15:08] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX 
+[14:15:08] Modify product: UPF0336 protein Rv0637 => hypothetical protein
+[14:15:08] Modify product: Probable cystathionine beta-synthase Rv1077 => putative cystathionine beta-synthase
+[14:15:08] Modify product: Nucleotide-binding protein SCO4614 => Nucleotide-binding protein
+[14:15:08] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
+[14:15:08] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[14:15:08] Modify product: Probable 2-succinylbenzoate--CoA ligase => putative 2-succinylbenzoate--CoA ligase
+[14:15:08] Modify product: Uncharacterized protein Rv0525 => putative protein
+[14:15:08] Modify product: Uncharacterized protein Rv0498 => putative protein
+[14:15:08] Modify product: Uncharacterized ATP-dependent helicase YprA => putative ATP-dependent helicase YprA
+[14:15:08] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[14:15:08] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
+[14:15:08] Modify product: Probable lipoprotein aminopeptidase LpqL => putative lipoprotein aminopeptidase LpqL
+[14:15:08] Modify product: Putative hydro-lyase PSPTO_5379 => Putative hydro-lyase
+[14:15:08] Modify product: Probable cold shock protein A => putative cold shock protein A
+[14:15:08] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[14:15:08] Modify product: UPF0371 protein DIP2346 => hypothetical protein
+[14:15:08] Modify product: Putative acyltransferase Rv0859 => Putative acyltransferase
+[14:15:08] Modify product: Acetyltransferase PA3944 => Acetyltransferase
+[14:15:08] Modify product: Uncharacterized protein Rv0088 => putative protein
+[14:15:08] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
+[14:15:08] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein
+[14:15:08] Modify product: Uncharacterized glycosyl hydrolase MT2062 => putative glycosyl hydrolase
+[14:15:08] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[14:15:08] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[14:15:08] Modify product: Probable siderophore transport system permease protein YfhA => putative siderophore transport system permease protein YfhA
+[14:15:08] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV
+[14:15:08] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK
+[14:15:08] Modify product: Uncharacterized N-acetyltransferase Rv2669 => putative N-acetyltransferase
+[14:15:08] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[14:15:08] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[14:15:08] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[14:15:08] Modify product: Probable glycerol uptake facilitator protein => putative glycerol uptake facilitator protein
+[14:15:08] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[14:15:08] Modify product: Probable M18 family aminopeptidase 2 => putative M18 family aminopeptidase 2
+[14:15:08] Cleaned 150 /product names
+[14:15:08] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.sprot.tmp.348397.faa
+[14:15:08] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.sprot.tmp.348397.blast
+[14:15:08] Labelling remaining 1075 proteins as 'hypothetical protein'
+[14:15:08] Possible /pseudo 'IS256 family transposase ISMlu1' at NZ_CP042169.1 position 663236
+[14:15:08] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP042169.1 position 1149627
+[14:15:08] Possible /pseudo 'Iron-sulfur cluster assembly SufBD family protein' at NZ_CP042169.1 position 1234071
+[14:15:08] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP042169.1 position 1522733
+[14:15:08] Possible /pseudo 'IS256 family transposase ISMlu1' at NZ_CP042169.1 position 2261917
+[14:15:08] Found 912 unique /gene codes.
+[14:15:08] Fixed 2 duplicate /gene - mrpD_1 mrpD_2
+[14:15:08] Fixed 2 duplicate /gene - hin_1 hin_2
+[14:15:08] Fixed 3 duplicate /gene - ywjA_1 ywjA_2 ywjA_3
+[14:15:08] Fixed 2 duplicate /gene - glgC_1 glgC_2
+[14:15:08] Fixed 2 duplicate /gene - pdhC_1 pdhC_2
+[14:15:08] Fixed 2 duplicate /gene - ziaR_1 ziaR_2
+[14:15:08] Fixed 2 duplicate /gene - citE_1 citE_2
+[14:15:08] Fixed 2 duplicate /gene - fprA_1 fprA_2
+[14:15:08] Fixed 2 duplicate /gene - tcrX_1 tcrX_2
+[14:15:08] Fixed 2 duplicate /gene - ydbD_1 ydbD_2
+[14:15:08] Fixed 6 duplicate /gene - mmgC_1 mmgC_2 mmgC_3 mmgC_4 mmgC_5 mmgC_6
+[14:15:08] Fixed 2 duplicate /gene - acdA_1 acdA_2
+[14:15:08] Fixed 2 duplicate /gene - liaR_1 liaR_2
+[14:15:08] Fixed 2 duplicate /gene - bkdA_1 bkdA_2
+[14:15:08] Fixed 2 duplicate /gene - gyrA_1 gyrA_2
+[14:15:08] Fixed 2 duplicate /gene - ydhK_1 ydhK_2
+[14:15:08] Fixed 2 duplicate /gene - nrtD_1 nrtD_2
+[14:15:08] Fixed 2 duplicate /gene - bkdB_1 bkdB_2
+[14:15:08] Fixed 5 duplicate /gene - acsA_1 acsA_2 acsA_3 acsA_4 acsA_5
+[14:15:08] Fixed 2 duplicate /gene - lysG_1 lysG_2
+[14:15:08] Fixed 2 duplicate /gene - gyrB_1 gyrB_2
+[14:15:08] Fixed 2 duplicate /gene - yheS_1 yheS_2
+[14:15:08] Fixed 2 duplicate /gene - lnrK_1 lnrK_2
+[14:15:08] Fixed 2 duplicate /gene - acp_1 acp_2
+[14:15:08] Fixed 3 duplicate /gene - stp_1 stp_2 stp_3
+[14:15:08] Fixed 2 duplicate /gene - iscS_1 iscS_2
+[14:15:08] Fixed 2 duplicate /gene - fcs_1 fcs_2
+[14:15:08] Fixed 2 duplicate /gene - mcr_1 mcr_2
+[14:15:08] Fixed 2 duplicate /gene - trpB_1 trpB_2
+[14:15:08] Fixed 2 duplicate /gene - map_1 map_2
+[14:15:08] Fixed 2 duplicate /gene - qorA_1 qorA_2
+[14:15:08] Fixed 4 duplicate /gene - merA_1 merA_2 merA_3 merA_4
+[14:15:08] Fixed 2 duplicate /gene - hsdM_1 hsdM_2
+[14:15:08] Fixed 2 duplicate /gene - def_1 def_2
+[14:15:08] Fixed 2 duplicate /gene - mgtA_1 mgtA_2
+[14:15:08] Fixed 3 duplicate /gene - czcD_1 czcD_2 czcD_3
+[14:15:08] Fixed 2 duplicate /gene - lolD_1 lolD_2
+[14:15:08] Fixed 3 duplicate /gene - echA8_1 echA8_2 echA8_3
+[14:15:08] Fixed 2 duplicate /gene - fadB_1 fadB_2
+[14:15:08] Fixed 2 duplicate /gene - metB_1 metB_2
+[14:15:08] Fixed 2 duplicate /gene - kdgR_1 kdgR_2
+[14:15:08] Fixed 2 duplicate /gene - ktrB_1 ktrB_2
+[14:15:08] Fixed 2 duplicate /gene - yghA_1 yghA_2
+[14:15:08] Fixed 2 duplicate /gene - gabT_1 gabT_2
+[14:15:08] Fixed 2 duplicate /gene - copB_1 copB_2
+[14:15:08] Fixed 4 duplicate /gene - cmtR_1 cmtR_2 cmtR_3 cmtR_4
+[14:15:08] Fixed 2 duplicate /gene - lepB_1 lepB_2
+[14:15:08] Fixed 2 duplicate /gene - accA3_1 accA3_2
+[14:15:08] Fixed 3 duplicate /gene - lcfB_1 lcfB_2 lcfB_3
+[14:15:08] Fixed 3 duplicate /gene - ettA_1 ettA_2 ettA_3
+[14:15:08] Fixed 2 duplicate /gene - lspA_1 lspA_2
+[14:15:08] Fixed 2 duplicate /gene - idsA2_1 idsA2_2
+[14:15:08] Fixed 2 duplicate /gene - lysE_1 lysE_2
+[14:15:08] Fixed 2 duplicate /gene - rlmP_1 rlmP_2
+[14:15:08] Fixed 2 duplicate /gene - rspR_1 rspR_2
+[14:15:08] Fixed 2 duplicate /gene - opuBB_1 opuBB_2
+[14:15:08] Fixed 2 duplicate /gene - fadA6_1 fadA6_2
+[14:15:08] Fixed 3 duplicate /gene - pepN_1 pepN_2 pepN_3
+[14:15:08] Fixed 2 duplicate /gene - copA_1 copA_2
+[14:15:08] Fixed 2 duplicate /gene - gabD1_1 gabD1_2
+[14:15:08] Fixed 60 colliding /gene names.
+[14:15:08] Adding /locus_tag identifiers
+[14:15:08] Assigned 2312 locus_tags to CDS and RNA features.
+[14:15:08] Writing outputs to /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/
+[14:15:09] Generating annotation statistics file
+[14:15:09] Generating Genbank and Sequin files
+[14:15:09] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.15.6 from https://github.com/tseemann/prokka' -Z \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.err -i \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.fsa 2> /dev/null
+[14:15:14] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/errorsummary.val
+[14:15:14] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.dr
+[14:15:14] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.fixedproducts
+[14:15:14] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.ecn
+[14:15:14] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.val
+[14:15:14] Repairing broken .GBK output that tbl2asn produces...
+[14:15:14] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.gbf > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_002008305\.4_ASM200830v4_genomic\/ASM200830v4_genomic\.gbk
+[14:15:14] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.gbf
+[14:15:14] Output files:
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.txt
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.fsa
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.faa
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.sqn
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.log
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.gbk
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.fna
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.tsv
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.err
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.tbl
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.ffn
+[14:15:14] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.gff
+[14:15:14] Annotation finished successfully.
+[14:15:14] Walltime used: 2.43 minutes
+[14:15:14] If you use this result please cite the Prokka paper:
+[14:15:14] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
+[14:15:14] Type 'prokka --citation' for more details.
+[14:15:14] Thank you, come again.

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_002008305.4_ASM200830v4_genomic/ASM200830v4_genomic.txt

@@ -0,0 +1,8 @@
+organism: Micrococcus species strain 
+contigs: 1
+bases: 2522703
+CDS: 2252
+rRNA: 6
+repeat_region: 2
+tRNA: 52
+tmRNA: 2

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.log

@@ -0,0 +1,404 @@
+[14:15:14] This is prokka 1.15.6
+[14:15:14] Written by Torsten Seemann <torsten.seemann@gmail.com>
+[14:15:14] Homepage is https://github.com/tseemann/prokka
+[14:15:14] Local time is Wed May 20 14:15:14 2026
+[14:15:14] You are root
+[14:15:14] Operating system is linux
+[14:15:14] You have BioPerl 1.7.8
+[14:15:14] System has 104 cores.
+[14:15:14] Will use maximum of 4 cores.
+[14:15:14] Annotating as >>> Bacteria <<<
+[14:15:14] Generating locus_tag from '/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_003691675.1_ASM369167v1_genomic.fna' contents.
+[14:15:14] Setting --locustag MHAAABBN from MD5 61aaabb71c296516a41965ae3e32dce1
+[14:15:14] Creating new output folder: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic
+[14:15:14] Running: mkdir -p \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic
+[14:15:14] Using filename prefix: ASM369167v1_genomic.XXX
+[14:15:14] Setting HMMER_NCPU=1
+[14:15:14] Writing log to: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.log
+[14:15:14] Command: /225040511/miniconda3/envs/biomni_e1/bin/prokka --outdir /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic --prefix ASM369167v1_genomic --genus Micrococcus --force --quiet --cpus 4 /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_003691675.1_ASM369167v1_genomic.fna
+[14:15:14] Looking for 'aragorn' - found /225040511/miniconda3/envs/biomni_e1/bin/aragorn
+[14:15:14] Determined aragorn version is v1.2 from 'ARAGORN v1.2.41 Dean Laslett'
+[14:15:14] Looking for 'barrnap' - found /225040511/miniconda3/envs/biomni_e1/bin/barrnap
+[14:15:14] Determined barrnap version is v0.9 from 'barrnap 0.9'
+[14:15:14] Looking for 'blastp' - found /225040511/miniconda3/envs/biomni_e1/bin/blastp
+[14:15:15] Determined blastp version is v2.17 from 'blastp: 2.17.0+'
+[14:15:15] Looking for 'cmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/cmpress
+[14:15:15] Determined cmpress version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[14:15:15] Looking for 'cmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/cmscan
+[14:15:15] Determined cmscan version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[14:15:15] Looking for 'egrep' - found /usr/bin/egrep
+[14:15:15] Looking for 'find' - found /usr/bin/find
+[14:15:15] Looking for 'grep' - found /usr/bin/grep
+[14:15:15] Looking for 'hmmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmpress
+[14:15:15] Determined hmmpress version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[14:15:15] Looking for 'hmmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmscan
+[14:15:15] Determined hmmscan version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[14:15:15] Looking for 'java' - found /225040511/miniconda3/envs/biomni_e1/bin/java
+[14:15:15] Looking for 'makeblastdb' - found /225040511/miniconda3/envs/biomni_e1/bin/makeblastdb
+[14:15:15] Determined makeblastdb version is v2.17 from 'makeblastdb: 2.17.0+'
+[14:15:15] Looking for 'minced' - found /225040511/miniconda3/envs/biomni_e1/bin/minced
+[14:15:15] Determined minced version is v4.2 from 'minced 0.4.2'
+[14:15:15] Looking for 'parallel' - found /225040511/miniconda3/envs/biomni_e1/bin/parallel
+[14:15:15] Determined parallel version is 20260422 from 'GNU parallel 20260422'
+[14:15:15] Looking for 'prodigal' - found /225040511/miniconda3/envs/biomni_e1/bin/prodigal
+[14:15:15] Determined prodigal version is v2.6 from 'Prodigal V2.6.3: February, 2016'
+[14:15:15] Looking for 'prokka-genbank_to_fasta_db' - found /225040511/miniconda3/envs/biomni_e1/bin/prokka-genbank_to_fasta_db
+[14:15:15] Looking for 'sed' - found /225040511/miniconda3/envs/biomni_e1/bin/sed
+[14:15:15] Looking for 'tbl2asn' - found /225040511/miniconda3/envs/biomni_e1/bin/tbl2asn
+[14:15:15] Determined tbl2asn version is v25.7 from 'tbl2asn 25.7   arguments:'
+[14:15:15] Using genetic code table 11.
+[14:15:15] Loading and checking input file: /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_003691675.1_ASM369167v1_genomic.fna
+[14:15:15] Wrote 1 contigs totalling 2483045 bp.
+[14:15:15] Predicting tRNAs and tmRNAs
+[14:15:15] Running: aragorn -l -gc11  -w \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.fna
+[14:15:18] 1 tRNA-Arg c[1808,1882] 35 (acg)
+[14:15:18] 2 tRNA-Ser c[19025,19116] 35 (gct)
+[14:15:18] 3 tRNA-Ser c[27701,27789] 35 (tga)
+[14:15:18] 4 tRNA-Thr c[29506,29581] 35 (cgt)
+[14:15:18] 5 tRNA-Pro [58221,58297] 35 (cgg)
+[14:15:18] 6 tRNA-Thr [71190,71266] 35 (tgt)
+[14:15:18] 7 tRNA-Val [73193,73268] 35 (cac)
+[14:15:18] 8 tRNA-Arg c[89404,89479] 35 (cct)
+[14:15:18] 9 tRNA-Leu [193769,193845] 35 (taa)
+[14:15:18] 10 tRNA-Gln [239494,239567] 33 (ttg)
+[14:15:18] 11 tRNA-Ala [304945,305042] 36 (ggc)
+[14:15:18] 12 tRNA-Asn [348161,348234] 33 (gtt)
+[14:15:18] 13 tRNA-Met [405585,405659] 35 (cat)
+[14:15:18] 14 tmRNA [501489,501858] 96,134 AESKRTDFALAA*
+[14:15:18] 15 tRNA-Arg c[534746,534819] 34 (ccg)
+[14:15:18] 16 tRNA-Leu c[591118,591199] 35 (tag)
+[14:15:18] 17 tRNA-Lys c[591838,591915] 35 (ctt)
+[14:15:18] 18 tRNA-Gln [613023,613095] 34 (ctg)
+[14:15:18] 19 tRNA-Glu [613150,613223] 35 (ctc)
+[14:15:18] 20 tRNA-Glu [613352,613426] 35 (ctc)
+[14:15:18] 21 tRNA-Val [688216,688291] 35 (tac)
+[14:15:18] 22 tRNA-His c[706792,706867] 34 (gtg)
+[14:15:18] 23 tRNA-Arg c[714045,714120] 35 (tct)
+[14:15:18] 24 tRNA-Ala c[726298,726387] 31 (cgc)
+[14:15:18] 25 tRNA-Gly c[728393,728465] 33 (tcc)
+[14:15:18] 26 tRNA-Pro [729519,729593] 35 (tgg)
+[14:15:18] 27 tRNA-Ala [767922,767997] 34 (ggc)
+[14:15:18] 28 tRNA-Ala [769384,769460] 35 (ggc)
+[14:15:18] 29 tRNA-Gly c[819075,819153] 36 (gcc)
+[14:15:18] 30 tRNA-Val c[819180,819252] 33 (gac)
+[14:15:18] 31 tRNA-Cys c[819310,819381] 33 (gca)
+[14:15:18] 32 tRNA-Gly c[819399,819473] 35 (gcc)
+[14:15:18] 33 tRNA-Leu [856740,856823] 35 (caa)
+[14:15:18] 34 tRNA-Leu c[943927,944012] 35 (gag)
+[14:15:18] 35 tRNA-Ile [1031141,1031235] 35 (gat)
+[14:15:18] 36 tRNA-Pro c[1221167,1221243] 35 (ggg)
+[14:15:18] 37 tRNA-Met c[1323928,1324002] 35 (cat)
+[14:15:18] 38 tRNA-Trp c[1554138,1554211] 34 (cca)
+[14:15:18] 39 tRNA-Met c[1571869,1571943] 35 (cat)
+[14:15:18] 40 tRNA-Thr c[1572003,1572075] 33 (ggt)
+[14:15:18] 41 tRNA-Tyr c[1583298,1583381] 35 (gta)
+[14:15:18] 42 tRNA-Gly [1712060,1712133] 33 (ccc)
+[14:15:18] 43 tRNA-Ala c[1796278,1796351] 34 (cgc)
+[14:15:18] 44 tRNA-Ile [2161862,2161936] 35 (gat)
+[14:15:18] 45 tRNA-Ala [2162167,2162240] 34 (tgc)
+[14:15:18] 46 tRNA-Leu [2194570,2194655] 35 (cag)
+[14:15:18] 47 tRNA-Lys [2282484,2282557] 34 (ttt)
+[14:15:18] 48 tRNA-Glu [2297408,2297481] 35 (ttc)
+[14:15:18] 49 tRNA-Asp [2297597,2297671] 35 (gtc)
+[14:15:18] 50 tRNA-Phe [2297743,2297818] 34 (gaa)
+[14:15:18] 51 tRNA-Ser [2399680,2399766] 35 (gga)
+[14:15:18] 52 tRNA-Ser c[2481526,2481616] 35 (cga)
+[14:15:18] Found 52 tRNAs
+[14:15:18] Predicting Ribosomal RNAs
+[14:15:18] Running Barrnap with 4 threads
+[14:15:19] 1 NZ_CP033200.1 52172 16S ribosomal RNA
+[14:15:19] 2 NZ_CP033200.1 54136 23S ribosomal RNA
+[14:15:19] 3 NZ_CP033200.1 57419 5S ribosomal RNA
+[14:15:19] 4 NZ_CP033200.1 1248129 5S ribosomal RNA
+[14:15:19] 5 NZ_CP033200.1 1248436 23S ribosomal RNA
+[14:15:19] 6 NZ_CP033200.1 1251963 16S ribosomal RNA
+[14:15:19] Found 6 rRNAs
+[14:15:19] Skipping ncRNA search, enable with --rfam if desired.
+[14:15:19] Total of 57 tRNA + rRNA features
+[14:15:19] Searching for CRISPR repeats
+[14:15:20] Found 0 CRISPRs
+[14:15:20] Predicting coding sequences
+[14:15:20] Contigs total 2483045 bp, so using single mode
+[14:15:20] Running: prodigal -i \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.fna -c -m -g 11 -p single -f sco -q
+[14:15:25] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP033200.1:303125..305518 on + strand
+[14:15:25] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP033200.1:348194..348526 on - strand
+[14:15:26] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP033200.1:706238..706813 on + strand
+[14:15:26] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP033200.1:726040..726513 on + strand
+[14:15:26] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP033200.1:1030719..1032098 on - strand
+[14:15:27] Found 2257 CDS
+[14:15:27] Connecting features back to sequences
+[14:15:27] Not using genus-specific database. Try --usegenus to enable it.
+[14:15:27] Annotating CDS, please be patient.
+[14:15:27] Will use 4 CPUs for similarity searching.
+[14:15:27] There are still 2257 unannotated CDS left (started with 2257)
+[14:15:27] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS with 4 CPUs
+[14:15:27] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.IS\.tmp\.350379\.faa | parallel --gnu --plain -j 4 --block 95321 --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\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.IS\.tmp\.350379\.blast 2> /dev/null
+[14:15:42] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.IS.tmp.350379.faa
+[14:15:42] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.IS.tmp.350379.blast
+[14:15:43] There are still 2193 unannotated CDS left (started with 2257)
+[14:15:43] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR with 4 CPUs
+[14:15:43] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.AMR\.tmp\.350379\.faa | parallel --gnu --plain -j 4 --block 93206 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.AMR\.tmp\.350379\.blast 2> /dev/null
+[14:16:05] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.AMR.tmp.350379.faa
+[14:16:05] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.AMR.tmp.350379.blast
+[14:16:05] There are still 2191 unannotated CDS left (started with 2257)
+[14:16:05] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot with 4 CPUs
+[14:16:05] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.sprot\.tmp\.350379\.faa | parallel --gnu --plain -j 4 --block 92947 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.sprot\.tmp\.350379\.blast 2> /dev/null
+[14:17:14] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase
+[14:17:14] Modify product: Probable helicase HelY => putative helicase HelY
+[14:17:14] Modify product: Uncharacterized protein Rv1488 => putative protein
+[14:17:14] Modify product: Probable cytochrome c oxidase polypeptide 4 => putative cytochrome c oxidase polypeptide 4
+[14:17:14] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1
+[14:17:14] Modify product: Protein Rv2204c => Protein
+[14:17:14] Modify product: Uncharacterized protein Rv2206 => putative protein
+[14:17:14] Modify product: UPF0053 protein Rv2366c => hypothetical protein
+[14:17:15] Modify product: Probable DNA polymerase III subunit delta => putative DNA polymerase III subunit delta
+[14:17:15] Modify product: DegV domain-containing protein SA1258 => DegV domain-containing protein
+[14:17:15] Modify product: Probable replication restart protein PriA => putative replication restart protein PriA
+[14:17:15] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein
+[14:17:15] Modify product: Uncharacterized transporter Rv1999c => putative transporter
+[14:17:15] Modify product: Uncharacterized protein MSMEG_2731/MSMEI_2664 => putative protein/MSMEI_2664
+[14:17:15] Modify product: Probable transcriptional regulatory protein Rv2603c => putative transcriptional regulatory protein
+[14:17:15] Modify product: Uncharacterized protein YdhK => putative protein YdhK
+[14:17:15] Modify product: Probable cytosol aminopeptidase => putative cytosol aminopeptidase
+[14:17:15] Modify product: Uncharacterized RNA pseudouridine synthase Rv1540 => putative RNA pseudouridine synthase
+[14:17:15] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW
+[14:17:15] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1830 => putative HTH-type transcriptional regulator
+[14:17:15] Modify product: Uncharacterized protein Rv1829 => putative protein
+[14:17:15] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1828 => putative HTH-type transcriptional regulator
+[14:17:15] Modify product: Probable cadmium-transporting ATPase => putative cadmium-transporting ATPase
+[14:17:15] Modify product: Uncharacterized protein Rv1708 => putative protein
+[14:17:15] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
+[14:17:15] Modify product: Uncharacterized protein Rv0102 => putative protein
+[14:17:15] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB 
+[14:17:15] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB 
+[14:17:15] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[14:17:15] Modify product: Aldo-keto reductase MSMEG_2408/MSMEI_2347 => Aldo-keto reductase/MSMEI_2347
+[14:17:15] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA
+[14:17:15] Modify product: Uncharacterized methyltransferase Rv3342 => putative methyltransferase
+[14:17:15] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
+[14:17:15] Modify product: Protein MG115 homolog => Protein MG115 
+[14:17:15] Modify product: Probable acetyl-CoA acetyltransferase => putative acetyl-CoA acetyltransferase
+[14:17:15] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit A => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit A
+[14:17:15] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B
+[14:17:15] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[14:17:15] Modify product: Uncharacterized protein Rv1841c => putative protein
+[14:17:15] Modify product: Uncharacterized HIT-like protein Rv0759c => putative HIT-like protein
+[14:17:15] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ
+[14:17:15] Modify product: Uncharacterized protein Rv1324 => putative protein
+[14:17:15] Modify product: Uncharacterized protein Rv1339 => putative protein
+[14:17:15] Modify product: Probable malate:quinone oxidoreductase => putative malate:quinone oxidoreductase
+[14:17:15] Modify product: Putative peroxiredoxin Rv2521 => Putative peroxiredoxin
+[14:17:15] Modify product: Protein Rv2993c => Protein
+[14:17:15] Modify product: RNA/DNA methyltransferase Rv2966c => RNA/DNA methyltransferase
+[14:17:15] Modify product: Probable N-succinyldiaminopimelate aminotransferase DapC => putative N-succinyldiaminopimelate aminotransferase DapC
+[14:17:15] Modify product: Uncharacterized protein Rv2926c => putative protein
+[14:17:15] Modify product: Uncharacterized protein Rv2901c => putative protein
+[14:17:15] Modify product: Uncharacterized protein Rv2242 => putative protein
+[14:17:15] Modify product: Uncharacterized protein Rv2239c => putative protein
+[14:17:15] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 
+[14:17:15] Modify product: Probable cadmium-transporting ATPase => putative cadmium-transporting ATPase
+[14:17:15] Modify product: Alpha-(1->6)-mannopyranosyltransferase Rv1459c => Alpha-(1->6)-mannopyranosyltransferase
+[14:17:15] Modify product: Thioredoxin-like reductase Rv2466c => Thioredoxin-like reductase
+[14:17:15] Modify product: Uncharacterized oxidoreductase Rv0484c => putative oxidoreductase
+[14:17:15] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase
+[14:17:15] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ
+[14:17:15] Modify product: Uncharacterized SufE-like protein Rv3284 => putative SufE-like protein
+[14:17:15] Modify product: Uncharacterized protein Rv2895c => putative protein
+[14:17:15] Modify product: Putative methyltransferase Rv1407 => Putative methyltransferase
+[14:17:15] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB 
+[14:17:15] Modify product: Uncharacterized protein Rv1841c => putative protein
+[14:17:15] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[14:17:15] Modify product: Uncharacterized membrane protein Rv2723 => putative membrane protein
+[14:17:15] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase
+[14:17:15] Modify product: Nucleotide-binding protein Rv1421 => Nucleotide-binding protein
+[14:17:15] Modify product: Probable cell division protein WhiA => putative cell division protein WhiA
+[14:17:15] Modify product: Iron-sulfur cluster assembly SufBD family protein SA0778 => Iron-sulfur cluster assembly SufBD family protein
+[14:17:15] Modify product: Iron-sulfur cluster assembly SufBD family protein Rv1462 => Iron-sulfur cluster assembly SufBD family protein
+[14:17:15] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[14:17:15] Modify product: Uncharacterized SURF1-like protein Rv2235 => putative SURF1-like protein
+[14:17:15] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA
+[14:17:15] Modify product: Uncharacterized protein Rv1276c => putative protein
+[14:17:15] Modify product: Phosphate-specific transport system accessory protein PhoU homolog 2 => Phosphate-specific transport system accessory protein PhoU 
+[14:17:15] Modify product: Uncharacterized tRNA/rRNA methyltransferase Rv3579c => putative tRNA/rRNA methyltransferase
+[14:17:15] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[14:17:15] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[14:17:15] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
+[14:17:15] Modify product: Probable hydrolase sll0100 => putative hydrolase
+[14:17:15] Modify product: Uncharacterized protein YihR => putative protein YihR
+[14:17:15] Modify product: Putative transport protein Rv0205 => Putative transport protein
+[14:17:16] Modify product: Uncharacterized metal-dependent hydrolase TatD => putative metal-dependent hydrolase TatD
+[14:17:16] Modify product: Probable phosphomannomutase => putative phosphomannomutase
+[14:17:16] Modify product: pH-sensitive adenylate cyclase Rv1264 => pH-sensitive adenylate cyclase
+[14:17:16] Modify product: UPF0182 protein MSMEG_1959/MSMEI_1915 => hypothetical protein
+[14:17:16] Modify product: Uncharacterized protein YlbL => putative protein YlbL
+[14:17:16] Modify product: Probable O-methyltransferase Rv1220c => putative O-methyltransferase
+[14:17:16] Modify product: Probable aminotransferase Rv1178 => putative aminotransferase
+[14:17:16] Modify product: Uncharacterized lipoprotein Rv2585c => putative lipoprotein
+[14:17:16] Modify product: Probable bacterial non-heme ferritin => putative bacterial non-heme ferritin
+[14:17:16] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating]
+[14:17:16] Modify product: Protein Rv2133c => Protein
+[14:17:16] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564
+[14:17:16] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[14:17:16] Modify product: Uncharacterized protein Rv3421c => putative protein
+[14:17:16] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX 
+[14:17:16] Modify product: UPF0336 protein Rv0637 => hypothetical protein
+[14:17:16] Modify product: Probable cystathionine beta-synthase Rv1077 => putative cystathionine beta-synthase
+[14:17:16] Modify product: Nucleotide-binding protein SCO4614 => Nucleotide-binding protein
+[14:17:16] Modify product: Probable 2-succinylbenzoate--CoA ligase => putative 2-succinylbenzoate--CoA ligase
+[14:17:16] Modify product: Uncharacterized protein Rv0525 => putative protein
+[14:17:16] Modify product: Uncharacterized protein Rv0498 => putative protein
+[14:17:16] Modify product: Uncharacterized ATP-dependent helicase YprA => putative ATP-dependent helicase YprA
+[14:17:16] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO
+[14:17:16] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[14:17:16] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
+[14:17:16] Modify product: Probable lipoprotein aminopeptidase LpqL => putative lipoprotein aminopeptidase LpqL
+[14:17:16] Modify product: Putative hydro-lyase PSPTO_5379 => Putative hydro-lyase
+[14:17:16] Modify product: Probable cold shock protein A => putative cold shock protein A
+[14:17:16] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
+[14:17:16] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[14:17:16] Modify product: UPF0371 protein DIP2346 => hypothetical protein
+[14:17:16] Modify product: Putative acyltransferase Rv0859 => Putative acyltransferase
+[14:17:16] Modify product: Probable cation-transporting ATPase G => putative cation-transporting ATPase G
+[14:17:16] Modify product: Acetyltransferase PA3944 => Acetyltransferase
+[14:17:16] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
+[14:17:16] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein
+[14:17:16] Modify product: Uncharacterized glycosyl hydrolase MT2062 => putative glycosyl hydrolase
+[14:17:16] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[14:17:16] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[14:17:16] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV
+[14:17:16] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK
+[14:17:16] Modify product: Uncharacterized N-acetyltransferase Rv2669 => putative N-acetyltransferase
+[14:17:16] Modify product: Putative glutaredoxin Rv3198A => Putative glutaredoxinA
+[14:17:16] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[14:17:16] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[14:17:16] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[14:17:16] Modify product: Probable glycerol uptake facilitator protein => putative glycerol uptake facilitator protein
+[14:17:16] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN
+[14:17:16] Modify product: Probable M18 family aminopeptidase 2 => putative M18 family aminopeptidase 2
+[14:17:16] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
+[14:17:16] Modify product: Protein Rv0786c => Protein
+[14:17:16] Modify product: UPF0312 protein SA2479 => hypothetical protein
+[14:17:16] Modify product: Probable glycerophosphodiester phosphodiesterase 2 => putative glycerophosphodiester phosphodiesterase 2
+[14:17:16] Modify product: Putative low molecular weight protein-tyrosine-phosphatase slr0328 => Putative low molecular weight protein-tyrosine-phosphatase
+[14:17:16] Modify product: Putative 2-hydroxyacid dehydrogenase SA2098 => Putative 2-hydroxyacid dehydrogenase
+[14:17:16] Modify product: Probable glycerophosphodiester phosphodiesterase 1 => putative glycerophosphodiester phosphodiesterase 1
+[14:17:16] Modify product: UPF0045 protein Rv1898 => hypothetical protein
+[14:17:16] Modify product: Universal stress protein MT2698 => Universal stress protein
+[14:17:17] Modify product: Probable inactive lipase Rv1592c => putative inactive lipase
+[14:17:17] Modify product: Uncharacterized protein Rv2895c => putative protein
+[14:17:17] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[14:17:17] Modify product: Probable malonic semialdehyde reductase RutE => putative malonic semialdehyde reductase RutE
+[14:17:17] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[14:17:17] Modify product: Probable 3-hydroxyisobutyrate dehydrogenase => putative 3-hydroxyisobutyrate dehydrogenase
+[14:17:17] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
+[14:17:17] Modify product: Probable glycine dehydrogenase (decarboxylating) => putative glycine dehydrogenase (decarboxylating)
+[14:17:17] Cleaned 149 /product names
+[14:17:17] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.sprot.tmp.350379.faa
+[14:17:17] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.sprot.tmp.350379.blast
+[14:17:17] Labelling remaining 1052 proteins as 'hypothetical protein'
+[14:17:17] Possible /pseudo 'Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit' at NZ_CP033200.1 position 293656
+[14:17:17] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP033200.1 position 349294
+[14:17:17] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP033200.1 position 359107
+[14:17:17] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP033200.1 position 830592
+[14:17:17] Possible /pseudo 'Iron-sulfur cluster assembly SufBD family protein' at NZ_CP033200.1 position 913532
+[14:17:17] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP033200.1 position 1211439
+[14:17:17] Possible /pseudo 'IS481 family transposase ISKrh2' at NZ_CP033200.1 position 1212507
+[14:17:17] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP033200.1 position 1444134
+[14:17:17] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP033200.1 position 1787569
+[14:17:17] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP033200.1 position 2427741
+[14:17:17] Found 921 unique /gene codes.
+[14:17:17] Fixed 2 duplicate /gene - liaR_1 liaR_2
+[14:17:17] Fixed 2 duplicate /gene - lolD_1 lolD_2
+[14:17:17] Fixed 2 duplicate /gene - rspR_1 rspR_2
+[14:17:17] Fixed 2 duplicate /gene - lnrK_1 lnrK_2
+[14:17:17] Fixed 2 duplicate /gene - gabD1_1 gabD1_2
+[14:17:17] Fixed 2 duplicate /gene - lspA_1 lspA_2
+[14:17:17] Fixed 3 duplicate /gene - accA3_1 accA3_2 accA3_3
+[14:17:17] Fixed 4 duplicate /gene - merR1_1 merR1_2 merR1_3 merR1_4
+[14:17:17] Fixed 2 duplicate /gene - def_1 def_2
+[14:17:17] Fixed 2 duplicate /gene - mntH_1 mntH_2
+[14:17:17] Fixed 2 duplicate /gene - gsiA_1 gsiA_2
+[14:17:17] Fixed 2 duplicate /gene - idsA2_1 idsA2_2
+[14:17:17] Fixed 2 duplicate /gene - glgC_1 glgC_2
+[14:17:17] Fixed 3 duplicate /gene - acdA_1 acdA_2 acdA_3
+[14:17:17] Fixed 2 duplicate /gene - echA8_1 echA8_2
+[14:17:17] Fixed 3 duplicate /gene - cadA_1 cadA_2 cadA_3
+[14:17:17] Fixed 2 duplicate /gene - sad_1 sad_2
+[14:17:17] Fixed 5 duplicate /gene - mmgC_1 mmgC_2 mmgC_3 mmgC_4 mmgC_5
+[14:17:17] Fixed 2 duplicate /gene - metB_1 metB_2
+[14:17:17] Fixed 2 duplicate /gene - yghA_1 yghA_2
+[14:17:17] Fixed 2 duplicate /gene - bkdB_1 bkdB_2
+[14:17:17] Fixed 2 duplicate /gene - qorA_1 qorA_2
+[14:17:17] Fixed 3 duplicate /gene - pepN_1 pepN_2 pepN_3
+[14:17:17] Fixed 2 duplicate /gene - galE_1 galE_2
+[14:17:17] Fixed 2 duplicate /gene - lysG_1 lysG_2
+[14:17:17] Fixed 2 duplicate /gene - tcrX_1 tcrX_2
+[14:17:17] Fixed 2 duplicate /gene - gyrB_1 gyrB_2
+[14:17:17] Fixed 5 duplicate /gene - acsA_1 acsA_2 acsA_3 acsA_4 acsA_5
+[14:17:17] Fixed 4 duplicate /gene - merA_1 merA_2 merA_3 merA_4
+[14:17:17] Fixed 2 duplicate /gene - fprA_1 fprA_2
+[14:17:17] Fixed 2 duplicate /gene - hbd_1 hbd_2
+[14:17:17] Fixed 2 duplicate /gene - gyrA_1 gyrA_2
+[14:17:17] Fixed 2 duplicate /gene - uvrA_1 uvrA_2
+[14:17:17] Fixed 2 duplicate /gene - iscS_1 iscS_2
+[14:17:17] Fixed 6 duplicate /gene - lcfB_1 lcfB_2 lcfB_3 lcfB_4 lcfB_5 lcfB_6
+[14:17:17] Fixed 2 duplicate /gene - yheS_1 yheS_2
+[14:17:17] Fixed 2 duplicate /gene - ktrB_1 ktrB_2
+[14:17:17] Fixed 2 duplicate /gene - rlmP_1 rlmP_2
+[14:17:17] Fixed 2 duplicate /gene - gabT_1 gabT_2
+[14:17:17] Fixed 3 duplicate /gene - ywjA_1 ywjA_2 ywjA_3
+[14:17:17] Fixed 5 duplicate /gene - czcD_1 czcD_2 czcD_3 czcD_4 czcD_5
+[14:17:17] Fixed 2 duplicate /gene - map_1 map_2
+[14:17:17] Fixed 2 duplicate /gene - bkdA_1 bkdA_2
+[14:17:17] Fixed 2 duplicate /gene - crt_1 crt_2
+[14:17:17] Fixed 2 duplicate /gene - citE_1 citE_2
+[14:17:17] Fixed 2 duplicate /gene - hin_1 hin_2
+[14:17:17] Fixed 3 duplicate /gene - ziaR_1 ziaR_2 ziaR_3
+[14:17:17] Fixed 2 duplicate /gene - trpB_1 trpB_2
+[14:17:17] Fixed 2 duplicate /gene - yknY_1 yknY_2
+[14:17:17] Fixed 2 duplicate /gene - acp_1 acp_2
+[14:17:17] Fixed 2 duplicate /gene - ettA_1 ettA_2
+[14:17:17] Fixed 2 duplicate /gene - lysE_1 lysE_2
+[14:17:17] Fixed 2 duplicate /gene - fadB_1 fadB_2
+[14:17:17] Fixed 2 duplicate /gene - mrpD_1 mrpD_2
+[14:17:17] Fixed 4 duplicate /gene - cmtR_1 cmtR_2 cmtR_3 cmtR_4
+[14:17:17] Fixed 2 duplicate /gene - abaF_1 abaF_2
+[14:17:17] Fixed 2 duplicate /gene - lepB_1 lepB_2
+[14:17:17] Fixed 2 duplicate /gene - pdhC_1 pdhC_2
+[14:17:17] Fixed 3 duplicate /gene - stp_1 stp_2 stp_3
+[14:17:17] Fixed 2 duplicate /gene - ideR_1 ideR_2
+[14:17:17] Fixed 2 duplicate /gene - paaJ_1 paaJ_2
+[14:17:17] Fixed 61 colliding /gene names.
+[14:17:17] Adding /locus_tag identifiers
+[14:17:17] Assigned 2315 locus_tags to CDS and RNA features.
+[14:17:17] Writing outputs to /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/
+[14:17:18] Generating annotation statistics file
+[14:17:18] Generating Genbank and Sequin files
+[14:17:18] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.15.6 from https://github.com/tseemann/prokka' -Z \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.err -i \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.fsa 2> /dev/null
+[14:17:23] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/errorsummary.val
+[14:17:23] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.dr
+[14:17:23] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.fixedproducts
+[14:17:23] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.ecn
+[14:17:23] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.val
+[14:17:23] Repairing broken .GBK output that tbl2asn produces...
+[14:17:23] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.gbf > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_003691675\.1_ASM369167v1_genomic\/ASM369167v1_genomic\.gbk
+[14:17:23] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.gbf
+[14:17:23] Output files:
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.gff
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.faa
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.fsa
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.sqn
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.log
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.gbk
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.err
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.tsv
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.fna
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.tbl
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.txt
+[14:17:23] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.ffn
+[14:17:23] Annotation finished successfully.
+[14:17:23] Walltime used: 2.15 minutes
+[14:17:23] If you use this result please cite the Prokka paper:
+[14:17:23] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
+[14:17:23] Type 'prokka --citation' for more details.
+[14:17:23] Share and enjoy!

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_003691675.1_ASM369167v1_genomic/ASM369167v1_genomic.txt

@@ -0,0 +1,7 @@
+organism: Micrococcus species strain 
+contigs: 1
+bases: 2483045
+CDS: 2257
+rRNA: 6
+tRNA: 51
+tmRNA: 1

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.log

@@ -0,0 +1,409 @@
+[14:20:04] This is prokka 1.15.6
+[14:20:04] Written by Torsten Seemann <torsten.seemann@gmail.com>
+[14:20:04] Homepage is https://github.com/tseemann/prokka
+[14:20:04] Local time is Wed May 20 14:20:04 2026
+[14:20:04] You are root
+[14:20:04] Operating system is linux
+[14:20:04] You have BioPerl 1.7.8
+[14:20:04] System has 104 cores.
+[14:20:04] Will use maximum of 4 cores.
+[14:20:04] Annotating as >>> Bacteria <<<
+[14:20:04] Generating locus_tag from '/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_020097155.1_ASM2009715v1_genomic.fna' contents.
+[14:20:04] Setting --locustag NAFOICDF from MD5 7af82cdfdf673547dbdda9b46abe35e9
+[14:20:04] Creating new output folder: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic
+[14:20:04] Running: mkdir -p \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic
+[14:20:04] Using filename prefix: ASM2009715v1_genomic.XXX
+[14:20:04] Setting HMMER_NCPU=1
+[14:20:04] Writing log to: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.log
+[14:20:04] Command: /225040511/miniconda3/envs/biomni_e1/bin/prokka --outdir /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic --prefix ASM2009715v1_genomic --genus Micrococcus --force --quiet --cpus 4 /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_020097155.1_ASM2009715v1_genomic.fna
+[14:20:04] Looking for 'aragorn' - found /225040511/miniconda3/envs/biomni_e1/bin/aragorn
+[14:20:04] Determined aragorn version is v1.2 from 'ARAGORN v1.2.41 Dean Laslett'
+[14:20:04] Looking for 'barrnap' - found /225040511/miniconda3/envs/biomni_e1/bin/barrnap
+[14:20:04] Determined barrnap version is v0.9 from 'barrnap 0.9'
+[14:20:04] Looking for 'blastp' - found /225040511/miniconda3/envs/biomni_e1/bin/blastp
+[14:20:04] Determined blastp version is v2.17 from 'blastp: 2.17.0+'
+[14:20:04] Looking for 'cmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/cmpress
+[14:20:04] Determined cmpress version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[14:20:04] Looking for 'cmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/cmscan
+[14:20:04] Determined cmscan version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[14:20:04] Looking for 'egrep' - found /usr/bin/egrep
+[14:20:04] Looking for 'find' - found /usr/bin/find
+[14:20:04] Looking for 'grep' - found /usr/bin/grep
+[14:20:04] Looking for 'hmmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmpress
+[14:20:04] Determined hmmpress version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[14:20:04] Looking for 'hmmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmscan
+[14:20:04] Determined hmmscan version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[14:20:04] Looking for 'java' - found /225040511/miniconda3/envs/biomni_e1/bin/java
+[14:20:04] Looking for 'makeblastdb' - found /225040511/miniconda3/envs/biomni_e1/bin/makeblastdb
+[14:20:04] Determined makeblastdb version is v2.17 from 'makeblastdb: 2.17.0+'
+[14:20:04] Looking for 'minced' - found /225040511/miniconda3/envs/biomni_e1/bin/minced
+[14:20:04] Determined minced version is v4.2 from 'minced 0.4.2'
+[14:20:04] Looking for 'parallel' - found /225040511/miniconda3/envs/biomni_e1/bin/parallel
+[14:20:05] Determined parallel version is 20260422 from 'GNU parallel 20260422'
+[14:20:05] Looking for 'prodigal' - found /225040511/miniconda3/envs/biomni_e1/bin/prodigal
+[14:20:05] Determined prodigal version is v2.6 from 'Prodigal V2.6.3: February, 2016'
+[14:20:05] Looking for 'prokka-genbank_to_fasta_db' - found /225040511/miniconda3/envs/biomni_e1/bin/prokka-genbank_to_fasta_db
+[14:20:05] Looking for 'sed' - found /225040511/miniconda3/envs/biomni_e1/bin/sed
+[14:20:05] Looking for 'tbl2asn' - found /225040511/miniconda3/envs/biomni_e1/bin/tbl2asn
+[14:20:05] Determined tbl2asn version is v25.7 from 'tbl2asn 25.7   arguments:'
+[14:20:05] Using genetic code table 11.
+[14:20:05] Loading and checking input file: /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_020097155.1_ASM2009715v1_genomic.fna
+[14:20:05] Wrote 1 contigs totalling 2648900 bp.
+[14:20:05] Predicting tRNAs and tmRNAs
+[14:20:05] Running: aragorn -l -gc11  -w \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.fna
+[14:20:08] 1 tRNA-Thr [23831,23905] 35 (cgt)
+[14:20:08] 2 tRNA-Ser [25613,25702] 35 (tga)
+[14:20:08] 3 tRNA-Ser [34500,34589] 35 (gct)
+[14:20:08] 4 tRNA-Arg [44549,44623] 35 (acg)
+[14:20:08] 5 tRNA-Ser [48866,48956] 35 (cga)
+[14:20:08] 6 tRNA-Ser c[123884,123970] 35 (gga)
+[14:20:08] 7 tRNA-Phe c[216059,216132] 34 (gaa)
+[14:20:08] 8 tRNA-Asp c[216209,216283] 35 (gtc)
+[14:20:08] 9 tRNA-Glu c[216411,216484] 35 (ttc)
+[14:20:08] 10 tRNA-Lys c[236009,236082] 34 (ttt)
+[14:20:08] 11 tRNA-Leu c[378294,378380] 35 (cag)
+[14:20:08] 12 tRNA-Ala c[394181,394256] 34 (tgc)
+[14:20:08] 13 tRNA-Ile c[394518,394592] 35 (gat)
+[14:20:08] 14 tRNA-Cys c[735912,735985] 33 (gca)
+[14:20:08] 15 tRNA-Ala [862821,862894] 34 (cgc)
+[14:20:08] 16 tRNA-Gly c[947540,947613] 33 (ccc)
+[14:20:08] 17 tRNA-Tyr [1090601,1090684] 35 (gta)
+[14:20:08] 18 tRNA-Thr [1100166,1100238] 33 (ggt)
+[14:20:08] 19 tRNA-Met [1100295,1100370] 35 (cat)
+[14:20:08] 20 tRNA-Trp [1121659,1121732] 34 (cca)
+[14:20:08] 21 tRNA-Pro [1362720,1362802] 30 (cgg)
+[14:20:08] 22 tRNA-Met [1368187,1368261] 35 (cat)
+[14:20:08] 23 tRNA-Pro [1472482,1472558] 35 (ggg)
+[14:20:08] 24 tRNA-Leu [1661164,1661238] 34 (cag)
+[14:20:08] 25 tRNA-Leu [1723662,1723746] 35 (gag)
+[14:20:08] 26 tRNA-Leu c[1808867,1808950] 35 (caa)
+[14:20:08] 27 tRNA-Gly [1838729,1838803] 35 (gcc)
+[14:20:08] 28 tRNA-Cys [1838821,1838892] 33 (gca)
+[14:20:08] 29 tRNA-Val [1838952,1839024] 33 (gac)
+[14:20:08] 30 tRNA-Gly [1839052,1839128] 35 (gcc)
+[14:20:08] 31 tRNA-Ala c[1925883,1925956] 34 (ggc)
+[14:20:08] 32 tRNA-Ala c[1928569,1928642] 34 (ggc)
+[14:20:08] 33 tRNA-Pro c[1984088,1984162] 35 (tgg)
+[14:20:08] 34 tRNA-Gly [1985242,1985315] 33 (tcc)
+[14:20:08] 35 tRNA-Arg [2000923,2000997] 35 (tct)
+[14:20:08] 36 tRNA-His [2008317,2008392] 34 (gtg)
+[14:20:08] 37 tRNA-Val c[2036310,2036385] 35 (tac)
+[14:20:08] 38 tRNA-Glu c[2101403,2101476] 35 (ctc)
+[14:20:08] 39 tRNA-Glu c[2101599,2101672] 35 (ctc)
+[14:20:08] 40 tRNA-Gln c[2101767,2101839] 34 (ctg)
+[14:20:08] 41 tRNA-Lys [2126513,2126588] 34 (ctt)
+[14:20:08] 42 tRNA-Leu [2127243,2127329] 36 (tag)
+[14:20:08] 43 tRNA-Arg [2185231,2185306] 34 (ccg)
+[14:20:08] 44 tmRNA c[2221406,2221775] 96,134 AESKRTDFALAA*
+[14:20:08] 45 tRNA-Met c[2315976,2316051] 35 (cat)
+[14:20:08] 46 tRNA-Asn c[2376323,2376396] 33 (gtt)
+[14:20:08] 47 tRNA-Arg c[2429206,2429304] 39 (gcg)
+[14:20:08] 48 tRNA-Gln c[2472861,2472933] 33 (ttg)
+[14:20:08] tRNA [2484226,2484318] is a pseudo/wacky gene - skipping.
+[14:20:08] 50 tRNA-Leu c[2516175,2516251] 35 (taa)
+[14:20:08] 51 tRNA-Arg [2609511,2609587] 35 (cct)
+[14:20:08] 52 tRNA-Val c[2625786,2625861] 35 (cac)
+[14:20:08] 53 tRNA-Thr c[2630042,2630118] 35 (tgt)
+[14:20:08] 54 tRNA-Arg [2633219,2633293] 36 (gcg)
+[14:20:08] 55 tRNA-Pro c[2648208,2648284] 35 (cgg)
+[14:20:08] Found 54 tRNAs
+[14:20:08] Predicting Ribosomal RNAs
+[14:20:08] Running Barrnap with 4 threads
+[14:20:09] 1 NZ_CP083691.1 42 5S ribosomal RNA
+[14:20:09] 2 NZ_CP083691.1 341 23S ribosomal RNA
+[14:20:09] 3 NZ_CP083691.1 3844 16S ribosomal RNA
+[14:20:09] 4 NZ_CP083691.1 1441080 16S ribosomal RNA
+[14:20:09] 5 NZ_CP083691.1 1443023 23S ribosomal RNA
+[14:20:09] 6 NZ_CP083691.1 1446292 5S ribosomal RNA
+[14:20:09] Found 6 rRNAs
+[14:20:09] Skipping ncRNA search, enable with --rfam if desired.
+[14:20:09] Total of 59 tRNA + rRNA features
+[14:20:09] Searching for CRISPR repeats
+[14:20:09] Found 0 CRISPRs
+[14:20:09] Predicting coding sequences
+[14:20:09] Contigs total 2648900 bp, so using single mode
+[14:20:09] Running: prodigal -i \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.fna -c -m -g 11 -p single -f sco -q
+[14:20:16] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP083691.1:1362267..1363679 on - strand
+[14:20:17] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP083691.1:1661087..1662364 on + strand
+[14:20:17] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP083691.1:2428948..2429241 on + strand
+[14:20:17] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP083691.1:2632558..2634669 on - strand
+[14:20:17] Found 2432 CDS
+[14:20:17] Connecting features back to sequences
+[14:20:17] Not using genus-specific database. Try --usegenus to enable it.
+[14:20:17] Annotating CDS, please be patient.
+[14:20:17] Will use 4 CPUs for similarity searching.
+[14:20:18] There are still 2432 unannotated CDS left (started with 2432)
+[14:20:18] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS with 4 CPUs
+[14:20:18] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.IS\.tmp\.353088\.faa | parallel --gnu --plain -j 4 --block 101093 --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\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.IS\.tmp\.353088\.blast 2> /dev/null
+[14:20:33] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.IS.tmp.353088.faa
+[14:20:33] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.IS.tmp.353088.blast
+[14:20:34] There are still 2376 unannotated CDS left (started with 2432)
+[14:20:34] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR with 4 CPUs
+[14:20:34] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.AMR\.tmp\.353088\.faa | parallel --gnu --plain -j 4 --block 99367 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.AMR\.tmp\.353088\.blast 2> /dev/null
+[14:20:58] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.AMR.tmp.353088.faa
+[14:20:58] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.AMR.tmp.353088.blast
+[14:20:59] There are still 2375 unannotated CDS left (started with 2432)
+[14:20:59] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot with 4 CPUs
+[14:20:59] Running: cat \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.sprot\.tmp\.353088\.faa | parallel --gnu --plain -j 4 --block 99220 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.sprot\.tmp\.353088\.blast 2> /dev/null
+[14:22:13] Modify product: Uncharacterized ATP-dependent helicase YprA => putative ATP-dependent helicase YprA
+[14:22:13] Modify product: Uncharacterized protein Rv0498 => putative protein
+[14:22:13] Modify product: Uncharacterized protein Rv0525 => putative protein
+[14:22:13] Modify product: Probable 2-succinylbenzoate--CoA ligase => putative 2-succinylbenzoate--CoA ligase
+[14:22:13] Modify product: Nucleotide-binding protein SCO4614 => Nucleotide-binding protein
+[14:22:13] Modify product: UPF0336 protein Rv0504c => hypothetical protein
+[14:22:13] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX 
+[14:22:13] Modify product: Uncharacterized protein Rv3421c => putative protein
+[14:22:13] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[14:22:13] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564
+[14:22:13] Modify product: Protein Rv2133c => Protein
+[14:22:13] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating]
+[14:22:13] Modify product: Probable bacterial non-heme ferritin => putative bacterial non-heme ferritin
+[14:22:13] Modify product: Uncharacterized lipoprotein Rv2585c => putative lipoprotein
+[14:22:13] Modify product: Probable aminotransferase Rv1178 => putative aminotransferase
+[14:22:13] Modify product: Probable O-methyltransferase Rv1220c => putative O-methyltransferase
+[14:22:13] Modify product: Uncharacterized protein Rv0007 => putative protein
+[14:22:13] Modify product: Probable M18 family aminopeptidase 2 => putative M18 family aminopeptidase 2
+[14:22:13] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[14:22:13] Modify product: Uncharacterized membrane protein Rv0364 => putative membrane protein
+[14:22:13] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[14:22:13] Modify product: Uncharacterized N-acetyltransferase Rv2669 => putative N-acetyltransferase
+[14:22:13] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK
+[14:22:13] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV
+[14:22:13] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[14:22:13] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[14:22:13] Modify product: Uncharacterized glycosyl hydrolase MT2062 => putative glycosyl hydrolase
+[14:22:13] Modify product: Probable membrane transporter protein XF_0764 => putative membrane transporter protein
+[14:22:13] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein
+[14:22:13] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
+[14:22:13] Modify product: Uncharacterized protein Rv0088 => putative protein
+[14:22:13] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[14:22:13] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[14:22:13] Modify product: Acetyltransferase PA3944 => Acetyltransferase
+[14:22:13] Modify product: Uncharacterized tRNA/rRNA methyltransferase Rv3579c => putative tRNA/rRNA methyltransferase
+[14:22:13] Modify product: Phosphate-specific transport system accessory protein PhoU homolog 2 => Phosphate-specific transport system accessory protein PhoU 
+[14:22:13] Modify product: Uncharacterized protein DR_1314 => putative protein
+[14:22:13] Modify product: Uncharacterized protein Rv1276c => putative protein
+[14:22:13] Modify product: Acetyl- and succinyl-CoA transferase Rv0802c => Acetyl- and succinyl-CoA transferase
+[14:22:13] Modify product: Probable glycine dehydrogenase (decarboxylating) => putative glycine dehydrogenase (decarboxylating)
+[14:22:13] Modify product: UPF0324 inner membrane protein YeiH => hypothetical protein
+[14:22:13] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
+[14:22:13] Modify product: Probable 3-hydroxyisobutyrate dehydrogenase => putative 3-hydroxyisobutyrate dehydrogenase
+[14:22:13] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[14:22:13] Modify product: Probable malonic semialdehyde reductase RutE => putative malonic semialdehyde reductase RutE
+[14:22:13] Modify product: UPF0225 protein YchJ => hypothetical protein
+[14:22:13] Modify product: Probable D,D-dipeptide transport system permease protein DdpC => putative D,D-dipeptide transport system permease protein DdpC
+[14:22:13] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR
+[14:22:13] Modify product: Uncharacterized protein Rv0034 => putative protein
+[14:22:13] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[14:22:13] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[14:22:14] Modify product: Universal stress protein MT2698 => Universal stress protein
+[14:22:14] Modify product: UPF0045 protein Rv1898 => hypothetical protein
+[14:22:14] Modify product: Probable glycerophosphodiester phosphodiesterase 1 => putative glycerophosphodiester phosphodiesterase 1
+[14:22:14] Modify product: Uncharacterized protein YagA => putative protein YagA
+[14:22:14] Modify product: Probable glycerophosphodiester phosphodiesterase 2 => putative glycerophosphodiester phosphodiesterase 2
+[14:22:14] Modify product: Probable glycerophosphodiester phosphodiesterase 2 => putative glycerophosphodiester phosphodiesterase 2
+[14:22:14] Modify product: Uncharacterized HTH-type transcriptional regulator Rv2282c => putative HTH-type transcriptional regulator
+[14:22:14] Modify product: Uncharacterized protein YdhK => putative protein YdhK
+[14:22:14] Modify product: Putative acyltransferase Rv0859 => Putative acyltransferase
+[14:22:14] Modify product: UPF0371 protein DIP2346 => hypothetical protein
+[14:22:14] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[14:22:14] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
+[14:22:14] Modify product: Probable cold shock protein A => putative cold shock protein A
+[14:22:14] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv2564 => putative ABC transporter ATP-binding protein
+[14:22:14] Modify product: Putative hydro-lyase PSPTO_5379 => Putative hydro-lyase
+[14:22:14] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
+[14:22:14] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[14:22:14] Modify product: Uncharacterized protein YlbL => putative protein YlbL
+[14:22:14] Modify product: UPF0182 protein MSMEG_1959/MSMEI_1915 => hypothetical protein
+[14:22:14] Modify product: Uncharacterized protein Rv1708 => putative protein
+[14:22:14] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1828 => putative HTH-type transcriptional regulator
+[14:22:14] Modify product: Uncharacterized protein Rv1829 => putative protein
+[14:22:14] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1830 => putative HTH-type transcriptional regulator
+[14:22:14] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW
+[14:22:14] Modify product: Uncharacterized RNA pseudouridine synthase Rv1540 => putative RNA pseudouridine synthase
+[14:22:14] Modify product: Probable cytosol aminopeptidase => putative cytosol aminopeptidase
+[14:22:14] Modify product: Probable transcriptional regulatory protein Rv2603c => putative transcriptional regulatory protein
+[14:22:14] Modify product: Uncharacterized transporter Rv1999c => putative transporter
+[14:22:14] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein
+[14:22:14] Modify product: Probable replication restart protein PriA => putative replication restart protein PriA
+[14:22:14] Modify product: DegV domain-containing protein SPy_1493/M5005_Spy1226 => DegV domain-containing protein/M5005_Spy1226
+[14:22:14] Modify product: Probable DNA polymerase III subunit delta => putative DNA polymerase III subunit delta
+[14:22:14] Modify product: UPF0053 protein Rv2366c => hypothetical protein
+[14:22:14] Modify product: Uncharacterized protein Rv2206 => putative protein
+[14:22:14] Modify product: Protein Rv2204c => Protein
+[14:22:14] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1
+[14:22:14] Modify product: Probable cytochrome c oxidase polypeptide 4 => putative cytochrome c oxidase polypeptide 4
+[14:22:14] Modify product: Probable cytochrome c oxidase subunit 3 => putative cytochrome c oxidase subunit 3
+[14:22:14] Modify product: Probable helicase HelY => putative helicase HelY
+[14:22:14] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase
+[14:22:14] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA
+[14:22:14] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[14:22:14] Modify product: Iron-sulfur cluster assembly SufBD family protein Rv1462 => Iron-sulfur cluster assembly SufBD family protein
+[14:22:14] Modify product: Iron-sulfur cluster assembly SufBD family protein SA0778 => Iron-sulfur cluster assembly SufBD family protein
+[14:22:14] Modify product: Probable protein-export membrane protein SecG => putative protein-export membrane protein SecG
+[14:22:14] Modify product: Probable cell division protein WhiA => putative cell division protein WhiA
+[14:22:14] Modify product: Nucleotide-binding protein Rv1421 => Nucleotide-binding protein
+[14:22:14] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase
+[14:22:14] Modify product: Uncharacterized membrane protein Rv2723 => putative membrane protein
+[14:22:14] Modify product: Putative methyltransferase Rv1407 => Putative methyltransferase
+[14:22:14] Modify product: Uncharacterized SufE-like protein Rv3284 => putative SufE-like protein
+[14:22:14] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase
+[14:22:14] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase
+[14:22:14] Modify product: Uncharacterized oxidoreductase Rv0484c => putative oxidoreductase
+[14:22:14] Modify product: Thioredoxin-like reductase Rv2466c => Thioredoxin-like reductase
+[14:22:14] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[14:22:14] Modify product: Uncharacterized protein Rv2239c => putative protein
+[14:22:14] Modify product: Uncharacterized protein Rv2242 => putative protein
+[14:22:14] Modify product: Uncharacterized protein Rv2901c => putative protein
+[14:22:14] Modify product: Uncharacterized protein Rv2926c => putative protein
+[14:22:14] Modify product: Probable N-succinyldiaminopimelate aminotransferase DapC => putative N-succinyldiaminopimelate aminotransferase DapC
+[14:22:14] Modify product: RNA/DNA methyltransferase Rv2966c => RNA/DNA methyltransferase
+[14:22:14] Modify product: Uncharacterized protein SA1069 => putative protein
+[14:22:14] Modify product: Uncharacterized HTH-type transcriptional regulator RhmR => putative HTH-type transcriptional regulator RhmR
+[14:22:14] Modify product: Protein Rv2993c => Protein
+[14:22:14] Modify product: Putative peroxiredoxin Rv2521 => Putative peroxiredoxin
+[14:22:14] Modify product: Probable malate:quinone oxidoreductase => putative malate:quinone oxidoreductase
+[14:22:14] Modify product: Uncharacterized protein Rv1339 => putative protein
+[14:22:14] Modify product: Uncharacterized protein Rv1324 => putative protein
+[14:22:14] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ
+[14:22:14] Modify product: Uncharacterized HIT-like protein Rv0759c => putative HIT-like protein
+[14:22:14] Modify product: Uncharacterized protein Rv1841c => putative protein
+[14:22:14] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[14:22:14] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B
+[14:22:14] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit A => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit A
+[14:22:14] Modify product: Probable acetyl-CoA acetyltransferase => putative acetyl-CoA acetyltransferase
+[14:22:14] Modify product: Probable pyridine nucleotide-disulfide oxidoreductase RclA => putative pyridine nucleotide-disulfide oxidoreductase RclA
+[14:22:14] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
+[14:22:14] Modify product: Uncharacterized methyltransferase Rv3342 => putative methyltransferase
+[14:22:14] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA
+[14:22:14] Modify product: Aldo-keto reductase MSMEG_2408/MSMEI_2347 => Aldo-keto reductase/MSMEI_2347
+[14:22:14] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[14:22:14] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
+[14:22:15] Modify product: Probable phosphomannomutase => putative phosphomannomutase
+[14:22:15] Modify product: Uncharacterized metal-dependent hydrolase TatD => putative metal-dependent hydrolase TatD
+[14:22:15] Modify product: Putative transport protein Rv0205 => Putative transport protein
+[14:22:15] Modify product: Uncharacterized protein YihR => putative protein YihR
+[14:22:15] Modify product: Probable hydrolase sll0100 => putative hydrolase
+[14:22:15] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
+[14:22:15] Modify product: KsdD-like steroid dehydrogenase MSMEG_5835 => KsdD-like steroid dehydrogenase
+[14:22:15] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[14:22:15] Cleaned 142 /product names
+[14:22:15] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.sprot.tmp.353088.faa
+[14:22:15] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.sprot.tmp.353088.blast
+[14:22:15] Labelling remaining 1241 proteins as 'hypothetical protein'
+[14:22:15] Possible /pseudo 'L-histidine transporter HutT' at NZ_CP083691.1 position 212391
+[14:22:15] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP083691.1 position 345484
+[14:22:15] Possible /pseudo 'IS3 family transposase ISAar24' at NZ_CP083691.1 position 355422
+[14:22:15] Possible /pseudo 'putative FMNH2-dependent monooxygenase SfnC' at NZ_CP083691.1 position 632215
+[14:22:15] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP083691.1 position 655537
+[14:22:15] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP083691.1 position 684632
+[14:22:15] Possible /pseudo 'Trk system potassium uptake protein TrkA' at NZ_CP083691.1 position 1575506
+[14:22:15] Possible /pseudo 'Iron-sulfur cluster assembly SufBD family protein' at NZ_CP083691.1 position 1752937
+[14:22:15] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP083691.1 position 1917679
+[14:22:15] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP083691.1 position 1955537
+[14:22:15] Possible /pseudo 'Signal peptidase I' at NZ_CP083691.1 position 2052459
+[14:22:15] Possible /pseudo 'Fructose-bisphosphate aldolase class 1' at NZ_CP083691.1 position 2333642
+[14:22:15] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP083691.1 position 2348254
+[14:22:15] Possible /pseudo 'Multidrug resistance protein EbrB' at NZ_CP083691.1 position 2364117
+[14:22:15] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP083691.1 position 2367636
+[14:22:15] Found 923 unique /gene codes.
+[14:22:15] Fixed 2 duplicate /gene - czcD_1 czcD_2
+[14:22:15] Fixed 2 duplicate /gene - lepB_1 lepB_2
+[14:22:15] Fixed 2 duplicate /gene - ideR_1 ideR_2
+[14:22:15] Fixed 2 duplicate /gene - gpmA_1 gpmA_2
+[14:22:15] Fixed 2 duplicate /gene - ebrB_1 ebrB_2
+[14:22:15] Fixed 2 duplicate /gene - copB_1 copB_2
+[14:22:15] Fixed 2 duplicate /gene - degU_1 degU_2
+[14:22:15] Fixed 2 duplicate /gene - rlmP_1 rlmP_2
+[14:22:15] Fixed 2 duplicate /gene - iscS_1 iscS_2
+[14:22:15] Fixed 2 duplicate /gene - ppa_1 ppa_2
+[14:22:15] Fixed 2 duplicate /gene - rspR_1 rspR_2
+[14:22:15] Fixed 2 duplicate /gene - paaJ_1 paaJ_2
+[14:22:15] Fixed 2 duplicate /gene - lysE_1 lysE_2
+[14:22:15] Fixed 2 duplicate /gene - glpQ2_1 glpQ2_2
+[14:22:15] Fixed 3 duplicate /gene - ricR_1 ricR_2 ricR_3
+[14:22:15] Fixed 2 duplicate /gene - pdxT_1 pdxT_2
+[14:22:15] Fixed 2 duplicate /gene - bkdA_1 bkdA_2
+[14:22:15] Fixed 2 duplicate /gene - dprA_1 dprA_2
+[14:22:15] Fixed 2 duplicate /gene - metB_1 metB_2
+[14:22:15] Fixed 2 duplicate /gene - map_1 map_2
+[14:22:15] Fixed 3 duplicate /gene - hutT_1 hutT_2 hutT_3
+[14:22:15] Fixed 2 duplicate /gene - gyrB_1 gyrB_2
+[14:22:15] Fixed 5 duplicate /gene - hin_1 hin_2 hin_3 hin_4 hin_5
+[14:22:15] Fixed 2 duplicate /gene - fda_1 fda_2
+[14:22:15] Fixed 5 duplicate /gene - acsA_1 acsA_2 acsA_3 acsA_4 acsA_5
+[14:22:15] Fixed 2 duplicate /gene - pepN_1 pepN_2
+[14:22:15] Fixed 2 duplicate /gene - dmoA_1 dmoA_2
+[14:22:15] Fixed 2 duplicate /gene - uvrA_1 uvrA_2
+[14:22:15] Fixed 2 duplicate /gene - acp_1 acp_2
+[14:22:15] Fixed 2 duplicate /gene - oatA_1 oatA_2
+[14:22:15] Fixed 2 duplicate /gene - gap2_1 gap2_2
+[14:22:15] Fixed 2 duplicate /gene - fadJ_1 fadJ_2
+[14:22:15] Fixed 2 duplicate /gene - lysG_1 lysG_2
+[14:22:15] Fixed 2 duplicate /gene - gyrA_1 gyrA_2
+[14:22:15] Fixed 2 duplicate /gene - glgC_1 glgC_2
+[14:22:15] Fixed 2 duplicate /gene - eno_1 eno_2
+[14:22:15] Fixed 3 duplicate /gene - yghA_1 yghA_2 yghA_3
+[14:22:15] Fixed 2 duplicate /gene - bkdB_1 bkdB_2
+[14:22:15] Fixed 2 duplicate /gene - gsiA_1 gsiA_2
+[14:22:15] Fixed 4 duplicate /gene - siwR_1 siwR_2 siwR_3 siwR_4
+[14:22:15] Fixed 2 duplicate /gene - yajO_1 yajO_2
+[14:22:15] Fixed 3 duplicate /gene - merA_1 merA_2 merA_3
+[14:22:15] Fixed 2 duplicate /gene - cobB_1 cobB_2
+[14:22:15] Fixed 2 duplicate /gene - posA_1 posA_2
+[14:22:15] Fixed 3 duplicate /gene - lcfB_1 lcfB_2 lcfB_3
+[14:22:15] Fixed 2 duplicate /gene - ktrB_1 ktrB_2
+[14:22:15] Fixed 2 duplicate /gene - lolD_1 lolD_2
+[14:22:15] Fixed 2 duplicate /gene - trpB_1 trpB_2
+[14:22:15] Fixed 2 duplicate /gene - lsr2_1 lsr2_2
+[14:22:15] Fixed 2 duplicate /gene - trkA_1 trkA_2
+[14:22:15] Fixed 2 duplicate /gene - tcrX_1 tcrX_2
+[14:22:15] Fixed 2 duplicate /gene - liaR_1 liaR_2
+[14:22:15] Fixed 2 duplicate /gene - stp_1 stp_2
+[14:22:15] Fixed 4 duplicate /gene - sfnC_1 sfnC_2 sfnC_3 sfnC_4
+[14:22:15] Fixed 2 duplicate /gene - ettA_1 ettA_2
+[14:22:15] Fixed 2 duplicate /gene - mrpD_1 mrpD_2
+[14:22:15] Fixed 2 duplicate /gene - hutI_1 hutI_2
+[14:22:15] Fixed 2 duplicate /gene - suhB_1 suhB_2
+[14:22:15] Fixed 2 duplicate /gene - accA3_1 accA3_2
+[14:22:15] Fixed 2 duplicate /gene - yknY_1 yknY_2
+[14:22:15] Fixed 2 duplicate /gene - echA8_1 echA8_2
+[14:22:15] Fixed 2 duplicate /gene - fprA_1 fprA_2
+[14:22:15] Fixed 2 duplicate /gene - ywjA_1 ywjA_2
+[14:22:15] Fixed 2 duplicate /gene - pdhC_1 pdhC_2
+[14:22:15] Fixed 2 duplicate /gene - adh_1 adh_2
+[14:22:15] Fixed 2 duplicate /gene - mmgC_1 mmgC_2
+[14:22:15] Fixed 66 colliding /gene names.
+[14:22:15] Adding /locus_tag identifiers
+[14:22:15] Assigned 2492 locus_tags to CDS and RNA features.
+[14:22:15] Writing outputs to /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/
+[14:22:16] Generating annotation statistics file
+[14:22:16] Generating Genbank and Sequin files
+[14:22:16] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.15.6 from https://github.com/tseemann/prokka' -Z \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.err -i \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.fsa 2> /dev/null
+[14:22:20] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/errorsummary.val
+[14:22:20] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.dr
+[14:22:20] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.fixedproducts
+[14:22:20] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.ecn
+[14:22:20] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.val
+[14:22:20] Repairing broken .GBK output that tbl2asn produces...
+[14:22:20] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.gbf > \/225040511\/project\/Biomanus\/experiments\/ablation\/results\/biomanus\/bioagentbench\/comparative\-genomics_20260520_140937\/prokka_output\/GCF_020097155\.1_ASM2009715v1_genomic\/ASM2009715v1_genomic\.gbk
+[14:22:20] Deleting unwanted file: /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.gbf
+[14:22:20] Output files:
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.txt
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.log
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.gbk
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.tsv
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.gff
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.err
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.ffn
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.fna
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.tbl
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.fsa
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.faa
+[14:22:20] /225040511/project/Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.sqn
+[14:22:20] Annotation finished successfully.
+[14:22:20] Walltime used: 2.27 minutes
+[14:22:20] If you use this result please cite the Prokka paper:
+[14:22:20] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
+[14:22:20] Type 'prokka --citation' for more details.
+[14:22:20] Thank you, come again.

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260520_140937/prokka_output/GCF_020097155.1_ASM2009715v1_genomic/ASM2009715v1_genomic.txt

@@ -0,0 +1,7 @@
+organism: Micrococcus species strain 
+contigs: 1
+bases: 2648900
+CDS: 2432
+rRNA: 6
+tRNA: 53
+tmRNA: 1

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260522_115630/agent_runtime/biomni_data/runtime_mcp_configs/runtime_mcp_20260522_115726_409997.yaml

@@ -0,0 +1,68 @@
+mcp_servers:
+  prokka:
+    enabled: true
+    description: 'Installs packages: prokka. Copies scripts: prokka_server.py. Default
+      command: ["python", "/app/prokka_server.py"] | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_prokka/app/prokka_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_prokka/app/prokka_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_prokka/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_prokka/app/prokka_server.py
+    packages:
+    - prokka
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/prokka.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2025.18.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: prokka
+      description: Tool bound for operation sequence_feature_extraction
+      inputSchema:
+        properties: {}
+        required: []
+  orthofinder:
+    enabled: true
+    description: 'Installs packages: orthofinder. Copies scripts: orthofinder_server.py.
+      Default command: ["python", "/app/orthofinder_server.py"] | Resolved source
+      server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_orthofinder/app/orthofinder_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_orthofinder/app/orthofinder_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_orthofinder/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_orthofinder/app/orthofinder_server.py
+    packages:
+    - orthofinder
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/orthofinder.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2025.18.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: run_orthofinder
+      description: Tool bound for operation database_lookup
+      inputSchema:
+        properties: {}
+        required: []

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260522_115630/orthofinder_output/results/Results_May22/Resolved_Gene_Trees/OG0000000_tree.txt

@@ -0,0 +1 @@
+(((TT9_LFPAFLNI_02102:5e-09,TT9_LFPAFLNI_02106:0.00288249)n2:0.0206525,(SA211_MHAAABBN_00352:0.042443,(AS2_ACLBLIBL_01505:0.25879,AS2_ACLBLIBL_02339:0.304882)n4:0.287255)n3:0.0287259)n1:0.0103334,((((SA211_MHAAABBN_00041:0.0194533,((((AS2_ACLBLIBL_01499:0,AS2_ACLBLIBL_02472:0)n12:5e-09,AS2_ACLBLIBL_02613:0.00287677)n11:5e-09,AS2_ACLBLIBL_00779:0.0758185)n10:0.00356263,(((AS2_ACLBLIBL_01768:0,AS2_ACLBLIBL_02336:0)n15:5e-09,AS2_ACLBLIBL_02637:0.00289763)n14:5e-09,AS2_ACLBLIBL_00146:5e-09)n13:0.0419983)n9:0.0311409)n8:0.0442562,(SA211_MHAAABBN_01118:0.00999489,(AS2_ACLBLIBL_02632:0.0613057,(AS2_ACLBLIBL_00044:5e-09,(AS2_ACLBLIBL_00556:0.00288709,AS2_ACLBLIBL_00692:5e-09)n19:6e-09)n18:0.0411965)n17:0.016226)n16:0.0374734)n7:0.0251797,(SA211_MHAAABBN_00012:0.00638885,(((TT9_LFPAFLNI_00274:0,TT9_LFPAFLNI_01546:0)n23:0.0164863,((SA211_MHAAABBN_00312:0.011895,(KBS0714_MOLHKGIG_01952:5e-09,KBS0714_MOLHKGIG_01337:0.0432482)n26:0.0130261)n25:0.00430081,((SA211_MHAAABBN_01818:5e-09,(KBS0714_MOLHKGIG_02278:5e-09,KBS0714_MOLHKGIG_02111:4.5e-09)n29:5e-10)n28:0.00292862,((KBS0714_MOLHKGIG_02068:0.00889823,SA211_MHAAABBN_01821:0.0119179)n31:0.0277276,(KBS0714_MOLHKGIG_00064:0.00555023,SA211_MHAAABBN_02077:0.0151318)n32:0.00168131)n30:0.00313267)n27:0.000313267)n24:3.48074e-05)n22:0.00929313,(TT9_LFPAFLNI_00879:5e-09,(SA211_MHAAABBN_01236:0.00942898,((SA211_MHAAABBN_01968:0.00515122,(TT9_LFPAFLNI_01997:0.00693576,TT9_LFPAFLNI_00518:0.0138941)n37:0.00300346)n36:0.00298165,(SA211_MHAAABBN_01160:0.00385663,(TT9_LFPAFLNI_01570:0.00291278,(TT9_LFPAFLNI_00800:6e-09,TT9_LFPAFLNI_01175:0.00288019)n40:0.0057635)n39:0.00225029)n38:0.000250032)n35:0.000721651)n34:8.01834e-05)n33:0.0169932)n21:0.0232115)n20:0.0122406)n6:0.0171617,((SA211_MHAAABBN_00137:5e-09,SA211_MHAAABBN_01971:0.0353709)n42:0.00702144,(AS2_ACLBLIBL_00227:0.0028477,(AS2_ACLBLIBL_01737:0,AS2_ACLBLIBL_02555:0)n44:0.00300792)n43:0.0388917)n41:0.0043213)n5:0.0103334)n0;

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260522_115630/orthofinder_output/results/Results_May22/Resolved_Gene_Trees/OG0000001_tree.txt

@@ -0,0 +1 @@
+((((KBS0714_MOLHKGIG_01202:0,KBS0714_MOLHKGIG_02030:0)n3:5e-09,(TT9_LFPAFLNI_02197:0,TT9_LFPAFLNI_02214:0)n4:0.00229901)n2:0.0374546,(AS2_ACLBLIBL_00896:0.129812,AS2_ACLBLIBL_00691:5e-09)n5:0.0222373)n1:0.00854126,((AS2_ACLBLIBL_02671:0.00463497,KBS0714_MOLHKGIG_00603:0.0022846)n7:0.0370793,(((SA211_MHAAABBN_01127:6e-09,(KBS0714_MOLHKGIG_01394:0.00226318,TT9_LFPAFLNI_01996:5e-09)n11:5e-09)n10:5e-09,((TT9_LFPAFLNI_01344:0.00226378,SA211_MHAAABBN_01126:0.0256487)n13:0.00284986,(((KBS0714_MOLHKGIG_02266:5e-09,(KBS0714_MOLHKGIG_02231:0.00295219,(KBS0714_MOLHKGIG_02065:0.00346372,KBS0714_MOLHKGIG_02229:0.00575251)n18:0.0037022)n17:5e-09)n16:0.00942842,((KBS0714_MOLHKGIG_00174:0,KBS0714_MOLHKGIG_00589:0,KBS0714_MOLHKGIG_00713:0,KBS0714_MOLHKGIG_01399:0)n20:5e-09,KBS0714_MOLHKGIG_02226:0.00702547)n19:0.00231511)n15:0.0223782,(KBS0714_MOLHKGIG_00623:0.0113824,(KBS0714_MOLHKGIG_02064:0.0669303,KBS0714_MOLHKGIG_02232:0.0564105)n22:0.00503245)n21:0.00246314)n14:0.0750864)n12:0.00834293)n9:0.127967,((KBS0714_MOLHKGIG_01504:0.144721,AS2_ACLBLIBL_02500:5e-09)n24:6e-09,((KBS0714_MOLHKGIG_01505:0.111616,(KBS0714_MOLHKGIG_00602:0,KBS0714_MOLHKGIG_01070:0,KBS0714_MOLHKGIG_02271:0)n27:5e-09)n26:0.00460815,AS2_ACLBLIBL_00721:0.00189813)n25:0.000210903)n23:0.0103769)n8:0.0265346)n6:0.00854126)n0;

Biomanus/experiments/ablation/results/biomanus/bioagentbench/comparative-genomics_20260522_115630/orthofinder_output/results/Results_May22/Resolved_Gene_Trees/OG0000008_tree.txt

@@ -0,0 +1 @@
+((KBS0714_MOLHKGIG_02227:0.026191,(TT9_LFPAFLNI_01016:0,TT9_LFPAFLNI_01158:0)n2:0.00373267)n1:2.5e-09,(SA211_MHAAABBN_00092:0,SA211_MHAAABBN_00343:0,SA211_MHAAABBN_01013:0,SA211_MHAAABBN_01394:0,SA211_MHAAABBN_02284:0,TT9_LFPAFLNI_00606:0,TT9_LFPAFLNI_01349:0,TT9_LFPAFLNI_02164:0,((KBS0714_MOLHKGIG_01398:0.0719037,(KBS0714_MOLHKGIG_01502:0.00443704,KBS0714_MOLHKGIG_02225:0.46793)n6:0.00244087)n5:0.0621436,KBS0714_MOLHKGIG_00711:0)n4:0)n3:5e-09)n0;