Mercurial > repos > iuc > tooldistillator_summarize

annotate test-data/gtdbtk/log_file.txt @ 11:f4f71128f097 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator commit 5afafa93bbb331db2e3f2e700714ff60bf467b27
author iuc
date Wed, 05 Nov 2025 12:59:52 +0000
parents 7fe1fe92de41
children
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7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
iuc
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1 [2025-05-20 11:11:56] INFO: GTDB-Tk v2.3.2
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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2 [2025-05-20 11:11:56] INFO: gtdbtk classify_wf --genome_dir input_dir --extension .fasta --out_dir output_dir --cpus 32 --min_perc_aa 10 --min_af 0.65 --skip_ani_screen
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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3 [2025-05-20 11:11:56] INFO: Using GTDB-Tk reference data version r214: /shared/ifbstor1/galaxy/mutable-data/tool-data/gtdbtk_database_versioned/full_database_release_214_downloaded_2024-10-03
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
iuc
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4 [2025-05-20 11:11:57] INFO: Identifying markers in 4 genomes with 32 threads.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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5 [2025-05-20 11:11:57] TASK: Running Prodigal V2.6.3 to identify genes.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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6 [2025-05-20 11:12:39] INFO: Completed 4 genomes in 42.03 seconds (10.51 seconds/genome).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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7 [2025-05-20 11:12:39] TASK: Identifying TIGRFAM protein families.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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8 [2025-05-20 11:12:44] INFO: Completed 4 genomes in 4.86 seconds (1.22 seconds/genome).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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9 [2025-05-20 11:12:44] TASK: Identifying Pfam protein families.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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10 [2025-05-20 11:12:45] INFO: Completed 4 genomes in 0.41 seconds (9.72 genomes/second).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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11 [2025-05-20 11:12:45] INFO: Annotations done using HMMER 3.4 (Aug 2023).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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12 [2025-05-20 11:12:45] TASK: Summarising identified marker genes.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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13 [2025-05-20 11:12:45] INFO: Completed 4 genomes in 0.12 seconds (34.17 genomes/second).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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14 [2025-05-20 11:12:45] INFO: Done.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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15 [2025-05-20 11:12:45] INFO: Aligning markers in 4 genomes with 32 CPUs.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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16 [2025-05-20 11:12:45] INFO: Processing 4 genomes identified as bacterial.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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17 [2025-05-20 11:12:54] INFO: Read concatenated alignment for 80,789 GTDB genomes.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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18 [2025-05-20 11:12:54] TASK: Generating concatenated alignment for each marker.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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19 [2025-05-20 11:12:56] INFO: Completed 4 genomes in 0.04 seconds (113.21 genomes/second).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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20 [2025-05-20 11:12:57] TASK: Aligning 120 identified markers using hmmalign 3.4 (Aug 2023).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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21 [2025-05-20 11:13:00] INFO: Completed 120 markers in 1.45 seconds (82.61 markers/second).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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22 [2025-05-20 11:13:01] TASK: Masking columns of bacterial multiple sequence alignment using canonical mask.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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23 [2025-05-20 11:15:22] INFO: Completed 80,793 sequences in 2.36 minutes (34,274.14 sequences/minute).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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24 [2025-05-20 11:15:22] INFO: Masked bacterial alignment from 41,084 to 5,035 AAs.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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25 [2025-05-20 11:15:22] INFO: 0 bacterial user genomes have amino acids in <10.0% of columns in filtered MSA.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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26 [2025-05-20 11:15:22] INFO: Creating concatenated alignment for 80,793 bacterial GTDB and user genomes.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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27 [2025-05-20 11:15:49] INFO: Creating concatenated alignment for 4 bacterial user genomes.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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28 [2025-05-20 11:15:49] INFO: Done.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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29 [2025-05-20 11:15:50] TASK: Placing 4 bacterial genomes into backbone reference tree with pplacer using 32 CPUs (be patient).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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30 [2025-05-20 11:15:50] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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31 [2025-05-20 11:18:29] INFO: Calculating RED values based on reference tree.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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32 [2025-05-20 11:18:29] INFO: 4 out of 4 have an class assignments. Those genomes will be reclassified.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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33 [2025-05-20 11:18:29] TASK: Placing 3 bacterial genomes into class-level reference tree 3 (1/2) with pplacer using 32 CPUs (be patient).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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34 [2025-05-20 11:27:00] INFO: Calculating RED values based on reference tree.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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35 [2025-05-20 11:27:03] TASK: Traversing tree to determine classification method.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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36 [2025-05-20 11:27:03] INFO: Completed 3 genomes in 0.01 seconds (528.27 genomes/second).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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37 [2025-05-20 11:27:03] TASK: Calculating average nucleotide identity using FastANI (v1.32).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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38 [2025-05-20 11:27:17] INFO: Completed 380 comparisons in 13.43 seconds (28.29 comparisons/second).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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39 [2025-05-20 11:27:17] INFO: 3 genome(s) have been classified using FastANI and pplacer.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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40 [2025-05-20 11:27:17] TASK: Placing 1 bacterial genomes into class-level reference tree 2 (2/2) with pplacer using 32 CPUs (be patient).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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41 [2025-05-20 11:33:00] INFO: Calculating RED values based on reference tree.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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42 [2025-05-20 11:33:03] TASK: Traversing tree to determine classification method.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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43 [2025-05-20 11:33:03] INFO: Completed 1 genome in 0.00 seconds (1,061.58 genomes/second).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
iuc
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44 [2025-05-20 11:33:03] TASK: Calculating average nucleotide identity using FastANI (v1.32).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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45 [2025-05-20 11:33:06] INFO: Completed 122 comparisons in 2.93 seconds (41.69 comparisons/second).
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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46 [2025-05-20 11:33:06] INFO: 1 genome(s) have been classified using FastANI and pplacer.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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47 [2025-05-20 11:33:06] INFO: Note that Tk classification mode is insufficient for publication of new taxonomic designations. New designations should be based on one or more de novo trees, an example of which can be produced by Tk in de novo mode.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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48 [2025-05-20 11:33:06] INFO: Done.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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49 [2025-05-20 11:33:06] INFO: Removing intermediate files.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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50 [2025-05-20 11:33:06] INFO: Intermediate files removed.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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51 [2025-05-20 11:33:06] INFO: Done.