Mercurial > repos > iuc > tooldistillator_summarize
view test-data/gtdbtk/log_file.txt @ 7:7fe1fe92de41 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
| author | iuc |
|---|---|
| date | Tue, 15 Jul 2025 09:51:56 +0000 |
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[2025-05-20 11:11:56] INFO: GTDB-Tk v2.3.2 [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 [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 [2025-05-20 11:11:57] INFO: Identifying markers in 4 genomes with 32 threads. [2025-05-20 11:11:57] TASK: Running Prodigal V2.6.3 to identify genes. [2025-05-20 11:12:39] INFO: Completed 4 genomes in 42.03 seconds (10.51 seconds/genome). [2025-05-20 11:12:39] TASK: Identifying TIGRFAM protein families. [2025-05-20 11:12:44] INFO: Completed 4 genomes in 4.86 seconds (1.22 seconds/genome). [2025-05-20 11:12:44] TASK: Identifying Pfam protein families. [2025-05-20 11:12:45] INFO: Completed 4 genomes in 0.41 seconds (9.72 genomes/second). [2025-05-20 11:12:45] INFO: Annotations done using HMMER 3.4 (Aug 2023). [2025-05-20 11:12:45] TASK: Summarising identified marker genes. [2025-05-20 11:12:45] INFO: Completed 4 genomes in 0.12 seconds (34.17 genomes/second). [2025-05-20 11:12:45] INFO: Done. [2025-05-20 11:12:45] INFO: Aligning markers in 4 genomes with 32 CPUs. [2025-05-20 11:12:45] INFO: Processing 4 genomes identified as bacterial. [2025-05-20 11:12:54] INFO: Read concatenated alignment for 80,789 GTDB genomes. [2025-05-20 11:12:54] TASK: Generating concatenated alignment for each marker. [2025-05-20 11:12:56] INFO: Completed 4 genomes in 0.04 seconds (113.21 genomes/second). [2025-05-20 11:12:57] TASK: Aligning 120 identified markers using hmmalign 3.4 (Aug 2023). [2025-05-20 11:13:00] INFO: Completed 120 markers in 1.45 seconds (82.61 markers/second). [2025-05-20 11:13:01] TASK: Masking columns of bacterial multiple sequence alignment using canonical mask. [2025-05-20 11:15:22] INFO: Completed 80,793 sequences in 2.36 minutes (34,274.14 sequences/minute). [2025-05-20 11:15:22] INFO: Masked bacterial alignment from 41,084 to 5,035 AAs. [2025-05-20 11:15:22] INFO: 0 bacterial user genomes have amino acids in <10.0% of columns in filtered MSA. [2025-05-20 11:15:22] INFO: Creating concatenated alignment for 80,793 bacterial GTDB and user genomes. [2025-05-20 11:15:49] INFO: Creating concatenated alignment for 4 bacterial user genomes. [2025-05-20 11:15:49] INFO: Done. [2025-05-20 11:15:50] TASK: Placing 4 bacterial genomes into backbone reference tree with pplacer using 32 CPUs (be patient). [2025-05-20 11:15:50] INFO: pplacer version: v1.1.alpha19-0-g807f6f3 [2025-05-20 11:18:29] INFO: Calculating RED values based on reference tree. [2025-05-20 11:18:29] INFO: 4 out of 4 have an class assignments. Those genomes will be reclassified. [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). [2025-05-20 11:27:00] INFO: Calculating RED values based on reference tree. [2025-05-20 11:27:03] TASK: Traversing tree to determine classification method. [2025-05-20 11:27:03] INFO: Completed 3 genomes in 0.01 seconds (528.27 genomes/second). [2025-05-20 11:27:03] TASK: Calculating average nucleotide identity using FastANI (v1.32). [2025-05-20 11:27:17] INFO: Completed 380 comparisons in 13.43 seconds (28.29 comparisons/second). [2025-05-20 11:27:17] INFO: 3 genome(s) have been classified using FastANI and pplacer. [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). [2025-05-20 11:33:00] INFO: Calculating RED values based on reference tree. [2025-05-20 11:33:03] TASK: Traversing tree to determine classification method. [2025-05-20 11:33:03] INFO: Completed 1 genome in 0.00 seconds (1,061.58 genomes/second). [2025-05-20 11:33:03] TASK: Calculating average nucleotide identity using FastANI (v1.32). [2025-05-20 11:33:06] INFO: Completed 122 comparisons in 2.93 seconds (41.69 comparisons/second). [2025-05-20 11:33:06] INFO: 1 genome(s) have been classified using FastANI and pplacer. [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. [2025-05-20 11:33:06] INFO: Done. [2025-05-20 11:33:06] INFO: Removing intermediate files. [2025-05-20 11:33:06] INFO: Intermediate files removed. [2025-05-20 11:33:06] INFO: Done.