[2023-10-21 23:59:10] INFO: GTDB-Tk v2.3.0
[2023-10-21 23:59:10] INFO: gtdbtk classify_wf --batchfile gems_genome_paths.tsv --out_dir gtdbtk_r214 --mash_db gtdb_r214.msh --mash_max_distance 0.1 -x gz --cpus 86 --pplacer_cpus 64
[2023-10-21 23:59:10] INFO: Using GTDB-Tk reference data version r214: /srv/db/gtdbtk/official/release214
[2023-10-21 23:59:15] INFO: Loading reference genomes.
[2023-10-21 23:59:16] INFO: Using Mash version 2.3
[2023-10-21 23:59:16] INFO: Creating Mash sketch file: gtdbtk_r214/classify/ani_screen/intermediate_results/mash/gtdbtk.user_query_sketch.msh
[2023-10-22 00:01:11] INFO: Completed 52,515 genomes in 1.93 minutes (27,264.58 genomes/minute).
[2023-10-22 00:01:11] INFO: Creating Mash sketch file: gtdb_r214.msh
[2023-10-22 00:04:39] INFO: Completed 85,205 genomes in 3.47 minutes (24,587.59 genomes/minute).
[2023-10-22 00:04:39] INFO: Calculating Mash distances.
[2023-10-22 01:18:49] INFO: Calculating ANI with FastANI v1.32.
[2023-10-22 02:33:10] INFO: Completed 417,036 comparisons in 74.15 minutes (5,624.42 comparisons/minute).
[2023-10-22 03:02:40] INFO: Summary of results saved to: gtdbtk_r214/classify/ani_screen/gtdbtk.ar53.ani_summary.tsv
[2023-10-22 03:02:40] INFO: Summary of results saved to: gtdbtk_r214/classify/ani_screen/gtdbtk.bac120.ani_summary.tsv
[2023-10-22 03:02:40] INFO: 35552 genome(s) have been classified using the ANI pre-screening step.
[2023-10-22 03:02:40] INFO: Done.
[2023-10-22 03:03:00] INFO: Identifying markers in 16,963 genomes with 86 threads.
[2023-10-22 03:03:01] TASK: Running Prodigal V2.6.3 to identify genes.
[2023-10-22 03:53:48] INFO: Completed 16,963 genomes in 50.80 minutes (333.95 genomes/minute).
[2023-10-22 03:58:23] TASK: Identifying TIGRFAM protein families.
[2023-10-22 04:18:37] INFO: Completed 16,963 genomes in 20.25 minutes (837.79 genomes/minute).
[2023-10-22 04:18:37] TASK: Identifying Pfam protein families.
[2023-10-22 04:20:11] INFO: Completed 16,963 genomes in 1.56 minutes (10,879.29 genomes/minute).
[2023-10-22 04:20:11] INFO: Annotations done using HMMER 3.3.2 (Nov 2020).
[2023-10-22 04:20:11] TASK: Summarising identified marker genes.
[2023-10-22 04:26:31] INFO: Completed 16,963 genomes in 6.33 minutes (2,678.09 genomes/minute).
[2023-10-22 04:26:32] INFO: Done.
[2023-10-22 04:26:36] INFO: Aligning markers in 16,963 genomes with 86 CPUs.
[2023-10-22 04:26:36] INFO: Processing 15,612 genomes identified as bacterial.
[2023-10-22 04:26:43] INFO: Read concatenated alignment for 80,789 GTDB genomes.
[2023-10-22 04:26:43] TASK: Generating concatenated alignment for each marker.
[2023-10-22 04:26:59] INFO: Completed 15,612 genomes in 10.15 seconds (1,538.06 genomes/second).
[2023-10-22 04:27:02] TASK: Aligning 120 identified markers using hmmalign 3.3.2 (Nov 2020).
[2023-10-22 04:31:18] INFO: Completed 120 markers in 4.15 minutes (28.95 markers/minute).
[2023-10-22 04:31:22] TASK: Masking columns of bacterial multiple sequence alignment using canonical mask.
[2023-10-22 04:33:56] INFO: Completed 96,401 sequences in 2.57 minutes (37,486.30 sequences/minute).
[2023-10-22 04:33:56] INFO: Masked bacterial alignment from 41,084 to 5,035 AAs.
[2023-10-22 04:33:56] INFO: 0 bacterial user genomes have amino acids in <10.0% of columns in filtered MSA.
[2023-10-22 04:33:56] INFO: Creating concatenated alignment for 96,401 bacterial GTDB and user genomes.
[2023-10-22 04:34:26] INFO: Creating concatenated alignment for 15,612 bacterial user genomes.
[2023-10-22 04:34:31] INFO: Processing 1,351 genomes identified as archaeal.
[2023-10-22 04:34:31] INFO: Read concatenated alignment for 4,416 GTDB genomes.
[2023-10-22 04:34:31] TASK: Generating concatenated alignment for each marker.
[2023-10-22 04:34:36] INFO: Completed 1,351 genomes in 0.96 seconds (1,405.72 genomes/second).
[2023-10-22 04:34:36] TASK: Aligning 53 identified markers using hmmalign 3.3.2 (Nov 2020).
[2023-10-22 04:34:49] INFO: Completed 53 markers in 8.03 seconds (6.60 markers/second).
[2023-10-22 04:34:49] TASK: Masking columns of archaeal multiple sequence alignment using canonical mask.
[2023-10-22 04:34:55] INFO: Completed 5,767 sequences in 5.58 seconds (1,034.32 sequences/second).
[2023-10-22 04:34:55] INFO: Masked archaeal alignment from 13,540 to 10,135 AAs.
[2023-10-22 04:34:55] INFO: 0 archaeal user genomes have amino acids in <10.0% of columns in filtered MSA.
[2023-10-22 04:34:55] INFO: Creating concatenated alignment for 5,767 archaeal GTDB and user genomes.
[2023-10-22 04:34:58] INFO: Creating concatenated alignment for 1,351 archaeal user genomes.
[2023-10-22 04:34:58] INFO: Done.
[2023-10-22 04:35:15] TASK: Placing 1,351 archaeal genomes into reference tree with pplacer using 64 CPUs (be patient).
[2023-10-22 04:35:15] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
[2023-10-22 04:45:00] INFO: Calculating RED values based on reference tree.
[2023-10-22 04:45:01] TASK: Traversing tree to determine classification method.
[2023-10-22 04:45:01] INFO: Completed 1,351 genomes in 0.15 seconds (9,062.20 genomes/second).
[2023-10-22 04:45:11] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 04:47:12] INFO: Completed 18,740 comparisons in 2.02 minutes (9,294.61 comparisons/minute).
[2023-10-22 04:48:46] INFO: 2 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 04:48:46] WARNING: 3 of 3047 genomes have a warning (see summary file).
[2023-10-22 04:48:55] TASK: Placing 15,612 bacterial genomes into backbone reference tree with pplacer using 64 CPUs (be patient).
[2023-10-22 04:48:55] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
[2023-10-22 05:18:12] INFO: Calculating RED values based on reference tree.
[2023-10-22 05:19:28] INFO: 15603 out of 15612 have an class assignments. Those genomes will be reclassified.
[2023-10-22 05:19:28] TASK: Placing 3,710 bacterial genomes into class-level reference tree 7 (1/8) with pplacer using 64 CPUs (be patient).
[2023-10-22 05:36:57] INFO: Calculating RED values based on reference tree.
[2023-10-22 05:37:00] TASK: Traversing tree to determine classification method.
[2023-10-22 05:37:02] INFO: Completed 3,710 genomes in 2.07 seconds (1,793.50 genomes/second).
[2023-10-22 05:37:14] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 05:43:18] INFO: Completed 51,548 comparisons in 6.05 minutes (8,521.55 comparisons/minute).
[2023-10-22 05:47:51] INFO: 1 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 05:47:53] TASK: Placing 2,967 bacterial genomes into class-level reference tree 3 (2/8) with pplacer using 64 CPUs (be patient).
[2023-10-22 06:08:26] INFO: Calculating RED values based on reference tree.
[2023-10-22 06:08:29] TASK: Traversing tree to determine classification method.
[2023-10-22 06:08:32] INFO: Completed 2,967 genomes in 3.17 seconds (936.05 genomes/second).
[2023-10-22 06:08:54] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 06:34:19] INFO: Completed 133,804 comparisons in 25.35 minutes (5,278.63 comparisons/minute).
[2023-10-22 06:37:49] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 06:37:51] TASK: Placing 1,965 bacterial genomes into class-level reference tree 1 (3/8) with pplacer using 64 CPUs (be patient).
[2023-10-22 06:52:50] INFO: Calculating RED values based on reference tree.
[2023-10-22 06:52:53] TASK: Traversing tree to determine classification method.
[2023-10-22 06:52:55] INFO: Completed 1,965 genomes in 2.04 seconds (962.10 genomes/second).
[2023-10-22 06:53:14] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 07:11:37] INFO: Completed 83,528 comparisons in 18.35 minutes (4,552.01 comparisons/minute).
[2023-10-22 07:14:12] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 07:14:13] TASK: Placing 1,747 bacterial genomes into class-level reference tree 6 (4/8) with pplacer using 64 CPUs (be patient).
[2023-10-22 07:27:00] INFO: Calculating RED values based on reference tree.
[2023-10-22 07:27:03] TASK: Traversing tree to determine classification method.
[2023-10-22 07:27:04] INFO: Completed 1,747 genomes in 0.96 seconds (1,819.33 genomes/second).
[2023-10-22 07:27:19] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 07:32:30] INFO: Completed 25,308 comparisons in 5.17 minutes (4,894.73 comparisons/minute).
[2023-10-22 07:34:19] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 07:34:20] TASK: Placing 1,513 bacterial genomes into class-level reference tree 4 (5/8) with pplacer using 64 CPUs (be patient).
[2023-10-22 07:46:31] INFO: Calculating RED values based on reference tree.
[2023-10-22 07:46:34] TASK: Traversing tree to determine classification method.
[2023-10-22 07:46:35] INFO: Completed 1,513 genomes in 1.15 seconds (1,317.85 genomes/second).
[2023-10-22 07:46:44] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 08:01:17] INFO: Completed 64,754 comparisons in 14.51 minutes (4,462.03 comparisons/minute).
[2023-10-22 08:03:07] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 08:03:08] TASK: Placing 1,491 bacterial genomes into class-level reference tree 8 (6/8) with pplacer using 64 CPUs (be patient).
[2023-10-22 08:08:44] INFO: Calculating RED values based on reference tree.
[2023-10-22 08:08:45] TASK: Traversing tree to determine classification method.
[2023-10-22 08:08:46] INFO: Completed 1,491 genomes in 0.23 seconds (6,515.10 genomes/second).
[2023-10-22 08:08:53] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 08:13:25] INFO: Completed 22,010 comparisons in 4.51 minutes (4,878.10 comparisons/minute).
[2023-10-22 08:15:14] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 08:15:14] TASK: Placing 1,317 bacterial genomes into class-level reference tree 5 (7/8) with pplacer using 64 CPUs (be patient).
[2023-10-22 08:24:35] INFO: Calculating RED values based on reference tree.
[2023-10-22 08:24:37] TASK: Traversing tree to determine classification method.
[2023-10-22 08:24:39] INFO: Completed 1,317 genomes in 1.34 seconds (979.23 genomes/second).
[2023-10-22 08:24:47] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 08:37:03] INFO: Completed 79,424 comparisons in 12.23 minutes (6,495.88 comparisons/minute).
[2023-10-22 08:38:40] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 08:38:41] TASK: Placing 893 bacterial genomes into class-level reference tree 2 (8/8) with pplacer using 64 CPUs (be patient).
[2023-10-22 08:50:24] INFO: Calculating RED values based on reference tree.
[2023-10-22 08:50:27] TASK: Traversing tree to determine classification method.
[2023-10-22 08:50:27] INFO: Completed 893 genomes in 0.53 seconds (1,697.05 genomes/second).
[2023-10-22 08:50:36] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2023-10-22 08:53:57] INFO: Completed 21,210 comparisons in 3.34 minutes (6,357.37 comparisons/minute).
[2023-10-22 08:54:51] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2023-10-22 08:54:51] WARNING: 90 of 49468 genomes have a warning (see summary file).
[2023-10-22 08:54:56] 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.
[2023-10-22 08:54:56] INFO: Done.
[2023-10-22 08:54:56] INFO: Removing intermediate files.
[2023-10-22 09:05:12] INFO: Intermediate files removed.
[2023-10-22 09:05:12] INFO: Done.