GTDB R214

Use of LTP 2022_01 Use of Pfam_lite and Tigrfam_lite

Manual NCBI Taxonomy for genomes

• GCF_000019505.1
• GCF_013342135.1
• GCF_017569205.1
• GCF_016595145.1
• GCA_934667915.1
• GCF_000347295.2

I had to reprocess pfam for genomes:

• GCA_024224895.1
• GCA_000765055.1

GTDB Taxonomy propagation log:

[2022-11-18 14:08:38] INFO: Reading GTDB taxonomy of genome in previous release:
[2022-11-18 14:08:49] INFO:   353569 of 353569 (100.0%) genomes in previous NCBI release had a GTDB taxonomy string
[2022-11-18 14:08:49] INFO:   65703 genomes were identified as representatives
[2022-11-18 14:08:49] INFO: Identifying unchanged genomes in current NCBI release:
[2022-11-18 14:09:02] INFO:   343135 (97.0%) genomes unchanged in current NCBI release
[2022-11-18 14:09:02] INFO:   10434 (3.0%) genomes absent or modified in current NCBI release
[2022-11-18 14:09:02] INFO:   64031 representatives unchanged in current GTDB release
[2022-11-18 14:09:02] INFO: Identifying genomes that have changed databases or version:
[2022-11-18 14:09:05] INFO:   3678 (1.0%) genomes moved from GenBank to RefSeq
[2022-11-18 14:09:05] INFO:   3364 (1.0%) genomes moved from RefSeq to GenBank
[2022-11-18 14:09:05] INFO:   1049 (0.3%) genomes have a new version number
[2022-11-18 14:09:05] INFO: There are 2343 genomes not present in the current release.
[2022-11-18 14:09:05] INFO: 929 of these were representatives.

[2022-11-23 14:33:05] WARNING: GCA_021829835.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 15.0%; Ar = 69.67%).
[2022-11-23 14:33:05] WARNING: GCA_021832495.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 17.5%; Ar = 59.84%).
[2022-11-23 14:33:05] WARNING: GCA_021832525.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 45.0%; Ar = 9.02%).
[2022-11-23 14:33:13] WARNING: GCA_934846365.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 94.17%; Ar = 14.75%).
[2022-11-23 14:33:15] WARNING: GCA_020850135.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 20.83%; Ar = 88.52%).
[2022-11-23 14:33:18] WARNING: GCA_021832035.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 89.17%; Ar = 11.48%).
[2022-11-23 14:33:18] WARNING: GCA_021832025.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 11.67%; Ar = 48.36%).
[2022-11-23 14:33:19] WARNING: GCA_934833245.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 97.5%; Ar = 15.57%).
[2022-11-23 14:33:21] WARNING: GCA_020062985.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 19.17%; Ar = 68.85%).
[2022-11-23 14:33:22] WARNING: GCA_023379625.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 9.17%; Ar = 42.62%).
[2022-11-23 14:33:23] WARNING: GCA_021835805.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 10.83%; Ar = 68.03%).
[2022-11-23 14:33:25] WARNING: GCA_021836825.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 81.67%; Ar = 9.02%).
[2022-11-23 14:33:25] WARNING: GCA_021832065.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 81.67%; Ar = 14.75%).
[2022-11-23 14:33:28] WARNING: GCA_021325135.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 20.83%; Ar = 95.08%).
[2022-11-23 14:33:30] WARNING: GCA_934860235.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 97.5%; Ar = 15.57%).
[2022-11-23 14:33:31] WARNING: GCA_020625105.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 22.5%; Ar = 97.54%).
[2022-11-23 14:33:31] WARNING: GCA_021832005.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 7.5%; Ar = 38.52%).
[2022-11-23 14:33:31] WARNING: GCA_020061885.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 6.67%; Ar = 28.69%).
[2022-11-23 14:33:37] WARNING: GCA_934876485.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 96.67%; Ar = 15.57%).
[2022-11-23 14:33:44] WARNING: GCA_020626585.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 23.33%; Ar = 82.79%).
[2022-11-23 14:33:44] WARNING: GCA_021829365.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 12.5%; Ar = 50.82%).
[2022-11-23 14:33:44] WARNING: GCA_020625985.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 28.33%; Ar = 99.18%).
[2022-11-23 14:33:44] WARNING: GCA_024231195.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 28.33%; Ar = 86.07%).
[2022-11-23 14:33:45] WARNING: GCA_020056285.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 11.67%; Ar = 58.2%).
[2022-11-23 14:33:46] WARNING: GCA_022424145.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 10.83%; Ar = 22.13%).
[2022-11-23 14:33:50] WARNING: GCA_021832825.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 12.5%; Ar = 53.28%).
[2022-11-23 14:33:52] WARNING: GCA_934869045.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 88.33%; Ar = 15.57%).
[2022-11-23 14:33:54] WARNING: GCA_020055025.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 55.0%; Ar = 9.84%).
[2022-11-23 14:33:57] WARNING: GCA_020626965.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 20.83%; Ar = 83.61%).
[2022-11-23 14:33:57] WARNING: GCA_021836645.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 13.33%; Ar = 66.39%).
[2022-11-23 14:33:58] WARNING: GCA_024206195.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 21.67%; Ar = 83.61%).
[2022-11-23 14:33:58] WARNING: GCA_021836665.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 49.17%; Ar = 10.66%).
[2022-11-23 14:34:01] WARNING: GCA_021829385.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 59.17%; Ar = 6.56%).
[2022-11-23 14:34:04] WARNING: GCA_023136575.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 55.0%; Ar = 40.16%).
[2022-11-23 14:34:09] WARNING: GCA_021829855.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 53.33%; Ar = 9.02%).
[2022-11-23 14:34:10] WARNING: GCA_020627045.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 18.33%; Ar = 65.57%).
[2022-11-23 14:34:11] WARNING: GCA_021323995.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 17.5%; Ar = 90.16%).
[2022-11-23 14:34:11] WARNING: GCA_934876005.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 92.5%; Ar = 11.48%).
[2022-11-23 14:34:16] WARNING: GCA_020850325.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 94.17%; Ar = 18.03%).
[2022-11-23 14:34:23] WARNING: GCA_021836785.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 11.67%; Ar = 54.92%).
[2022-11-23 14:34:23] WARNING: GCA_934883135.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 97.5%; Ar = 15.57%).
[2022-11-23 14:34:23] WARNING: GCA_020627075.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 15.83%; Ar = 71.31%).
[2022-11-23 14:34:24] WARNING: GCA_019428815.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 17.5%; Ar = 60.66%).
[2022-11-23 14:34:24] WARNING: GCA_023475455.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 78.33%; Ar = 17.21%).
[2022-11-23 14:34:31] WARNING: GCA_021835745.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 45.83%; Ar = 8.2%).
[2022-11-23 14:34:36] WARNING: GCA_020626885.1: NCBI (d__Bacteria) and GTDB (d__Archaea) domains disagree in domain report (Bac = 23.33%; Ar = 90.98%).
[2022-11-23 14:34:36] WARNING: GCA_023143585.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 60.0%; Ar = 36.89%).
[2022-11-23 14:34:44] WARNING: GCA_934859225.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 85.83%; Ar = 14.75%).
[2022-11-23 14:34:47] WARNING: GCA_021836545.1: NCBI (d__Archaea) and GTDB (d__Bacteria) domains disagree in domain report (Bac = 66.67%; Ar = 11.48%).