GTDB R232

I had to manually create a md5sum.txt for GCA_0354320051 as it was missing in R226

We had to manually delete GCA_964261755.1,GCA_965643355.1 as they were not a proper Genome Assembly more like all the bins in the same file for multiple MAGS.

Calling Tigrfam: [2025-09-18 06:16:45] WARNING: Skipping /tmp/tmprgd5x2xo/GCA_046042695.1_protein.faa because it is empty [2025-09-18 06:16:45] WARNING Skipping /tmp/tmprgd5x2xo/GCA_046042695.1_protein.faa because it is empty marker_manager.py:508 [2025-09-18 06:35:27] WARNING: Skipping /tmp/tmpp234pkaq/GCA_000722035.1_protein.faa because it is empty [2025-09-18 06:35:27] WARNING Skipping /tmp/tmpp234pkaq/GCA_000722035.1_protein.faa because it is empty marker_manager.py:508 [2025-09-18 06:52:29] WARNING: Skipping /tmp/tmpa1kniyqg/GCA_000722025.1_protein.faa because it is empty [2025-09-18 06:52:29] WARNING Skipping /tmp/tmpa1kniyqg/GCA_000722025.1_protein.faa because it is empty marker_manager.py:508 [2025-09-18 08:32:04] WARNING: Skipping /tmp/tmpujr9wbxr/GCA_000722095.1_protein.faa because it is empty [2025-09-18 08:32:04] WARNING Skipping /tmp/tmpujr9wbxr/GCA_000722095.1_protein.faa because it is empty marker_manager.py:508 [2025-09-18 09:38:51] WARNING: Skipping /tmp/tmpx01dcrrr/GCA_002870245.1_protein.faa because it is empty [2025-09-18 09:38:51] WARNING Skipping /tmp/tmpx01dcrrr/GCA_002870245.1_protein.faa because it is empty marker_manager.py:508 Finished processing 33528 of 33533 (99.99%) items.

GCA_046042695.1 was removed from the process, prodigal files were empty annd Genbank flagged this as fragmented (8,000 contigs)

Adding NCBI Taxonomy manually

I had to manually had the ncbi taxonomy to 3 genomes:

GCA_001447355.1
GCF_030803925.1
GCF_900142255.1

Same species for the 3 genomes

UPDATE metadata_taxonomy SET ncbi_taxonomy='d__Bacteria;p__Bacillota;c__Bacilli;o__Bacillales;f__Alicyclobacillaceae;g__Alicyclobacillus;s__Alicyclobacillus tolerans'
WHERE id=1207321;
UPDATE metadata_taxonomy SET ncbi_taxonomy_unfiltered='d__Bacteria;x__Bacillati;p__Bacillota;c__Bacilli;o__Bacillales;f__Alicyclobacillaceae;g__Alicyclobacillus;s__Alicyclobacillus tolerans'
WHERE id=1207321;