Checkm2 metadata

Add CheckM v2 information

To update Checkm2 information for genomes in GTDB, We only run genomes that have been processed in the Checkm v1 step. We then use the ncbi_assembly_metadata.tsv file generated previously to select the tranlation table of interest.

gtdb_migration_tk prepare_checkm2 --checkm_summary_genbank /srv/db/gtdb/metadata/release<#>/checkm/genbank/checkm.profiles.tsv --checkm_summary_refseq /srv/db/gtdb/metadata/release<#>/checkm/refseq/checkm.profiles.tsv -g /srv/db/gtdb/genomes/ncbi/release<#>/genome_dirs.tsv -o /srv/db/gtdb/metadata/release<#>/checkm2/ -l logs/prepare_checkm2.log -m /srv/db/gtdb/metadata/release<#>/metadata_tables/ncbi_assembly_metadata.tsv

This creates a checkm_cmds.lst file in /srv/db/gtdb/metadata/release<#>/checkm2/

Because checkm1 is already installed in the gtdb-migration-tk env, I havent installed Checkm2 yet.
so for now the pipeline is:

conda activate checkm2_1.0.2
sh checkm_cmds.lst

Once all the commands are run, we join the results to 2 tables ( one with all checkm2 information, one with only fields required for the database):

gtdb_migration_tk join_checkm2 --checkm2_output_dir checkm2 -o . -l join_checkm2.log
gtdb_migration_tk update_metadata_db --hostname watson.ace.uq.edu.au -u gtdb -p ecogenomicsgtdb -d gtdb_pierre_r226 --metadata_table checkm2.quality_report_for_database.tsv --metadata_table_desc /srv/db//gtdb/metadata/release220/checkm2/metadata_checkm2_desc.tsv --genome_list /srv/db/gtdb/metadata//release226/export_metadata/metadata_r226_before_checkm.tsv -l update_checkm2_r226.log