Seqcode parsing - Ecogenomics/GTDBNCBI GitHub Wiki

Pull information from Seqcode, generates a metadata table and push this information to the Database

Create folder in metadata

mkdir metadata/seqcode
cd metadata/seqcode

Pull the data for the website

gtdb_migration_tk generate_seqcode_table -o . -g /srv/db/gtdb/genomes/ncbi/release214/genome_dirs.tsv

Push the metadata table to GTDB database

gtdb_migration_tk update_metadata_db --hostname watson.ace.uq.edu.au -u gtdb -p <password> -d gtdb_pierre_r220 --metadata_table seqcode_table.tsv --metadata_table_desc /srv/db/gtdb/metadata/metadata_seqcode.desc.tsv -l /srv/db/gtdb/genomes/ncbi/release220/logs/update_metadata_db_seqcode.tsv

Update the type_designation columns

Once Seqcode and NCBI and LPSN data are in the database, we need to update the columns gtdb_type_designation_ncbi_taxa_sources and gtdb_type_designation_ncbi_taxa to reflect all the information we have from these 3 sources.

gtdb_migration_tk update_type_designation --hostname watson.ace.uq.edu.au -u gtdb -p <password> -d gtdb_pierre_r220