Generate Ribosomal Metadata

Generate Ribosomal Metadata:

Identifies, extracts, and taxonomically classifies 16S and 23S rRNA genes in genomes against SILVA

• check if a new version of SILVA has been released. If so, download this and update the rna_silva.py script to point to the new SILVA data and to store results in a new directory (i.e., currently rna_silva_132).
• see Update Silva
• need to run for 16S, 23S, and 5S rRNA genes

Current silva version: 138.2

module load blast (optional)
gtdb_migration_tk rna_silva -v <current_silva#> -r ssu -g /srv/db/gtdb/genomes/ncbi/release<release#>/genome_dirs.tsv -c 40 -l logs/rna_silva_<current_silva#>_ssu.log --rerun

Identifies, extracts, and taxonomically classifies 16S rRNA genes in genomes against the Living Tree Project (LTP)

• check if a new version of LTP has been released. If so, download this and update the rna_ltp.py script to point to the new LTP data and to store results in a new directory (i.e., currently rna_ltp_132).
• need to run for 16S

Current LTP version: 08_2023
Current SSU version: 138.2

gtdb_migration_tk rna_ltp -g /srv/db/gtdb/genomes/ncbi/release<release#>/refseq/genome_dirs.tsv --ltp_version 132 --ssu_version 138.1 -c 30 --all
gtdb_migration_tk rna_ltp -g /srv/db/gtdb/genomes/ncbi/release<release#>/genbank/genome_dirs.tsv --ltp_version 132 --ssu_version 138.1 -c 30 --all