Gtdbtk - gtdb to ncbi


Can I use kbase for gtdb-tk classification and then use the output files from that to run gtdb to script?

The directory layout provided by Kbase isn’t what the script expects. You can fix things by moving all the data files in the root directory into ./runtime_output/classify, i.e. cp * ./runtime_output/classify, and then running the script from the root directory:

> --gtdbtk_output_dir runtime_output --output_file ncbi_translation.tsv --ar53_metadata_file ar53_metadata_r220.tsv.gz --bac120_metadata_file bac120_metadata_r220.tsv.gz