Hi
Can I use kbase for gtdb-tk classification and then use the output files from that to run gtdb to ncbi_majority.vote.py script?
The directory layout provided by Kbase isn’t what the gtdb_to_ncbi_majority_vote.py 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:
> gtdb_to_ncbi_majority_vote.py --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