Error creating db

[pgcudahy]

Hello Jody, excited for the new tool. I tried installing today with mamba install -c bioconda ntm-profiler=0.1.1 but when I ran ntm-profiler update_db I got this

tb-profiler error report

• OS: linux
• Program version: 4.1.1
• Program call:

{'prefix': 'Mycobacteroides_abscessus_subsp._abscessus', 'csv': 'Mycobacteroides_abscessus.csv', 'load': True, 'watchlist': None, 'match_ref': None, 'other_annotations': None, 'custom': False, 'db_name': None, 'db_commit': None, 'db_author': None, 'db_date': None, 'func': <function create_resistance_db at 0x2b18f78213a0>}

Traceback:

  File "/gpfs/ysm/project/cohen_theodore/pgc29/conda_envs/ntmprofiler2/bin/ntm-profiler", line 460, in <module>
    args.func(args)
  File "/gpfs/ysm/project/cohen_theodore/pgc29/conda_envs/ntmprofiler2/bin/ntm-profiler", line 245, in create_resistance_db
    tbp.create_db(args)
  File "/gpfs/ysm/project/cohen_theodore/pgc29/conda_envs/ntmprofiler2/lib/python3.9/site-packages/tbprofiler/db.py", line 506, in create_db
    if args.include_original_mutation:

Value:

'Namespace' object has no attribute 'include_original_mutation'

I tried to trace the issue in db.py but couldn't find it. Instead I tried rewinding the tb-profiler version back to when the latest release of ntm-profiler was made (mamba install -c bioconda ntm-profiler=0.1.1 tb-profiler=4.0.2) and now ntm-profiler update_db works. So some change made since then has caused the error.

Best,
Patrick

[jodyphelan]

Hi @pgcudahy ,

Thanks for testing it out! I'll check that out, there were some potential breaking changes between tb-profiler v4.0 and 4.1 so I'll check that and make sure the conda recipes are using the correct versions!

Jody

[jodyphelan]

Hi @pgcudahy, just a little update on this. In latest release of the default database I have switched to using genomes and their taxonomy labels from GTDB. This should hopefully mean better classification, although it is still possible that a genome won't be classified if it falls outside of a clade in GTDB. As a fallback, the latest release of ntm-profiler will now use mash to report the 10 closest mycobacterium sequences together with the mash proxy for average nucleotide identity to give an idea of what species it might be.