troubleshooting first run errors

[slschnorr]

Hello,

I'm trying bigscape cluster for the first time. It is a centrally installed conda env on our cluster. I made a simple call just to get started:

bigscape cluster -i isolates/gbks/ -o bigscape/isolates/ -p resources/HMMs/Pfam-A.hmm --mix

and it resulted in the error:

AttributeError: 'NoneType' object has no attribute 'decode'

Seems to involve generating the HMM profile index from the HMM database I specified. I did add a few extra custom HMMs, so these miss an ACC entry and DESC entry. Could that be the problem?

Traceback output here:

Traceback (most recent call last):
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/bin/bigscape", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/big_scape/__main__.py", l                                        ine 51, in main
    cli()
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/click/core.py", line 1157                                        , in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/click/core.py", line 1078                                        , in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/click/core.py", line 1688                                        , in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/click/core.py", line 1434                                        , in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/click/core.py", line 783,                                         in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/click/decorators.py", lin                                        e 33, in new_func
    return f(get_current_context(), *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/big_scape/cli/cluster_cli                                        .py", line 159, in cluster
    run_bigscape(ctx.obj)
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/big_scape/run_bigscape.py                                        ", line 164, in run_bigscape
    HMMer.init(run["pfam_path"])
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/big_scape/hmm/hmmer.py",                                         line 109, in init
    HMMer.profile_index = gen_profile_index(HMMer.profiles)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lisc/app/conda/miniforge3/envs/bigscape-2.0.0-beta.6/lib/python3.11/site-packages/big_scape/hmm/hmmer.py",                                         line 554, in gen_profile_index
    index[profile.accession.decode()[:7]] = idx
          ^^^^^^^^^^^^^^^^^^^^^^^^

[slschnorr]

Nevermind I will answer my own question - yes the missing ACC and DESC of my custom hmm profiles that were merged with the database were the problem.