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IDOPs with -t option throws errors #2

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maxnest opened this issue Apr 21, 2023 · 0 comments
Open

IDOPs with -t option throws errors #2

maxnest opened this issue Apr 21, 2023 · 0 comments

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@maxnest
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maxnest commented Apr 21, 2023

Dear colleagues,
Thank you for a useful program. However, I had a few problems running the program with -t arguments:

  1. I installed the program according to the instructions: conda create -n idops -c gamb-go -c bioconda idops
  2. Further, when starting the program (idops --verbosity --output ~/idops_test -t Bt_19_43_splitted_prokka.faa) python gives an error: AttributeError: 'MultipleSeqAlignment' object has no attribute '_alphabet'
  3. We managed to solve the problem by installing an older version of biopython in the idops environment: python -m pip install biopython==1.72
  4. After starting, the program again gives an error, but this time it says that it cannot find the required model in the directory:
    File "/home/maksim/anaconda3/envs/idops/lib/python3.8/subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
    subprocess.CalledProcessError: Command '['hmmalign', '-o', '/tmp/tmpsdxrh2ck', '/home/maksim/anaconda3/envs/idops/lib/python3.8/site-packages/idops/ressources/hmms /CryM6.hmm', '-']' returned non-zero exit status 1.
  5. Indeed, the number of models in the /ressources/hmms/ directory differs in the conda version (linux-64/idops-0.2.2-py38_171616.tar.bz2) from the version linux-64/idops-0.2.2-py38_0.tar version .bz2. As a temporary solution, I move the models from linux-64/idops-0.2.2-py38_0.tar.bz2 to the appropriate directory
  6. Further, when starting idops, it gives the following error:
    File "/home/maksim/anaconda3/envs/idops/bin/idops", line 33, in
    sys.exit(load_entry_point('idops==0.2.2', 'console_scripts', 'idops')())
    File "/home/maksim/anaconda3/envs/idops/lib/python3.8/site-packages/idops/idops.py", line 36, in main
    make_trees(df_scan, args)
    File "/home/maksim/anaconda3/envs/idops/lib/python3.8/site-packages/idops/tree/make_trees.py", line 23, in make_trees
    aln = hmmalign_hits(model, df_group)
    File "/home/maksim/anaconda3/envs/idops/lib/python3.8/site-packages/idops/tree/make_trees.py", line 85, in hmmalign_hits
    open(os.path.join(os.path.dirname(idops.file), "resources", "seqdb",
    FileNotFoundError: [Errno 2] No such file or directory: '/home/maksim/anaconda3/envs/idops/lib/python3.8/site-packages/idops/ressources/seqdb/.faa'

Given all the difficulties that have arisen, let me ask you how I can solve them.
I would be grateful for any information.
Thank you

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