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Created by Michal Zeman@valzip

Test workflow and common run fails at RGI step at biopython

Hi! I was testing your software and I wasn't able to pass the test workflow (same problem is in normal workflow).

Data were single WGS genome in separate contigs.

Is it problem of my dependencies or some typo in the code?

Tested system:

Linux Mint 19.3 Tricia based on Ubuntu 18.04 bionic

conda 4.10.1

python 3.8.3.final.0

although when I have conda environment active

python version is 3.6.4

and biopython 1.78

Error in rule run_RGI:
    jobid: 46
    output: /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/PathoFact_intermediate/AMR/RGI_results/Cl3778/group_1.RGI.txt
    log: /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/logs/Cl3778/group_1.RGI.log (check log file(s) for error message)
    conda-env: /home/kuskus/Software/PathoFact/.snakemake/conda/efe64355
    shell:
        rgi main --input_sequence /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/splitted/Cl3778/group_1.fasta --output_file /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/PathoFact_intermediate/AMR/RGI_results/Cl3778/group_1.RGI --input_type protein --local --clean  &> /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/logs/Cl3778/group_1.RGI.log
        (exited with non-zero exit code)

Log file contains several lines:

Traceback (most recent call last):
  File "/home/kuskus/Software/PathoFact/.snakemake/conda/efe64355/bin/rgi", line 2, in <module>
    from app.MainBase import MainBase
  File "/home/kuskus/Software/PathoFact/.snakemake/conda/efe64355/lib/python3.6/site-packages/app/MainBase.py", line 1, in <module>
    from app.settings import *
  File "/home/kuskus/Software/PathoFact/.snakemake/conda/efe64355/lib/python3.6/site-packages/app/settings.py", line 7, in <module>
    from Bio.Alphabet import generic_dna
  File "/home/kuskus/.local/lib/python3.6/site-packages/Bio/Alphabet/__init__.py", line 21, in <module>
    "Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.