Error in rule virtual_digest

[MichelMoser]

Hi,

I run into an error in the virtual_digest rule.

Looks like Bio.Alphabet was dropped after biopython 1.78 but required by the rule.

Could you provide a fix for it?

Error in rule virtual_digest:
    jobid: 107
    output: /net/cn-1/mnt/SCRATCH/michelmo/Projects/Ssalmo/PORE_C/resultsAltoAll/virtual_digest/DpnII_altoAll.vd.catalog.yaml, /net/cn-1/mnt/SCRATCH/michelmo/Projects/Ssalmo/PORE_C/resultsAltoAll/virtual_digest/DpnII_altoAll.vd.fragments.parquet, /net/cn-1/mnt/SCRATCH/michelmo/Projects/Ssalmo/PORE_C/resultsAltoAll/virtual_digest/DpnII_altoAll.vd.digest_stats.csv
    log: /net/cn-1/mnt/SCRATCH/michelmo/Projects/Ssalmo/PORE_C/resultsAltoAll/virtual_digest/DpnII_altoAll.vd.catalog.yaml.log (check log file(s) for error message)
    conda-env: /net/fs-1/home01/michelmo/tools/Pore-C-Snakemake/.snakemake/conda/5b6cb3e2
    shell:
        pore_c --dask-scheduler-port 0 --dask-num-workers 10 refgenome virtual-digest /net/cn-1/mnt/SCRATCH/michelmo/Projects/Ssalmo/PORE_C/resultsAltoAll/refgenome/altoAll.rg.fa DpnII /net/cn-1/mnt/SCRATCH/michelmo/Projects/Ssalmo/PORE_C/resultsAltoAll/virtual_digest/DpnII_altoAll.vd -n 10 2> /net/cn-1/mnt/SCRATCH/michelmo/Projects/Ssalmo/PORE_C/resultsAltoAll/virtual_digest/DpnII_altoAll.vd.catalog.yaml.log
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Thu Dec  2 14:15:43 2021]
Finished job 125.
3 of 137 steps (2%) done
[Thu Dec  2 14:15:45 2021]
Finished job 151.
4 of 137 steps (3%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Inspection of the log file shows:

File "/mnt/users/michelmo/.local/lib/python3.8/site-packages/Bio/Alphabet/__init__.py", line 20, in <module>
    raise ImportError(
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.

Thank you,
Michel

[vmurigneu]

Hello, I encountered a similar issue when using the Pore-C-Snakemake pipeline within a conda environment, can you help

Thank you
Valentine