CMSeq image is not working?

[nkleinbo]

When calling polymut.py in the CMSeq image, the following error occurs. Input files are valid gff and bam/bai files.

However, the image is only used in the wCMSeqWorkflowFile workflow, which seems not to be used currently?

Traceback (most recent call last):
  File "/usr/local/bin/polymut.py", line 11, in <module>
    load_entry_point('CMSeq==1.0.0', 'console_scripts', 'polymut.py')()
  File "/usr/local/bin/cmseq/polymut.py", line 36, in polymut_from_file
    dominanceArray, mutationStats = i.easy_polymorphism_rate(minqual=args.minqual,mincov=args.mincov,dominant_frq_thrsh=args.dominant_frq_thrsh)
  File "/usr/local/bin/cmseq/cmseq.py", line 366, in easy_polymorphism_rate
    from Bio.Alphabet import IUPAC
  File "/usr/local/lib/python3.6/dist-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.