NameError: free variable 'mask' referenced before assignment in enclosing scope

[kstagaman]

checkm was working totally fine for me just a few days ago, but now even running the checkm test gives me this following error:

checkm test ~/checkm_test_results
[2024-01-31 17:56:43] INFO: CheckM v1.2.2
[2024-01-31 17:56:43] INFO: checkm test /home/checkm_test_results
[2024-01-31 17:56:43] INFO: CheckM data: /home/checkm_databases
[2024-01-31 17:56:43] INFO: [CheckM - Test] Processing E.coli K12-W3310 to verify operation of CheckM.
[2024-01-31 17:56:43] INFO: [Step 1]: Verifying tree command.
[2024-01-31 17:56:43] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2024-01-31 17:56:43] INFO: Identifying marker genes in 1 bins with 1 threads:
    Finished processing 1 of 1 (100.00%) bins.
[2024-01-31 17:56:55] INFO: Saving HMM info to file.
[2024-01-31 17:56:55] INFO: Calculating genome statistics for 1 bins with 1 threads:
    Finished processing 1 of 1 (100.00%) bins.
[2024-01-31 17:56:55] INFO: Extracting marker genes to align.
[2024-01-31 17:56:55] INFO: Parsing HMM hits to marker genes:
    Finished parsing hits for 1 of 1 (100.00%) bins.
[2024-01-31 17:56:55] INFO: Extracting 43 HMMs with 1 threads:
    Finished extracting 43 of 43 (100.00%) HMMs.
[2024-01-31 17:56:56] INFO: Aligning 43 marker genes with 1 threads:
Process Process-8:ing 0 of 43 (0.00%) marker genes.
Traceback (most recent call last):
  File "/_admin/build/bld/python/ntjcyzuaylge/lib/python3.10/multiprocessing/process.py", line
 314, in _bootstrap
    self.run()
  File "/_admin/build/bld/python/ntjcyzuaylge/lib/python3.10/multiprocessing/process.py", line
 108, in run
    self._target(*self._args, **self._kwargs)
  File "/home/.local/lib/python3.10/site-packages/checkm/hmmerAligner.py", line 272, in _alignMarkerParallel
    self._alignMarker(markerId, markerSeqs[markerId], markerStats[markerId], bReportHitStats, alignOutputDir, hmmModelFi
les[markerId], bKeepUnmaskedAlign)
  File "/home/.local/lib/python3.10/site-packages/checkm/hmmerAligner.py", line 297, in _alignMarker
    self._maskAlignment(alignSeqFile, makedSeqFile)
  File "/home/.local/lib/python3.10/site-packages/checkm/hmmerAligner.py", line 356, in _maskAlignment
    maskedSeq = ''.join([seq[i] for i in range(0, len(seq)) if mask[i] == 'x'])
  File "/home/.local/lib/python3.10/site-packages/checkm/hmmerAligner.py", line 356, in <listcomp>
    maskedSeq = ''.join([seq[i] for i in range(0, len(seq)) if mask[i] == 'x'])
NameError: free variable 'mask' referenced before assignment in enclosing scope

[donovan-h-parks]

I am unable to reproduce this error. Perhaps your system has insufficient memory to run CheckM: https://github.com/Ecogenomics/CheckM/wiki/Installation#system-requirements.