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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
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checkm was working totally fine for me just a few days ago, but now even running the checkm test gives me this following error:
The text was updated successfully, but these errors were encountered: