A error when assess MAGs #404
Description
[2024-11-03 13:25:38] INFO: CheckM v1.2.2
[2024-11-03 13:25:38] INFO: checkm lineage_wf -x fa binsA binsA.checkm -t 48 --tmpdir binsA.tmp --pplacer_threads 40
[2024-11-03 13:25:38] INFO: CheckM data: /mnt/z/lcb/miniconda3/checkm_data
[2024-11-03 13:25:38] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2024-11-03 13:25:41] INFO: Identifying marker genes in 176 bins with 48 threads:
Finished processing 176 of 176 (100.00%) bins.
[2024-11-03 13:27:50] INFO: Saving HMM info to file.
[2024-11-03 13:27:50] INFO: Calculating genome statistics for 176 bins with 48 threads:
Finished processing 176 of 176 (100.00%) bins.
[2024-11-03 13:27:51] INFO: Extracting marker genes to align.
[2024-11-03 13:27:51] INFO: Parsing HMM hits to marker genes:
Finished parsing hits for 176 of 176 (100.00%) bins.
[2024-11-03 13:27:57] INFO: Extracting 43 HMMs with 48 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
[2024-11-03 13:27:57] INFO: Aligning 43 marker genes with 48 threads:
Finished aligning 43 of 43 (100.00%) marker genes.
[2024-11-03 13:27:57] INFO: Reading marker alignment files.
[2024-11-03 13:27:57] INFO: Concatenating alignments.
[2024-11-03 13:27:57] INFO: Placing 176 bins into the genome tree with pplacer (be patient).
[2024-11-03 13:32:16] INFO: { Current stage: 0:06:37.230 || Total: 0:06:37.230 }
[2024-11-03 13:32:16] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets.
[2024-11-03 13:32:16] INFO: Reading HMM info from file.
Unexpected error: <class 'ValueError'>
Traceback (most recent call last):
File "/mnt/z/lcb/miniconda3/bin/checkm", line 856, in
checkmParser.parseOptions(args)
File "/mnt/z/lcb/miniconda3/lib/python3.12/site-packages/checkm/main.py", line 980, in parseOptions
self.lineageSet(options)
File "/mnt/z/lcb/miniconda3/lib/python3.12/site-packages/checkm/main.py", line 249, in lineageSet
resultsParser.analyseResults(options.tree_dir,
File "/mnt/z/lcb/miniconda3/lib/python3.12/site-packages/checkm/resultsParser.py", line 63, in analyseResults
binStats = self.parseBinStats(outDir, binStatsFile)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/z/lcb/miniconda3/lib/python3.12/site-packages/checkm/resultsParser.py", line 155, in parseBinStats
binStats[lineSplit[0]] = ast.literal_eval(lineSplit[1])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/z/lcb/miniconda3/lib/python3.12/ast.py", line 112, in literal_eval
return _convert(node_or_string)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/z/lcb/miniconda3/lib/python3.12/ast.py", line 101, in _convert
return dict(zip(map(_convert, node.keys),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/z/lcb/miniconda3/lib/python3.12/ast.py", line 111, in _convert
return _convert_signed_num(node)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/z/lcb/miniconda3/lib/python3.12/ast.py", line 85, in _convert_signed_num
return _convert_num(node)
^^^^^^^^^^^^^^^^^^
File "/mnt/z/lcb/miniconda3/lib/python3.12/ast.py", line 76, in _convert_num
_raise_malformed_node(node)
File "/mnt/z/lcb/miniconda3/lib/python3.12/ast.py", line 73, in _raise_malformed_node
raise ValueError(msg + f': {node!r}')
ValueError: malformed node or string on line 1: <ast.Call object at 0x71f3a61a1e90>