A error when assess MAGs

[liangchengbo]

[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>

[zehanna]

Hi, I get the same error, could you solve it by now? Cheers