Uncaught exception: Multiprocessing.Child_error

[zoubohao]

When I was running checkm with the following command: checkm lineage, it raised up error:

[2022-11-15 11:33:51] INFO: CheckM v1.2.1 [2022-11-15 11:33:51] INFO: checkm lineage_wf -t 25 --pplacer_threads 25 -x fasta -f ../AllData/RealDataBinningModels/MaxBin_Data/HLJ/DeepurifyTempOut/FilterOutput/family_checkm.txt --reduced_tree ../AllData/RealDataBinningModels/MaxBin_Data/HLJ/DeepurifyTempOut/FilterOutput/family_filter ../AllData/RealDataBinningModels/MaxBin_Data/HLJ/DeepurifyTempOut/FilterOutput/family_filter/checkmTempOut [2022-11-15 11:33:51] INFO: CheckM data: /home/zoubh/Softwares/checkm_database/ [2022-11-15 11:33:51] INFO: [CheckM - tree] Placing bins in reference genome tree. [2022-11-15 11:33:54] INFO: Identifying marker genes in 831 bins with 25 threads: Finished processing 831 of 831 (100.00%) bins. [2022-11-15 11:34:06] INFO: Saving HMM info to file. [2022-11-15 11:34:06] INFO: Calculating genome statistics for 831 bins with 25 threads: Finished processing 831 of 831 (100.00%) bins. [2022-11-15 11:34:08] INFO: Extracting marker genes to align. [2022-11-15 11:34:08] INFO: Parsing HMM hits to marker genes: Finished parsing hits for 831 of 831 (100.00%) bins. [2022-11-15 11:34:34] INFO: Extracting 43 HMMs with 25 threads: Finished extracting 43 of 43 (100.00%) HMMs. [2022-11-15 11:34:34] INFO: Aligning 43 marker genes with 25 threads: Finished aligning 43 of 43 (100.00%) marker genes. [2022-11-15 11:34:36] INFO: Reading marker alignment files. [2022-11-15 11:34:36] INFO: Concatenating alignments. [2022-11-15 11:34:36] INFO: Placing 831 bins into the genome tree with pplacer (be patient). Uncaught exception: Multiprocessing.Childerror() Fatal error: exception Multiprocessing.Childerror() Uncaught exception: Sys_error("../AllData/RealDataBinningModels/MaxBin_Data/HLJ/DeepurifyTempOut/FilterOutput/family_filter/checkmTempOut/storage/tree/concatenated.pplacer.json: No such file or directory") Fatal error: exception Sys_error("../AllData/RealDataBinningModels/MaxBin_Data/HLJ/DeepurifyTempOut/FilterOutput/family_filter/checkmTempOut/storage/tree/concatenated.pplacer.json: No such file or directory") [2022-11-15 11:36:16] INFO: { Current stage: 0:02:24.785 || Total: 0:02:24.785 } [2022-11-15 11:36:16] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets. [2022-11-15 11:36:16] INFO: Reading HMM info from file. [2022-11-15 11:36:16] INFO: Parsing HMM hits to marker genes: Finished parsing hits for 831 of 831 (100.00%) bins. [2022-11-15 11:36:40] INFO: Determining marker sets for each genome bin.

Unexpected error: <class 'FileNotFoundError'> Traceback (most recent call last): File "/home/zoubh/.local/bin/checkm", line 856, in checkmParser.parseOptions(args) File "/home/zoubh/.local/lib/python3.10/site-packages/checkm/main.py", line 980, in parseOptions self.lineageSet(options) File "/home/zoubh/.local/lib/python3.10/site-packages/checkm/main.py", line 261, in lineageSet treeParser.getBinMarkerSets(options.tree_dir, options.marker_file, File "/home/zoubh/.local/lib/python3.10/site-packages/checkm/treeParser.py", line 485, in getBinMarkerSets tree = dendropy.Tree.get_from_path(treeFile, schema='newick', rooting="force-rooted", preserve_underscores=True) File "/home/zoubh/.local/lib/python3.10/site-packages/dendropy/datamodel/basemodel.py", line 216, in get_from_path with open(src, "r", newline=None) as fsrc: FileNotFoundError: [Errno 2] No such file or directory: '../AllData/RealDataBinningModels/MaxBin_Data/HLJ/DeepurifyTempOut/FilterOutput/family_filter/checkmTempOut/storage/tree/concatenated.tre

############### It can not be the out of memory since the memory of my machine is 256GB. I also checked the log output of pplacer, it seems there is no error in it...... Thanks for answering.

[azat-badretdin]

I noticed that the path to the file is relative, which might be a result of specifying relative path in the data installation root. If this is the case, maybe specifying an absolute path could help?

[zoubohao]

I appreciate your advice. I'll try using the absolute path to test if this issue persists.

[zoubohao]

This issue has been solved. The issue comes from a bug from pplacer. I changed the version of pplacer to the last one and this issue has gone.

Thanks for giving advices.