Unexpected error: <class 'RecursionError'>

[MingyueCheng]

Command: checkm lineage_wf -x fa -t 20 --pplacer_threads 20 --tmpdir ./checkm_tmp ./bin ./checkm

Can anybody help me ！！ Many thanks to you！! I just wanna get a summary table of 3W metagenomic bins, with completeness, contamination, strain heterogeneity... and some other things like these. Did this error occur because of the large number of bins?

[2022-12-24 19:34:28] INFO: CheckM v1.2.2
[2022-12-24 19:34:28] INFO: checkm lineage_wf -x fa -t 20 --pplacer_threads 20 --tmpdir ./checkm_tmp ./bin ./checkm
[2022-12-24 19:34:28] INFO: CheckM data: /opt/service/miniconda3/envs/r4_py37_env/checkm_data
[2022-12-24 19:34:28] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2022-12-24 20:51:16] INFO: Identifying marker genes in 33728 bins with 20 threads:
[2022-12-25 05:16:17] INFO: Saving HMM info to file.
[2022-12-25 05:16:28] INFO: Calculating genome statistics for 33728 bins with 20 threads:
[2022-12-25 05:20:48] INFO: Extracting marker genes to align.
[2022-12-25 05:20:48] INFO: Parsing HMM hits to marker genes:
[2022-12-25 05:53:53] INFO: Extracting 43 HMMs with 20 threads:
[2022-12-25 05:53:55] INFO: Aligning 43 marker genes with 20 threads:
[2022-12-25 06:09:50] INFO: Reading marker alignment files.
[2022-12-25 06:09:53] INFO: Concatenating alignments.
[2022-12-25 06:09:56] INFO: Placing 33728 bins into the genome tree with pplacer (be patient).
[2022-12-25 09:57:01] INFO: { Current stage: 14:22:33.383 || Total: 14:22:33.383 }
[2022-12-25 09:57:03] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets.
[2022-12-25 09:57:03] INFO: Reading HMM info from file.
[2022-12-25 09:57:15] INFO: Parsing HMM hits to marker genes:
[2022-12-25 10:22:47] INFO: Determining marker sets for each genome bin.

Unexpected error: <class 'RecursionError'>

#ERROR detail:
Traceback (most recent call last):
File "/opt/service/miniconda3/envs/r4_py37_env/bin/checkm", line 856, in
checkmParser.parseOptions(args)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/checkm/main.py", line 980, in parseOptions
self.lineageSet(options)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/checkm/main.py", line 265, in lineageSet
resultsParser, options.unique, options.multi)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/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 "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/datamodel/basemodel.py", line 219, in get_from_path
**kwargs)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/datamodel/treemodel.py", line 2663, in _parse_and_create_from_stream
global_annotations_target=None)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/dataio/ioservice.py", line 375, in read_tree_lists
global_annotations_target=global_annotations_target)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/dataio/newickreader.py", line 326, in _read
tree_factory=tree_factory):
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/dataio/newickreader.py", line 304, in tree_iter
taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/dataio/newickreader.py", line 386, in _parse_tree_statement
is_internal_node=None)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/dataio/newickreader.py", line 562, in _parse_tree_node_description
is_internal_node=is_new_internal_node,
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/dataio/newickreader.py", line 562, in _parse_tree_node_description
is_internal_node=is_new_internal_node,
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/dataio/newickreader.py", line 562, in _parse_tree_node_description
is_internal_node=is_new_internal_node,
[Previous line repeated 979 more times]
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/dataio/newickreader.py", line 553, in _parse_tree_node_description
new_node = tree.node_factory();
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/datamodel/treemodel.py", line 3027, in node_factory
return Node(**kwargs)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/datamodel/treemodel.py", line 1028, in init
length=kwargs.pop("edge_length", None))
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/datamodel/treemodel.py", line 1002, in edge_factory
return Edge(**kwargs)
File "/opt/service/miniconda3/envs/r4_py37_env/lib/python3.7/site-packages/dendropy/datamodel/treemodel.py", line 747, in init
basemodel.DataObject.init(self, label=kwargs.pop("label", None))
RecursionError: maximum recursion depth exceeded while calling a Python object

[MingyueCheng]

Or should I split the bins into different directories and run the commend separately? Will the results be different from that by taking them all to the CheckM?

I noticed that there was a step to replace all of the bins into the reference tree. The document mentioned that "All genomes to be analyzed must reside in a single bins directory."

I am afraid that if I analyzed these bins in different batches, the results will be influenced.

By the way, I just wanna get a summary table reporting the completeness, contamination, strain heterogeneity. What is the most convenient and efficient way to achieve this goal using CheckM? Many thanks for your help!

[donovan-h-parks]

You may find this helpful:
https://github.com/Ecogenomics/CheckM/wiki/Bugs-and-Feature-Requests#processing-large-numbers-of-genomes

CheckM results are independent for each genome.