CheckM failing at pplacer step

[priscalim00]

Hi! Thank you for your efforts in developing and maintaining CheckM. I'm attempting to run dRep which utilizes CheckM for the filtering step. However I'm running into issues with CheckM failing. I've looked through the dRep and CheckM log files and determined that the error is arising during the pplacer step, but I'm not able to figure out what the error is or how to fix it. I've looked through the other issues on this page and haven't found a solution.

I installed dRep using conda and used checkm data setRoot to direct it to the directory containing the CheckM database. I also ran conda list to check the packages installed and confirmed that I have the following packages installed:

• checkm-genome: 1.2.2
• hmmer: 3.4
• pplacer: 1.1.alpha19
• prodigal: 2.6.3

However, when I attempt to run checkm test ~/checkm_test_results, I encounter the following error:

[2024-06-28 13:46:01] INFO: CheckM v1.2.2
[2024-06-28 13:46:01] INFO: checkm test /nas/longleaf/home/prisca/checkm_test_results
[2024-06-28 13:46:01] INFO: CheckM data: data/reference/CheckM
[2024-06-28 13:46:01] INFO: [CheckM - Test] Processing E.coli K12-W3310 to verify operation of CheckM.
[2024-06-28 13:46:01] INFO: [Step 1]: Verifying tree command.
[2024-06-28 13:46:01] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2024-06-28 13:46:01] INFO: Identifying marker genes in 1 bins with 1 threads:
Finished processing 1 of 1 (100.00%) bins.
[2024-06-28 13:46:14] INFO: Saving HMM info to file.
[2024-06-28 13:46:14] INFO: Calculating genome statistics for 1 bins with 1 threads:
Finished processing 1 of 1 (100.00%) bins.
[2024-06-28 13:46:14] INFO: Extracting marker genes to align.
[2024-06-28 13:46:14] INFO: Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 1 (100.00%) bins.
[2024-06-28 13:46:14] INFO: Extracting 43 HMMs with 1 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
[2024-06-28 13:46:15] INFO: Aligning 43 marker genes with 1 threads:
Finished aligning 43 of 43 (100.00%) marker genes.
[2024-06-28 13:46:16] INFO: Reading marker alignment files.
[2024-06-28 13:46:16] INFO: Concatenating alignments.
[2024-06-28 13:46:16] INFO: Placing 1 bins into the genome tree with pplacer (be patient).
[2024-06-28 13:47:30] INFO: { Current stage: 0:01:28.584 || Total: 0:01:28.584 }

Unexpected error: <class 'ValueError'>
Traceback (most recent call last):
File "/users/p/r/prisca/miniconda3/envs/drep/bin/checkm", line 856, in
checkmParser.parseOptions(args)
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/site-packages/checkm/main.py", line 1031, in parseOptions
self.test(options)
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/site-packages/checkm/main.py", line 940, in test
verifyEcoli.run(self, options.output_dir)
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/site-packages/checkm/test/test_ecoli.py", line 67, in run
self.verifyTree(options.output_dir)
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/site-packages/checkm/test/test_ecoli.py", line 127, in verifyTree
binStats = ResultsParser(None).parseBinStats(outdir, DefaultValues.BIN_STATS_PHYLO_OUT)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/site-packages/checkm/resultsParser.py", line 155, in parseBinStats
binStats[lineSplit[0]] = ast.literal_eval(lineSplit[1])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/ast.py", line 112, in literal_eval
return _convert(node_or_string)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/ast.py", line 101, in _convert
return dict(zip(map(_convert, node.keys),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/ast.py", line 111, in _convert
return _convert_signed_num(node)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/ast.py", line 85, in _convert_signed_num
return _convert_num(node)
^^^^^^^^^^^^^^^^^^
File "/users/p/r/prisca/miniconda3/envs/drep/lib/python3.12/ast.py", line 76, in _convert_num
_raise_malformed_node(node)
File "/users/p/r/prisca/miniconda3/envs/drep/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 0x7ff462a10050>

I've increased the memory up to 256gb and got the same output, so I'm confident it's not a memory issue which leaves me pretty stumped on what to try next. Thanks for any suggestions you might have!

[priscalim00]

I just wanted to post an update for anyone who might be facing a similar issue.

I decided to try installing CheckM into it's own conda environment and run the checkm test ~/checkm_test_results command, and well everything worked just fine! I also tested checkm on one of my samples and got an output with no errors. So, it seems like CheckM is not getting installed properly via the dRep installation. I've no idea what went wrong on that end, I might reach out to the dRep folks and see if they can figure out the root cause. But for now, I think running CheckM separately and parsing the output results into dRep is a decent workaround.

[donovan-h-parks]

Hi. I think this relates to a recent change in numpy that breaks older version of CheckM. This was addressed in CheckM v1.2.3 which was released a few days ago.

[priscalim00]

Oh thanks for letting me know! That definitely explains the issues I was facing.

[Sayyed-Hammad-Ullah-BS-Zoology-Student]

I am facing the following issue while i run checkm, what is the root of the issue and how to resolve it:

(04_checkm_quast) sayyed_hammad_ullah@Hammad:/mnt/c/Users/PMLS/Desktop/Genome_assembly$ checkm lineage_wf -t 4 -r --tab_table --file bacteroides -x fasta /mnt/c/Users/PMLS/Desktop/Genome_assembly/unicycler_assemblies/ /mnt/c/Users/PMLS/Desktop/Genome_assembly/checkm/checkm_results/
[2024-09-03 17:44:57] INFO: CheckM v1.2.3
[2024-09-03 17:44:57] INFO: checkm lineage_wf -t 4 -r --tab_table --file bacteroides -x fasta /mnt/c/Users/PMLS/Desktop/Genome_assembly/unicycler_assemblies/ /mnt/c/Users/PMLS/Desktop/Genome_assembly/checkm/checkm_results/
[2024-09-03 17:44:57] INFO: CheckM data: /home/sayyed_hammad_ullah/miniconda3/envs/04_checkm_quast/checkm_data
[2024-09-03 17:44:57] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2024-09-03 17:44:57] INFO: Identifying marker genes in 1 bins with 4 threads:
Finished processing 1 of 1 (100.00%) bins.
[2024-09-03 17:45:01] INFO: Saving HMM info to file.
[2024-09-03 17:45:01] INFO: Calculating genome statistics for 1 bins with 4 threads:
Finished processing 1 of 1 (100.00%) bins.
[2024-09-03 17:45:01] INFO: Extracting marker genes to align.
[2024-09-03 17:45:01] INFO: Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 1 (100.00%) bins.
[2024-09-03 17:45:01] INFO: Extracting 43 HMMs with 4 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
[2024-09-03 17:45:01] INFO: Aligning 43 marker genes with 4 threads:
Finished aligning 43 of 43 (100.00%) marker genes.
[2024-09-03 17:45:02] INFO: Reading marker alignment files.
[2024-09-03 17:45:02] INFO: Concatenating alignments.
[2024-09-03 17:45:02] INFO: Placing 1 bins into the genome tree with pplacer (be patient).
Killed
[2024-09-03 17:45:49] ERROR: pplacer exited with code: 35072

Controlled exit resulting from an unrecoverable error or warning.

[donovan-h-parks]

Hi Sayyed,

This looks like you are running out of memory. You can find the CheckM system requirements here: https://github.com/Ecogenomics/CheckM/wiki/Installation#system-requirements

Cheers,
Donovan

[Sayyed-Hammad-Ullah-BS-Zoology-Student]

[like] SAYYED HAMMAD ULLAH reacted to your message:

…

________________________________ From: Donovan H. Parks ***@***.***> Sent: Tuesday, September 3, 2024 2:27:33 PM To: Ecogenomics/CheckM ***@***.***> Cc: SAYYED HAMMAD ULLAH ***@***.***>; Comment ***@***.***> Subject: Re: [Ecogenomics/CheckM] CheckM failing at pplacer step (Issue #400) Hi Sayyed, This looks like you are running out of memory. You can find the CheckM system requirements here: https://github.com/Ecogenomics/CheckM/wiki/Installation#system-requirements Cheers, Donovan — Reply to this email directly, view it on GitHub<#400 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BKKMX7HEE2B3QSHETWHPNC3ZUXBNLAVCNFSM6AAAAABKCKGOSGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRWGY3TANZWG4>. You are receiving this because you commented.Message ID: ***@***.***>