Check-M test fails at step two. about checkm

[donovan-h-parks]

Helllo Ashmita,

Pplacer appears to be crashing which is likely because you are running out of memory. CheckM requires ~32Gb to place genomes into its full reference tree. You can reduce this to just under 16Gb by using the --reduced_tree flag. Alternatively, you can use the taxonomy_wf if you know the taxonomic identity of the bins you wish to process with CheckM.

[donovan-h-parks]

Hello Ashmita,

Can you please post the full output from CheckM. It is clear what the problem is just from the IOError message. Also, you might just try running CheckM on a set of your own bins/genomes to see if that works or at least provides a more informative error message.

Cheers,
Donovan

[Ashmita005]

Hello Donovan

So as requested I have used Check M on a set of my own bins and here is the full output received.

ashmita@ashmita-VirtualBox:~/Documents/programms$ checkm lineage_wf -t 5 -x fa /home/ashmita/Documents/bins /home/ashmita/Documents/resultscm

---

[CheckM - tree] Placing bins in reference genome tree.

---

Identifying marker genes in 26 bins with 5 threads:
Finished processing 26 of 26 (100.00%) bins.
Saving HMM info to file.

Calculating genome statistics for 26 bins with 5 threads:
Finished processing 26 of 26 (100.00%) bins.

Extracting marker genes to align.
Parsing HMM hits to marker genes:
Finished parsing hits for 26 of 26 (100.00%) bins.
Extracting 43 HMMs with 5 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
Aligning 43 marker genes with 5 threads:
Finished aligning 43 of 43 (100.00%) marker genes.

Reading marker alignment files.
Concatenating alignments.
Placing 26 bins into the genome tree with pplacer (be patient).
Killed
Uncaught exception: Sys_error("/home/ashmita/Documents/resultscm/storage/tree/concatenated.pplacer.json: No such file or directory")
Fatal error: exception Sys_error("/home/ashmita/Documents/resultscm/storage/tree/concatenated.pplacer.json: No such file or directory")

{ Current stage: 0:01:39.226 || Total: 0:01:39.226 }

---

[CheckM - lineage_set] Inferring lineage-specific marker sets.

---

Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 26 of 26 (100.00%) bins.

Determining marker sets for each genome bin.

Unexpected error: <type 'exceptions.IOError'>
Traceback (most recent call last):
File "/usr/local/bin/checkm", line 710, in
checkmParser.parseOptions(args)
File "/usr/local/lib/python2.7/dist-packages/checkm/main.py", line 1241, in parseOptions
self.lineageSet(options)
File "/usr/local/lib/python2.7/dist-packages/checkm/main.py", line 226, in lineageSet
resultsParser, options.unique, options.multi)
File "/usr/local/lib/python2.7/dist-packages/checkm/treeParser.py", line 477, in getBinMarkerSets
tree = dendropy.Tree.get_from_path(treeFile, schema='newick', rooting="force-rooted", preserve_underscores=True)
File "/usr/local/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line 217, in get_from_path
with open(src, "r", newline=None) as fsrc:
File "/usr/local/lib/python2.7/dist-packages/dendropy/utility/filesys.py", line 60, in pre_py34_open
buffering=buffering)
IOError: [Errno 2] No such file or directory: '/home/ashmita/Documents/resultscm/storage/tree/concatenated.tre'

It is roughly the same error as when I try to run the installation test..

Your help will be appreciated
Thank you
Ashmita

[Ashmita005]

Thank you Donovan, It now works

[Buuntu]

@dparks1134 I get this error too when running CheckM under AWS Batch

[donovan-h-parks]

It is likely a memory issue. CheckM requires ~32Gb to place genomes into its full reference tree. You can reduce this to just under 16Gb by using the --reduced_tree flag. Alternatively, you can use the taxonomy_wf if you know the taxonomic identity of the bins you wish to process with CheckM.

[Buuntu]

@dparks1134 Yep that's the issue, when setting an AWS Batch job to run with a minimum amount of memory of 32 GB, it works fine. Would it not be useful for CheckM to error out at the start or at least give a warning if the memory requirements are not met?