CHECKM_LINEAGEWF failing with exit status 1

[carleton-envbiotech]

CHECKM_LINEAGEWF failing with exit status 1

[jfy133]

Thanks for the report!

EOFerror implies to me that there is an empty input file or corrupted database somewhere...

If you go into the reported work directory, can you inspect the input files to see if they do have something in them?

[carleton-envbiotech]

Working through the work directory, I see the following:

• A directory called checkm_data_2015_01_16 that has multiple subdirectory within it
• An input_bins directory that contains a single .fa file, as would be expected
• An additional directory called: MEGAHIT-DASTool-unclassified-dastool_refined_unbinned-NitrifyingPelletDNA_Week4_Sulphatereduction_DNARNAkit_rep3_S14_wf after the sample name that initiated this process.
• Notably, the 'bin' subdirectory within the above-mentioned directory is empty, as is the 'storage' directory.
• Using 'cat' to open the checkm.log only returns this, which looks like where the process encountered an error:

[2024-02-22 09:26:07] INFO: CheckM v1.2.1 [2024-02-22 09:26:07] INFO: checkm lineage_wf -t 10 -f MEGAHIT-DASTool-unclassified-dastool_refined_unbinned-NitrifyingPelletDNA_Week4_Sulphatereduction_DNARNAkit_rep3_S14_wf.tsv --tab_table --pplacer_threads 10 -x fa input_bins/ MEGAHIT-DASTool-unclassified-dastool_refined_unbinned-NitrifyingPelletDNA_Week4_Sulphatereduction_DNARNAkit_rep3_S14_wf [2024-02-22 09:26:07] INFO: CheckM data: checkm_data_2015_01_16 [2024-02-22 09:26:07] INFO: [CheckM - tree] Placing bins in reference genome tree. [2024-02-22 09:26:08] INFO: Identifying marker genes in 1 bins with 10 threads:

[jfy133]

Looking at the checkm issues, I think it maybe you have run out of memory for the checkm process.

You shoulf increase the memory for that errored process in your custom config file too, as you've already done for others it seems

[carleton-envbiotech]

I obtained this error message even after adjusting the configuration to look like the following excerpt:

process { withName: GTDBTK_CLASSIFYWF { cpus = 32 memory = 256.GB } withName: CHECKM_QC { cpus = 32 memory = 256.GB } }

[jfy133]

Gah. Could you try running the command manually (.command.sh) with a local copy of checkM? That way we can isolate the error whether it's the pipeline doing something wrong or thetool...

[jfy133]

@carleton-envbiotech my feeling is either still memory, this seems to be REALLY common issue with checkm, and results in very similar errors.

I note that your configuration in teh except woudn't work without new lines - was that just a quick type out?

process { 
        withName: GTDBTK_CLASSIFYWF { 
                cpus = 32
                memory = 256.GB 
        } 
        withName: CHECKM_QC { 
                cpus = 32 
                memory = 256.GB 
        }
}

Works for me for example

Otherwise, maybe it's the wrong database file being passed to it... the nf-core/mag docs for --checkm_db says it shoujld be this below, but looks like you have a different name in the command above (it might be the same contents, IDK)

default: https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/auxillary_files/gtdbtk_r214_data.tar.gz```

[jfy133]

Going to close for now, as I think ti's a memory issue rather than a pipeline error