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I'm running nf-core/mag on a metagenomics dataset and wanted to include a taxonomic classification via CAT. The main module CAT runs, but then runs into the following issue:
nf-core/mag execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: null.
The full error message was:
Error executing process > 'NFCORE_MAG:MAG:CAT_SUMMARY'
Caused by:
Process `NFCORE_MAG:MAG:CAT_SUMMARY` input file name collision -- There are multiple input files for each of the following file names: SPAdes-DASTool-group-0.ORF2LCA.names.txt.gz, SPAdes-DASTool-group-0.bin2classification.names.txt.gz, MEGAHIT-DASTool-group-0.bin2classification.names.txt.gz, MEGAHIT-DASTool-group-0.ORF2LCA.names.txt.gz
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
As the names suggest I'm using SPAdes and MEGAHIT, MaxBin2, Metabat2 and DAS Tool (Which seems to be the Problem here) and --postbinning_input "both".
I tracked down the problem to the naming convention within the CAT module:
CAT module hard codes file names in the commands themselves, rather than using the now standard Prefix, and thus the 'unbinned' information gets removed when writing files, resulting in the overwriting of bins and unbins of a given sampe...
Description of the bug
Hi there,
I'm running nf-core/mag on a metagenomics dataset and wanted to include a taxonomic classification via CAT. The main module
CAT
runs, but then runs into the following issue:As the names suggest I'm using SPAdes and MEGAHIT, MaxBin2, Metabat2 and DAS Tool (Which seems to be the Problem here) and
--postbinning_input "both"
.I tracked down the problem to the naming convention within the
CAT
module:mag/modules/local/cat.nf
Line 31 in 66cf53a
Which does not account for the naming of the unbinned DasTool file.
If you need any more information/files I can of course provide them.
Command used and terminal output
nextflow run nf-core/mag -r 2.3.0 -profile cfc --input "../samplesheet.csv" --host_genome "mm10" --save_hostremoved_reads --cat_db ../cat_db/CAT_prepare_20210107.tar.gz --coassemble_group --refine_bins_dastool --postbinning_input "both" --busco_auto_lineage_prok --save_busco_reference --busco_download_path "../busco-data.ezlab.org/v5/data" --skip_concoct --skip_prokka --outdir "results_with_cat" -c "../QMCOK_mag.config" --email [email protected] -resume
Relevant files
No response
System information
Nextflow version 23.04.1 build 5866
Hardware: HPC Cluster
Executor: slurs
Container engine: Singularity
nf-core/mag: 2.3.0
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