I keep getting this error when running CONCOCT when it hits a negative control in nf-core/mag:

ERROR ~ Error executing process > 'NFCORE_MAG:mag:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (Negative-Control-X007)'

Caused by:

`Process

NFCORE_MAG:mag:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (Negative-Control-X007)

terminated with an error exit status (255)`

Command executed:

concoct \

\

--threads 12 \

--coverage_file MEGAHIT-CONCOCT-Negative-Control-X007.tsv \

--composition_file MEGAHIT-CONCOCT-Negative-Control-X007.fasta \

-b MEGAHIT-CONCOCT-Negative-Control-X007

cat <<-END_VERSIONS > versions.yml

"NFCORE_MAG:mag:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT":

concoct: $(echo $(concoct --version 2> /dev/null) | sed 's/concoct //g' )

END_VERSIONS

Command exit status:

255

Command output:

(empty)

Command error:

/usr/local/lib/python3.9/site-packages/concoct/__init__.py:1: UserWarning: pkg_resources is deprecated as an API. See <https://setuptools.pypa.io/en/latest/pkg_resources.html>. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.

import pkg_resources # part of setuptools

Up and running. Check MEGAHIT-CONCOCT-Negative-Control-X007_log.txt for progress

Work dir:

/datastore/userdata/daniel/Long_lake_NRCan_collaboration/Full_scale_study/Sequences_redownloaded/work/56/20d4bac486fdc337d2e42b0d884256

Container:

/datastore/userdata/daniel/Long_lake_NRCan_collaboration/quay.io-biocontainers-concoct-1.1.0--py39h8907335_8.img

Tip: when you have fixed the problem you can continue the execution adding the option

-resume` to the run command line`

-- Check '.nextflow.log' file for details

ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

Any sense of how to adjust the custom config file or pass a command to CONCOCT to deal with this so it doesn’t keep killing the pipeline? None of the other binners I used ran into this issue for this negative control

Hi @Daniel Gregoire! You can change errorStrategy for concoct so it doesn't stop the pipeline:

process {
  withName: CONCOCT_CONCOCT {
    errorStrategy = 'ignore'
  }
}

Save this as

nextflow.config

in your launch directory, or use a different filename and pass it explicitly with

-c

when running the pipeline.

Ended up using --skip_concoct and because it had processed 42/43 samples (the one that isn’t working being the negative control), I think it preserved the CONCOCT bins for downstream processing. Even still, I’ll adjust the config file for future runs, thanks @Diego Alvarez Saravia