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nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples
https://nf-co.re/viralrecon
MIT License
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ERROR in Script plasmidID #349

Closed AroobAlhumaidy closed 1 year ago

AroobAlhumaidy commented 1 year ago

Description of the bug

Hello everyone,

I'm running Viralrecon for monkeypox, and facing an error:

The error:

ERROR in Script plasmidID on or near line 868; exiting with status 1
MESSAGE:  See ./logs/plasmidID.log for more information.
command: gff_to_bed.sh -i ./NO_GROUP/pmseq_V300081052_28_+_V300081052_30/data/pmseq_V300081052_28_+_V300081052_30".gff" -L

Is there any solution?

Thanks,

Command used and terminal output


time nextflow run nf-core/viralrecon \
    --input viralrecon.samplesheet.csv  \
    --outdir results  \
    -c custom.config \
    --max_cpus 60 \
    --max_memory '300.GB' \
    --memory-swap '-1' \
    --platform illumina \
    --protocol metagenomic \
    --genome 'NC_063383.1' \
    --nextclade_dataset_name 'hMPXV' \
    -profile docker

Relevant files

nextflow.log custom.config.txt

System information

EDIT by @maxulysse: removed extra triple quotes + fix viralrecon version

drpatelh commented 1 year ago

--skip_plasmidid will be set to true by default which indirectly will fix this issue. Quite a few bugs have propped up that may not be fixed in the short-term. See https://github.com/nf-core/viralrecon/pull/360/commits/5b59dc83cfa4172ebc5b564f4522dd45006ced00