Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Pipeline run #339

@Mau-sumi-lab

Description

@Mau-sumi-lab

Description of the bug

I have been trying to run a test data miseq35147139, it's throwing me an error:
ERROR ~ Error executing process > 'NFCORE_DEMULTIPLEX:DEMULTIPLEX:SAMSHEE (run1)'

Caused by:
Process NFCORE_DEMULTIPLEX:DEMULTIPLEX:SAMSHEE (run1) terminated with an error exit status (4)

Command executed:

Run validation command and capture output

python -m samshee run1.lane1_no_adapters.csv > run1.lane1_no_adapters_formatted.csv

cat <<-END_VERSIONS > versions.yml
"NFCORE_DEMULTIPLEX:DEMULTIPLEX:SAMSHEE":
samshee: $( python -m pip show --version samshee | grep "Version" | sed -e "s/Version: //g" )
python: $( python --version | sed -e "s/Python //g" )
END_VERSIONS

Command exit status:
4

Command output:
(empty)

Command error:
failed writing output: validator #0 ({'$ref': 'urn:samshee:illuminav2/v1'}) raised validation errors:

  • $.Header: 'FileFormatVersion' is a required property
  • $.Header: 'Experiment Name' does not match '^[a-zA-Z0-9_]+$'
  • $.Reads: [{'151': 151}] is not of type 'object'

Work dir:
/mnt/sk01sm01/users/mausumi/demultiplex/work/41/0499dc73f9ffb2888c7e6a4a43757a

Container:
/mnt/sk01sm01/users/mausumi/demultiplex/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-87-874139c488abfe0d65786bdbafea96a0768554c1a5e8e70a332708954b96dee7-data.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

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

the pipeline_sheet.csv is:
id,samplesheet,lane,flowcell
run1,mausumi/demultiplex/miseq_35147139_samplesheet.csv,1,mausumi/demultiplex/miseq_35147139

Command used and terminal output

nextflow run nf-core/demultiplex -r 1.6.1 -profile singularity --input pipeline_sheet.csv --outdir results

Relevant files

No response

System information

nextflow version: 25.04.4
executor: local
container engine: singularity
OS: Linux
version of nf-core/demultiplex: 1.6.1

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't working

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions