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Description
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 resultsRelevant 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