pipeline:runArtic (1)'
Habibk91 opened this issue · 2 comments
Habibk91 commented
Operating System
Windows 11
Other Linux
wsl
Workflow Version
23.04.1
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-artic -c myconfig.cfg --fastq 'positive_ctrl/' --sample 'barcode12/' --scheme_version 'Midnight-ONT/V3' --out_dir 'barcode12_results/'
Workflow Execution - CLI Execution Profile
custom
What happened?
Hello, i got this error after executing the nexflow pipeline. it seems there's an error with the runArtic pipeline trying to move a file into a non-existent directory. even after creating the directories, i still get the same error. any help ?
Relevant log output
ERROR ~ Error executing process > 'pipeline:runArtic (1)'
Caused by:
Process `pipeline:runArtic (1)` terminated with an error exit status (1)
Command executed:
run_artic.sh barcode12/ seqs.fastq.gz 150 1200 r941_min_hac_variant_g507 SARS-CoV-2 SARS-CoV-2 Midnight-ONT/V3 4 0 200
bcftools stats barcode12/.pass.named.vcf.gz > barcode12/.pass.named.stats
Command exit status:
1
Command output:
Moving input: 'seqs.fastq.gz' to 'barcode12//barcode12/.fastq.gz'
Command error:
Moving input: 'seqs.fastq.gz' to 'barcode12//barcode12/.fastq.gz'
mv: cannot move 'seqs.fastq.gz' to 'barcode12//barcode12/.fastq.gz': No such file or directory
Work dir:
/home/habib-msi/data/work/fa/41cea993052fbf3a78b674a553cfcd
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for detailsApplication activity log entry
No response
cjalder commented
Hi, thanks for highlighting the issue. I think it may have to do with the trailing / in your --sample parameter. Can you try running with --sample 'barcode12' and see if the error persists?