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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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pipeline:runArtic (1)' #84

Closed Habibk91 closed 1 year ago

Habibk91 commented 1 year ago

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 details

Application activity log entry

No response

cjalder commented 1 year ago

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?

Habibk91 commented 1 year ago

Thank you very much @cjalder, it worked perfectly.