Error with data on NFS storage

[angelovangel]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.1.0-g09db777

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-clone-validation --fastq /home/nfs/../fastq_pass --sample_sheet /home/nfs/../samplesheet.csv --out_dir /home/nfs/../assembly --threads 12

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

ERROR ~ Error executing process > 'validate_sample_sheet' Command error: WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. /usr/bin/env: 'python3': No such file or directory

Strangely, this happens only when the inputs for the pipeline are on NFS mounts. Permissions are ok, e.g. some output is written there. Tried to use process.scratch = true but didn't solve it. It works after copying the fastq and samplesheet inputs to a local storage. I see the same behaviour with all other epi2me pipelines..

Relevant log output

`Caused by:
  Process `validate_sample_sheet` terminated with an error exit status (127)

Command executed:

  workflow-glue check_sample_sheet sample_sheet.csv

Command exit status:
  127

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  /usr/bin/env: 'python3': No such file or directory`

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[sarahjeeeze]

Hi, this looks like an issue related to your environment so perhaps ask your system admin or whoever manages your docker, you could also try singularity with -profile singularity

[angelovangel]

Thanks!