Unable to pull singularity image?

[forty2wallabyway]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

24.04.3

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-flu \ --downsample 50 \ --fastq 'wf-flu-demo/fastq' \ --sample_sheet 'wf-flu-demo/sample_sheet.csv' \ -profile singularity

Workflow Execution - CLI Execution Profile

singularity

What happened?

Command error: FATAL: container creation failed: mount /proc/self/fd/4->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/4: kernel reported a bad superblock for squashfs image partition, possible causes are that your kernel doesn't support the compression algorithm or the image is corrupted

Relevant log output

ERROR ~ Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (255)

Command executed:

  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  bcftools --version | head -1 | sed 's/ /,/' >> versions.txt
  samtools --version | grep samtools | head -1 | sed 's/ /,/' >> versions.txt

Command exit status:
  255

Command output:
  (empty)

Command error:
  FATAL:   container creation failed: mount /proc/self/fd/4->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/4: kernel reported a bad superblock for squashfs image partition, possible causes are that your kernel doesn't support the compression algorithm or the image is corrupted

Application activity log entry

No response

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

no

Other demo data information

No response

[nrhorner]

Hi @forty2wallabyway This might be related to a singularity bug that was fixed in v3.5.1. https://github.com/apptainer/singularity/issues/5466

Which version are you using?

[forty2wallabyway]

Thanks @nrhorner I was using v3.5.0 and updating to a newer version solved my issue!