Closed forty2wallabyway closed 1 month ago
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?
Thanks @nrhorner I was using v3.5.0 and updating to a newer version solved my issue!
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
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