Podman permissions issue

[emilybfox]

Description of the bug

When running CorgiSNPs with the podman profile, execution is cancelled/terminated right after the nextflow workflow shows up and starts to run due to a permissions issue.

Thank you for your time, and let me know if more information is needed.

Command used and terminal output

command used:
nextflow run DOH-JDJ0303/CorgiSNPs \
    -r main \
    -profile podman \
    --input samplesheet.csv \
    --outdir results/ \
    --db db/ \
    --push true


terminal output:
ERROR ~ Error executing process > 'DOHJDJ0303_CORGISNPS:CORGISNPS:PREPARE:FASTP (C1)'
...
Command exit status:
126
Command output:
(empty)
Command error:
Error: pasta failed with exit code 1:
netns dir open: Permission denied, exiting

Relevant files

No response

System information

Nextflow version = 24.10.5
Hardware = Linux server (SSH into)
Executor = local (bash)
Container engine = Podman (v.5.6.2)

[DOH-JDJ0303]

Hi @emilybfox. Thank you for creating this request! 😄 Looking into this my hunch is that it may be something specific to your machine rather than the workflow. Would you mind running the two commands below to see if you get the same error:

First command

podman run \
    --rm \
    community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690 \
    fastp

Second command

podman run \
    --rm \
    --network=host \
    community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690 \
    fastp

If you only get an error for the first command then it would indicate there is an issue with your installation of podman, which I might be able to help with 😅

[emilybfox]

Hi @emilybfox. Thank you for creating this request! 😄 Looking into this my hunch is that it may be something specific to your machine rather than the workflow. Would you mind running the two commands below to see if you get the same error:

First command

podman run
--rm
community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690
fastp
Second command

podman run
--rm
--network=host
community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690
fastp
If you only get an error for the first command then it would indicate there is an issue with your installation of podman, which I might be able to help with 😅

Thank you so much Jared! It looks like I do only get an error with the first command, so I will work on fixing my installation of podman😅. I appreciate your help! 😄