Salmon job stuck in running state despite completed outputs (collection job)

usegalaxy.org support
1

Hello Galaxy team,

I am experiencing an issue with a Salmon quantification job run on a dataset collection. Although the output files (e.g., quant.sf) are fully generated and viewable for all samples, the parent Salmon job continues to show as “running/queued” and has not transitioned to a completed state.

As a result, downstream tools (e.g., tximport) remain queued and do not start, likely because the scheduler considers the upstream job active.

Key details:

  • Tool: Salmon quant

  • Input: Paired-end RNA-seq dataset collection

  • Outputs: quant.sf files are present and viewable

  • Issue: Job state not resolving at the collection level

  • Downstream jobs blocked: tximport remains queued

This appears to be a job state / scheduler bookkeeping issue rather than a tool failure.

Could you please advise or reset the job state so downstream analysis can proceed?

Thank you for your help.

Best regards,
smmarwansalih

2

Hi @Marwan_Salih

Sometimes Galaxy does not update the job status. Click at Galaxy icon in the top left corner of Galaxy window. This action should update the screen content.

Hope that helps.

Kind regards,

Igor