When I’m not featureCounts, it says the job is paused. Use the “Resume Paused Jobs” in the history menu to resume. The job tab turned blue. Also, before this, on RNA STAR result, there is an error occurred setting the metadata for this dataset and it still didn’t change after I set it manually or retry auto-detection. Can anyone help on this?
This usually means that the resulting BAM was empty (no hits).
Please try at least one rerun to eliminate cluster issues. For the errored dataset, click on the rerun icon to bring up the tool form again. It will have a new option to “resume” downstream jobs/dependencies. Set that option to true to replace the old/paused output with the new output, and submit the job.
If the mapping job fails again, the next step is to troubleshoot the inputs and parameters. Quick items to check:
- Are the fastq inputs intact, with content, and not in an error state?
- Did you run QA/QC on the fastq data?
- If you are using a custom genome, is the fasta formatted correctly?
I added some tags to your post that will search other Q&A for the checks above. If you cannot solve the problem, please post back a few more details about how the rerun worked, what you checked, and where you are working (URL if a public Galaxy server, or describe if another platform).
Let’s start there. Thanks!