6 months ago by
United States
Hi,
It looks like your Stringtie jobs completed, as well as some Cufflinks jobs. The Cuffdiff jobs are still queued (started up earlier today).
Your analysis does have a problem unrelated to the cluster queue. Specifically, the options for HISAT2 need to be set differently when the result is input to Cufflinks versus Stringtie. It looks like this reporting option was not set when creating HISAT2 BAMs input to Cufflinks. I didn't check the Stringtie input HISAT2 BAMs, but you should. If both are not corrected, the results from downstream tools will not be scientifically valid, or the jobs will fail (error). You'll need to rerun HISAT2 with the proper settings, then rerun the downstream tools.
Galaxy tutorials, including those for RNA-seq: https://galaxyproject.org/learn/
Tutorials using Galaxy Main
These work at Galaxy Main https://usegalaxy.org and often at other public Galaxies.
- RNA-seq: Introduction - an introductory tutorial for transcriptome analysis.
- RNA-seq: Discovering and quantifying new transcripts - an in-depth transcriptome analysis example.
Galaxy Training Network
GTN network tutorial's tools will work at various public Galaxy servers. Find out which public server(s) support any particular tutorial under "Galaxy instances". Some will also have a pre-configured Galaxy Docker available and this is noted on the tutorial group's landing page.
- RNA-seq tutorials are under the group >> Transcriptomics
More about jobs:
Jobs are run in the order submitted, are added to a master queue (all users), then execute. Concurrency quotas are in place to help ensure equal access for everyone, whether running individual jobs or batch jobs.
Important: Unless you detect an input/setting problem and need to rerun to correct those, queued jobs should be left queued. When jobs are deleted/rerun, the new jobs are added back at the end of the queue, extending wait time. Permanently delete any jobs queued that you no longer wish to run or have already used to start a rerun. This clears them from the server quicker. Note that jobs that are already executing (yellow) will take longer to clear/free up job concurrency quotas.
FAQs: https://galaxyproject.org/support/
Thanks! Jen, Galaxy team
