featureCount doesn't work on GVL/Galaxy

I can’t get featureCounts to complete on my GVL/Galaxy instance running on AWS. If I download the same HISAT2 output and use the same built-in reference (hg19) on the public server, the job completes just fine. Any thoughts?

Hi @mitchellgc, Can you provide some more information on what happens. What specific error message (if any) do you get. Can you also provide the Galaxy server logs? Also, the size of the instance that you launched, and any other pertinent information would be useful.

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If I select View Error Logs in the admin console on Galaxy, it says “No Errors Available.” Unfortunately, the console won’t launch from GVL (503 Service Temporarily Unavailable), so I can’t get any other logs. The server is running on Amazon elastic cloud.

The featureCounts job ran until it finally timed out with the error that it had taken linger than the specified time.

So just to verify, the upload issue has been resolved? Was that related to the size of the node?

Regarding the console not launching, are you able to access the cloudman console?

If so, you can edit the Galaxy app settings (3 dot icon on the Galaxy app panel), and specify a different timeout for the k8s_walltime_limit in job_conf.yml.

You can try bumping that up to a larger number.