cvmfs error when running RNA STAR -- Resolved 09/16/2022, please rerun any failures


I was running RNA STAR and got this error: |Job Start Time|2022-09-15 23:24:13|

FATAL: could not open image /cvmfs/ failed to retrieve path for /cvmfs/ lstat /cvmfs/ transport endpoint is not connected

Which is an error that I see has been popping up from last month. I am wondering if there is an issue with the cvmfs dependency once again.

Please let me know if there is a different issue that I can try on my end. Otherwise, I would like to know when I should try re-running the workflow.

All the best,

I ran the same workflow with the same datasets this morning: |Job Start Time| 2022-09-16 11:38:29
and STAR was able to successfully finish mapping! It did not run into the same cvmfs error.

I don’t know how the error resolved itself, but I wanted to let you all know.


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Yes, the problem was temporary and server-side at earlier today.

Rerunning is the solution :slight_smile: