Error running Smart-Seq2 workflow on Terra

9 views

Skip to first unread message

David Lieb

unread,

Jul 18, 2023, 4:21:47 PM7/18/23

to cumulus...@googlegroups.com

Hi,

I'm trying to run the latest version of the Cumulus Smart-Seq2 workflow (v 2.4.1) on Terra and get this error:

Job smartseq2.run_rsem_pe:0:1 exited with return code 127 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.

The only error I could find in the log file is "strato: command not found" after rsem has run. I've attached the log file here.

Can you tell what's going on? FWIW, this is the first time I've used this workflow.

Thanks!

David

run_rsem_pe-0.log

Yiming Yang

unread,

Jan 20, 2024, 7:09:37 PM1/20/24

to David Lieb, cumulus...@googlegroups.com

Hi David,

Hope this email finds you well.

The issue on missing stratocumulus package has been fixed several months ago. In case I forgot to inform you, please retry the workflow, and let me know if the issue still persists.

Sincerely,

Yiming

--
You received this message because you are subscribed to the Google Groups "Cumulus Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cumulus-suppo...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cumulus-support/CAN%3DjmYtYHmvr_NK0f_CKuwkPepC78cNf%2Bcyag5xTjBNSFW284g%40mail.gmail.com.