Open feltus opened 1 year ago
Sorry for the slow response. I can't seem to duplicate the problem. Are you still having the issue?
What file system are you using? I think we have non-standard set ups...
On Mon, Mar 6, 2023 at 8:13 PM Stephen Ficklin @.***> wrote:
Sorry for the slow response. I can't seem to duplicate the problem. Are you still having the issue?
— Reply to this email directly, view it on GitHub https://github.com/SystemsGenetics/GEMmaker/issues/277#issuecomment-1457315617, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABLBGLABAKXVWAGSYPXGWH3W22DS3ANCNFSM6AAAAAAVF4ULCU . You are receiving this because you were assigned.Message ID: @.***>
-- F. Alex Feltus, Ph.D. Professor, Clemson University - Department of Genetics & Biochemistry https://www.clemson.edu/science/departments/genetics-biochemistry/people/profiles/FFELTUS Chief Science Officer, Praxis AI LLC https://praxis-ai.com/ Member, CU Center for Human Genetics https://www.clemson.edu/science/research/chg.html Member, CU-MUSC Biomedical Data Science & Informatics Program https://www.cs.clemson.edu/bdsi/
Description of the bug
My students and I are having several issues with GEMmaker on our cluster. The most important and consistent issue is GEMMaker is running through the workflow VERY QUICKLY and quitting without writing results. It is happening with SRA pulls and with the test run like this:
module add openjdk/11.0.15_10-gcc/9.5.0 nextflow pull systemsgenetics/gemmaker nextflow run systemsgenetics/gemmaker -profile test,singularity
OR if I do a 'real' rn like this:
extflow run systemsgenetics/gemmaker -profile singularity \
Error and .nexftflow.log below.
Command used and terminal output
Relevant files
No response
System information
No response