Question: Problem with Trinity/Unicycler at https://usegalaxy.org -- Unicycler fixed, Trinity OPEN, follow for updates
3
gravatar for j_pasook
21 days ago by
j_pasook40
j_pasook40 wrote:

Hi,

I've tried to execute my work using Trinity (Beta) via Galaxy. Every time I execute it shows this error to me;

Can't locate Sys/Hostname.pm: Permission denied at /opt/packages/trinity/2.2.0/PerlLib/HPC/FarmIt.pm line 13. BEGIN failed--compilation aborted at /opt/packages/trinity/2.2.0/PerlLib/HPC/FarmIt.pm line 13. Compilation failed in require at /opt/packages/trinity/2.2.0/PerlLib/HPC/GridRunner.pm line 10. BEGIN failed--compilation aborted at /opt/packages/trinity/2.2.0/PerlLib/HPC/GridRunner.pm line 10. Compilation failed in require at /opt/packages/trinity/2.2.0/Trinity line 29.

I don't know it is because of my data or a server. Please help

Thanks

ADD COMMENTlink modified 13 days ago by Jennifer Hillman Jackson25k • written 21 days ago by j_pasook40

Hello, This might be related to some other known issues with the server at https://usegalaxy.org. Please follow this post for updates: https://biostar.usegalaxy.org/p/28860/.

I'll also run a test Trinity job to see if that cluster is also problematic - it was last week, then passed as Ok, yet other jobs that run there (Unicycler) are still erroring. It could be a distinct issue, more feedback once the tests complete.

Thanks for reporting the problem, Jen, Galaxy team

ADD REPLYlink written 21 days ago by Jennifer Hillman Jackson25k
1

Thanks!! I will look forward to it. Hoping that it'll get fixed soon

ADD REPLYlink written 20 days ago by j_pasook40

I confirmed the problem with a test run: https://github.com/galaxyproject/usegalaxy-playbook/issues/152#issuecomment-407475285

More feedback once this is fixed.

ADD REPLYlink written 20 days ago by Jennifer Hillman Jackson25k
4
gravatar for Jennifer Hillman Jackson
17 days ago by
United States
Jennifer Hillman Jackson25k wrote:

UPDATE 7-27-2018

Status:

  • Unicycler -- jobs should run correctly now (passed tests). Please let us know if you encounter a server error from a job started mid-day today or later.

  • Trinity -- jobs are still failing server-side, we are working on this still

Thanks! Jen, Galaxy team

ADD COMMENTlink written 17 days ago by Jennifer Hillman Jackson25k

Is there any ETA on the fix for Trinity?

ADD REPLYlink written 9 days ago by nathanshaner20
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