TRINITY taking forever

Question: TRINITY taking forever

19 months ago by

bcking2 • 20 wrote:

I am trying to build a transcriptome from RNA NGS data in FASTQ format using TRINITY. It has been well over three days and it still shows that the analysis data sets are "waiting" to be processed. Is that normal?

Thanks!

Brian

assembly trinity galaxy rna-seq • 658 views

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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by bcking2 • 20

Thanks for reporting the issue. We are looking into the problem and will reply when resolved. Jen, Galaxy team

ADD REPLY • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The issue has been corrected with the Trinity connection to Bridges at PSC this morning.

Due to the nature of the problem, any current Trinity jobs should be re-run. Use the "rerun" double arrow button within the current gray dataset to start these quickly up as an exact run of the originals. Then you can permanently delete those older stalled Trinity runs.

Anyone with stalled Trinity jobs from this week should do the same. The rerun/delete instructions are specific to this tool, this specific problem, at this particular time.

Thanks again for reporting the problem and your patience while we made the correction. Please let us know if your jobs does not start up within the next 24 hours (likely will start sooner).

Jen, Galaxy team

ADD COMMENT • link modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

luca.marisaldi • 30

luca.marisaldi • 30 wrote:

Hi Jennifer,

I write you to report that once again, apparently, Trinity seems not working. Even if I did exactly what you said and also performed separately a small trial, the Trinity step always shows "waiting to run".

Hope this issue is going to fixed soon because after almost a week of troubles I would need to proceed further with my analysis.

Thank you for your help!

Luca

ADD COMMENT • link written 19 months ago by luca.marisaldi • 30

A second correction has been made. Please see this post for details: https://biostar.usegalaxy.org/p/22682/#22692

Thanks for testing again and the follow-up. Should you or others have problems again, please let us know.

Jen, Galaxy team

ADD REPLY • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Update:

Trinity was corrected again mid-day Friday 4/28/17 EST. Please re-run any jobs that failed.

If you have jobs that were started after that time, those will also need to be re-run (and the original grey jobs deleted/purged).

Sorry for the inconvenience, Jen, Galaxy team

ADD COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k

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