Question: TRINITY taking forever
1
gravatar for bcking2
4 months ago by
bcking210
bcking210 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 • 220 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson22k • written 4 months ago by bcking210

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

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson22k
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson22k 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 COMMENTlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson22k
0
gravatar for luca.marisaldi
4 months ago by
luca.marisaldi30 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 COMMENTlink written 4 months ago by luca.marisaldi30
1

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 REPLYlink written 4 months ago by Jennifer Hillman Jackson22k
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson22k 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 COMMENTlink written 3 months ago by Jennifer Hillman Jackson22k
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