Question: Queue times to run Trinity?
0
gravatar for gg832
4 months ago by
gg83210
gg83210 wrote:

Hello,

I'm rather new to Galaxy. I'm trying to run de novo assembly for RNAseq data using Trinity on Galaxy (at usegalaxy.org). I have paried-end 150 bp reads. Total size for both data sets is approximately 126 GB. The job has been queued now for more than three days. Is this normal? I used all of the default parameters. I just want to make sure there wasn't something else I was supposed to do when I submitted the data for assembly, like specify a compute resource or notify the admins that I was submitting a job that would probably take a while to run?

Thanks in advance!

trinity galaxy rna-seq • 229 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson22k • written 4 months ago by gg83210

Thanks for reporting the issue. We are looking into this and will provide feedback soon. Thanks, 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 and your assembly job should start up now.

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson22k

Thank you, Jen! Since the job still indicates that it is 'waiting to run,' do you know how long it normally takes to begin a run? I know that it can vary depending on usage, but I'd just like to have a rough estimate so I know when to reach out to you guys if it's taking too long. If this assembly is successful, I have one more data set that I would like to run, which would be used to compare to the current data set.

ADD REPLYlink written 4 months ago by gg83210

Trinity still not running. Any update?

Thanks.

ADD REPLYlink written 4 months ago by gg83210

Trinity still not working.

M

ADD REPLYlink written 4 months ago by magdawarzecha610
0
gravatar for gg832
3 months ago by
gg83210
gg83210 wrote:

After 10 days, my run finally resulted in a "Remote job server could not determine this job's state." error. I searched this issue again, and found this answer: https://biostar.usegalaxy.org/p/22642/#22674, so I resubmitted the run. Fingers crossed!

ADD COMMENTlink written 3 months ago by gg83210
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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