Question: Queue times to run Trinity?
0
gravatar for gg832
19 months ago by
gg83220
gg83220 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 • 759 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by gg83220

Thanks for reporting the issue. We are looking into this and will provide feedback soon. Thanks, Jen, Galaxy team

ADD REPLYlink written 19 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k 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 19 months ago by Jennifer Hillman Jackson25k

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 19 months ago by gg83220

Trinity still not running. Any update?

Thanks.

ADD REPLYlink written 19 months ago by gg83220

Trinity still not working.

M

ADD REPLYlink written 19 months ago by magdawarzecha610
0
gravatar for gg832
19 months ago by
gg83220
gg83220 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 19 months ago by gg83220
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k 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 19 months ago by Jennifer Hillman Jackson25k
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