Question: FASTQ Groomer is taking a long time to process one file
gravatar for msh
3.1 years ago by
United States
msh0 wrote:


I'm using the Main Galaxy instance to process RNA-seq FASTQ files. I used the batch mode to run 6 datasets through the FASTQ Groomer tool. 5 of the files were processed fairly quickly, but the 6th has been "running" for over 24 hours now. 

I'm not sure if there is a problem with the server, or if there is a problem with this particular file. Should I delete the job that seems stalled and re-run, or keep waiting? 


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ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by msh0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The usual advice given is to never restart a job. Jobs are never "lost" even if delayed for some reason like a transient cluster issue. These will either execute or fail. There are quotas on how many jobs can be run by any user at any one time. So I wonder if the "24 hrs" includes wait time (grey) while the other jobs processed (yellow to green).

That said, in this specific case, if the job has been executing (yellow) for more than 24 hours that is unexpected. I would go ahead and re-run it and then permanently delete the one executing (this will get it to exit quickly).

If the job takes longer the next pass through, the content is likely a factor. Just let the job run to completion. And consider running FastQC on the original dataset. If you need to double check the correct settings to use with the Groomer, the info here for Fastq Datatype QA should help.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k

Thanks Jen, 

I will try re-running as you suggest. And yes, it's been executing (yellow) for more than a day. Other jobs have run to completion during the time that this particular file stayed yellow. 

ADD REPLYlink written 3.1 years ago by msh0
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