Question: My program is running for more than 14 hrs without completing execution; how to stop it or rerun it
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gravatar for vasumk1953
5 months ago by
vasumk19530
vasumk19530 wrote:

I am running Read or replace read groups, after loading the data files and quality check with FASTQC and mapping them into BAM format MWA-MEM. This is an assignment in week 4 of Genomic Data Science with Galaxy, a coursera course. The program has been running in Galaxy for ore than 14 hours. I am unable to modify it. Should I stop it or wait. Please advise

queue job usegalaxy.org galaxy • 163 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by vasumk19530
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

It is best to allow queued jobs to stay queued. Deleting and rerunning will extend wait time as the restarted job is added back to the end of the queue.

Other problems might lead to what looks like a queued job. For example, double check that the inputs are all in a success (green) state, with no warnings.

FAQs:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k

Ps: The jobs have completed now.

There is one problem with the BWA-MEM runs that may have impacted runtime (yellow datasets, not grey like queued datasets): the paired-end data was entered in the wrong order. Correct this under the option "Single or Paired-end reads". The first set of reads are "forward" and correspond to datasets with "R1" in the name. The second set of reads are "reverse" named with "R2".

Rerun this mapping step for all three jobs.

Hope that helps!

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
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