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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
6 months ago by
vasumk1953 • 0
vasumk1953 • 0 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 • 195 views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by vasumk1953 • 0
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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