Question: Jobs taking forever and not running
gravatar for bscarpe
6 weeks ago by
bscarpe0 wrote:

For the last 3 weeks I have not been able to get a job to run in galaxy on this server. Is this a problem of backlog or something specific to me?

galaxy • 99 views
ADD COMMENTlink modified 6 weeks ago by Jennifer Hillman Jackson25k • written 6 weeks ago by bscarpe0

Sorry, I will add a little more detail. I have been trying to run DeepTools - BamCompare jobs on RNAseq BAM files that were output from HISAT2? The jobs are running for a long time and eventually terminating due to taking to long to run. I ran the first replicate through without any problems a few weeks ago but I am stuck with this replicate.

Any suggestions? Brandon

ADD REPLYlink written 6 weeks ago by bscarpe0
gravatar for Jennifer Hillman Jackson
6 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


The history you were working in has been permanently deleted (purged) and the rest are empty. I don't see anything obviously wrong with the input BAMs (all runs based on the same genome, have results, around the same mapping rates, similar size).

As far as I can tell, the job was simply too large to run at the public server Galaxy Main with the given parameters/content. Using "Ignore duplicates" might be a factor -- instead, these could be removed first with the tool RmDup in a distinct step to break the job up. You could also try pre-filtering the BAM on other attributes: mapping quality, properly paired reads, exclude unmapped, etc. Downsampling or setting a larger bin size are also options.

If all else fails and/or changing the run parameters doesn't meet your research goals, moving to your own Galaxy where more resources can be allocated would be the solution.

FAQ: My job ended with an error. What can I do?

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 weeks ago by Jennifer Hillman Jackson25k

Thanks Jen! This is super helpful

ADD REPLYlink written 26 days ago by bscarpe0
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