Question: why Tophat very very slow on the galaxy project last 2 days?
gravatar for Fat.eldefrawy
7 months ago by
Fat.eldefrawy10 wrote:

Hi everybody, I was using Tophat last week it was a little bit fast, now I'm trying to run a job with the same data set have been used last week, but the job hanged without any progress. this also occurs when running cufflink jobs I rerun the jobs many times, unfortunately, wasn't lucky. any explanation, please Fat

ADD COMMENTlink modified 7 months ago • written 7 months ago by Fat.eldefrawy10
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


It looks like your jobs have now completed. It is better to not delete/rerun jobs that are queued, as the original job placement is lost, and the new job is added back at the end of the queue, extending wait time.

We are doing some cluster upgrades, which may be contributing to longer wait times. Jobs that fail for exceeding resources have a different error message than usual reported (we are updating this). Until done, this means that others working on the same server are likely doing many reruns for job failures of this type (by not understanding the new reporting). This should all be cleared up soon -- once done, we'll remove the banner on the server with the notification and update our support FAQs as needed.

Also - the Cuffdiff failures are probably because the reference annotation (galGal5) input is a mismatch for the reference genome (galGal4) used for mapping/BAM inputs.

Support FAQs:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
gravatar for Fat.eldefrawy
7 months ago by
Fat.eldefrawy10 wrote:

Hello Jen, Thanks for the kind response, I have used galGal4 ( from iGenome) as reference annotation and also used galGal4 as a reference genome but still get the error reference annotation., Does the archiving time version of galGal4 may make mismatch? as galGal4 annotation (iGenom) has 3 archived GtF files with different dates, I have used the one archived on -2015-07-17-14-31-25 do you think I have to try either archive-2014-05-23-16-03-55 or archive-2013-03-06-09-55-59? Fat

ADD COMMENTlink written 7 months ago by Fat.eldefrawy10

You could try that, but I am wondering if there is some other problem going on. This data should be a match -- once UCSC releases a genome, it does not change. Reference annotation created against that genome can change but the underlying links between the base genome/build do not (genome source/build and related dataset chromosome length/names are the anchors) - and that should be consistent with this data source.

Would you please send in a new bug report from this test? In the comments, please include:

  1. A link to this post to connect the two
  2. The exact link you used to download the iGenomes archive
  3. The paths inside the archive to the two files you uploaded and used in the failed job(s): -- a) path to genome fasta file -- b) path to GTF annotation file.

Please leave all inputs and the error datasets, plus any test/reformatting datasets, left as active (not deleted/purged) so we can review and provide feedback. I'll send details back via email and post a summary back here only if there is a larger problem with the source data, tool/server issue, etc (info that will help others, generalized).

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson25k
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