User: brian.hermann

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1 year, 11 months ago
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3 years, 3 months ago
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Posts by brian.hermann

<prev • 44 results • page 1 of 5 • next >
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Comment: C: TopHat jobs failing - Failed to find or download one or more job outputs from re
... Hi Jen, I wanted to touch base with you again about my troubles running these kinds of jobs on usealaxy.org. I am now routinely (100%) obtaining the following error "Remote job server indicated a problem running or monitoring this job." I have tried rerunning the jobs, but it seems to be persistent ...
written 2.4 years ago by brian.hermann40
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How to resolve Cufflinks Fatal error: Matched on ERROR
... Hi, I've been running some RNA-seq analysis jobs on the Galaxy test server with PapAnu2 built-in and TopHat ran fine, but Cufflinks failed with the following error. I noticed the banner on Usegalaxy indicating some jobs were running on Jetstream and noted the job was queued for Jetstream. I couldn' ...
cufflinks software error written 2.4 years ago by brian.hermann40 • updated 2.4 years ago by Jennifer Hillman Jackson25k
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Comment: C: TopHat jobs failing - Failed to find or download one or more job outputs from re
... Thanks Jen, this is very helpful. Thanks for all you and your team do to provide outstanding informatics infrastructure. Best, Brian From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Monday, May 02, 2016 7:43 PM To: Brian Hermann Brian.Hermann@utsa.edu Sub ...
written 2.5 years ago by brian.hermann40
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TopHat jobs failing - Failed to find or download one or more job outputs from remote server.
... Hi, I seem to be running into a problem on the galaxy test server (due to availability of a new genome annotation - PapAnu2). I am receiving the following errors from the test server: "Failed to find or download one or more job outputs from remote server" and "Failed to communicate with remote job ...
galaxy tophat written 2.5 years ago by brian.hermann40 • updated 2.5 years ago by Jennifer Hillman Jackson25k
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Papio Anubis 2.0 genome annotation
... Hello, I was wondering if there was a possibility of adding the papAnu_2.0 annotation as a built-in genome for gene expression tools such as TopHat. Thanks very much for considering this request.   Best, Brian ...
galaxy built-in genome baboon written 2.7 years ago by brian.hermann40 • updated 2.6 years ago by Jennifer Hillman Jackson25k
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Comment: C: Random tool failures
... I tried rerunning some of the jobs overnight and they seemed to be doing fine (no failures) until ~8am ET this morning, although they were running slowly. ...
written 2.7 years ago by brian.hermann40
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Comment: C: Random tool failures
...  Hi Jennifer, As you suggested, I reran a batch of jobs that had previously failed and still getting error outs.  See below for an example from tophat.  One of the tophat jobs completed, but most failed.  I guess I will sit tight until I hear back again from you whether there are additional issues. ...
written 2.7 years ago by brian.hermann40
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Comment: C: Random tool failures
... Hi Jennifer, I reran some cuffnorm jobs (on Usegalaxy.org) and had the same result (see below).  I noticed that some of the jobs from the previous batch did complete correctly even after this post, but none (so far) on the re-run.  Thanks for your help. Best, Brian   Traceback (most recent cal ...
written 2.7 years ago by brian.hermann40
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Answer: A: Random tool failures
... hi Jen, Thanks for your reply.  I thought I was running these on the main usegalaxy.org server.  I noticed that queued jobs starting running again, so perhaps this was just overloaded clusters?  I submitted bug reports referencing this post and will leave the files. Will re-run today and let you kn ...
written 2.7 years ago by brian.hermann40
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Random tool failures
... Hi, I've encountered a series of tool failures over the past day or so, the most recent being TopHat and Cuffnorm runs on a dataset collection.  The most recent failures were due to "failure preparing job" and "failure preparing job script" and "Cluster could not complete job." I noted the followin ...
galaxy written 2.7 years ago by brian.hermann40

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