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Question: Bowtie2/BWA-MEM remain waiting to run for several days in Main server. Is it only in my account?
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gravatar for David Wilson
3.4 years ago by
David Wilson • 30
Spain
David Wilson • 30 wrote:

Hi all,

I've been trying to run Bowtie2 and BWA-MEM with several datasets and in different histories in the Galaxy Main Server. I waited for several Bowtie2/BWA-MEM jobs to start for 2 days with no success. Other tools work as expected. Has anyone had the same problem? I other words, is it a problem with the tools?

 

Thanks

 

David
bwa software error bowtie • 1.0k views
ADD COMMENT • link •
modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by David Wilson • 30
0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There were some issues with the long running cluster Stampede this week that is linked to job delays and certain failures. Even if you started these jobs on the default cluster, it is possible they were moved to Stampede due to the size of the job.

In short, leave current jobs in the queue so that they will execute and give any failed jobs one re-run before reporting a problem with the tool (unless it clearly fails for memory or wall-time: Support see section 2.8). Both are the quickest paths for getting work done on http//usegalaxy.org.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
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