Question: BWA-MEM crashes on clean sample data
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jenn.drummond • 10 wrote:
I'm trying to run a course demo on the main usegalaxy.org site, and BWA-MEM is crashing with an error that really doesn't look like my problem -- it can't find samtools. How can something that simple be broken on the main site?
Error: no such directory: /jetstream/scratch0/main/jobs/15863592/conda-env/bin
Fatal error: Exit code 127 ()
/jetstream/scratch0/main/jobs/15863592/command.sh: line 68: samtools: command not found
The workflow is at https://usegalaxy.org/u/jennformatics/h/coursera-project-1. Any ideas?
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modified 18 months ago
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Jennifer Hillman Jackson ♦ 25k
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18 months ago by
jenn.drummond • 10
Problem was transient, as suggested in the comments.
The Galaxy Main server was updated later yesterday. It is possible that there was a problem introduced. Or that a job failed due to timing versus the update.
Would you please rerun the job one time to eliminate a transient problem (server or cluster). If it fails again, please leave all datasets related the job undeleted in the history, then send an error report (bug icon) for one of the failed jobs. Please include a link to this biostars post in the comments.
We appreciate the feedback about the problem! If the rerun does work, please let us know as well. Jen, Galaxy team
UPDATE: Our administrator has identified a likely cause and is testing. More soon.
Yes, it's working now. Thanks for the quick reply! I was pretty frustrated -- uploading the data to usegalaxy.org was already my last resort, after many failed attempts to get a local instance running BWA-MEM, so having that not work was just the last straw! :)