Question: BWA-MEM crashes on clean sample data
gravatar for jenn.drummond
4 months ago by
jenn.drummond10 wrote:

I'm trying to run a course demo on the main 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/ line 68: samtools: command not found

The workflow is at Any ideas?

bwa-mem • 105 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson22k • written 4 months ago by jenn.drummond10

Problem was transient, as suggested in the comments.

ADD REPLYlink written 4 months ago by jenn.drummond10

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.

ADD REPLYlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson22k

Yes, it's working now. Thanks for the quick reply! I was pretty frustrated -- uploading the data to 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! :)

ADD REPLYlink written 4 months ago by jenn.drummond10
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson22k wrote:


Thanks for sending this in. Our administrator made a change to the server for this and a few other tools this morning. The problem was newly introduced last night during a software update.

It is Ok to rerun the jobs now as long as the targetted cluster is either Stampede or the Default cluster (we call it Roundup). The other cluster available is Jetstream (the other clusters are for testing only). Jetstream is still producing the error and should be avoided, or expect jobs to continue to fail when run there until the final changes are made (fail by chance when no cluster is chosen or if choosing Jetstream specifically).

The cluster for a job can be user-specified for several tools, including this tone, at the end of the list of tool form options. Usually the last one. Help:

Thanks again and please let us know if future runs are a problem.

Jen, Galaxy team

ADD COMMENTlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson22k
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