Question: Continued problems since Galaxy update
gravatar for cgamper1
2.6 years ago by
United States
cgamper110 wrote:


I have been unable to make any progress in running an RNAseq analysis using HISAT2 on a collection of samples. When I posted the job on Friday, it appeared to complete but only 2 of the 3 samples in the collection generated BAM file output. The third was blank. To rerun and keep it as a collection (which I would like to do for the downstream analysis), Galaxy requires reposting alignment of all 3 samples rather than rerunning the individual missing one. When I posted this job it took about 12 hours for the first of the 3 datasets to transition from grey to yellow but this first dataset undergoing analysis wasn't complete even after about 24 hours and the other 2 remained grey (not run). The HISAT run should only require less than half an hour of compute resources so I am not sure why these jobs never post or complete. This Galaxy upgrade has been an entirely frustrating experience. Time to downgrade? Perhaps I can run each file individually and put the BAM output in a collection instead?


software error • 622 views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by cgamper110
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


There were server issues until just a small time ago. Jobs can be re-run now.

At this time, it might be best to run the failed jobs then create a collection after that.

The version of Galaxy running is the core problem - other recent configuration changes are the primary reason for failures. These should resolve shortly. If work is urgent, using a local or cloud Galaxy might be a good option.

Thanks for your patience and our apologies for the recent job issues, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
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