Question: Continued problems since Galaxy update
0
gravatar for cgamper1
21 months ago by
cgamper110
United States
cgamper110 wrote:

Hi,

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?

Chris

software error • 422 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson24k • written 21 months ago by cgamper110
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

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. https://wiki.galaxyproject.org/BigPicture/Choices

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

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 107 users visited in the last hour