Question: "Unable to finish job" but no errors, data seems to be there?
gravatar for Brian Griffiths
3.2 years ago by
United States
Brian Griffiths20 wrote:


I am running a local instance of galaxy on a dual-xeon chip MB with 128 GB of ram.

I installed tophat, but when I run my fastq files through it I get "Unable to finish job."

The history turns red, and it says no errors were logged. There appears to be full datasets, but they are still marked as not finishing.

I've googled around, but the solutions seem to be related to hardware limitations (not enough RAM, which I think I'm fine on).

I tried to copy the output, but then I accidentally shut down the processes with ctrl c (windows user :/ ) and it scrolled off the page.

Does anybody know what I can do to fix this?



tophat • 1.3k views
ADD COMMENTlink modified 10 months ago by yusheng_tan0 • written 3.2 years ago by Brian Griffiths20
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


If this was a straightforward memory problem with the job, the error message would have noted that. There is likely some other issue with the local.

This is a simple thing to double check, but it is good to eliminate it: is there enough disk space available to write the final output files? 

The Galaxy log may have more details about the failure. You can share those here for more troubleshooting help. 

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

Ended up being bit having sam tools installed locally. I saw that suggestion a few questions down. It works now. :)

ADD REPLYlink written 3.2 years ago by Brian Griffiths20

Yes, that will cause many problems. Usually this is detected early on, during the first upload or other starting functions. That this tool suite should be installed first on any Galaxy instance should probably be added to our wiki. I will work with our team to put this in a few high-visibility places. Thanks for letting us know! Jen

ADD REPLYlink written 3.2 years ago by Jennifer Hillman Jackson25k
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