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Question: "Unable to finish job" but no errors, data seems to be there?
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gravatar for Brian Griffiths
3.2 years ago by
Brian Griffiths • 20
United States
Brian Griffiths • 20 wrote:

Hi,

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?

Thanks,

Brian
tophat • 1.3k views
ADD COMMENT • link •
modified 10 months ago by yusheng_tan • 0 • written 3.2 years ago by Brian Griffiths • 20
1
gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
1

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

ADD REPLY • link written 3.2 years ago by Brian Griffiths • 20

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 REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
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