Hello, I'm repeatedly getting a runtime error with GATK, the unified genotyper. My workflow has worked with a number of my paired end samples, but for a couple of them I keep getting the error. Any help is greatly appreciated. Thanks! -Matt
Where are you working? On most servers, you can click on the bug icon to review details about the error. Information may also be on the "Info" page under stdout/stderr (accessed by clicking on the "i" circle icon). GATK often provides very detailed messages about the problem - generally formatting or other input problems. If working on Main, it could be that the job is too large to run on the server.
If you are working on Main (http://usegalaxy.org) and are still not sure what the problem is after reviewing the error logs, you can send in the bug report and we can provide feedback.
Thanks, Jen, Galaxy team