Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: GATK runtime error
0
gravatar for labella.matthew
4.2 years ago by
labella.matthew • 0
United States
labella.matthew • 0 wrote:

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 
runtime error alignment galaxy gatk • 1.0k views
ADD COMMENT • link •
modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by labella.matthew • 0
0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi 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
ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 174 users visited in the last hour