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Question: HELP! A Runtime Error in Running Unified Genotyper
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gravatar for liyingcai2014
4.1 years ago by
liyingcai2014 • 10
China
liyingcai2014 • 10 wrote:

Hi,

I'm having problems in running the workflow of cloudmap.

When it gets to "Unified Genotyper". It shows runtime error.

Please give me some suggestions!

Thanks a lot,

Yi
unified genotyper runtime error cloudmap • 1.1k views
ADD COMMENT • link •
modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by liyingcai2014 • 10

One suggestion I have is that you provide enough details in your question to enable someone to understand or at least make a guess about what the specific cause might be. If you get a chance to complete a bug report form during the error reporting process, that would make it easier.  

 

ADD REPLY • link modified 4.1 years ago • written 4.1 years ago by fubar ♦ 1.1k
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There are two known issues with this tool (captured here: https://trello.com/c/plQYSCvS).
Perhaps one of these applies to your case?

Problem 1:
This tool produces an error when the option "Genotype likelihoods calculation model to employ:" is set as "BOTH". When either of the two alternatives are selected individually instead, the job runs without issue. Occurs with both custom reference genomes or when using hg_g1k_v37.

Problem 2:
Same exact error is reported for some datasets when this option is set to "INDEL" and the Rod file is the dbSNP vcf from the GATK bundle. It is not clear if this is a resource issue.

If so, then try to work-around for the first, and try an alternate reference file for the second.

Just a guess, but seemed worth sharing. Best, Jen, Galaxy team

 
ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks. Actually, When I increased the value of mapping quality, it got through.

Best,

Yi

ADD REPLY • link written 4.1 years ago by liyingcai2014 • 10
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