Question: HELP! A Runtime Error in Running Unified Genotyper
gravatar for liyingcai2014
3.4 years ago by
liyingcai201410 wrote:


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,


ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson24k • written 3.4 years ago by liyingcai201410

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 REPLYlink modified 3.4 years ago • written 3.4 years ago by fubar1.1k
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson24k wrote:


There are two known issues with this tool (captured here:
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 COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson24k

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



ADD REPLYlink written 3.4 years ago by liyingcai201410
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