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# UnifiedGenotyper Error

Member

HI,

I am using UG to call both SNP and INDELS across 179 different samples for RAD sequencing. I keep getting this error:

##### ERROR ------------------------------------------------------------------------------------------

The odd thing is while it repeatedly happens, it never throws the exact same error. It's always at a different place in the alignment. I tried rerunning the whole pipeline with the 8/16 nightly build (including reduce reads) and it is still doing this. I've tried with and without using a BED interval file as well.

Is there any way to get GATK to just not output a call and keep going?

Thanks!

Tagged:

• Member

To update this, it has something to do with ReduceReads. My non-reduced bams just finished without errors.

• Member

Now, I've had both reduced and non-reduced bam files produce this error.

Hi there,

Could you upload test files that reproduce the error, so that we can try to debug this locally? Instructions are in the FAQs.

• Member
edited August 2013

I have uploaded a small sample of my barflies, along with the interval file, reference, and a file that contains the exact command I was using. It is called UG.error.zip. I've had these test files both pass and fail, so please try running it a few time. Thanks.

Hi there,

I was able to reproduce your error after 5 attempts, but unfortunately it takes a long time to get there. I'll try to narrow down the issue to something more quickly repeatable. At this rate though I can't guarantee that we'll be able to fix this anytime soon. But we'll try. Thanks for the test files!

• Member

Thanks for your efforts. I am happy to see that you were at least able to repeat the error. For now, I have just split up my interval file and have a catch statement in my pipeline to rerun any partition of the intervals that fails (I realize Queue can do this, but my original analysis pipeline wasn't using it). I am also seeing about a ~20% failure rate. Hope that it can eventually be figured out!

Jon