Stack trace Issue with UG Indel calling.

srynearson1srynearson1 Member
edited October 2013 in Ask the GATK team

Hello all,

I have narrowed down this issue to UG Indel caller.
I am currently running UG will an additional 136 1000Genome individuals to be call at the same time my variants of interest. I run my SNP and Indel calls separate as per GATK best practices. But have noticed this issue only with my Indel calls.

This is the command I'm running:

java
-Xmx32g
-jar
-Djava.io.tmpdir=/tmp/
/home/srynearson/GenomeAnalysisTK-nightly-oct/GenomeAnalysisTK.jar
-T UnifiedGenotyper
-R /home/srynearson/cAPTUrE/references/human_g1k_v37.fasta
-I [each of the 1000Genome .bam files]
-I [each of my variants of interest .bam files]
--num_threads 15
--standard_min_confidence_threshold_for_calling 30.0
--standard_min_confidence_threshold_for_emitting 30.0
--output_mode EMIT_VARIANTS_ONLY
--num_cpu_threads_per_data_thread 2
--genotype_likelihoods_model INDEL

And this is the error I get:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Alignment 88304365 | 67S24M1D8M1S
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:574)
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:438)
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(ReadUtils.java:434)
at org.broadinstitute.sting.gatk.walkers.annotator.BaseQualityRankSumTest.getElementForRead(BaseQualityRankSumTest.java:76)
at org.broadinstitute.sting.gatk.walkers.annotator.RankSumTest.getElementForRead(RankSumTest.java:200)
at org.broadinstitute.sting.gatk.walkers.annotator.RankSumTest.fillQualsFromLikelihoodMap(RankSumTest.java:179)
at org.broadinstitute.sting.gatk.walkers.annotator.RankSumTest.annotate(RankSumTest.java:102)
at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:192)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateGenotypes(UnifiedGenotyperEngine.java:560)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:234)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:367)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version nightly-2013-10-04-ge260355):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Alignment 88304365 | 67S24M1D8M1S
ERROR ------------------------------------------------------------------------------------------

I have confirmed prior files and the SNP file runs to completion.

Any ideas?
Thanks!

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Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hmm, this looks like an issue we've seen with reads that are soft-clipped. Can you try running the region around this read again with -rf BadCigar ?

  • Okay so I tried it again adding -rf BadCigar and same error. So I tried a different data set and again got the same error in the same step:

    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Alignment 88304365 | 67S24M1D8M1S

    I'm using the Bundle for all my references and knowns. Do you think this is some problem with the reference? This seem very strange given different data sets.

  • Strange, I ran the exact same data set, and command line, but this time no errors. Seems to be a strange internal thing. By reading through the forum, I have noticed others have experienced the same behavior.

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