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Created 2013-10-06 17:28:09 | Updated 2013-10-06 17:29:10 | Tags: indel
Comments (4)

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!


Created 2013-05-11 21:57:53 | Updated | Tags: reducereads
Comments (2)

Hello all thank for the great work.

I have run into an issue with ReduceReads and I was hoping you could offer some insite. I'm getting the following stack trace issue (attached file). I looked around the forums, and others who were getting stack trace issue using ReduceReads were told code fixes would remedy the issue so I thought I would check with you. I also ran samtools flagstat.