Hello,
I am running the GATK WDL best practices pipeline with the sample data from the Google Cloud (https://github.com/broadinstitute/wdl/blob/develop/scripts/broad_pipelines/PublicPairedSingleSampleWf_160927.wdl). The pipeline hits an error close to the end, at the HaplotypeCaller scatter.
The failing command is being run like this:
INFO 01:07:19,794 HelpFormatter - --------------------------------------------------------------------------------
INFO 01:07:19,797 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 01:07:19,797 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 01:07:19,797 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 01:07:19,800 HelpFormatter - Program Args: -T HaplotypeCaller -R /home/dnanexus/execution/inputs/Homo_sapiens_assembly38.fasta -o NA12878.vcf.gz -I /home/dnanexus/execution/inputs/NA12878.bam -L /home/dnanexus/execution/inputs/scattered.interval_list -ERC GVCF --max_alternate_alleles 3 -variant_index_parameter 128000 -variant_index_type LINEAR -contamination 0 --read_filter OverclippedRead
The error is:
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.IllegalStateException: Updating last read seen in the traversal with read H06HDADXX130110:2:1101:10101:44450 2/2 250b aligned read. with span chr1:59003339-59003543 but this occurs before the previously seen read chr1:117920599-117920848
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.rememberLastReadLocation(TraverseActiveRegions.java:426)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:354)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
Runs with other interval lists succeed, but this one fails. The interval list is attached. Any ideas would be appreciated.
Thanks,
Ohad.