Hi,
I'm trying to build a pon with GATK 3.7-0 to use with mutect2. For that, I've downloaded 80 exome bam files from the 1000g project (GBR, TSI, IBS and CEU populations).
For most of them, when I try to use the artifact_dectection_mode, I get a GATK runtime error saying 'READ_MAX_LENGTH must be > 0 but got 0'.
To try you can, for example, download ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00116/exome_alignment/HG00116.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam
I'm using the b37 reference files from the bundle_gatk_2_8 and the bed file of SureSelect6 from Agilent .
Here the full stack trace and command line :
INFO 09:42:32,040 HelpFormatter - ------------------------------------------------------------------------------------
INFO 09:42:32,045 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 09:42:32,045 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 09:42:32,045 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 09:42:32,045 HelpFormatter - [Thu Apr 06 09:42:32 GMT 2017] Executing on Linux 2.6.18-275.12.1.el5.573g0000 amd64
INFO 09:42:32,045 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b25
INFO 09:42:32,049 HelpFormatter - Program Args: -T MuTect2 -I:tumor /data/misc/mutect2/pon/1000g_bam/HG00116.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam --db
snp /data/highlander/reference/bundle_gatk_2_8/b37/dbsnp_138.b37.vcf --artifact_detection_mode -L /data/highlander/reference/bundle_gatk_2_8/b37/capture.sureselect6.bed -R /data/highlander/reference/bundle_gatk_2_8/b37/human_g1k_v37.fasta -o /data/misc/mutect2/pon/1000g_vcf_normal/HG00116.vcf.gz
INFO 09:42:32,062 HelpFormatter - Executing as lifescope@n3 on Linux 2.6.18-275.12.1.el5.573g0000 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b25.
INFO 09:42:32,062 HelpFormatter - Date/Time: 2017/04/06 09:42:32
INFO 09:42:32,062 HelpFormatter - ------------------------------------------------------------------------------------
INFO 09:42:32,063 HelpFormatter - ------------------------------------------------------------------------------------
...
ERROR --
ERROR stack trace
java.lang.IllegalArgumentException: READ_MAX_LENGTH must be > 0 but got 0
at org.broadinstitute.gatk.utils.pairhmm.PairHMM.initialize(PairHMM.java:126)
at org.broadinstitute.gatk.utils.pairhmm.N2MemoryPairHMM.initialize(N2MemoryPairHMM.java:60)
at org.broadinstitute.gatk.utils.pairhmm.LoglessPairHMM.initialize(LoglessPairHMM.java:66)
at org.broadinstitute.gatk.utils.pairhmm.PairHMM.initialize(PairHMM.java:159)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.initializePairHMM(PairHMMLikelihoodCalculationEngine.java:267)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngine.java:282)
at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:644)
at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:171)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
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:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: READ_MAX_LENGTH must be > 0 but got 0
ERROR ------------------------------------------------------------------------------------------
Am I doing something wrong or is it some kind of bug :-) ?
Thank you in advance for your help
Raphael