IllegalArgumentException while executing MuTect

HoondyHoondy Posts: 1Member

Hello fellow muTect experts,

I am executing muTect 1.1.4 for the first time. I using the following arguments

java -Xmx2g -jar $mutect --analysis_type MuTect --reference_sequence $ref --cosmic $cosmic --dbsnp $dbsnp --input_file:normal $input4 --input_file:tumor $input1 --out A_call_stats.out --coverage_file A_coverage.wig.txt

and it seems to work fine until I saw this exception msg. It says comparison method violates its general contract and I am not sure what it means.

INFO 10:37:18,258 HelpFormatter - --------------------------------------------------------------------------------- INFO 10:37:18,278 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012/11/08 10:30:02 INFO 10:37:18,278 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 10:37:18,278 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 10:37:18,282 HelpFormatter - Program Args: --analysis_type MuTect --reference_sequence /comm/home/dhlee/Library/human_v37/human_g1k_v37.fasta --cosmic /comm/home/dhlee/Library/human_v37/Cosmic_Sorted_Merged_v63_300113.vcf --dbsnp /comm/home/dhlee/Library/human_v37/dbsnp_137.b37.vcf --input_file:normal /comm/home/dhlee/Analysis/20130129_NGS/s_7_8.recal.bam --input_file:tumor /comm/home/dhlee/Analysis/20130129_NGS/s_1_2.recal.bam --out A_call_stats.out --coverage_file A_coverage.wig.txt INFO 10:37:18,282 HelpFormatter - Date/Time: 2013/02/15 10:37:18 INFO 10:37:18,282 HelpFormatter - --------------------------------------------------------------------------------- INFO 10:37:18,283 HelpFormatter - --------------------------------------------------------------------------------- INFO 10:37:18,440 ArgumentTypeDescriptor - Dynamically determined type of /comm/home/dhlee/Library/human_v37/dbsnp_137.b37.vcf to be VCF INFO 10:37:18,574 ArgumentTypeDescriptor - Dynamically determined type of /comm/home/dhlee/Library/human_v37/Cosmic_Sorted_Merged_v63_300113.vcf to be VCF INFO 10:37:18,581 GenomeAnalysisEngine - Strictness is SILENT INFO 10:37:19,054 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE Target Coverage: 1000
INFO 10:37:19,061 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 10:37:19,376 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.31 INFO 10:37:19,803 RMDTrackBuilder - Loading Tribble index from disk for file /comm/home/dhlee/Library/human_v37/dbsnp_137.b37.vcf INFO 10:37:22,330 RMDTrackBuilder - Loading Tribble index from disk for file /comm/home/dhlee/Library/human_v37/Cosmic_Sorted_Merged_v63_300113.vcf INFO 10:37:22,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 10:37:22,865 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 10:37:34,286 MuTect - [MUTECTOR] Processed 1000021 reads in 9274 ms INFO 10:37:40,672 MuTect - [MUTECTOR] Processed 2000721 reads in 6386 ms INFO 10:37:43,984 MuTect - [MUTECTOR] Processed 3000721 reads in 3312 ms INFO 10:37:46,216 MuTect - [MUTECTOR] Processed 4000917 reads in 2232 ms INFO 10:37:50,936 MuTect - [MUTECTOR] Processed 5001109 reads in 4720 ms INFO 10:37:53,860 ProgressMeter - 1:368649 3.60e+05 31.0 s 86.0 s 0.0% 72.4 h 72.4 h INFO 10:37:55,905 MuTect - [MUTECTOR] Processed 6001110 reads in 4969 ms INFO 10:37:57,043 MuTect - [MUTECTOR] Processed 7001327 reads in 1138 ms INFO 10:37:58,876 MuTect - [MUTECTOR] Processed 8001498 reads in 1833 ms INFO 10:38:01,653 MuTect - [MUTECTOR] Processed 9001501 reads in 2777 ms INFO 10:38:01,676 MuTect - [MUTECTOR] Inspected 1000 potential candidates INFO 10:38:03,389 MuTect - [MUTECTOR] Processed 10001597 reads in 1736 ms Error processing 1:1110991 java.lang.IllegalArgumentException: Comparison method violates its general contract! at java.util.TimSort.mergeLo(TimSort.java:747) at java.util.TimSort.mergeAt(TimSort.java:483) at java.util.TimSort.mergeForceCollapse(TimSort.java:426) at java.util.TimSort.sort(TimSort.java:223) at java.util.TimSort.sort(TimSort.java:173) at java.util.Arrays.sort(Arrays.java:659) at java.util.Collections.sort(Collections.java:217) at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:480) at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:34) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93) INFO 10:38:08,226 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.RuntimeException: java.lang.IllegalArgumentException: Comparison method violates its general contract! at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:712) at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:34) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93) Caused by: java.lang.IllegalArgumentException: Comparison method violates its general contract! at java.util.TimSort.mergeLo(TimSort.java:747) at java.util.TimSort.mergeAt(TimSort.java:483) at java.util.TimSort.mergeForceCollapse(TimSort.java:426) at java.util.TimSort.sort(TimSort.java:223) at java.util.TimSort.sort(TimSort.java:173) at java.util.Arrays.sort(Arrays.java:659) at java.util.Collections.sort(Collections.java:217) at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:480) ... 14 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-25-g2a68eab):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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: java.lang.IllegalArgumentException: Comparison method violates its general contract!
ERROR --------------------------------------------------------------------------------------------------------------------------------------------

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