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Error - MuTect 1.1.4 and java 1.7.0_09 used

I met an error while using MuTect 1.1.4 on java 1.7.0_09.

]$ java -version
java version "1.7.0_09-icedtea"
OpenJDK Runtime Environment (rhel-2.3.4.1.el6_3-x86_64)
OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)

The command line is below:

java  -Xmx5g -jar  muTect-1.1.4.jar  --analysis_type MuTect  --reference_sequence  /lustre/DB_Analy/HG_19_Proton/hg19.fasta  --dbsnp  dbsnp_138.hg19.sort.vcf  --cosmic  reorder.mod.vcf  --input_file:normal  2014_01_28_Lim___Geun_Normal.bam  --input_file:tumor  2014_01_28_Lim___Geun_Tumor.bam  --out  example.call_stats.txt  --coverage_file example.coverage.wig.txt

and the error messages:

INFO  13:11:24,238 HelpFormatter - ---------------------------------------------------------------------------------
INFO  13:11:24,240 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012/11/08 10:30:02
INFO  13:11:24,240 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  13:11:24,240 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  13:11:24,244 HelpFormatter - Program Args: --analysis_type MuTect --reference_sequence /lustre/DB_Analy/HG_19_Proton/hg19.fasta --dbsnp dbsnp_138.hg19.sort.vcf --cosmic reorder.mod.vcf --input_file:normal 2014_01_28_Lim___Geun_Normal.bam --input_file:tumor 2014_01_28_Lim___Geun_Tumor.bam --out example.call_stats.txt --coverage_file example.coverage.wig.txt
INFO  13:11:24,244 HelpFormatter - Date/Time: 2014/02/21 13:11:24
INFO  13:11:24,244 HelpFormatter - ---------------------------------------------------------------------------------
INFO  13:11:24,244 HelpFormatter - ---------------------------------------------------------------------------------
INFO  13:11:24,263 ArgumentTypeDescriptor - Dynamically determined type of dbsnp_138.hg19.sort.vcf to be VCF
INFO  13:11:24,268 ArgumentTypeDescriptor - Dynamically determined type of reorder.mod.vcf to be VCF
INFO  13:11:24,275 GenomeAnalysisEngine - Strictness is SILENT
INFO  13:11:24,319 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE Target Coverage: 1000
INFO  13:11:24,326 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO  13:11:24,716 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.39
INFO  13:11:24,735 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_138.hg19.sort.vcf
INFO  13:11:24,849 RMDTrackBuilder - Loading Tribble index from disk for file reorder.mod.vcf
INFO  13:11:24,936 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  13:11:24,937 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
Error processing chr1:6529709
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.mergeCollapse(TimSort.java:410)
        at java.util.TimSort.sort(TimSort.java:214)
        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)
##### 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)
(........)
##### 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 ------------------------------------------------------------------------------------------

Searching here the forum, this sort of issues are found when new version of java (1.7) goes with MuTect old one,
or old java with MuTect new. And the latest MuTect seems to go well with java 1.7.
So I'm still in trouble. I can not figure out what's wrong there.

Answers

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