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Welcome to the MuTect Support Forum

kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭
edited October 2012 in MuTect v1

Welcome to the MuTect support forum. I'll do my best to answer any questions you have regarding MuTect, how to optimally run it, and how to interpret the results. The current documentation, though sparse, is located at

https://confluence.broadinstitute.org/display/CGATools/MuTect

To ask a new question, please create a new discussion thread using the "Ask a Question" button in the left hand side menu.

Welcome, and thank you for using MuTect for all your somatic point detection needs ;)

Kristian Cibulskis, Author of MuTect
Broad Institute, Cancer Genome Analysis

Post edited by Geraldine_VdAuwera on
Tagged:

Answers

  • Hi

    I am new and I tried to run Mutect but this is the errorr that I faced

    ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:

    ERROR contig reads = chrM / 16571
    ERROR contig reference = chrM / 16569.
    ERROR reads contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_gl000193_random, chr4_gl000194_random, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
    ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]

    could you please help me?

  • AlessandroAlessandro Member

    Hi!
    I'm trying to run muTect, I report this error message

    Error processing chr1:136456
    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:471)
    at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:32)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:168)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:156)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:229)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:200)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:44)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociBase.traverse(TraverseLociBase.java:61)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociBase.traverse(TraverseLociBase.java:16)
    at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:70)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
    at java.lang.Thread.run(Thread.java:722)
    at org.broadinstitute.sting.utils.threading.EfficiencyMonitoringThreadFactory$TrackingThread.run(EfficiencyMonitoringThreadFactory.java:154)

    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:714)
    at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:32)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:168)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:156)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:229)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:200)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:44)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociBase.traverse(TraverseLociBase.java:61)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociBase.traverse(TraverseLociBase.java:16)
    at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:70)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
    at java.lang.Thread.run(Thread.java:722)
    at org.broadinstitute.sting.utils.threading.EfficiencyMonitoringThreadFactory$TrackingThread.run(EfficiencyMonitoringThreadFactory.java:154)
    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.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:471)
    ... 15 more

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.1-202-g2fe6a31):
    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 ------------------------------------------------------------------------------------------

    Could you help me please?=)

  • vyellapavyellapa Member

    Are you using -nt or -nct options? If so, I dont think Mutect supports it.

    Naji

    Its looks like the bam was aligned to a different reference compared to what youre providing to Mutect. Are you sure its the same reference?

  • rgfowlerrgfowler Member

    I have the same error as Alessandro, and I did use the same reference for alignment and mutect. Since mine was run with a different version of the GATK, but I won't clutter with a dump unless it would help, since it looks very similar. Is there any further guidance available now?

    Thanks,
    Jerry

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