MuTect - No tribble type error

SebBatSebBat BuffaloMember
edited October 2015 in MuTect v1

hi all

I'm trying to run MuTect over paired tumor-normal bam files but I can't get past the following error:

ERROR A USER ERROR has occurred (version 2.2-25-g2a68eab)
ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:

ERROR Name FeatureType Documentation
ERROR BCF2 VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_bcf2_BCF2Codec.html
ERROR VCF VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html

none of the links actually sends to a working page.
the command line is the following:

java -jar muTect-1.1.4.jar \
--analysis_type MuTect \
--reference_sequence /genomes/hg19_reordered.fa \
--dbsnp dbsnp_138_hg19_reordered.vcf \
--cosmic b37_cosmic_v54_120711_reordered.vcf \
--input_file /ExomeSeq/Normal_sorted_group.bam \
--input_file /ExomeSeq/Tumor_sorted_group.bam \
--out /ExomeSeq/MuTectOutput/calls.txt \
--coverage_file ExomeSeq/MuTectOutput/coverage.txt

and the "reordered" simply indicates that the chrs are in the order 1-->22,X,Y,M

any help would be golden

thanks

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    This error usually happens when a VCF index file is corrupted. You can try deleting the VCF index files; they will be regenerated automatically by the program when you run on the VCFs. Let me know if that doesn't work for you.

    Sorry about the broken links -- they're due to a change in codebase structure several versions ago.

    By the way you may want to try using the latest version of MuTect, which you can get on the GATK downloads page.

  • SebBatSebBat BuffaloMember
    edited October 2015

    by using the last version (and deleting the index file) (it seems it can't find GATK?) I get the following error instead:

    Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
    at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
    Could not find the main class: org.broadinstitute.sting.gatk.CommandLineGATK. Program will exit.

  • SebBatSebBat BuffaloMember
    edited October 2015

    loading java 1.8 here's a new error...looks like I'm collecting them :)

    Running MuTect

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

    java.lang.ExceptionInInitializerError
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:167)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:57)
    at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:66)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:106)
    Caused by: java.lang.NullPointerException
    at org.reflections.Reflections.scan(Reflections.java:220)
    at org.reflections.Reflections.scan(Reflections.java:166)
    at org.reflections.Reflections.(Reflections.java:94)
    at org.broadinstitute.sting.utils.classloader.PluginManager.(PluginManager.java:79)
    ... 4 more

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.1-0-g72492bb):
    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 http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Code exception (see stack trace for error itself)
    ERROR ------------------------------------------------------------------------------------------

    if the new version doesn't work, any way I can fix the first error? deleting the index files didn't do it

    also, it seems that the cosmic vcf file that I got from the mutect site doesn't have a header..maybe a possible cause of the error?
    thanks

    Post edited by SebBat on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ugh, my bad. I meant to say 1.6 and 1.7, respectively. Java 1.8 isn't supported yet. Sorry about that! It's been a long day.

  • SebBatSebBat BuffaloMember

    lol no worries, it's friday :wink: !
    it seems that it's working using the latest MuTect 1.1.7 and Java 1.7.0_25.
    the analysis is running, I'll go back tonite and see if it completed and post the results

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