Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

Regards
GATK Staff

a problem about "ExceptionInInitializerError" from running Mutect1.1.7.jar

xdzperfectxdzperfect Beijing Institute of genomicsMember

Dear mutect developers,
When I using the following command to do calling snp \indel,
$java -Xmx1g -jar $mutect_bin/mutect-1.1.7.jar \
--analysis_type MuTect \
--reference_sequence $GATK_ref/2.8/ucsc.hg19.fasta \
--cosmic $GATK_ref/2.8/hg19_cosmic_v54_120711.vcf \
--dbsnp $GATK_ref/2.8/dbsnp_132_b37.leftAligned.vcf \
--intervals 1:1-249250621 \
--input_file:normal $normal/chr1.merged.uniqPairs.sort.dupMarked.addGR.order.realn.bam \
--input_file:tumor $primary/chr1.merged.uniqPairs.sort.dupMarked.addGR.order.realn.bam \
--out chr1_n6Vp5_call_stats.txt \
--coverage_file chr1_n6Vp5_coverage.wig.txt

***************

I got problem:

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 ------------------------------------------------------------------------------------------

I'm confused by that ,could you tell me how to conquer it,thank you!

Xu,ZhengZheng
Beijing Institute of Genomics,Chinese Academy of Sciences

Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    Are you using Java version 1.7? No other version is supported. Other versions may cause errors similar to this.

  • xdzperfectxdzperfect Beijing Institute of genomicsMember

    Hi Geraldine_VdAuwera
    thanks for you kind help,I just using java 1.8,so I change it ,but when I using java 1.7,command as following:
    java -Xmx8g -jar $mutect_bin/mutect-1.1.7.jar \
    --analysis_type MuTect \
    --reference_sequence $GATK_ref/2.8/ucsc.hg19.fasta \
    --cosmic $Mutect_ref/hg19_cosmic_v54_120711.vcf \
    --dbsnp $Mutect_ref/dbsnp_132_b37.leftAligned.vcf \
    --intervals chr1:1-249250621 \
    --input_file:normal $normal \
    --input_file:tumor $primary \
    --out chr1_n6Vp5_call_stats.txt \
    --coverage_file chr1_n6Vp5_coverage.wig.txt
    I got error as following:

    ERROR MESSAGE: Input files /leofs/ciwm_group/xuzhzh/rawdata/Mutect_ref/dbsnp_132_b37.leftAligned.vcf and reference have incompatible contigs: No overlapping contigs found.
    ERROR /leofs/ciwm_group/xuzhzh/rawdata/Mutect_ref/dbsnp_132_b37.leftAligned.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT]
    ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, 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_ctg5_hap1, 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]

    ****************

    after search at Forum,I know maybe I shold change ref,because I use ucsc.hg19.fasta.So I change it by using" human_g1k_v37.fasta"
    commond as following:
    java -Xmx8g -jar $mutect_bin/mutect-1.1.7.jar \
    --analysis_type MuTect \
    --reference_sequence $Mutect_ref/human_g1k_v37.fasta \
    --cosmic $Mutect_ref/hg19_cosmic_v54_120711.vcf \
    --dbsnp $Mutect_ref/dbsnp_132_b37.leftAligned.vcf \
    --intervals chr1:1-249250621 \
    --input_file:normal $normal \
    --input_file:tumor $primary \
    --out chr1_n6Vp5_call_stats.txt \
    --coverage_file chr1_n6Vp5_coverage.wig.txt


    BUT,I also get error as following:

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

    java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
    at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:171)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:324)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:308)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:267)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:213)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:140)
    at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208)
    at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:973)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:767)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:284)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)
    Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
    at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:167)
    ... 14 more
    Caused by: java.io.EOFException
    at org.broad.tribble.util.LittleEndianInputStream.readFully(LittleEndianInputStream.java:134)
    at org.broad.tribble.util.LittleEndianInputStream.readLong(LittleEndianInputStream.java:76)
    at org.broad.tribble.index.linear.LinearIndex$ChrIndex.read(LinearIndex.java:268)
    at org.broad.tribble.index.AbstractIndex.read(AbstractIndex.java:359)
    at org.broad.tribble.index.linear.LinearIndex.(LinearIndex.java:98)
    ... 19 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: java.lang.reflect.InvocationTargetException
    ERROR ------------------------------------------------------------------------------------------

    could you help me? thank you!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    You can Try deleting the index files and regenerating them.

  • xdzperfectxdzperfect Beijing Institute of genomicsMember

    I'm try again,while I still get the same error report.~~(>_<)~~
    I using the following command to create new index:
    igvtools index dbsnp_132_b37.leftAligned_attachCHROM.vcf
    igvtools index dbsnp_132.b37.leftAligned.vcf
    igvtools index hg19_cosmic_v54_120711_attachCHROM.vcf
    igvtools index hg19_cosmic_v54_120711.vcf
    java -jar $picard-tools/CreateSequenceDictionary.jar \
    R=human_g1k_v37.fasta \
    O=human_g1k_v37.dict
    samtools faidx human_g1k_v37.fasta


    and get the index as following:
    -rw-r----- 1 xuzhzh ciwm_group 4578627615 Oct 13 16:21 dbsnp_132_b37.leftAligned.vcf
    -rw-r--r-- 1 xuzhzh ciwm_group 286663 Oct 19 10:23 dbsnp_132_b37.leftAligned.vcf.idx
    -rw-r----- 1 xuzhzh ciwm_group 994591 Oct 13 16:18 hg19_cosmic_v54_120711.vcf
    -rw-r--r-- 1 xuzhzh ciwm_group 589039 Oct 19 10:14 hg19_cosmic_v54_120711.vcf.idx
    -rw-r--r-- 1 xuzhzh ciwm_group 11265 Oct 15 09:29 human_g1k_v37.dict
    -rw-r--r-- 1 xuzhzh ciwm_group 3153506519 Oct 14 21:07 human_g1k_v37.fasta
    -rw-r--r-- 1 xuzhzh ciwm_group 2746 Oct 19 2015 human_g1k_v37.fasta.fai


    Could you tell me how to conquer it ,thank you!

Sign In or Register to comment.