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SVGenotyper Error

jfarrelljfarrell Member ✭✭

Any suggestions for the error below? SVGenotyper was running on 229 bam files-just this one failure occurred.

INFO  22:45:09,990 SVGenotyper - Genotyping site: CNP . DEL 7 70447662 70447736 70447987 70448060
INFO  22:45:09,990 SVGenotyper - GenotypingDepthModule processing site . ...
#DBG: Sun Apr 19 22:45:09 EDT 2015 RCC start: 1
#DBG: Sun Apr 19 22:45:10 EDT 2015 RCC done: 1
INFO  22:45:10,016 SVGenotyper - Computing expected counts ...
INFO  22:45:10,023 SVGenotyper - Computing expected counts done.
INFO  22:45:10,023 SVGenotyper - Computing effective length ...

INFO  22:45:34,047 ProgressMeter -        Starting         0.0    37.7 m    3737.0 w      100.0%    37.7 m       0.0 s
#ERR: SAM record: 264685269     99      7       70447672        21      85M235D16M      =       70448205        634     GTATTATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTAT    BBCFFFFFHGHHGIJIFHIIIIHJIIJGIIJJHGIGGHGGI?DCIEHIJJDHIJJDFHGFFGHJGIIIJJJEHGECEHFEEDFFFFFFFDECCC>@[email protected]    RG:Z:C27PG.1    NH:i:1  NM:i:237
#ERR: junction: ._1 658 1-358 7:70447377-70447734 301-658 7:70447990-70448347 GGATTACAGATATGAGCCACTTTGCCCATCCCCTGTGAATTATTTTTAATTTTTATTTATTTATTTCAGTTTCTACACACAACACTGACCTATAAATTACAGTCTTCTGTCCCTTTATCCGCTAGGGTCTTTATACTTTTCAATCAATTTATAGAAACTGTTTATTTATTTATTTTTCTATTTTTTGATGTATATTATAGTAATTTACATATTTATGGGGTACATGTGCTTGTTACATGCATTGAATGTGTAATGATCAAGTCAGGGTCATTGAGGTATCCACCACCTTGTATGTTTATCATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTTATGAGTTGGTATCCTATCTTCCAGTTACTTTCAAAGATACATAATATTGGCCGGGCGTGGTGGCTCACTCCTGTAATCTCAGCACTTTGGGAGGCTGAGGTGGGTGGATCACGAGGTCAGGAGTTCGAGACCCACCTGGCCAACATAGTGAAAACCCGTTTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGACACGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCATTTGGACCTGGGAGGCGGAGGTTGCAGTGAGCCAAGACTGCGCCATTGCACTCCA
#ERR: ._1 J GGATTACAGATATGAGCCACTTTGCCCATCCCCTGTGAATTATTTTTAATTTTTATTTATTTATTTCAGTTTCTACACACAACACTGACCTATAAATTACAGTCTTCTGTCCCTTTATCCGCTAGGGTCTTTATACTTTTCAATCAATTTATAGAAACTGTTTATTTATTTATTTTTCTATTTTTTGATGTATATTATAGTAATTTACATATTTATGGGGTACATGTGCTTGTTACATGCATTGAATGTGTAATGATCAAGTCAGGGTCATTGAGGTATCCACCACCTTGTATGTTTATCATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTTATGAGTTGGTATCCTATCTTCCAGTTACTTTCAAAGATACATAATATTGGCCGGGCGTGGTGGCTCACTCCTGTAATCTCAGCACTTTGGGAGGCTGAGGTGGGTGGATCACGAGGTCAGGAGTTCGAGACCCACCTGGCCAACATAGTGAAAACCCGTTTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGACACGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCATTTGGACCTGGGAGGCGGAGGTTGCAGTGAGCCAAGACTGCGCCATTGCACTCCA
#ERR: ._1   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
#ERR: ._1 L GGATTACAGATATGAGCCACTTTGCCCATCCCCTGTGAATTATTTTTAATTTTTATTTATTTATTTCAGTTTCTACACACAACACTGACCTATAAATTACAGTCTTCTGTCCCTTTATCCGCTAGGGTCTTTATACTTTTCAATCAATTTATAGAAACTGTTTATTTATTTATTTTTCTATTTTTTGATGTATATTATAGTAATTTACATATTTATGGGGTACATGTGCTTGTTACATGCATTGAATGTGTAATGATCAAGTCAGGGTCATTGAGGTATCCACCACCTTGTATGTTTATCATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTT
#ERR: ._1 J GGATTACAGATATGAGCCACTTTGCCCATCCCCTGTGAATTATTTTTAATTTTTATTTATTTATTTCAGTTTCTACACACAACACTGACCTATAAATTACAGTCTTCTGTCCCTTTATCCGCTAGGGTCTTTATACTTTTCAATCAATTTATAGAAACTGTTTATTTATTTATTTTTCTATTTTTTGATGTATATTATAGTAATTTACATATTTATGGGGTACATGTGCTTGTTACATGCATTGAATGTGTAATGATCAAGTCAGGGTCATTGAGGTATCCACCACCTTGTATGTTTATCATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTTATGAGTTGGTATCCTATCTTCCAGTTACTTTCAAAGATACATAATATTGGCCGGGCGTGGTGGCTCACTCCTGTAATCTCAGCACTTTGGGAGGCTGAGGTGGGTGGATCACGAGGTCAGGAGTTCGAGACCCACCTGGCCAACATAGTGAAAACCCGTTTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGACACGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCATTTGGACCTGGGAGGCGGAGGTTGCAGTGAGCCAAGACTGCGCCATTGCACTCCA
#ERR: ._1                                                                                                                                                                                                                                                                                                               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
#ERR: ._1 R GGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTTATGAGTTGGTATCCTATCTTCCAGTTACTTTCAAAGATACATAATATTGGCCGGGCGTGGTGGCTCACTCCTGTAATCTCAGCACTTTGGGAGGCTGAGGTGGGTGGATCACGAGGTCAGGAGTTCGAGACCCACCTGGCCAACATAGTGAAAACCCGTTTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGACACGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCATTTGGACCTGGGAGGCGGAGGTTGCAGTGAGCCAAGACTGCGCCATTGCACTCCA
#ERR:            70447677     70448047
#ERR: TGTTTATC | ATTTTTAT ... TTGGTATT | TATGAGTT
#ERR: TGTTTATC | ATTTTTAT ... TTGGTATT | TATGAGTT
#ERR:      300                           359
#ERR: junctionEnd: R
#ERR: refExtentStart: 70447672
#ERR: refExtentEnd: 70448007
#ERR: junctionLength: 658
#ERR: junctionLeftFlankLength: 358
#ERR: junctionRightFlankLength: 358
Error: Exception processing cnp: Internal error: junctionOffset = -18
CNP: . 7:70447662-70448060
INFO  22:45:35,239 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Internal error: junctionOffset = -18
        at org.broadinstitute.sv.genotyping.SplitReadMapper.annotateSplitReadMapped(SplitReadMapper.java:431)
        at org.broadinstitute.sv.genotyping.SplitReadMapper.annotateSplitRead(SplitReadMapper.java:187)
        at org.broadinstitute.sv.genotyping.SplitReadMapper.getSplitReadsInternal(SplitReadMapper.java:146)
        at org.broadinstitute.sv.genotyping.SplitReadMapper.getSplitReads(SplitReadMapper.java:128)
        at org.broadinstitute.sv.genotyping.SplitReadMapper.getSplitReads(SplitReadMapper.java:106)
        at org.broadinstitute.sv.genotyping.GenotypingSplitReadModule.getSplitReads(GenotypingSplitReadModule.java:506)
        at org.broadinstitute.sv.genotyping.GenotypingSplitReadModule.getSplitReadGenotypingReads(GenotypingSplitReadModule.java:371)
        at org.broadinstitute.sv.genotyping.GenotypingSplitReadModule.genotypeSample(GenotypingSplitReadModule.java:119)
        at org.broadinstitute.sv.genotyping.GenotypingSplitReadModule.genotypeCnp(GenotypingSplitReadModule.java:85)
        at org.broadinstitute.sv.genotyping.GenotypingSplitReadModule.genotypeCnp(GenotypingSplitReadModule.java:39)
        at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnpInternal(GenotypingAlgorithm.java:141)
        at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnp(GenotypingAlgorithm.java:106)
        at org.broadinstitute.sv.genotyping.SVGenotyperWalker.processVCFFile(SVGenotyperWalker.java:265)
        at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:211)
        at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:56)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:106)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
        at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
        at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
        at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
##### 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: Internal error: junctionOffset = -18
##### ERROR ------------------------------------------------------------------------------------------
INFO  22:45:40,695 QGraph - Writing incremental jobs reports...
INFO  22:45:40,698 QGraph - 1 Pend, 278 Run, 1 Fail, 0 Done

Best Answer

Answers

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    Thanks for the report.
    I will try to recreate this from the info provided - I'll let you know if I'm not able to.

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    I'm not able to exactly recreate this error. I'm not sure I'm able to faithfully recreate the input VCF record from the logged output.
    Can you send me (or post) the input VCF record?

  • jfarrelljfarrell Member ✭✭

    It is one of the variants below (it ran after removing both of these). Most likely it was the second one. The site vcf input used for genotyping contained deletion sites from the GONL WGS and were not from the GenomeSTRiP discovery of the actual bam files being genotyped.

    7 70447676 . CATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGAGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATG
    GGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATT C . Inaccessible AC=244;AF=0.161;AN=1534;CIEND=-3,71;CIPOS=-15,60;END=70447989;NFAFF=136;SOURCE=Breakdancer,MATE-CLEVER,SOAPdenovo;SVLEN=-313;SVTYPE=DEL
    7 70447791 . TATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTA
    TGGGTTGGTATTATTTTATGGGTTGGTATTATTATTTTATGGGTTGGTATTATTTTTATGGGTTGGTATTATTATTTTATGAGTTGGTA T . Inaccessible AC=20;AF=0.013;AN=1534;CIEND=-7,0;CIPOS=-43,0;END=70
    448027;NFAFF=16;SOURCE=Breakdancer,MATE-CLEVER;SVLEN=-236;SVTYPE=DEL

  • jfarrelljfarrell Member ✭✭

    Thanks Bob for the quick fix! I will test it out.

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