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VariantsToBinaryPed runtime error

I have a multisample WES gVCF file processed all of the way through GenotypeGVCFs. I have used GATK 4.0.6 for everything. Now that I wish to convert my gVCF to PLINK format, I have to use GATK 3. But using VariantsToBinaryPed from GATK 3.8 (I've tried 3.7 as well) I am getting a runtime error. I originally had multiallelic sites and thought that would be the issue, but after using SelectVariant and keeping only the biallelic sites the runtime issue remains the same.

Previous issues similar to mine that have been solved had the top item on the stack trace reading through the metadata file. For me it is the gVCF file itself, with a function called getGQLog10FromLikelihoods. I'm currently trying GenotypeGVCFs from 3.8 to see if this is compatible.

INFO  09:17:44,576 HelpFormatter - Date/Time: 2018/07/24 09:17:44 
INFO  09:17:44,576 HelpFormatter - ------------------------------------------------------------------------------------ 
INFO  09:17:44,577 HelpFormatter - ------------------------------------------------------------------------------------ 
INFO  09:17:44,616 NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/kk2252/sandbox/gatk3.jar!/com/intel/gkl/native/libgkl_compression.so 
INFO  09:17:44,650 GenomeAnalysisEngine - Deflater: IntelDeflater 
INFO  09:17:44,651 GenomeAnalysisEngine - Inflater: IntelInflater 
INFO  09:17:44,651 GenomeAnalysisEngine - Strictness is SILENT 
INFO  09:17:44,816 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO  09:17:44,999 GenomeAnalysisEngine - Preparing for traversal 
INFO  09:17:45,003 GenomeAnalysisEngine - Done preparing for traversal 
INFO  09:17:45,004 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  09:17:45,004 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  09:17:45,004 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
##### ERROR --
##### ERROR stack trace 
java.lang.ArrayIndexOutOfBoundsException: -1
    at htsjdk.variant.variantcontext.GenotypeLikelihoods.getGQLog10FromLikelihoods(GenotypeLikelihoods.java:220)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.checkGQIsGood(VariantsToBinaryPed.java:442)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.getStandardEncoding(VariantsToBinaryPed.java:406)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.getEncoding(VariantsToBinaryPed.java:398)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.writeIndividualMajor(VariantsToBinaryPed.java:282)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.map(VariantsToBinaryPed.java:267)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.map(VariantsToBinaryPed.java:103)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
##### 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 https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: -1
##### ERROR ------------------------------------------------------------------------------------------

Answers

  • I see that there is an open thread of people having this issue.

  • kohlkopfkohlkopf Member
    edited July 2018

    The tool writes the .bim file until it chokes on a record. In the following, the first two records are written to the .bim fiile but the program seems to choke on the third. It does not make it in to the .bim file.

    1   11601123    .   C   T   3887.66 .   AC=20;AF=0.435;AN=46;BaseQRankSum=-5.150e-01;ClippingRankSum=0.00;DP=435;ExcessHet=0.7918;FS=0.567;MLEAC=21;MLEAF=0.457;MQ=58.03;MQRankSum=-1.737e+00;QD=19.25;ReadPosRankSum=0.391;SOR=0.631   GT:AD:DP:GQ:PGT:PID:PL  0/0:22,0:22:63:.:.:0,63,945 0/1:13,2:15:42:0|1:11601097_G_T:42,0,832    ./.:0,0:.:.:0|1:11601097_G_T    0/1:14,4:18:99:0|1:11601097_G_T:120,0,1270  0/1:8,6:14:99:0|1:11601097_G_T:225,0,1189   0/0:35,0:35:90:.:.:0,90,1070    0/1:18,3:21:99:0|1:11601097_G_T:114,0,744   0/0:37,0:37:99:.:.:0,100,1041   0/0:32,0:32:87:.:.:0,87,1305    0/0:22,0:22:60:.:.:0,60,724 1/1:0,10:10:30:1|1:11601097_G_T:450,30,0    1/1:0,11:11:33:1|1:11601097_G_T:495,33,0    0/0:25,0:25:40:.:.:0,40,745 0/0:21,0:21:60:.:.:0,60,900 0/1:15,7:22:99:0|1:11601097_G_T:237,0,1078  1/1:0,9:9:27:1|1:11601097_G_T:405,27,0  0/0:22,0:22:54:.:.:0,54,810 0/1:21,5:26:99:0|1:11601097_G_T:147,0,867   1/1:0,15:15:45:1|1:11601097_G_T:675,45,0    1/1:0,5:5:15:1|1:11601097_G_T:225,15,0  0/0:12,0:12:0:.:.:0,0,244   0/1:5,2:7:63:0|1:11601097_G_T:63,0,462  1/1:0,15:15:48:1|1:11601097_G_T:719,48,0    0/1:11,3:14:93:0|1:11601097_G_T:93,0,453
    1   11601129    .   GACAGCCAGGACT   G   3440.37 .   AC=20;AF=0.435;AN=46;BaseQRankSum=0.825;ClippingRankSum=0.00;DP=429;ExcessHet=0.7918;FS=8.604;MLEAC=20;MLEAF=0.435;MQ=57.83;MQRankSum=-1.465e+00;QD=17.46;ReadPosRankSum=0.210;SOR=1.245    GT:AD:DP:GQ:PGT:PID:PL  0/0:22,0:22:57:.:.:0,57,855 0/1:12,2:14:42:0|1:11601097_G_T:42,0,931    ./.:1,0:1:.:.:.:0,0,0   0/1:19,4:23:99:0|1:11601097_G_T:111,0,1486  0/1:8,5:13:99:0|1:11601097_G_T:183,0,1192   0/0:36,0:36:81:.:.:0,81,1215    0/1:21,3:24:63:0|1:11601097_G_T:63,0,873    0/0:35,0:35:90:.:.:0,90,1350    0/0:30,0:30:90:.:.:0,90,954 0/0:22,0:22:60:.:.:0,60,724 1/1:0,9:9:27:1|1:11601097_G_T:405,27,0  1/1:0,11:11:33:1|1:11601097_G_T:495,33,0    0/0:24,0:24:33:.:.:0,33,696 0/0:22,0:22:54:.:.:0,54,810 0/1:19,6:25:99:0|1:11601097_G_T:195,0,1321  1/1:0,8:8:24:1|1:11601097_G_T:360,24,0  0/0:20,0:20:51:.:.:0,51,765 0/1:22,4:26:99:0|1:11601097_G_T:144,0,909   1/1:0,11:11:33:1|1:11601097_G_T:495,33,0    1/1:0,5:5:18:1|1:11601097_G_T:250,18,0  0/0:8,0:8:24:.:.:0,24,258   0/1:6,1:7:24:0|1:11601097_G_T:24,0,467  1/1:0,16:16:48:1|1:11601097_G_T:719,48,0    0/1:9,3:12:90:0|1:11601097_G_T:90,0,495
    1   11601179    .   A   C   1572.75 .   AC=19;AF=0.396;AN=48;BaseQRankSum=1.61;ClippingRankSum=0.00;DP=466;ExcessHet=0.7918;FS=2.554;MLEAC=18;MLEAF=0.375;MQ=61.38;MQRankSum=-2.006e+00;QD=14.56;ReadPosRankSum=-6.300e-02;SOR=0.547    GT:AD:DP:GQ:PGT:PID:PL  0/0:21,0:21:60:.:.:0,60,900 0/1:17,2:19:23:0|1:11601179_A_C:23,0,1091   1/1:0,2:2:6:1|1:11601179_A_C:90,6,0 0/1:19,2:21:27:0|1:11601179_A_C:27,0,1600   0/0:15,0:15:0:.:.:0,0,296   0/0:40,0:40:99:.:.:0,101,1249   0/0:12,0:12:27:.:.:0,27,405 0/0:26,0:26:60:.:.:0,60,900 0/0:28,0:28:60:.:.:0,60,900 0/0:32,0:32:87:.:.:0,87,1305    1/1:0,4:4:12:1|1:11601179_A_C:175,12,0  1/1:0,7:7:21:1|1:11601179_A_C:316,21,0  0/1:14,3:17:84:0|1:11601179_A_C:84,0,581    0/0:22,0:22:63:.:.:0,63,699 0/0:20,0:20:63:0|1:11601179_A_C:0,63,1543   1/1:0,1:1:3:1|1:11601179_A_C:45,3,0 0/0:32,0:32:90:.:.:0,90,1350    0/1:11,1:12:6:0|1:11601179_A_C:6,0,501  1/1:0,5:5:15:1|1:11601179_A_C:201,15,0  1/1:0,6:6:18:1|1:11601179_A_C:250,18,0  0/0:13,0:13:36:.:.:0,36,540 0/1:14,2:16:42:0|1:11601179_A_C:42,0,843    1/1:0,11:11:33:1|1:11601179_A_C:440,33,0    0/0:19,0:19:33:.:.:0,33,557
    
    
    Post edited by kohlkopf on
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @kohlkopf
    Hi,

    Sorry for the delay. I am asking another developer now and will get back to you asap.

    -Sheila

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