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CatVariants Error

Any suggestions for this error from CatVariants?

John

INFO  17:02:46,100 HelpFormatter - -------------------------------------------------------
INFO  17:02:46,103 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
INFO  17:02:46,107 HelpFormatter - Program Args: -R /restricted/projectnb/casa/ref/human_g1k_v37_decoy.fasta --variant adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29/chr10_1-40200000/adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29.chr10_1-40200000.scalpel.vcf --variant adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29/chr10_40200000-85000000/adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29.chr10_40200000-85000000.scalpel.vcf --variant adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29/chr10_85000000-135534747/adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29.chr10_85000000-135534747.scalpel.vcf -out output.vcf
INFO  17:02:46,336 HelpFormatter - Executing as [email protected] on Linux 2.6.32-504.16.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_60-b27.
INFO  17:02:46,336 HelpFormatter - Date/Time: 2016/02/23 17:02:46
INFO  17:02:46,337 HelpFormatter - -------------------------------------------------------
INFO  17:02:46,337 HelpFormatter - -------------------------------------------------------
...
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.NullPointerException
        at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.setIndexSequenceDictionary(IndexingVariantContextWriter.java:178)
        at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.close(IndexingVariantContextWriter.java:133)
        at htsjdk.variant.variantcontext.writer.VCFWriter.close(VCFWriter.java:210)
        at org.broadinstitute.gatk.tools.CatVariants.execute(CatVariants.java:303)
        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.gatk.tools.CatVariants.main(CatVariants.java:311)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
##### 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 ------------------------------------------------------------------------------------------

more merge_CU001163.baylor.sh
java -cp /share/pkg/gatk/3.4-46/install/GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants \
-R /restricted/projectnb/casa/ref/human_g1k_v37_decoy.fasta \
--variant adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29/chr10_1-40200000/adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29.chr10_1-40200000.scalpel.vcf\
--variant adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29/chr10_40200000-85000000/adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29.chr10_40200
000-85000000.scalpel.vcf\
--variant adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29/chr10_85000000-135534747/adsp.sv.wgs.CU001163.baylor.bamsurgeon.2016_01_29.chr10_8500
0000-135534747.scalpel.vcf\
-out output.vcf

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Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @jfarrell
    Hi John,

    I think this is a bug that has been fixed in the latest version. Can you try upgrading and see if the error persists?

    Thanks,
    Sheila

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @jfarrell
    Hi John,

    Sorry. I just realized upgrading won't fix anything. Can you try deleting the index files and letting GATK regenerate them?

    Thanks,
    Sheila

  • jfarrelljfarrell Member ✭✭

    Which index files? For the fast reference (/restricted/projectnb/casa/ref/human_g1k_v37_decoy.fasta.fai)?

  • huongmeekshuongmeeks Salt Lake City, UtahMember
    edited March 2016

    Hi,

    I'm running into the same problem as John. I wanted to merge all vcf files in Human Genome 1000 (chr1-22 and X/Y) into one. It gave me the same stack trace error. I'm using the latest version of GATK (3.5).

    What should I do now?

    Thanks,
    Huong

    PS: Here is the code that I used:
    java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants -R hs37d5.fa.gz -V ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -V ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -out ALL.phase3_integrated_v2a.20130502.genotypes.vcf.gz -assumeSorted

    Here is the error that it produced:
    INFO 10:39:12,440 HelpFormatter - -------------------------------------------------------
    INFO 10:39:12,442 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
    INFO 10:39:12,446 HelpFormatter - Program Args: -R hs37d5.fa.gz -V ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -V ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -out ALL.phase3_integrated_v2a.20130502.genotypes.vcf.gz -assumeSorted
    INFO 10:39:12,457 HelpFormatter - Executing as [email protected] on Linux 2.6.32-573.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_95-mockbuild_2016_01_21_15_45-b00.
    INFO 10:39:12,457 HelpFormatter - Date/Time: 2016/03/16 10:39:12
    INFO 10:39:12,457 HelpFormatter - -------------------------------------------------------
    INFO 10:39:12,458 HelpFormatter - -------------------------------------------------------

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

    java.lang.NullPointerException
    at htsjdk.variant.variantcontext.VariantContextComparator.getSequenceNameList(VariantContextComparator.java:25)
    at htsjdk.variant.variantcontext.VariantContextComparator.(VariantContextComparator.java:76)
    at org.broadinstitute.gatk.tools.CatVariants$PositionComparator.(CatVariants.java:327)
    at org.broadinstitute.gatk.tools.CatVariants.execute(CatVariants.java:233)
    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.gatk.tools.CatVariants.main(CatVariants.java:312)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    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 ------------------------------------------------------------------------------------------

    Issue · Github
    by Sheila

    Issue Number
    727
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I see from the file names that those VCFs have probably been run through another program (shapeit). We've found that some third party tools produce output that is not entirely properly formatted, which then cause our tools to crash. You'll need to run ValidateVariants on those files to verify that they are valid VCFs before running GATK tools on them.

  • huongmeekshuongmeeks Salt Lake City, UtahMember

    Hi Geraldine,

    I did check on the file using ValidateVariants, and no failures was found. Do you have any other idea? Thank you for helping me out.

    Best,
    Huong Meeks

    Below is the code and the result:
    java -jar GenomeAnalysisTK.jar -T ValidateVariants -R $BING/work/data/1kG/seq/hs37d5.fa -V ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --validationTypeToExclude ALL

    Result:

    INFO 12:46:49,344 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:46:49,345 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
    INFO 12:46:49,346 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 12:46:49,346 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 12:46:49,349 HelpFormatter - Program Args: -T ValidateVariants -R /uufs/chpc.utah.edu/common/home/u0551462/work/data/1kG/seq/hs37d5.fa -V ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --validationTypeToExclude ALL
    INFO 12:46:49,358 HelpFormatter - Executing as [email protected] on Linux 2.6.32-573.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_95-mockbuild_2016_01_21_15_45-b00.
    INFO 12:46:49,358 HelpFormatter - Date/Time: 2016/03/16 12:46:49
    INFO 12:46:49,358 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:46:49,358 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:46:49,426 GenomeAnalysisEngine - Strictness is SILENT
    INFO 12:46:49,570 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    WARN 12:46:49,721 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
    INFO 12:46:49,786 GenomeAnalysisEngine - Preparing for traversal
    INFO 12:46:49,802 GenomeAnalysisEngine - Done preparing for traversal
    INFO 12:46:49,803 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 12:46:49,803 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 12:46:49,803 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
    INFO 12:47:19,806 ProgressMeter - 1:4601585 1428401.0 30.0 s 21.0 s 0.1% 5.7 h 5.7 h
    INFO 12:47:49,808 ProgressMeter - 1:9561554 2321420.0 60.0 s 25.0 s 0.3% 5.5 h 5.5 h
    INFO 12:48:19,809 ProgressMeter - 1:15206190 3363269.0 90.0 s 26.0 s 0.5% 5.2 h 5.1 h
    INFO 12:48:49,810 ProgressMeter - 1:20175095 4317547.0 120.0 s 27.0 s 0.6% 5.2 h 5.2 h
    INFO 12:49:19,811 ProgressMeter - 1:25614079 4903925.0 2.5 m 30.0 s 0.8% 5.1 h 5.1 h
    INFO 12:49:49,812 ProgressMeter - 1:31287375 6246254.0 3.0 m 28.0 s 1.0% 5.0 h 5.0 h
    INFO 12:50:19,814 ProgressMeter - 1:36874644 7207081.0 3.5 m 29.0 s 1.2% 5.0 h 4.9 h
    INFO 12:50:49,815 ProgressMeter - 1:42438099 7842476.0 4.0 m 30.0 s 1.4% 4.9 h 4.9 h
    INFO 12:51:19,816 ProgressMeter - 1:48061835 9084626.0 4.5 m 29.0 s 1.5% 4.9 h 4.8 h
    INFO 12:51:49,817 ProgressMeter - 1:53974482 1.012745E7 5.0 m 29.0 s 1.7% 4.8 h 4.8 h
    INFO 12:52:19,818 ProgressMeter - 1:59175176 1.0674287E7 5.5 m 30.0 s 1.9% 4.9 h 4.8 h
    INFO 12:52:49,820 ProgressMeter - 1:64838523 1.1323875E7 6.0 m 31.0 s 2.1% 4.8 h 4.7 h
    INFO 12:53:19,821 ProgressMeter - 1:70609022 1.1933518E7 6.5 m 32.0 s 2.3% 4.8 h 4.7 h
    INFO 12:53:49,822 ProgressMeter - 1:76219899 1.375146E7 7.0 m 30.0 s 2.4% 4.8 h 4.7 h
    INFO 12:54:19,824 ProgressMeter - 1:81570104 1.463793E7 7.5 m 30.0 s 2.6% 4.8 h 4.7 h
    INFO 12:54:49,825 ProgressMeter - 1:87141168 1.538338E7 8.0 m 31.0 s 2.8% 4.8 h 4.7 h
    INFO 12:55:19,826 ProgressMeter - 1:92888446 1.6450496E7 8.5 m 31.0 s 3.0% 4.8 h 4.6 h
    INFO 12:55:49,827 ProgressMeter - 1:98645090 1.6918306E7 9.0 m 31.0 s 3.1% 4.8 h 4.6 h
    INFO 12:56:19,828 ProgressMeter - 1:104160165 1.8252548E7 9.5 m 31.0 s 3.3% 4.8 h 4.6 h
    INFO 12:56:49,829 ProgressMeter - 1:109495735 1.9368038E7 10.0 m 30.0 s 3.5% 4.8 h 4.6 h
    INFO 12:57:19,833 ProgressMeter - 1:114983280 2.0301071E7 10.5 m 31.0 s 3.7% 4.8 h 4.6 h
    INFO 12:57:49,834 ProgressMeter - 1:120409444 2.1910073E7 11.0 m 30.0 s 3.8% 4.8 h 4.6 h
    INFO 12:58:19,835 ProgressMeter - 1:150628365 2.4174737E7 11.5 m 28.0 s 4.8% 4.0 h 3.8 h
    INFO 12:58:49,836 ProgressMeter - 1:156273297 2.5347859E7 12.0 m 28.0 s 5.0% 4.0 h 3.8 h
    INFO 12:59:19,838 ProgressMeter - 1:161513580 2.5850306E7 12.5 m 29.0 s 5.1% 4.0 h 3.8 h
    INFO 12:59:49,839 ProgressMeter - 1:166751529 2.6976235E7 13.0 m 28.0 s 5.3% 4.1 h 3.9 h
    INFO 13:00:19,840 ProgressMeter - 1:172152913 2.7460716E7 13.5 m 29.0 s 5.5% 4.1 h 3.9 h
    INFO 13:00:49,841 ProgressMeter - 1:177997201 2.8249422E7 14.0 m 29.0 s 5.7% 4.1 h 3.9 h
    INFO 13:01:19,845 ProgressMeter - 1:183118177 2.8840594E7 14.5 m 30.0 s 5.8% 4.1 h 3.9 h
    INFO 13:01:49,847 ProgressMeter - 1:188267864 2.959082E7 15.0 m 30.0 s 6.0% 4.2 h 3.9 h
    INFO 13:02:19,848 ProgressMeter - 1:192681825 3.1527222E7 15.5 m 29.0 s 6.1% 4.2 h 3.9 h
    INFO 13:02:49,849 ProgressMeter - 1:197940820 3.3405666E7 16.0 m 28.0 s 6.3% 4.2 h 4.0 h
    INFO 13:03:19,850 ProgressMeter - 1:203081177 3.4993086E7 16.5 m 28.0 s 6.5% 4.2 h 4.0 h
    INFO 13:03:34,759 ValidateVariants - Reference allele is too long (130) at position 1:205853579; skipping that record. Set --referenceWindowStop >= 130
    INFO 13:03:49,852 ProgressMeter - 1:209019234 3.5720807E7 17.0 m 28.0 s 6.7% 4.3 h 4.0 h
    INFO 13:04:19,853 ProgressMeter - 1:214494735 3.6281909E7 17.5 m 28.0 s 6.8% 4.3 h 4.0 h
    INFO 13:04:49,854 ProgressMeter - 1:219811748 3.6884817E7 18.0 m 29.0 s 7.0% 4.3 h 4.0 h
    INFO 13:05:19,855 ProgressMeter - 1:225367876 3.7457742E7 18.5 m 29.0 s 7.2% 4.3 h 4.0 h
    INFO 13:05:49,857 ProgressMeter - 1:230778431 3.8364509E7 19.0 m 29.0 s 7.4% 4.3 h 4.0 h
    INFO 13:06:19,858 ProgressMeter - 1:236096944 4.0027622E7 19.5 m 29.0 s 7.5% 4.3 h 4.0 h
    INFO 13:06:49,859 ProgressMeter - 1:241200107 4.1418654E7 20.0 m 28.0 s 7.7% 4.3 h 4.0 h
    INFO 13:07:19,861 ProgressMeter - 1:246365373 4.2786183E7 20.5 m 28.0 s 7.9% 4.4 h 4.0 h
    Successfully validated the input file. Checked 6468094 records with no failures.
    INFO 13:07:37,214 ProgressMeter - done 4.4637605E7 20.8 m 27.0 s 7.9% 4.4 h 4.0 h
    INFO 13:07:37,215 ProgressMeter - Total runtime 1247.41 secs, 20.79 min, 0.35 hours
    INFO 13:07:38,122 GATKRunReport - Uploaded run statistics report to AWS S3

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @huongmeeks You error is actually different from John's, now that I look at it more closely. And I see that you're running on OpenJDK, which is not supported. Can you confirm that you get the same error if you run on a machine with the Oracle JDK?

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