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GenotypeConcordance IndexOutOfBoundsException

JonRJonR IndianaMember
edited October 2019 in Ask the GATK team

I'm running the newest version of GATK4 GenotypeConcordance when I get this error.

ERROR: "java.lang.IndexOutOfBoundsException: Index: 0, Size: 0"

Yesterday I performed troubleshooting with a freshly installed version of GATK4 with:

  • conda install -c bioconda gatk4

The call VCF was created with a pipeline running the slightly older GATK 4.0. I have no problem running:

  • call sample vcf vs call sample vcf

It's only when I use:

  • call vcf vs truth vcf

that I have an issue. The truth vcf and the reference were both downloaded from the gatk resource bundle:

My pipeline uses bwa mem, fastp & GATK 4.0 but I'm troubleshooting with GATK 4.1.3.

COMMAND: gatk GenotypeConcordance -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O NA12891_GenotypeConcordance.txt -CS NA12891 -CV NA12891_HaplotypeCaller.SNP_filtered.vcf -TV dbsnp_138.hg38.vcf --INTERVALS NA12891_bait.interval_list
REFERENCE_MDSUM: 7ff134953dcca8c8997453bbb80b6b5e resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta
VCF_MDSUM: f7e1ef5c1830bfb33675b9c7cbaa4868 dbsnp_138.hg38.vcf

Running.....
==============================================

Using GATK jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk4/share/gatk4-4.1.3.0-0/gatk-package-4.1.3.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk4/share/gatk4-4.1.3.0-0/gatk-package-4.1.3.0-local.jar GenotypeConcordance -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O NA12891_GenotypeConcordance.txt -CS NA12891 -CV NA12891_HaplotypeCaller.SNP_filtered.vcf -TV dbsnp_138.hg38.vcf --INTERVALS NA12891_bait.interval_list
09:47:05.280 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk4/share/gatk4-4.1.3.0-0/gatk-package-4.1.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Oct 02 09:47:05 EDT 2019] GenotypeConcordance --TRUTH_VCF dbsnp_138.hg38.vcf --CALL_VCF NA12891_HaplotypeCaller.SNP_filtered.vcf --OUTPUT NA12891_GenotypeConcordance.txt --CALL_SAMPLE NA12891 --INTERVALS NA12891_bait.interval_list --REFERENCE_SEQUENCE resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --OUTPUT_VCF false --INTERSECT_INTERVALS true --MIN_GQ 0 --MIN_DP 0 --OUTPUT_ALL_ROWS false --USE_VCF_INDEX false --MISSING_SITES_HOM_REF false --IGNORE_FILTER_STATUS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Oct 02, 2019 9:47:07 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Wed Oct 02 09:47:07 EDT 2019] Executing as [email protected] on Linux 3.10.0-957.21.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.3.0
INFO 2019-10-02 09:47:07 GenotypeConcordance Starting to load intervals list(s).
INFO 2019-10-02 09:47:08 GenotypeConcordance Finished loading up intervals list(s).
[Wed Oct 02 09:47:09 EDT 2019] picard.vcf.GenotypeConcordance done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2530738176
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
at java.util.ArrayList.get(ArrayList.java:429)
at picard.vcf.GenotypeConcordance.doWork(GenotypeConcordance.java:325)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)

Best Answer

Answers

  • JonRJonR IndianaMember
    edited October 2019

    1st few lines of call vcf below
    tail -n +3400 NA12891_HaplotypeCaller.SNP_filtered.vcf | head

    ===================================================================

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891
    chr1 17385 . G A 10.20 gatk-best-practices AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;ClippingRankSum=0.000;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=40.00;MQRankSum=0.000;QD=0.51;ReadPosRankSum=-1.632;SOR=0.048 GT:AD:DP:GQ:PL 0/1:17,3:20:38:38,0,667
    chr1 941119 . A G 1608.77 PASS AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.36;SOR=1.387 GT:AD:DP:GQ:PL 1/1:0,39:39:99:1637,117,0
    chr1 946247 . G A 2088.77 PASS AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.73;SOR=1.480 GT:AD:DP:GQ:PL 1/1:0,52:52:99:2117,156,0
    chr1 948245 . A G 1212.77 PASS AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.97;SOR=2.019 GT:AD:DP:GQ:PL 1/1:0,30:30:90:1241,90,0
    chr1 952421 . A G 2702.77 PASS AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.96;QD=27.24;SOR=1.196 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2731,199,0
    chr1 953259 . T C 1892.77 PASS AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.38;QD=28.20;SOR=1.077 GT:AD:DP:GQ:PL 1/1:0,53:53:99:1921,159,0
    chr1 953279 . T C 1861.77 PASS AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.63;QD=25.00;SOR=1.562 GT:AD:DP:GQ:PL 1/1:0,48:48:99:1890,144,0
    chr1 953778 . G C 2570.77 PASS AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.56;SOR=1.651 GT:AD:DP:GQ:PL 1/1:0,56:56:99:2599,175,0
    chr1 953779 . A C 2570.77 PASS AC=2;AF=1.00;AN=2;DP=58;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.62;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,58:58:99:2599,175,0

  • bshifawbshifaw Member, Broadie, Moderator admin

    Do you get any errors after running ValidateVariants on the VCF?

  • JonRJonR IndianaMember
    edited November 2019

    There were no errors after running Validate Variants.

    See commands and log files below.

  • JonRJonR IndianaMember
    edited November 2019

    COMMAND: gatk-launch ValidateVariants -R /data/BIOINFORMATICS/RESOURCES/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -V R4c_FILTER_SNP/NA12891_HaplotypeCaller.SNP_filtered.vcf --dbsnp /data/BIOINFORMATICS/RESOURCES/VCF/broadinstitute-resource-bundle/dbsnp_138.hg38.vcf
    Using GATK jar /data/BIOINFORMATICS/SOFTWARES/ANACONDA_JN/ANACONDA_3/envs/seqCap/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar
    Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /data/BIOINFORMATICS/SOFTWARES/ANACONDA_JN/ANACONDA_3/envs/seqCap/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar ValidateVariants -R /data/BIOINFORMATICS/RESOURCES/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -V R4c_FILTER_SNP/NA12891_HaplotypeCaller.SNP_filtered.vcf --dbsnp /data/BIOINFORMATICS/RESOURCES/VCF/broadinstitute-resource-bundle/dbsnp_138.hg38.vcf
    15:53:57.966 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/BIOINFORMATICS/SOFTWARES/ANACONDA_JN/ANACONDA_3/envs/seqCap/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    15:53:58.094 INFO ValidateVariants - ------------------------------------------------------------
    15:53:58.094 INFO ValidateVariants - The Genome Analysis Toolkit (GATK) v4.0.0.0
    15:53:58.094 INFO ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
    15:53:58.094 INFO ValidateVariants - Executing as [email protected] on Linux v4.15.0-54-generic amd64
    15:53:58.095 INFO ValidateVariants - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_92-b15
    15:53:58.095 INFO ValidateVariants - Start Date/Time: November 11, 2019 3:53:57 PM EST
    15:53:58.095 INFO ValidateVariants - ------------------------------------------------------------
    15:53:58.095 INFO ValidateVariants - ------------------------------------------------------------
    15:53:58.095 INFO ValidateVariants - HTSJDK Version: 2.13.2
    15:53:58.095 INFO ValidateVariants - Picard Version: 2.17.2
    15:53:58.096 INFO ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 1
    15:53:58.096 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    15:53:58.096 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    15:53:58.096 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    15:53:58.096 INFO ValidateVariants - Deflater: IntelDeflater
    15:53:58.096 INFO ValidateVariants - Inflater: IntelInflater
    15:53:58.096 INFO ValidateVariants - GCS max retries/reopens: 20
    15:53:58.096 INFO ValidateVariants - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
    15:53:58.096 INFO ValidateVariants - Initializing engine
    15:53:58.613 INFO FeatureManager - Using codec VCFCodec to read file file:///data/BIOINFORMATICS/RESOURCES/VCF/broadinstitute-resource-bundle/dbsnp_138.hg38.vcf
    15:53:58.763 INFO FeatureManager - Using codec VCFCodec to read file file:///data/TARGET_ENRICHMENT_PIPELINE/VERSION_2019_11_07/seqcap19/R4c_FILTER_SNP/NA12891_HaplotypeCaller.SNP_filtered.vcf
    15:53:58.900 INFO ValidateVariants - Done initializing engine
    15:53:58.900 INFO ProgressMeter - Starting traversal
    15:53:58.900 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    15:54:09.890 INFO ProgressMeter - chr2:89851902 0.2 3000 16380.0
    15:54:20.967 INFO ProgressMeter - chr4:97972286 0.4 6000 16314.0
    15:54:32.440 INFO ProgressMeter - chr7:45083658 0.6 9000 16100.2
    15:54:43.854 INFO ProgressMeter - chr10:94403282 0.7 13000 17351.1
    15:54:55.246 INFO ProgressMeter - chr14:19827619 0.9 17000 18102.4
    15:55:06.593 INFO ProgressMeter - chr17:75093757 1.1 21000 18613.7
    15:55:16.776 INFO ProgressMeter - chr22:30538900 1.3 25000 19261.4
    15:55:18.953 INFO ProgressMeter - chr22:30538900 1.3 25719 19276.5
    15:55:18.953 INFO ProgressMeter - Traversal complete. Processed 25719 total variants in 1.3 minutes.
    15:55:18.954 INFO ValidateVariants - Shutting down engine
    [November 11, 2019 3:55:18 PM EST] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 1.35 minutes.
    Runtime.totalMemory()=2682781696

    COMMAND: gatk-launch GenotypeConcordance -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O R4j_COMPARE_TO_KNOWN_SNPS/NA12891_GenotypeConcordance.txt -CV R4c_FILTER_SNP/NA12891_HaplotypeCaller.SNP_filtered.vcf -TV /data/BIOINFORMATICS/RESOURCES/VCF/broadinstitute-resource-bundle/dbsnp_138.hg38.vcf --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12891_bait.interval_list

    16:05:30.947 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/BIOINFORMATICS/SOFTWARES/ANACONDA_JN/ANACONDA_3/envs/seqCap/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    [Mon Nov 11 16:05:30 EST 2019] GenotypeConcordance --TRUTH_VCF /data/BIOINFORMATICS/RESOURCES/VCF/broadinstitute-resource-bundle/dbsnp_138.hg38.vcf --CALL_VCF R4c_FILTER_SNP/NA12891_HaplotypeCaller.SNP_filtered.vcf --OUTPUT R4j_COMPARE_TO_KNOWN_SNPS/NA12891_GenotypeConcordance.txt --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12891_bait.interval_list --REFERENCE_SEQUENCE resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --OUTPUT_VCF false --INTERSECT_INTERVALS true --MIN_GQ 0 --MIN_DP 0 --OUTPUT_ALL_ROWS false --USE_VCF_INDEX false --MISSING_SITES_HOM_REF false --IGNORE_FILTER_STATUS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 1 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
    [Mon Nov 11 16:05:30 EST 2019] Executing as [email protected] on Linux 4.15.0-54-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Deflater: Intel; Inflater: Intel; Picard version: Version:4.0.0.0
    INFO 2019-11-11 16:05:30 GenotypeConcordance Starting to load intervals list(s).
    INFO 2019-11-11 16:05:31 GenotypeConcordance Finished loading up intervals list(s).
    [Mon Nov 11 16:05:31 EST 2019] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes.
    Runtime.totalMemory()=727711744
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:653)
    at java.util.ArrayList.get(ArrayList.java:429)
    at picard.vcf.GenotypeConcordance.doWork(GenotypeConcordance.java:331)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:269)
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:24)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:152)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
    at org.broadinstitute.hellbender.Main.main(Main.java:275)
    Using GATK jar /data/BIOINFORMATICS/SOFTWARES/ANACONDA_JN/ANACONDA_3/envs/seqCap/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar
    Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /data/BIOINFORMATICS/SOFTWARES/ANACONDA_JN/ANACONDA_3/envs/seqCap/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar GenotypeConcordance -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O R4j_COMPARE_TO_KNOWN_SNPS/NA12891_GenotypeConcordance.txt -CV R4c_FILTER_SNP/NA12891_HaplotypeCaller.SNP_filtered.vcf -TV /data/BIOINFORMATICS/RESOURCES/VCF/broadinstitute-resource-bundle/dbsnp_138.hg38.vcf --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12891_bait.interval_list

  • JonRJonR IndianaMember

    Sadly, I got the same error.

    I downloaded the file: somatic-hg38_af-only-gnomad.hg38.vcf.gz

    from here:

    https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38

    Thank you for the response.

  • JonRJonR IndianaMember
    edited November 2019

    ERROR Below

    =========================================
    COMMAND: gatk-launch GenotypeConcordance -R /data/BIOINFORMATICS/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O R4j_COMPARE_TO_KNOWN_SNPS/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_GenotypeConcordance.txt -CV R4c_FILTER_SNP/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_HaplotypeCaller.SNP_filtered.vcf -TV /data/BIOINFORMATICS/RESOURCES/somatic-hg38_af-only-gnomad.hg38.vcf.gz --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_bait.interval_list
    =========================================
    Using GATK jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/seqCap19/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar
    Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/seqCap19/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar GenotypeConcordance -R /data/BIOINFORMATICS/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O R4j_COMPARE_TO_KNOWN_SNPS/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_GenotypeConcordance.txt -CV R4c_FILTER_SNP/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_HaplotypeCaller.SNP_filtered.vcf -TV /data/BIOINFORMATICS/RESOURCES/somatic-hg38_af-only-gnomad.hg38.vcf.gz --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_bait.interval_list
    20:09:39.075 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/seqCap19/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    [Wed Nov 13 20:09:39 EST 2019] GenotypeConcordance --TRUTH_VCF /data/BIOINFORMATICS/RESOURCES/somatic-hg38_af-only-gnomad.hg38.vcf.gz --CALL_VCF R4c_FILTER_SNP/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_HaplotypeCaller.SNP_filtered.vcf --OUTPUT R4j_COMPARE_TO_KNOWN_SNPS/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_GenotypeConcordance.txt --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_bait.interval_list --REFERENCE_SEQUENCE /data/BIOINFORMATICS/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --OUTPUT_VCF false --INTERSECT_INTERVALS true --MIN_GQ 0 --MIN_DP 0 --OUTPUT_ALL_ROWS false --USE_VCF_INDEX false --MISSING_SITES_HOM_REF false --IGNORE_FILTER_STATUS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 1 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
    [Wed Nov 13 20:09:39 EST 2019] Executing as [email protected] on Linux 3.10.0-957.21.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_192-b01; Deflater: Intel; Inflater: Intel; Picard version: Version:4.0.0.0
    INFO 2019-11-13 20:09:39 GenotypeConcordance Starting to load intervals list(s).
    INFO 2019-11-13 20:09:39 GenotypeConcordance Finished loading up intervals list(s).
    [Wed Nov 13 20:09:39 EST 2019] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes.
    Runtime.totalMemory()=1637351424
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:657)
    at java.util.ArrayList.get(ArrayList.java:433)
    at picard.vcf.GenotypeConcordance.doWork(GenotypeConcordance.java:331)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:269)
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:24)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:152)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
    at org.broadinstitute.hellbender.Main.main(Main.java:275)

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @JonR

    Can you please try this with the latest GATK4.1.4.0 and let us know if the issue persists?

  • JonRJonR IndianaMember

    Ran with the most recent version of gatk4. Same issue

    COMMAND: gatk GenotypeConcordance -R /data/BIOINFORMATICS/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O R4j_COMPARE_TO_KNOWN_SNPS/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_GenotypeConcordance.txt -CV R4c_FILTER_SNP/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_HaplotypeCaller.SNP_filtered.vcf -TV /data/BIOINFORMATICS/RESOURCES/somatic-hg38_af-only-gnomad.hg38.vcf.gz --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_bait.interval_list

    ==========================================

    Using GATK jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk4/share/gatk4-4.1.4.1-0/gatk-package-4.1.4.1-local.jar
    Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk4/share/gatk4-4.1.4.1-0/gatk-package-4.1.4.1-local.jar GenotypeConcordance -R /data/BIOINFORMATICS/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O R4j_COMPARE_TO_KNOWN_SNPS/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_GenotypeConcordance.txt -CV R4c_FILTER_SNP/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_HaplotypeCaller.SNP_filtered.vcf -TV /data/BIOINFORMATICS/RESOURCES/somatic-hg38_af-only-gnomad.hg38.vcf.gz --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_bait.interval_list
    15:03:16.900 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk4/share/gatk4-4.1.4.1-0/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
    [Fri Dec 06 15:03:16 EST 2019] GenotypeConcordance --TRUTH_VCF /data/BIOINFORMATICS/RESOURCES/somatic-hg38_af-only-gnomad.hg38.vcf.gz --CALL_VCF R4c_FILTER_SNP/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_HaplotypeCaller.SNP_filtered.vcf --OUTPUT R4j_COMPARE_TO_KNOWN_SNPS/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_GenotypeConcordance.txt --INTERVALS R3n_BED_TO_INTERVAL_LIST/NA12878_HPrep_Rep2_8plex_MAD050_Cap003_S23_bait.interval_list --REFERENCE_SEQUENCE /data/BIOINFORMATICS/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --OUTPUT_VCF false --INTERSECT_INTERVALS true --MIN_GQ 0 --MIN_DP 0 --OUTPUT_ALL_ROWS false --USE_VCF_INDEX false --MISSING_SITES_HOM_REF false --IGNORE_FILTER_STATUS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
    Dec 06, 2019 3:03:17 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    [Fri Dec 06 15:03:17 EST 2019] Executing as [email protected] on Linux 3.10.0-1062.1.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.4.1
    INFO 2019-12-06 15:03:17 GenotypeConcordance Starting to load intervals list(s).
    INFO 2019-12-06 15:03:18 GenotypeConcordance Finished loading up intervals list(s).
    [Fri Dec 06 15:03:18 EST 2019] picard.vcf.GenotypeConcordance done. Elapsed time: 0.03 minutes.
    Runtime.totalMemory()=2300575744
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:653)
    at java.util.ArrayList.get(ArrayList.java:429)
    at picard.vcf.GenotypeConcordance.doWork(GenotypeConcordance.java:325)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
    at org.broadinstitute.hellbender.Main.main(Main.java:292)

    Issue · Github
    by bhanuGandham

    Issue Number
    1439
    State
    open
    Last Updated
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @JonR

    I am going to check with the dev team and get back to you.

  • JonRJonR IndianaMember
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