Error occur on VariantRecalibrator : Malformed floating point valueprior

WeichiWeichi Member
edited January 2 in Ask the GATK team

The problem is about VQSR. I have no idea how to fix this error:

A USER ERROR has occurred: Unknown file is malformed: Malformed floating point valueprior

The input vcf file is generate by HaplotypeCaller and resource are from broadinstitute.org/bundle.
My gatk version is v4.0.8.1

This is my code:
gatk --java-options -DGATK_STACKTRACE_ON_USER_EXCEPTION=true VariantRecalibrator \
-R human_g1k_v37.fasta \
-V NV0047-01_S14_gatk4.vcf \
-O raw.SNPs.recal \
-resource [hapmap,known=false,training=true,truth=true,prior=15.0]: hapmap_3.3.b37.vcf \
-resource [omni,known=false,training=true,truth=true,prior=12.0]: 1000G_omni2.5.b37.vcf \
-resource [dbsnp,known=true,training=false,truth=false,prior=2.0]: dbsnp_138.b37.vcf \
-resource [1000G,known=false,training=true,truth=false,prior=10.0]:1000G_phase1.snps.high_confidence.b37.vcf \
-an DP \ -an QD \ -an FS \ -an SOR \ -an MQ \ -an MQRankSum \ -an ReadPosRankSum \ -an InbreedingCoeff \
-mode SNP \ --tranches-file raw.SNPs.tranches \ -rscript-file recal.plots.R

and this is full error message:


A USER ERROR has occurred: Unknown file is malformed: Malformed floating point valueprior


org.broadinstitute.hellbender.exceptions.UserException$MalformedFile: Unknown file is malformed: Malformed floating point valueprior
at org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet.getDoubleAttributeOrElse(TrainingSet.java:67)
at org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet.(TrainingSet.java:41)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.onTraversalStart(VariantRecalibrator.java:423)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:891)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

Tagged:

Comments

  • WeichiWeichi Member

    Does it have any tools can check the vcf files ?

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Hello @Weichi - I agree that it would be best to check the VCF files for proper format. Here is a link that contains the command using GATKs ValidateVariants to check the VCF file formats. If you can run this and let me know your results we can continue to determine what other files might be causing your error.

  • WeichiWeichi Member

    Hi @SChaluvadi ,Thanks for your advise.
    This is my command for ValidateVariants :
    /pkg/biology/GATK/GATK_v4.0.8.1/gatk ValidateVariants -V NV0047-01_S14_gatk4.vcf
    /pkg/biology/GATK/GATK_v4.0.8.1/gatk ValidateVariants -V hapmap_3.3.b37.vcf
    /pkg/biology/GATK/GATK_v4.0.8.1/gatk ValidateVariants -V 1000G_omni2.5.b37.vcf
    /pkg/biology/GATK/GATK_v4.0.8.1/gatk ValidateVariants -V dbsnp_138.b37.vcf
    /pkg/biology/GATK/GATK_v4.0.8.1/gatk ValidateVariants -V 1000G_phase1.snps.high_confidence.b37.vcf

    And this is the result:
    (I didn't get any error message from GATKs ValidateVariants)

    Using GATK jar /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-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 /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar ValidateVariants -V /work2/weichi79/project016_VQSR/TMUH_set/NV0047-01_S14_gatk4.vcf
    12:49:06.610 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
    12:49:06.767 INFO ValidateVariants - ------------------------------------------------------------
    12:49:06.767 INFO ValidateVariants - The Genome Analysis Toolkit (GATK) v4.0.8.1
    12:49:06.767 INFO ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
    12:49:06.767 INFO ValidateVariants - Executing as [email protected] on Linux v3.10.0-514.el7.x86_64 amd64
    12:49:06.767 INFO ValidateVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13
    12:49:06.767 INFO ValidateVariants - Start Date/Time: January 4, 2019 12:49:06 PM CST
    12:49:06.767 INFO ValidateVariants - ------------------------------------------------------------
    12:49:06.767 INFO ValidateVariants - ------------------------------------------------------------
    12:49:06.767 INFO ValidateVariants - HTSJDK Version: 2.16.0
    12:49:06.768 INFO ValidateVariants - Picard Version: 2.18.7
    12:49:06.768 INFO ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    12:49:06.768 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    12:49:06.768 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    12:49:06.768 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    12:49:06.768 INFO ValidateVariants - Deflater: IntelDeflater
    12:49:06.768 INFO ValidateVariants - Inflater: IntelInflater
    12:49:06.768 INFO ValidateVariants - GCS max retries/reopens: 20
    12:49:06.768 INFO ValidateVariants - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
    12:49:06.768 INFO ValidateVariants - Initializing engine
    12:49:07.095 INFO FeatureManager - Using codec VCFCodec to read file file:///work2/weichi79/project016_VQSR/TMUH_set/NV0047-01_S14_gatk4.vcf
    12:49:07.299 INFO ValidateVariants - Done initializing engine
    12:49:07.299 INFO ProgressMeter - Starting traversal
    12:49:07.300 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    12:49:17.302 INFO ProgressMeter - 10:97608114 0.2 2934000 17604000.0
    12:49:23.951 INFO ProgressMeter - GL000192.1:483068 0.3 4964391 17889697.3
    12:49:23.951 INFO ProgressMeter - Traversal complete. Processed 4964391 total variants in 0.3 minutes.
    12:49:23.951 INFO ValidateVariants - Shutting down engine
    [January 4, 2019 12:49:23 PM CST] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.29 minutes.
    Runtime.totalMemory()=6951534592

    Using GATK jar /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-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 /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar ValidateVariants -V /work1/weichi79/GATK_dataset/vqsr/hapmap_3.3.b37.vcf
    12:49:25.477 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
    12:49:25.549 INFO ValidateVariants - ------------------------------------------------------------
    12:49:25.549 INFO ValidateVariants - The Genome Analysis Toolkit (GATK) v4.0.8.1
    12:49:25.549 INFO ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
    12:49:25.549 INFO ValidateVariants - Executing as [email protected] on Linux v3.10.0-514.el7.x86_64 amd64
    12:49:25.549 INFO ValidateVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13
    12:49:25.549 INFO ValidateVariants - Start Date/Time: January 4, 2019 12:49:25 PM CST
    12:49:25.549 INFO ValidateVariants - ------------------------------------------------------------
    12:49:25.549 INFO ValidateVariants - ------------------------------------------------------------
    12:49:25.550 INFO ValidateVariants - HTSJDK Version: 2.16.0
    12:49:25.550 INFO ValidateVariants - Picard Version: 2.18.7
    12:49:25.550 INFO ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    12:49:25.550 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    12:49:25.550 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    12:49:25.550 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    12:49:25.550 INFO ValidateVariants - Deflater: IntelDeflater
    12:49:25.550 INFO ValidateVariants - Inflater: IntelInflater
    12:49:25.550 INFO ValidateVariants - GCS max retries/reopens: 20
    12:49:25.550 INFO ValidateVariants - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
    12:49:25.550 INFO ValidateVariants - Initializing engine
    12:49:25.883 INFO FeatureManager - Using codec VCFCodec to read file file:///work1/weichi79/GATK_dataset/vqsr/hapmap_3.3.b37.vcf
    12:49:26.001 INFO ValidateVariants - Done initializing engine
    12:49:26.001 INFO ProgressMeter - Starting traversal
    12:49:26.001 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    12:49:31.493 INFO ProgressMeter - X:155073731 0.1 4165754 45519074.8
    12:49:31.494 INFO ProgressMeter - Traversal complete. Processed 4165754 total variants in 0.1 minutes.
    12:49:31.494 INFO ValidateVariants - Shutting down engine
    [January 4, 2019 12:49:31 PM CST] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.10 minutes.
    Runtime.totalMemory()=3787980800

    Using GATK jar /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-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 /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar ValidateVariants -V /work1/weichi79/GATK_dataset/vqsr/1000G_omni2.5.b37.vcf
    12:49:33.019 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
    12:49:33.091 INFO ValidateVariants - ------------------------------------------------------------
    12:49:33.091 INFO ValidateVariants - The Genome Analysis Toolkit (GATK) v4.0.8.1
    12:49:33.091 INFO ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
    12:49:33.091 INFO ValidateVariants - Executing as [email protected] on Linux v3.10.0-514.el7.x86_64 amd64
    12:49:33.091 INFO ValidateVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13
    12:49:33.091 INFO ValidateVariants - Start Date/Time: January 4, 2019 12:49:33 PM CST
    12:49:33.091 INFO ValidateVariants - ------------------------------------------------------------
    12:49:33.091 INFO ValidateVariants - ------------------------------------------------------------
    12:49:33.091 INFO ValidateVariants - HTSJDK Version: 2.16.0
    12:49:33.092 INFO ValidateVariants - Picard Version: 2.18.7
    12:49:33.092 INFO ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    12:49:33.092 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    12:49:33.092 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    12:49:33.092 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    12:49:33.092 INFO ValidateVariants - Deflater: IntelDeflater
    12:49:33.092 INFO ValidateVariants - Inflater: IntelInflater
    12:49:33.092 INFO ValidateVariants - GCS max retries/reopens: 20
    12:49:33.092 INFO ValidateVariants - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
    12:49:33.092 INFO ValidateVariants - Initializing engine
    12:49:33.401 INFO FeatureManager - Using codec VCFCodec to read file file:///work1/weichi79/GATK_dataset/vqsr/1000G_omni2.5.b37.vcf
    12:49:33.480 INFO ValidateVariants - Done initializing engine
    12:49:33.480 INFO ProgressMeter - Starting traversal
    12:49:33.481 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    12:49:37.129 INFO ProgressMeter - Y:22725379 0.1 2448222 40288897.4
    12:49:37.129 INFO ProgressMeter - Traversal complete. Processed 2448222 total variants in 0.1 minutes.
    12:49:37.129 INFO ValidateVariants - Shutting down engine
    [January 4, 2019 12:49:37 PM CST] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.07 minutes.
    Runtime.totalMemory()=3171418112

    Using GATK jar /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-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 /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar ValidateVariants -V /work1/weichi79/GATK_dataset/dbsnp_138.b37.vcf
    12:49:38.664 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
    12:49:38.736 INFO ValidateVariants - ------------------------------------------------------------
    12:49:38.736 INFO ValidateVariants - The Genome Analysis Toolkit (GATK) v4.0.8.1
    12:49:38.736 INFO ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
    12:49:38.736 INFO ValidateVariants - Executing as [email protected] on Linux v3.10.0-514.el7.x86_64 amd64
    12:49:38.736 INFO ValidateVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13
    12:49:38.736 INFO ValidateVariants - Start Date/Time: January 4, 2019 12:49:38 PM CST
    12:49:38.736 INFO ValidateVariants - ------------------------------------------------------------
    12:49:38.736 INFO ValidateVariants - ------------------------------------------------------------
    12:49:38.737 INFO ValidateVariants - HTSJDK Version: 2.16.0
    12:49:38.737 INFO ValidateVariants - Picard Version: 2.18.7
    12:49:38.737 INFO ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    12:49:38.737 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    12:49:38.737 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    12:49:38.737 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    12:49:38.737 INFO ValidateVariants - Deflater: IntelDeflater
    12:49:38.737 INFO ValidateVariants - Inflater: IntelInflater
    12:49:38.737 INFO ValidateVariants - GCS max retries/reopens: 20
    12:49:38.737 INFO ValidateVariants - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
    12:49:38.737 INFO ValidateVariants - Initializing engine
    12:49:39.039 INFO FeatureManager - Using codec VCFCodec to read file file:///work1/weichi79/GATK_dataset/dbsnp_138.b37.vcf
    12:49:39.269 INFO ValidateVariants - Done initializing engine
    12:49:39.269 INFO ProgressMeter - Starting traversal
    12:49:39.269 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    12:49:49.272 INFO ProgressMeter - 1:180226284 0.2 3256000 19532093.6
    12:49:59.272 INFO ProgressMeter - 2:92175939 0.3 6719000 20153976.9
    12:50:09.274 INFO ProgressMeter - 3:20725959 0.5 10239000 20474587.6
    12:50:19.275 INFO ProgressMeter - 3:192803301 0.7 13789000 20680397.9
    12:50:29.276 INFO ProgressMeter - 4:164503920 0.8 17380000 20853497.6
    12:50:39.275 INFO ProgressMeter - 5:146409116 1.0 20991000 20988901.1
    12:50:49.276 INFO ProgressMeter - 6:132529077 1.2 24572000 21059909.2
    12:50:59.278 INFO ProgressMeter - 7:130954017 1.3 28190000 21140386.0
    12:51:09.277 INFO ProgressMeter - 8:136456469 1.5 31809000 21204115.2
    12:51:19.279 INFO ProgressMeter - 10:33867353 1.7 35416000 21247475.3
    12:51:29.281 INFO ProgressMeter - 11:69263498 1.8 38990000 21264952.9
    12:51:39.283 INFO ProgressMeter - 12:103138777 2.0 42543000 21269018.6
    12:51:49.285 INFO ProgressMeter - 14:53850353 2.2 46003000 21229867.6
    12:51:59.284 INFO ProgressMeter - 16:21304349 2.3 49475000 21201451.3
    12:52:09.285 INFO ProgressMeter - 18:21790360 2.5 52996000 21196139.1
    12:52:19.285 INFO ProgressMeter - 20:39831512 2.7 56428000 21158384.2
    12:52:29.285 INFO ProgressMeter - X:95178372 2.8 60002000 21175183.5
    12:52:32.059 INFO ProgressMeter - MT:11547 2.9 61045456 21197565.6
    12:52:32.060 INFO ProgressMeter - Traversal complete. Processed 61045456 total variants in 2.9 minutes.
    12:52:32.060 INFO ValidateVariants - Shutting down engine
    [January 4, 2019 12:52:32 PM CST] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 2.89 minutes.
    Runtime.totalMemory()=8657567744

    Using GATK jar /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-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 /pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar ValidateVariants -V /work1/weichi79/GATK_dataset/vqsr/1000G_phase1.snps.high_confidence.b37.vcf
    12:52:33.596 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/pkg/biology/GATK/GATK_v4.0.8.1/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
    12:52:33.670 INFO ValidateVariants - ------------------------------------------------------------
    12:52:33.670 INFO ValidateVariants - The Genome Analysis Toolkit (GATK) v4.0.8.1
    12:52:33.670 INFO ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
    12:52:33.670 INFO ValidateVariants - Executing as [email protected] on Linux v3.10.0-514.el7.x86_64 amd64
    12:52:33.670 INFO ValidateVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13
    12:52:33.671 INFO ValidateVariants - Start Date/Time: January 4, 2019 12:52:33 PM CST
    12:52:33.671 INFO ValidateVariants - ------------------------------------------------------------
    12:52:33.671 INFO ValidateVariants - ------------------------------------------------------------
    12:52:33.671 INFO ValidateVariants - HTSJDK Version: 2.16.0
    12:52:33.671 INFO ValidateVariants - Picard Version: 2.18.7
    12:52:33.671 INFO ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    12:52:33.671 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    12:52:33.671 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    12:52:33.671 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    12:52:33.671 INFO ValidateVariants - Deflater: IntelDeflater
    12:52:33.671 INFO ValidateVariants - Inflater: IntelInflater
    12:52:33.671 INFO ValidateVariants - GCS max retries/reopens: 20
    12:52:33.671 INFO ValidateVariants - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
    12:52:33.671 INFO ValidateVariants - Initializing engine
    12:52:33.972 INFO FeatureManager - Using codec VCFCodec to read file file:///work1/weichi79/GATK_dataset/vqsr/1000G_phase1.snps.high_confidence.b37.vcf
    12:52:34.149 WARN IndexUtils - Feature file "/work1/weichi79/GATK_dataset/vqsr/1000G_phase1.snps.high_confidence.b37.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
    12:52:34.196 WARN IndexUtils - Index file /work1/weichi79/GATK_dataset/vqsr/1000G_phase1.snps.high_confidence.b37.vcf.idx is out of date (index older than input file). Use IndexFeatureFile to make a new index.
    12:52:34.198 INFO ValidateVariants - Done initializing engine
    12:52:34.198 INFO ProgressMeter - Starting traversal
    12:52:34.198 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    12:52:44.205 INFO ProgressMeter - 2:31099720 0.2 2492000 14947515.7
    12:52:54.202 INFO ProgressMeter - 3:56964447 0.3 5179000 15533893.2
    12:53:04.205 INFO ProgressMeter - 4:124475544 0.5 7898000 15792315.1
    12:53:14.205 INFO ProgressMeter - 6:14633930 0.7 10613000 15916714.6
    12:53:24.208 INFO ProgressMeter - 7:109647093 0.8 13300000 15957127.7
    12:53:34.211 INFO ProgressMeter - 9:81903293 1.0 16006000 16002799.4
    12:53:44.213 INFO ProgressMeter - 11:77367098 1.2 18696000 16021709.6
    12:53:54.214 INFO ProgressMeter - 13:94988716 1.3 21421000 16062537.5
    12:54:04.215 INFO ProgressMeter - 16:84567907 1.5 24133000 16085628.3
    12:54:14.216 INFO ProgressMeter - 21:15245336 1.7 26871000 16119698.5
    12:54:20.393 INFO ProgressMeter - X:155190417 1.8 28596441 16156942.0
    12:54:20.393 INFO ProgressMeter - Traversal complete. Processed 28596441 total variants in 1.8 minutes.
    12:54:20.393 INFO ValidateVariants - Shutting down engine
    [January 4, 2019 12:54:20 PM CST] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 1.78 minutes.
    Runtime.totalMemory()=2197291008

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @Weichi I am asking the GATK team what this error might indicate and will get back to you!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @Weichi A team member is looking into your inquiry but has been unable to reproduce the error that you are seeing. To help troubleshoot, can you share the file NV0047-01_S14_gatk4.vcf (or part of it if it is too large)?

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    The problem is simply that the way the command line is parsed has been changed and the documentation has not been updated - which we are working to resolve. The resource files should be passed as below:

    -resource hapmap,known=false,training=true,truth=true,prior=15:hapmap_3.3.b37.vcf

    Please note that there should be a space after "-resource" but NO space after the ":" between the prior value and the actual name of the file.

    Thanks!

  • WeichiWeichi Member

    Yes, it works!
    Thanks for your help!

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