The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*
Hello,
I've been using GATK Best Practices for Germline SNPs & Indels, workflow 2-4-JointGenotyping-B37 (after running the preceding ones), and after running for a week, the following two tasks failed. Any idea what's going on? Thanks!
Best, Oliver
2022/04/14 22:56:39 Starting container setup.
2022/04/14 22:56:41 Done container setup.
2022/04/14 22:56:43 Starting localization.
2022/04/14 22:56:52 Localization script execution started...
2022/04/14 22:56:52 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz
2022/04/14 22:56:55 Localizing input gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
2022/04/14 22:56:55 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx
2022/04/14 22:56:55 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf
2022/04/14 22:56:55 Localizing input gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi
2022/04/14 22:56:55 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi
Copying gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz...
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Copying gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx...
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Copying gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf...
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==> NOTE: You are performing a sequence of gsutil operations that may
run significantly faster if you instead use gsutil -m cp ... Please
see the -m section under "gsutil help options" for further information
about when gsutil -m can be advantageous.
Copying gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi...
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2022/04/14 22:57:22 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz.tbi -> /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz.tbi
2022/04/14 22:57:23 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz -> /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz
Copying gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz...
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2022/04/14 22:57:54 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-IndelsVariantRecalibrator/script -> /cromwell_root/script
2022/04/14 22:57:55 Localization script execution complete.
2022/04/14 22:58:08 Done localization.
2022/04/14 22:58:15 Running user action: docker run -v /mnt/local-disk:/cromwell_root -v /mnt/d-c74a541aa27f13cfe59c2f998a664729:/mnt/d9e025138b28caa42dd4006fc3636661:ro --entrypoint=/bin/bash broadinstitute/gatk@sha256:5c8ad33becf8541ede410de4c99b861ae13bbb0a2dfa7501dcd758be8fc3f36d /cromwell_root/script
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.15fa83e1
22:58:19.476 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:58:19.635 INFO VariantRecalibrator - ------------------------------------------------------------
22:58:19.636 INFO VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.4.0
22:58:19.636 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
22:58:19.636 INFO VariantRecalibrator - Executing as root@c1af2870e4a8 on Linux v5.10.107+ amd64
22:58:19.636 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
22:58:19.637 INFO VariantRecalibrator - Start Date/Time: April 14, 2022 10:58:19 PM GMT
22:58:19.637 INFO VariantRecalibrator - ------------------------------------------------------------
22:58:19.637 INFO VariantRecalibrator - ------------------------------------------------------------
22:58:19.638 INFO VariantRecalibrator - HTSJDK Version: 2.24.1
22:58:19.638 INFO VariantRecalibrator - Picard Version: 2.25.4
22:58:19.639 INFO VariantRecalibrator - Built for Spark Version: 2.4.5
22:58:19.639 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:58:19.639 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:58:19.639 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:58:19.639 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:58:19.639 INFO VariantRecalibrator - Deflater: IntelDeflater
22:58:19.639 INFO VariantRecalibrator - Inflater: IntelInflater
22:58:19.639 INFO VariantRecalibrator - GCS max retries/reopens: 20
22:58:19.640 INFO VariantRecalibrator - Requester pays: disabled
22:58:19.640 INFO VariantRecalibrator - Initializing engine
22:58:19.985 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf
22:58:20.048 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz
22:58:20.123 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
22:58:20.253 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz
22:58:20.516 INFO VariantRecalibrator - Done initializing engine
22:58:20.518 INFO TrainingSet - Found mills track: Known = false Training = true Truth = true Prior = Q12.0
22:58:20.518 INFO TrainingSet - Found axiomPoly track: Known = false Training = true Truth = false Prior = Q10.0
22:58:20.519 INFO TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0
22:58:20.533 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF.
22:58:20.558 INFO ProgressMeter - Starting traversal
22:58:20.558 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
22:58:22.437 INFO VariantRecalibrator - Shutting down engine
[April 14, 2022 10:58:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=24696061952
org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at 1:2156906 [VC /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz @ 1:2156906-2156909 Q3829.08 of type=INDEL alleles=[ATTT*, *, A, AT, ATT, ATTTT, ATTTTT] attr={AC=[2, 2, 1, 5, 2, 2], AF=[1.242e-03, 1.242e-03, 6.211e-04, 3.106e-03, 1.242e-03, 1.242e-03], AN=1610, AS_BaseQRankSum=[0.950, ., ., ., ., .], AS_FS=[0.000, 0.000, 0.000, 0.000, 2.963, .], AS_InbreedingCoeff=[0.1217, 0.1271, 0.1236, 0.1267, 0.1284, 0.1271], AS_MQ=[60.00, 60.00, 60.00, 60.00, 60.00, 0.00], AS_MQRankSum=[0.000, ., ., ., ., .], AS_QD=[33.28, 29.85, 27.79, 27.06, 29.86, 32.23], AS_ReadPosRankSum=[0.400, ., ., ., ., .], AS_SOR=[0.804, 0.180, 0.368, 0.804, 0.895, .], BaseQRankSum=1.35, DB=true, DP=44, ExcessHet=0.2996, FS=0.000, InbreedingCoeff=0.3346, MLEAC=[148, 79, 75, 238, 85, 79], MLEAF=[0.092, 0.049, 0.047, 0.148, 0.053, 0.049], MQ=60.00, MQRankSum=0.00, QD=33.81, ReadPosRankSum=0.619, SOR=0.693} GT=[] filters=
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:145)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.lang.IllegalStateException: Reference allele mismatch at position 1:2156904 :
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:427)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.parseTrainingSets(VariantDataManager.java:399)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addDatum(VariantRecalibrator.java:615)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addVariantDatum(VariantRecalibrator.java:578)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.lambda$consumeQueuedVariants$0(VariantRecalibrator.java:543)
at java.util.ArrayList.forEach(ArrayList.java:1257)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.consumeQueuedVariants(VariantRecalibrator.java:543)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.apply(VariantRecalibrator.java:522)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:139)
... 20 more
Caused by: java.lang.IllegalStateException: The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*
at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.determineReferenceAllele(GATKVariantContextUtils.java:237)
at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.isAlleleInList(GATKVariantContextUtils.java:166)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:425)
... 28 more
Using GATK jar /gatk/gatk-package-4.2.4.0-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 -Xms24g -jar /gatk/gatk-package-4.2.4.0-local.jar VariantRecalibrator -V /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz -O neph.indels.recal --tranches-file neph.indels.tranches --trust-all-polymorphic -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.5 -tranche 99.0 -tranche 97.0 -tranche 96.0 -tranche 95.0 -tranche 94.0 -tranche 93.5 -tranche 93.0 -tranche 92.0 -tranche 91.0 -tranche 90.0 -an FS -an ReadPosRankSum -an MQRankSum -an QD -an SOR -an DP --use-allele-specific-annotations -mode INDEL --max-gaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12 /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf -resource:axiomPoly,known=false,training=true,truth=false,prior=10 /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz -resource:dbsnp,known=true,training=false,truth=false,prior=2 /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
2022/04/14 22:58:24 Starting delocalization.
2022/04/14 22:58:25 Delocalization script execution started...
2022/04/14 22:58:25 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-IndelsVariantRecalibrator/memory_retry_rc
2022/04/14 22:58:27 Delocalizing output /cromwell_root/rc -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-IndelsVariantRecalibrator/rc
2022/04/14 22:58:29 Delocalizing output /cromwell_root/stdout -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-IndelsVariantRecalibrator/stdout
2022/04/14 22:58:30 Delocalizing output /cromwell_root/stderr -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-IndelsVariantRecalibrator/stderr
2022/04/14 22:58:32 Delocalizing output /cromwell_root/neph.indels.recal -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-IndelsVariantRecalibrator/neph.indels.recal
2022/04/14 22:58:33 Delocalizing output /cromwell_root/neph.indels.recal.idx -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-IndelsVariantRecalibrator/neph.indels.recal.idx
2022/04/14 22:58:35 Delocalizing output /cromwell_root/neph.indels.tranches -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-IndelsVariantRecalibrator/neph.indels.tranches
2022/04/14 22:58:36 Delocalization script execution complete.
2022/04/14 22:58:37 Done delocalization.
and also with:
2022/04/14 22:57:14 Starting container setup.
2022/04/14 22:57:16 Done container setup.
2022/04/14 22:57:19 Starting localization.
2022/04/14 22:57:33 Localization script execution started...
2022/04/14 22:57:33 Localizing input gs://gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz.tbi
2022/04/14 22:57:37 Localizing input gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
2022/04/14 22:57:37 Localizing input gs://gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz
2022/04/14 22:57:37 Localizing input gs://gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz
2022/04/14 22:57:37 Localizing input gs://gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz.tbi
2022/04/14 22:57:37 Localizing input gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi
2022/04/14 22:57:37 Localizing input gs://gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz
2022/04/14 22:57:37 Localizing input gs://gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi
Copying gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz...
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Copying gs://gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz...
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Copying gs://gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz...
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Copying gs://gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz.tbi...
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==> NOTE: You are performing a sequence of gsutil operations that may
run significantly faster if you instead use gsutil -m cp ... Please
see the -m section under "gsutil help options" for further information
about when gsutil -m can be advantageous.
Copying gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi...
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Copying gs://gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz...
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Copying gs://gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi...
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2022/04/14 22:58:35 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz.tbi -> /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz.tbi
2022/04/14 22:58:37 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz -> /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz
Copying gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz...
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2022/04/14 22:59:12 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SNPsVariantRecalibratorClassic/script -> /cromwell_root/script
2022/04/14 22:59:14 Localization script execution complete.
2022/04/14 22:59:19 Done localization.
2022/04/14 22:59:20 Running user action: docker run -v /mnt/local-disk:/cromwell_root -v /mnt/d-c74a541aa27f13cfe59c2f998a664729:/mnt/d9e025138b28caa42dd4006fc3636661:ro --entrypoint=/bin/bash broadinstitute/gatk@sha256:5c8ad33becf8541ede410de4c99b861ae13bbb0a2dfa7501dcd758be8fc3f36d /cromwell_root/script
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.d174fa90
22:59:26.591 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:59:27.304 INFO VariantRecalibrator - ------------------------------------------------------------
22:59:27.305 INFO VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.4.0
22:59:27.305 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
22:59:27.306 INFO VariantRecalibrator - Executing as root@3dc658b896b4 on Linux v5.10.107+ amd64
22:59:27.306 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
22:59:27.307 INFO VariantRecalibrator - Start Date/Time: April 14, 2022 10:59:26 PM GMT
22:59:27.307 INFO VariantRecalibrator - ------------------------------------------------------------
22:59:27.307 INFO VariantRecalibrator - ------------------------------------------------------------
22:59:27.308 INFO VariantRecalibrator - HTSJDK Version: 2.24.1
22:59:27.308 INFO VariantRecalibrator - Picard Version: 2.25.4
22:59:27.309 INFO VariantRecalibrator - Built for Spark Version: 2.4.5
22:59:27.309 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:59:27.309 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:59:27.309 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:59:27.309 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:59:27.310 INFO VariantRecalibrator - Deflater: IntelDeflater
22:59:27.310 INFO VariantRecalibrator - Inflater: IntelInflater
22:59:27.310 INFO VariantRecalibrator - GCS max retries/reopens: 20
22:59:27.311 INFO VariantRecalibrator - Requester pays: disabled
22:59:27.311 INFO VariantRecalibrator - Initializing engine
22:59:27.681 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz
22:59:27.905 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz
22:59:28.120 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz
22:59:28.233 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
22:59:28.312 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz
22:59:28.514 WARN IndexUtils - Feature file "file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
22:59:28.678 WARN IntelInflater - Zero Bytes Written : 0
22:59:28.697 INFO VariantRecalibrator - Done initializing engine
22:59:28.707 INFO TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0
22:59:28.708 INFO TrainingSet - Found omni track: Known = false Training = true Truth = true Prior = Q12.0
22:59:28.708 INFO TrainingSet - Found 1000G track: Known = false Training = true Truth = false Prior = Q10.0
22:59:28.709 INFO TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q7.0
22:59:28.723 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF.
22:59:28.754 INFO ProgressMeter - Starting traversal
22:59:28.755 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
22:59:38.698 INFO VariantRecalibrator - Shutting down engine
[April 14, 2022 10:59:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=10290200576
org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at 1:15213104 [VC /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz @ 1:15213104 Q315.15 of type=SNP alleles=[A*, G] attr={AC=1, AF=6.211e-04, AN=1610, AS_BaseQRankSum=-1.000, AS_FS=0.000, AS_InbreedingCoeff=0.3356, AS_MQ=60.00, AS_MQRankSum=0.000, AS_QD=29.61, AS_ReadPosRankSum=0.000, AS_SOR=0.223, BaseQRankSum=-9.670e-01, DB=true, DP=40, ExcessHet=0.0000, FS=0.000, InbreedingCoeff=0.3356, MLEAC=66, MLEAF=0.041, MQ=60.00, MQRankSum=0.00, QD=29.98, ReadPosRankSum=0.00, SOR=0.223} GT=[] filters=
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:145)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.lang.IllegalStateException: Reference allele mismatch at position 1:15212969 :
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:427)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.parseTrainingSets(VariantDataManager.java:399)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addDatum(VariantRecalibrator.java:615)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addVariantDatum(VariantRecalibrator.java:578)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.lambda$consumeQueuedVariants$0(VariantRecalibrator.java:543)
at java.util.ArrayList.forEach(ArrayList.java:1257)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.consumeQueuedVariants(VariantRecalibrator.java:543)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.apply(VariantRecalibrator.java:522)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:139)
... 20 more
Caused by: java.lang.IllegalStateException: The provided reference alleles do not appear to represent the same position, CAG* vs. CAC*
at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.determineReferenceAllele(GATKVariantContextUtils.java:237)
at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.isAlleleInList(GATKVariantContextUtils.java:166)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:425)
... 28 more
Using GATK jar /gatk/gatk-package-4.2.4.0-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 -Xms10g -jar /gatk/gatk-package-4.2.4.0-local.jar VariantRecalibrator -V /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz -O neph.snps.recal --tranches-file neph.snps.tranches --trust-all-polymorphic -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.8 -tranche 99.6 -tranche 99.5 -tranche 99.4 -tranche 99.3 -tranche 99.0 -tranche 98.0 -tranche 97.0 -tranche 90.0 -an QD -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an SOR -an DP --use-allele-specific-annotations -mode SNP --max-gaussians 6 -resource:hapmap,known=false,training=true,truth=true,prior=15 /cromwell_root/gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz -resource:omni,known=false,training=true,truth=true,prior=12 /cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz -resource:1000G,known=false,training=true,truth=false,prior=10 /cromwell_root/gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz -resource:dbsnp,known=true,training=false,truth=false,prior=7 /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
2022/04/14 22:59:41 Starting delocalization.
2022/04/14 22:59:42 Delocalization script execution started...
2022/04/14 22:59:42 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SNPsVariantRecalibratorClassic/memory_retry_rc
2022/04/14 22:59:44 Delocalizing output /cromwell_root/rc -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SNPsVariantRecalibratorClassic/rc
2022/04/14 22:59:46 Delocalizing output /cromwell_root/stdout -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SNPsVariantRecalibratorClassic/stdout
2022/04/14 22:59:47 Delocalizing output /cromwell_root/stderr -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SNPsVariantRecalibratorClassic/stderr
2022/04/14 22:59:49 Delocalizing output /cromwell_root/neph.snps.recal -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SNPsVariantRecalibratorClassic/neph.snps.recal
2022/04/14 22:59:51 Delocalizing output /cromwell_root/neph.snps.recal.idx -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SNPsVariantRecalibratorClassic/neph.snps.recal.idx
2022/04/14 22:59:52 Delocalizing output /cromwell_root/neph.snps.tranches -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/be0a714d-c873-4fc9-b20c-32c3cce1f5b0/JointGenotyping/c09f2466-8e33-4ae3-a5a2-326c114f79a5/call-SNPsVariantRecalibratorClassic/neph.snps.tranches
2022/04/14 22:59:54 Delocalization script execution complete.
2022/04/14 22:59:55 Done delocalization.
-
This error message is indicating that there is something wrong with your data. At the location mentioned in the error message, there is a reference mismatch issue. It looks related to a previous bug fix we put out in VariantRecalibrator to supply the location when this error comes up. https://gatk.broadinstitute.org/hc/en-us/community/posts/360074618292-New-version-of-GATK-leads-to-VariantRecalibrator-error-
Is there something with these two samples that could have led to this reference mismatch problem?
Best,
Genevieve
-
Hello,
I used GATK Best Practices workflows from beginning to end, including using the reference data that were provided with these workflows. If the references are inconsistent, how can this be caused by my sequencing data? Thanks!
Best, Oliver
-
Hello,
For 2-1-Processing-For-Variant-Discovery-B37, the input "hg38" for ref_name looks suspicious. Is it incorrect and is the correct value "b37"?
Could this be the cause for the error?
Thanks!
Best, Oliver
-
Yes, there might be an issue with how you are running the featured workspace. I'm looking into this further and will let you know when I have an update.
-
Thanks, looking forward!
-
Are you running the workflow on Terra? If so, can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.
- Toggle the "Share with support" button to "Yes"
- Click Save
Please provide us with a link to your workspace. We’ll be happy to take a closer look as soon as we can!
Best,
Samantha
-
Hello,
The workspace is here: https://app.terra.bio/#workspaces/amp-dcc-rfp15/Pollak_Nephrotic_Syndrome_Portal
The submission with the error is here: https://app.terra.bio/#workspaces/amp-dcc-rfp15/Pollak_Nephrotic_Syndrome_Portal/job_history/be0a714d-c873-4fc9-b20c-32c3cce1f5b0
And the workspace is shared with support now.
Thanks for looking into this!
Best, Oliver
-
Hello,
I was wondering if there is any update on this? Thanks!
Best, Oliver
-
Hi Oliver,
Sorry for the delayed response. It does seem like there is an error in the Featured Workspace where the ref_name input for the 2-1-Processing-For-Variant-Discovery-B37 workflow is incorrectly set to "hg38." The inputs.json in Github for this workflow does indeed set ref_name to "b37": https://github.com/gatk-workflows/gatk4-data-processing/blob/2.1.0/processing-for-variant-discovery-gatk4.b37.wgs.inputs.json.
I'll make this update in the workspace and test it out, but in the meantime, you can update the input in your workspace and try re-running the pipeline.
Best,
Samantha
-
Hello,
I reran it with "b37", but I'm still getting this error. Any ideas? Thanks!
2022/05/07 20:07:54 Starting container setup. 2022/05/07 20:07:56 Done container setup. 2022/05/07 20:07:58 Starting localization. 2022/05/07 20:08:08 Localization script execution started... 2022/05/07 20:08:08 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz 2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz 2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx 2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf 2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi 2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi Copying gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz... / [0 files][ 0.0 B/ 1.4 GiB] - - [0 files][ 64.7 MiB/ 1.4 GiB] \ | | [0 files][135.1 MiB/ 1.4 GiB] / / [0 files][187.7 MiB/ 1.4 GiB] - \ \ [0 files][249.0 MiB/ 1.4 GiB] | / / [0 files][316.6 MiB/ 1.4 GiB] - - [0 files][376.4 MiB/ 1.4 GiB] \ | | [0 files][450.7 MiB/ 1.4 GiB] / - - [0 files][525.4 MiB/ 1.4 GiB] \ \ [0 files][600.7 MiB/ 1.4 GiB] | / / [0 files][675.7 MiB/ 1.4 GiB] - \ \ [0 files][740.5 MiB/ 1.4 GiB] 72.5 MiB/s | | [0 files][810.1 MiB/ 1.4 GiB] 71.6 MiB/s / - - [0 files][885.1 MiB/ 1.4 GiB] 71.7 MiB/s \ | | [0 files][959.9 MiB/ 1.4 GiB] 71.5 MiB/s / / [0 files][ 1.0 GiB/ 1.4 GiB] 71.4 MiB/s - \ \ [0 files][ 1.1 GiB/ 1.4 GiB] 73.5 MiB/s | / / [0 files][ 1.1 GiB/ 1.4 GiB] 66.9 MiB/s - - [0 files][ 1.2 GiB/ 1.4 GiB] 65.2 MiB/s \ | | [0 files][ 1.2 GiB/ 1.4 GiB] 63.7 MiB/s / - - [0 files][ 1.3 GiB/ 1.4 GiB] 62.0 MiB/s \ \ [0 files][ 1.4 GiB/ 1.4 GiB] 60.0 MiB/s | / / [0 files][ 1.4 GiB/ 1.4 GiB] 65.6 MiB/s Operation completed over 1 objects/1.4 GiB. / [1 files][ 1.4 GiB/ 1.4 GiB] 64.6 MiB/s Copying gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx... / [1 files][ 1.4 GiB/ 1.4 GiB] 64.5 MiB/s - - [2 files][ 1.4 GiB/ 1.4 GiB] 60.3 MiB/s Copying gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf... - [2 files][ 1.4 GiB/ 1.5 GiB] 60.3 MiB/s \ | | [2 files][ 1.5 GiB/ 1.5 GiB] 62.2 MiB/s | [3 files][ 1.5 GiB/ 1.5 GiB] 43.3 MiB/s / Copying gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi... / [3 files][ 1.5 GiB/ 1.5 GiB] 43.2 MiB/s / [4 files][ 1.5 GiB/ 1.5 GiB] 41.2 MiB/s ==> NOTE: You are performing a sequence of gsutil operations that may run significantly faster if you instead use gsutil -m cp ... Please see the -m section under "gsutil help options" for further information about when gsutil -m can be advantageous. Copying gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi... / [4 files][ 1.5 GiB/ 1.5 GiB] 41.0 MiB/s / [5 files][ 1.5 GiB/ 1.5 GiB] 38.2 MiB/s 2022/05/07 20:08:38 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz.tbi -> /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz.tbi 2022/05/07 20:08:39 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz -> /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz Copying gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz... / [0 files][ 0.0 B/258.6 MiB] - - [0 files][ 59.3 MiB/258.6 MiB] \ | | [0 files][129.2 MiB/258.6 MiB] / / [0 files][178.3 MiB/258.6 MiB] - \ \ [0 files][251.0 MiB/258.6 MiB] Operation completed over 1 objects/258.6 MiB. \ [1 files][258.6 MiB/258.6 MiB] 2022/05/07 20:08:45 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/script -> /cromwell_root/script 2022/05/07 20:08:47 Localization script execution complete. 2022/05/07 20:08:51 Done localization. 2022/05/07 20:08:52 Running user action: docker run -v /mnt/local-disk:/cromwell_root -v /mnt/d-c74a541aa27f13cfe59c2f998a664729:/mnt/d9e025138b28caa42dd4006fc3636661:ro --entrypoint=/bin/bash broadinstitute/gatk@sha256:5c8ad33becf8541ede410de4c99b861ae13bbb0a2dfa7501dcd758be8fc3f36d /cromwell_root/script Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.df55fe54 20:08:56.917 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 20:08:57.090 INFO VariantRecalibrator - ------------------------------------------------------------ 20:08:57.091 INFO VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.4.0 20:08:57.091 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 20:08:57.091 INFO VariantRecalibrator - Executing as root@d31f73fa6011 on Linux v5.10.107+ amd64 20:08:57.091 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08 20:08:57.092 INFO VariantRecalibrator - Start Date/Time: May 7, 2022 8:08:56 PM GMT 20:08:57.092 INFO VariantRecalibrator - ------------------------------------------------------------ 20:08:57.092 INFO VariantRecalibrator - ------------------------------------------------------------ 20:08:57.093 INFO VariantRecalibrator - HTSJDK Version: 2.24.1 20:08:57.093 INFO VariantRecalibrator - Picard Version: 2.25.4 20:08:57.093 INFO VariantRecalibrator - Built for Spark Version: 2.4.5 20:08:57.094 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 20:08:57.094 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 20:08:57.094 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 20:08:57.094 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 20:08:57.094 INFO VariantRecalibrator - Deflater: IntelDeflater 20:08:57.094 INFO VariantRecalibrator - Inflater: IntelInflater 20:08:57.095 INFO VariantRecalibrator - GCS max retries/reopens: 20 20:08:57.095 INFO VariantRecalibrator - Requester pays: disabled 20:08:57.095 INFO VariantRecalibrator - Initializing engine 20:08:57.419 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf 20:08:57.481 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz 20:08:57.552 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz 20:08:57.684 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz 20:08:57.896 INFO VariantRecalibrator - Done initializing engine 20:08:57.900 INFO TrainingSet - Found mills track: Known = false Training = true Truth = true Prior = Q12.0 20:08:57.900 INFO TrainingSet - Found axiomPoly track: Known = false Training = true Truth = false Prior = Q10.0 20:08:57.900 INFO TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0 20:08:57.914 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF. 20:08:57.934 INFO ProgressMeter - Starting traversal 20:08:57.934 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 20:08:59.193 INFO VariantRecalibrator - Shutting down engine [May 7, 2022 8:08:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=24696061952 org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at 1:3418656 [VC /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz @ 1:3418656 Q49.04 of type=SNP alleles=[C*, T] attr={AC=2, AF=0.020, AN=100, AS_BaseQRankSum=., AS_FS=0.000, AS_InbreedingCoeff=0.3892, AS_MQ=60.00, AS_MQRankSum=., AS_QD=28.53, AS_ReadPosRankSum=., AS_SOR=0.693, DP=137, ExcessHet=0.0000, FS=0.000, InbreedingCoeff=0.3892, MLEAC=5, MLEAF=0.050, MQ=60.00, QD=35.48, SOR=1.609} GT=[] filters= at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:145) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485) at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Caused by: java.lang.IllegalStateException: Reference allele mismatch at position 1:3418653 : at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:427) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.parseTrainingSets(VariantDataManager.java:399) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addDatum(VariantRecalibrator.java:615) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addVariantDatum(VariantRecalibrator.java:578) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.lambda$consumeQueuedVariants$0(VariantRecalibrator.java:543) at java.util.ArrayList.forEach(ArrayList.java:1257) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.consumeQueuedVariants(VariantRecalibrator.java:543) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.apply(VariantRecalibrator.java:522) at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:139) ... 20 more Caused by: java.lang.IllegalStateException: The provided reference alleles do not appear to represent the same position, CCG* vs. CGC* at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.determineReferenceAllele(GATKVariantContextUtils.java:237) at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.isAlleleInList(GATKVariantContextUtils.java:166) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:425) ... 28 more Using GATK jar /gatk/gatk-package-4.2.4.0-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 -Xms24g -jar /gatk/gatk-package-4.2.4.0-local.jar VariantRecalibrator -V /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz -O neph.indels.recal --tranches-file neph.indels.tranches --trust-all-polymorphic -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.5 -tranche 99.0 -tranche 97.0 -tranche 96.0 -tranche 95.0 -tranche 94.0 -tranche 93.5 -tranche 93.0 -tranche 92.0 -tranche 91.0 -tranche 90.0 -an FS -an ReadPosRankSum -an MQRankSum -an QD -an SOR -an DP --use-allele-specific-annotations -mode INDEL --max-gaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12 /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf -resource:axiomPoly,known=false,training=true,truth=false,prior=10 /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz -resource:dbsnp,known=true,training=false,truth=false,prior=2 /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz 2022/05/07 20:09:03 Starting delocalization. 2022/05/07 20:09:04 Delocalization script execution started... 2022/05/07 20:09:04 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/memory_retry_rc 2022/05/07 20:09:06 Delocalizing output /cromwell_root/rc -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/rc 2022/05/07 20:09:08 Delocalizing output /cromwell_root/stdout -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/stdout 2022/05/07 20:09:10 Delocalizing output /cromwell_root/stderr -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/stderr 2022/05/07 20:09:11 Delocalizing output /cromwell_root/neph.indels.recal -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/neph.indels.recal 2022/05/07 20:09:13 Delocalizing output /cromwell_root/neph.indels.recal.idx -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/neph.indels.recal.idx 2022/05/07 20:09:14 Delocalizing output /cromwell_root/neph.indels.tranches -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/neph.indels.tranches 2022/05/07 20:09:16 Delocalization script execution complete. 2022/05/07 20:09:17 Done delocalization.Best, Oliver
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Hi Oliver Ruebenacker, thanks for the update. We're doing some testing to determine if this issue is coming from the featured workspace or your input data.
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Hello Genevieve,
Thanks for the update and I'm looking forward to the results of the test!
We've also looked deeper into the issue, and we noticed that while the variant called by GATK looked like this:
1 3418653 . CCG C 77.64 PASS AC=1;AF=0.010;AN=100;AS_BaseQRankSum=-0.500;AS_FS=0.000;AS_InbreedingCoeff=0.3458;AS_MQ=60.00;AS_MQRankSum=1.200;AS_QD=13.00;AS_ReadPosRankSum=-0.900;AS_SOR=0.693;BaseQRankSum=-4.310e-01;DP=171;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.3458;MLEAC=5;MLEAF=0.050;MQ=54.09;MQRankSum=1.28;QD=12.94;ReadPosRankSum=-8.420e-01;SOR=0.693
The file dbsnp_138.b37.vcf.gz provided as reference by Terra and included as input to the failing task looks like this:
1 3418653 rs369335009 CGC C,CG . . NOC;OTHERKG;RS=369335009;RSPOS=3418654;SAO=0;SSR=0;VC=DIV;VP=0x050000000001000002000210;WGT=1;dbSNPBuildID=138
So indeed there is a conflict. One solution might be to upgrade to a later dbsnp file.
Thanks!
Best, Oliver
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Sorry for the delay. We are still looking into this and will let you know once we have an update.
Best,
Samantha
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I've confirmed with the pipeline authors that the dbsnp file is indeed incorrect. I'll work on getting this updated in the featured workspace. Thank you for pointing this out!
Best,
Samantha
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Hi everyone,
Please, is there any updated version available for the dbSNP_b37 later than v138. It seems like I do have the same issues because of an error in the dbsnp_138.b37.vcf.gz file.
Looking forward to having your comments.
Best.
Ahmed -
Hi Ahmed,
We don't currently distribute a newer dbSNP VCF ourselves, but you could try downloading the latest release from NCBI (https://ftp.ncbi.nih.gov/snp/latest_release/VCF/) and see if substituting it for the dbSNP 138 VCF in your workflow resolves the issue.
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