Hi,

I have the following error. I tried to run ValidateVariants and no issues were recognized.

REQUIRED for all errors and issues:
a) GATK version used: not sure, it was from the WARP JointGenotyping step

b) Exact command used:

gatk --java-options "-Xms24000m -Xmx25000m" \
  VariantRecalibrator \
  -V /cromwell_root/fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz \
  -O vcf_cohort.indels.recal \
  --tranches-file vcf_cohort.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

 
c) Entire program log:

2023/08/21 20:19:30 Starting container setup. 2023/08/21 20:19:32 Done container setup. 2023/08/21 20:19:33 Starting localization. 2023/08/21 20:19:45 Localization script execution started... 2023/08/21 20:19:45 Localizing input gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz.tbi -> /cromwell_root/fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz.tbi 2023/08/21 20:19:48 Localizing input gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz -> /cromwell_root/fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz Copying gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz... / [0 files][ 0.0 B/ 7.3 MiB] / [1 files][ 7.3 MiB/ 7.3 MiB] Operation completed over 1 objects/7.3 MiB. 2023/08/21 20:19:50 Localizing input gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-IndelsVariantRecalibrator/script -> /cromwell_root/script 2023/08/21 20:19:52 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 2023/08/21 20:19:54 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 2023/08/21 20:19:54 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 2023/08/21 20:19:54 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 2023/08/21 20:19:54 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 2023/08/21 20:19:54 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][ 43.6 MiB/ 1.4 GiB] \ | | [0 files][ 95.1 MiB/ 1.4 GiB] / / [0 files][150.0 MiB/ 1.4 GiB] - \ \ [0 files][202.6 MiB/ 1.4 GiB] | / / [0 files][252.1 MiB/ 1.4 GiB] - - [0 files][295.4 MiB/ 1.4 GiB] \ | | [0 files][338.2 MiB/ 1.4 GiB] / - - [0 files][372.3 MiB/ 1.4 GiB] \ \ [0 files][424.4 MiB/ 1.4 GiB] | / / [0 files][478.8 MiB/ 1.4 GiB] - \ \ [0 files][534.0 MiB/ 1.4 GiB] 47.8 MiB/s | | [0 files][589.1 MiB/ 1.4 GiB] 50.0 MiB/s / - - [0 files][641.5 MiB/ 1.4 GiB] 53.7 MiB/s \ \ [0 files][681.4 MiB/ 1.4 GiB] 51.3 MiB/s | / / [0 files][728.1 MiB/ 1.4 GiB] 49.8 MiB/s - \ \ [0 files][761.6 MiB/ 1.4 GiB] 45.4 MiB/s | | [0 files][808.0 MiB/ 1.4 GiB] 43.6 MiB/s / - - [0 files][857.3 MiB/ 1.4 GiB] 43.0 MiB/s \ | | [0 files][902.1 MiB/ 1.4 GiB] 44.0 MiB/s / / [0 files][953.9 MiB/ 1.4 GiB] 45.0 MiB/s - \ \ [0 files][ 1006 MiB/ 1.4 GiB] 48.7 MiB/s | / / [0 files][ 1.0 GiB/ 1.4 GiB] 49.9 MiB/s - - [0 files][ 1.1 GiB/ 1.4 GiB] 50.3 MiB/s \ | | [0 files][ 1.1 GiB/ 1.4 GiB] 50.4 MiB/s / - - [0 files][ 1.2 GiB/ 1.4 GiB] 50.4 MiB/s \ \ [0 files][ 1.2 GiB/ 1.4 GiB] 50.1 MiB/s | / / [0 files][ 1.3 GiB/ 1.4 GiB] 49.7 MiB/s - \ \ [0 files][ 1.3 GiB/ 1.4 GiB] 49.5 MiB/s | | [0 files][ 1.4 GiB/ 1.4 GiB] 49.4 MiB/s / - - [0 files][ 1.4 GiB/ 1.4 GiB] 49.2 MiB/s \ Operation completed over 1 objects/1.4 GiB. \ [1 files][ 1.4 GiB/ 1.4 GiB] 48.0 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] 48.0 MiB/s \ [2 files][ 1.4 GiB/ 1.4 GiB] 46.4 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] 46.4 MiB/s | / / [2 files][ 1.5 GiB/ 1.5 GiB] 46.5 MiB/s - - [3 files][ 1.5 GiB/ 1.5 GiB] 35.1 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] 35.0 MiB/s \ [4 files][ 1.5 GiB/ 1.5 GiB] 31.5 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] 31.4 MiB/s \ [5 files][ 1.5 GiB/ 1.5 GiB] 29.4 MiB/s | 2023/08/21 20:20:31 Localization script execution complete. 2023/08/21 20:20:38 Done localization. 2023/08/21 20:20:39 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash us.gcr.io/broad-gatk/gatk@sha256:e7996ba655225c1cde0a1faec6a113e217758310af2cf99b00d61dae8ec6e9f2 /cromwell_root/script Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.2134704e 20:20:44.587 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 20:20:44.761 INFO VariantRecalibrator - ------------------------------------------------------------ 20:20:44.762 INFO VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.3.0.0 20:20:44.762 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 20:20:44.763 INFO VariantRecalibrator - Executing as root@e227705dffff on Linux v5.15.120+ amd64 20:20:44.763 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08 20:20:44.764 INFO VariantRecalibrator - Start Date/Time: August 21, 2023 8:20:44 PM GMT 20:20:44.764 INFO VariantRecalibrator - ------------------------------------------------------------ 20:20:44.764 INFO VariantRecalibrator - ------------------------------------------------------------ 20:20:44.765 INFO VariantRecalibrator - HTSJDK Version: 3.0.1 20:20:44.765 INFO VariantRecalibrator - Picard Version: 2.27.5 20:20:44.765 INFO VariantRecalibrator - Built for Spark Version: 2.4.5 20:20:44.766 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 20:20:44.766 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 20:20:44.766 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 20:20:44.766 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 20:20:44.767 INFO VariantRecalibrator - Deflater: IntelDeflater 20:20:44.767 INFO VariantRecalibrator - Inflater: IntelInflater 20:20:44.767 INFO VariantRecalibrator - GCS max retries/reopens: 20 20:20:44.767 INFO VariantRecalibrator - Requester pays: disabled 20:20:44.767 INFO VariantRecalibrator - Initializing engine 20:20:45.235 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 20:20:45.329 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 20:20:45.436 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz 20:20:45.614 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz 20:20:45.726 INFO VariantRecalibrator - Done initializing engine 20:20:45.730 INFO TrainingSet - Found mills track: Known = false Training = true Truth = true Prior = Q12.0 20:20:45.730 INFO TrainingSet - Found axiomPoly track: Known = false Training = true Truth = false Prior = Q10.0 20:20:45.730 INFO TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0 20:20:45.746 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF. 20:20:45.779 INFO ProgressMeter - Starting traversal 20:20:45.780 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 20:20:56.964 INFO ProgressMeter - 1:245133539 0.2 7000 37553.6 20:21:07.140 INFO ProgressMeter - 4:155410909 0.4 18000 50561.8 20:21:10.637 INFO VariantRecalibrator - Shutting down engine [August 21, 2023 8:21:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.43 minutes. Runtime.totalMemory()=24615321600 org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at 6:29912830 [VC /cromwell_root/fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz @ 6:29912830 Q18401.70 of type=SNP alleles=[T*, C] attr={AC=16, AF=1.00, AN=16, AS_BaseQRankSum=-0.050, AS_FS=0.000, AS_MQ=47.45, AS_MQRankSum=-0.100, AS_QD=32.28, AS_ReadPosRankSum=-0.250, AS_SOR=2.432, BaseQRankSum=1.77, DB=true, DP=617, ExcessHet=0.0000, FS=0.000, MLEAC=16, MLEAF=1.00, MQ=47.59, MQRankSum=1.21, QD=32.28, ReadPosRankSum=0.341, SOR=2.445} 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$OfRef.evaluateSequential(ForEachOps.java:173) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485) at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1095) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Caused by: java.lang.IllegalStateException: Reference allele mismatch at position 6:29912413 : at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:427) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.parseTrainingSets(VariantDataManager.java:399) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addDatum(VariantRecalibrator.java:621) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addVariantDatum(VariantRecalibrator.java:584) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.lambda$consumeQueuedVariants$0(VariantRecalibrator.java:549) at java.util.ArrayList.forEach(ArrayList.java:1257) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.consumeQueuedVariants(VariantRecalibrator.java:549) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.apply(VariantRecalibrator.java:528) at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:139) ... 20 more Caused by: java.lang.IllegalStateException: The provided reference alleles do not appear to represent the same position, TG* vs. TT* at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.determineReferenceAllele(GATKVariantContextUtils.java:238) at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.isAlleleInList(GATKVariantContextUtils.java:167) at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:425) ... 28 more Using GATK jar /gatk/gatk-package-4.3.0.0-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=2 -Xms24000m -Xmx25000m -jar /gatk/gatk-package-4.3.0.0-local.jar VariantRecalibrator -V /cromwell_root/fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-SitesOnlyGatherVcf/cacheCopy/vcf_cohort.sites_only.vcf.gz -O vcf_cohort.indels.recal --tranches-file vcf_cohort.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 2023/08/21 20:21:13 Starting delocalization. 2023/08/21 20:21:14 Delocalization script execution started... 2023/08/21 20:21:14 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-IndelsVariantRecalibrator/memory_retry_rc 2023/08/21 20:21:17 Delocalizing output /cromwell_root/rc -> gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-IndelsVariantRecalibrator/rc 2023/08/21 20:21:19 Delocalizing output /cromwell_root/stdout -> gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-IndelsVariantRecalibrator/stdout 2023/08/21 20:21:21 Delocalizing output /cromwell_root/stderr -> gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-IndelsVariantRecalibrator/stderr 2023/08/21 20:21:23 Delocalizing output /cromwell_root/vcf_cohort.indels.tranches -> gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-IndelsVariantRecalibrator/vcf_cohort.indels.tranches 2023/08/21 20:21:25 Delocalizing output /cromwell_root/vcf_cohort.indels.recal.idx -> gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-IndelsVariantRecalibrator/vcf_cohort.indels.recal.idx 2023/08/21 20:21:26 Delocalizing output /cromwell_root/vcf_cohort.indels.recal -> gs://fc-secure-7485ee0e-7fdc-4d21-bb21-13eecc505aa7/submissions/4c302257-426d-4fae-9df7-9a45914c4405/JointGenotyping/dbff565e-f85d-4561-b511-eef10258322c/call-IndelsVariantRecalibrator/vcf_cohort.indels.recal 2023/08/21 20:21:28 Delocalization script execution complete. 2023/08/21 20:21:29 Done delocalization.