Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.

a) GATK version used 4.1.5.0
b) Exact GATK commands used

c) The entire error log if applicable.

2020/03/10 03:00:07 Starting container setup. 2020/03/10 03:00:10 Done container setup. 2020/03/10 03:00:11 Starting localization. 2020/03/10 03:00:19 Localization script execution started... 2020/03/10 03:00:19 Localizing input gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0001-scattered.interval_list -> /cromwell_root/fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0001-scattered.interval_list 2020/03/10 03:00:20 Localizing input gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-CreatePanel/shard-1/attempt-3/script -> /cromwell_root/script 2020/03/10 03:00:21 Localizing input gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -> /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta 2020/03/10 03:00:54 Localizing input gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict -> /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict 2020/03/10 03:00:54 Localizing input gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai -> /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai Copying gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict... Copying gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai... / [0/2 files][ 0.0 B/725.2 KiB] 0% Done / [0/2 files][ 0.0 B/725.2 KiB] 0% Done / [1/2 files][725.2 KiB/725.2 KiB] 99% Done / [2/2 files][725.2 KiB/725.2 KiB] 100% Done Operation completed over 2 objects/725.2 KiB. 2020/03/10 03:00:56 Localization script execution complete. 2020/03/10 03:01:00 Done localization. 2020/03/10 03:01:01 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint= us.gcr.io/broad-gatk/gatk@sha256:bdde52f53347e8ae506da50ed82b8be1bfac1cdbc7a9b78efcf7ac582aa2d4d4 /bin/bash /cromwell_root/script Using GATK jar /root/gatk.jar defined in environment variable GATK_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 /root/gatk.jar GenomicsDBImport --genomicsdb-workspace-path pon_db -R /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-0/Mutect2/99642b02-4487-4099-881a-4e1ee2eb8ffd/call-Filter/cacheCopy/M_CH_024-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-1/Mutect2/2809c30f-4971-48fa-b7f8-95ec2f914797/call-Filter/cacheCopy/M_CH_034-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-2/Mutect2/3db395fe-fa86-4a56-9f8e-0c74816b9e66/call-Filter/cacheCopy/M_CH_037-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-3/Mutect2/c96a0220-465a-41ee-81db-e27d07ee2eb6/call-Filter/cacheCopy/M_CH_040-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-4/Mutect2/72e2711c-9425-4fe2-848a-5cd4258cab8b/call-Filter/cacheCopy/M_CH_041-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-5/Mutect2/83b55c95-68a7-4792-a66c-46fc461d0709/call-Filter/cacheCopy/M_CH_049-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-6/Mutect2/094435fa-7824-40f8-a3a0-1dd795357f49/call-Filter/cacheCopy/M_CH_070-filtered.vcf -V 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gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-11/Mutect2/c0669e5e-df93-44d0-b74e-f8e3043e7af9/call-Filter/cacheCopy/M_CH_129-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-12/Mutect2/f3382013-fc73-447b-a682-20c5d31c96f5/call-Filter/cacheCopy/M_CH_133-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-13/Mutect2/7fc39883-6aec-4af9-afa1-7e8a92691d8a/call-Filter/cacheCopy/M_CH_152-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-14/Mutect2/05c27a97-b975-4b1f-b4de-a53ed915609d/call-Filter/cacheCopy/M_CH_156-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-15/Mutect2/149a80df-69c4-44ec-9d7c-68f027b7395c/call-Filter/cacheCopy/M_CH_157-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-16/Mutect2/18903ffa-9617-41c4-b92e-862411436299/call-Filter/cacheCopy/M_CH_183-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-17/Mutect2/5eeccadf-3ee1-4c56-9fb7-6949a886b0e0/call-Filter/cacheCopy/M_CH_184-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-18/Mutect2/003ca618-82f5-4eda-b53b-1ea8bd15d9c2/call-Filter/cacheCopy/M_CH_189-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-19/Mutect2/c9d94516-c0b2-4f31-b17b-84dd09a62eea/call-Filter/cacheCopy/M_CH_203-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-20/Mutect2/3d5581a0-9367-4a2d-8792-ca186eb34cf9/call-Filter/cacheCopy/M_CH_205-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-21/Mutect2/e6265441-b8b1-454d-8f2f-dd4a7e03c85e/call-Filter/cacheCopy/M_CH_210-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-22/Mutect2/79bf9bf3-7835-4dc8-9e37-49771d4dba91/call-Filter/cacheCopy/M_CH_212-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-23/Mutect2/a7214f27-9b46-4202-b5e3-06245469adbb/call-Filter/cacheCopy/M_CH_216-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-24/Mutect2/7f404802-98d7-40e6-aa70-136bf07eb059/call-Filter/cacheCopy/M_CH_217-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-25/Mutect2/6a8466d8-04cb-457f-900d-223818770d36/call-Filter/cacheCopy/M_CH_222-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-26/Mutect2/8ef8e54d-872e-49d9-9a19-53ac971e8db2/call-Filter/cacheCopy/M_CH_245-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-27/Mutect2/43b43743-3899-4f24-8edc-952c4856ad26/call-Filter/cacheCopy/M_CH_275-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-28/Mutect2/af22710b-252d-425d-a6c9-b99952054bba/call-Filter/cacheCopy/M_CH_278-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-29/Mutect2/662d0c9e-9a7b-45f8-b72e-e38301d5dc2d/call-Filter/cacheCopy/M_CH_279-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-30/Mutect2/b7c0713b-e1b0-48d1-9e5b-edccdaebb87c/call-Filter/cacheCopy/M_CH_287-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-31/Mutect2/e0193584-6a4e-4050-90d0-41de7bdf6b90/call-Filter/cacheCopy/M_CH_292-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-32/Mutect2/b38e84c3-f0b1-4f12-8626-888ac260bcf4/call-Filter/cacheCopy/M_CH_304-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-33/Mutect2/ae8a08cb-295f-40bd-bb9c-ccd24931207c/call-Filter/cacheCopy/M_CH_312-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-34/Mutect2/7479ae00-c34f-4a1d-9b0b-b13c139865c4/call-Filter/cacheCopy/M_CH_314-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-35/Mutect2/b1829013-001a-42f5-b1ac-816df5853b2d/call-Filter/cacheCopy/M_CH_342-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-36/Mutect2/fd2c4a49-261a-4235-ab7a-e43ef15acaa3/call-Filter/cacheCopy/M_CH_363-filtered.vcf -L /cromwell_root/fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0001-scattered.interval_list Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.7bee3c7a 03:01:07.301 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 03:01:07.706 INFO GenomicsDBImport - ------------------------------------------------------------ 03:01:07.707 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.5.0 03:01:07.707 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 03:01:07.708 INFO GenomicsDBImport - Executing as root@ac242bf747d4 on Linux v4.19.87+ amd64 03:01:07.708 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03 03:01:07.709 INFO GenomicsDBImport - Start Date/Time: March 10, 2020 3:01:07 AM UTC 03:01:07.709 INFO GenomicsDBImport - ------------------------------------------------------------ 03:01:07.709 INFO GenomicsDBImport - ------------------------------------------------------------ 03:01:07.710 INFO GenomicsDBImport - HTSJDK Version: 2.21.2 03:01:07.710 INFO GenomicsDBImport - Picard Version: 2.21.9 03:01:07.711 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 03:01:07.711 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 03:01:07.712 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 03:01:07.712 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 03:01:07.713 INFO GenomicsDBImport - Deflater: IntelDeflater 03:01:07.713 INFO GenomicsDBImport - Inflater: IntelInflater 03:01:07.713 INFO GenomicsDBImport - GCS max retries/reopens: 20 03:01:07.713 INFO GenomicsDBImport - Requester pays: disabled 03:01:07.714 INFO GenomicsDBImport - Initializing engine 03:01:24.453 INFO FeatureManager - Using codec IntervalListCodec to read file file:///cromwell_root/fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0001-scattered.interval_list 03:01:24.623 INFO IntervalArgumentCollection - Processing 242193529 bp from intervals 03:01:25.045 INFO GenomicsDBImport - Done initializing engine 03:01:25.718 INFO GenomicsDBImport - Vid Map JSON file will be written to /cromwell_root/pon_db/vidmap.json 03:01:25.719 INFO GenomicsDBImport - Callset Map JSON file will be written to /cromwell_root/pon_db/callset.json 03:01:25.719 INFO GenomicsDBImport - Complete VCF Header will be written to /cromwell_root/pon_db/vcfheader.vcf 03:01:25.719 INFO GenomicsDBImport - Importing to array - /cromwell_root/pon_db/genomicsdb_array 03:01:25.719 INFO ProgressMeter - Starting traversal 03:01:25.720 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 03:01:40.360 INFO GenomicsDBImport - Importing batch 1 with 37 samples 03:01:52.018 INFO GenomicsDBImport - Shutting down engine [March 10, 2020 3:01:52 AM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.75 minutes. Runtime.totalMemory()=1081081856 *********************************************************************** A USER ERROR has occurred: Bad input: GenomicsDBImport does not support GVCFs with MNPs. MNP found at chr2:106435059 in VCF /a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-Mutect2/shard-26/Mutect2/8ef8e54d-872e-49d9-9a19-53ac971e8db2/call-Filter/cacheCopy/M_CH_245-filtered.vcf *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. 2020/03/10 03:01:53 Starting delocalization. 2020/03/10 03:01:54 Delocalization script execution started... 2020/03/10 03:01:54 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-CreatePanel/shard-1/attempt-3/memory_retry_rc 2020/03/10 03:01:54 Delocalizing output /cromwell_root/rc -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-CreatePanel/shard-1/attempt-3/rc 2020/03/10 03:01:56 Delocalizing output /cromwell_root/stdout -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-CreatePanel/shard-1/attempt-3/stdout 2020/03/10 03:01:58 Delocalizing output /cromwell_root/stderr -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-CreatePanel/shard-1/attempt-3/stderr 2020/03/10 03:01:59 Delocalizing output /cromwell_root/1-Mutect2_PON_37_Youngs.vcf.idx -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/a19bf1ef-4f7f-466b-a346-16930ac36941/Mutect2_Panel/b2b9da5d-73ca-45b0-92cd-fbd4a47dcf7f/call-CreatePanel/shard-1/attempt-3/1-Mutect2_PON_37_Youngs.vcf.idx Required file output '/cromwell_root/1-Mutect2_PON_37_Youngs.vcf.idx' does not exist.