Can you please provide
a) GATK version used: 4.1.5.0
b) Exact GATK commands used

c) The entire error log if applicable.

When running the 1-Mutect2_PON workspace, at the CreatePanel stage, some of the tasks will fail because they seem unable to locate the `.idx` files created earlier. Other tasks seems to run just fine. Below is one of the error logs.

2020/03/10 02:06:45 Starting container setup. 2020/03/10 02:06:48 Done container setup. 2020/03/10 02:06:49 Starting localization. 2020/03/10 02:06:55 Localization script execution started... 2020/03/10 02:06:55 Localizing input gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0003-scattered.interval_list -> /cromwell_root/fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0003-scattered.interval_list 2020/03/10 02:06:56 Localizing input gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-CreatePanel/shard-3/attempt-3/script -> /cromwell_root/script 2020/03/10 02:06:58 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 02:07:38 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 02:07:38 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][568.1 KiB/725.2 KiB] 78% Done / [2/2 files][725.2 KiB/725.2 KiB] 100% Done Operation completed over 2 objects/725.2 KiB. 2020/03/10 02:07:39 Localization script execution complete. 2020/03/10 02:07:46 Done localization. 2020/03/10 02:07:47 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/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-0/Mutect2/43e9805c-212b-4929-9479-323260f1c412/call-Filter/M_CH_024-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-1/Mutect2/d96fab6a-5227-4bcf-b018-74ffd41ea9b9/call-Filter/M_CH_034-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-2/Mutect2/c5b7a541-731d-4683-8f39-197d60d396b1/call-Filter/M_CH_037-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-3/Mutect2/cf13af63-f9b0-48a7-a9ab-048b80e148dd/call-Filter/M_CH_040-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-4/Mutect2/2fbdef51-2247-4a4c-8857-7c97ba7d0f2e/call-Filter/M_CH_041-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-5/Mutect2/3fe24f01-f9e5-43d1-970b-1e0525eda2fe/call-Filter/M_CH_049-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-6/Mutect2/b015e4e9-50c6-4adb-898e-1997e245b41e/call-Filter/M_CH_070-filtered.vcf -V 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gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-31/Mutect2/fbaf8b4f-c0e0-44f1-97f3-b2e69b5abebd/call-Filter/M_CH_292-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-32/Mutect2/117f9102-1551-4256-87e8-1c807625ca5b/call-Filter/M_CH_304-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-33/Mutect2/cad848fb-952c-486e-94b1-da77676bf3c5/call-Filter/M_CH_312-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-34/Mutect2/7a55889b-5fc2-49b9-a13f-968862922ff7/call-Filter/M_CH_314-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-35/Mutect2/d59c0c32-9ee3-4207-be64-115ef35b4d56/call-Filter/M_CH_342-filtered.vcf -V gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-36/Mutect2/1ce89951-101e-40ab-8add-aed5343b43c8/call-Filter/M_CH_363-filtered.vcf -L /cromwell_root/fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0003-scattered.interval_list Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.e83a16c9 02:07:52.482 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 02:07:52.814 INFO GenomicsDBImport - ------------------------------------------------------------ 02:07:52.815 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.5.0 02:07:52.815 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 02:07:52.816 INFO GenomicsDBImport - Executing as root@cd0178a256a0 on Linux v4.19.87+ amd64 02:07:52.816 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03 02:07:52.816 INFO GenomicsDBImport - Start Date/Time: March 10, 2020 2:07:52 AM UTC 02:07:52.816 INFO GenomicsDBImport - ------------------------------------------------------------ 02:07:52.816 INFO GenomicsDBImport - ------------------------------------------------------------ 02:07:52.817 INFO GenomicsDBImport - HTSJDK Version: 2.21.2 02:07:52.817 INFO GenomicsDBImport - Picard Version: 2.21.9 02:07:52.818 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 02:07:52.818 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 02:07:52.818 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 02:07:52.818 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 02:07:52.818 INFO GenomicsDBImport - Deflater: IntelDeflater 02:07:52.818 INFO GenomicsDBImport - Inflater: IntelInflater 02:07:52.819 INFO GenomicsDBImport - GCS max retries/reopens: 20 02:07:52.819 INFO GenomicsDBImport - Requester pays: disabled 02:07:52.819 INFO GenomicsDBImport - Initializing engine 02:08:09.029 INFO FeatureManager - Using codec IntervalListCodec to read file file:///cromwell_root/fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0003-scattered.interval_list 02:08:09.146 INFO IntervalArgumentCollection - Processing 190214555 bp from intervals 02:08:09.463 INFO GenomicsDBImport - Done initializing engine 02:08:10.070 INFO GenomicsDBImport - Vid Map JSON file will be written to /cromwell_root/pon_db/vidmap.json 02:08:10.071 INFO GenomicsDBImport - Callset Map JSON file will be written to /cromwell_root/pon_db/callset.json 02:08:10.071 INFO GenomicsDBImport - Complete VCF Header will be written to /cromwell_root/pon_db/vcfheader.vcf 02:08:10.071 INFO GenomicsDBImport - Importing to array - /cromwell_root/pon_db/genomicsdb_array 02:08:10.071 INFO ProgressMeter - Starting traversal 02:08:10.072 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 02:08:22.178 INFO GenomicsDBImport - Importing batch 1 with 37 samples 02:08:32.845 INFO GenomicsDBImport - Shutting down engine [March 10, 2020 2:08:32 AM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.67 minutes. Runtime.totalMemory()=1135083520 *********************************************************************** A USER ERROR has occurred: Bad input: GenomicsDBImport does not support GVCFs with MNPs. MNP found at chr4:113753806 in VCF /d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-Mutect2/shard-6/Mutect2/b015e4e9-50c6-4adb-898e-1997e245b41e/call-Filter/M_CH_070-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 02:08:34 Starting delocalization. 2020/03/10 02:08:35 Delocalization script execution started... 2020/03/10 02:08:35 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-CreatePanel/shard-3/attempt-3/memory_retry_rc 2020/03/10 02:08:35 Delocalizing output /cromwell_root/rc -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-CreatePanel/shard-3/attempt-3/rc 2020/03/10 02:08:36 Delocalizing output /cromwell_root/stdout -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-CreatePanel/shard-3/attempt-3/stdout 2020/03/10 02:08:38 Delocalizing output /cromwell_root/stderr -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-CreatePanel/shard-3/attempt-3/stderr 2020/03/10 02:08:39 Delocalizing output /cromwell_root/1-Mutect2_PON_37_Youngs.vcf.idx -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/d22a4efc-70c2-4707-ae2a-67d33d33fde9/Mutect2_Panel/10f975b3-afad-4676-8408-988fc84005c3/call-CreatePanel/shard-3/attempt-3/1-Mutect2_PON_37_Youngs.vcf.idx Required file output '/cromwell_root/1-Mutect2_PON_37_Youngs.vcf.idx' does not exist.