Hello GATK Team,

I'm running somatic variant calling (mutect2) on 108 Whole Exome Tumor-Normal samples in Terra. However, one of the samples keeps failing at `munmap_chunk(): invalid pointer` at  FilterAlignmentArtifacts task.

could you please shed some lights  on how i can what is happening and i'll be able to resolve this.

gatk version used; 4.1.8.0

workflow used; https://app.terra.bio/#workspaces/help-gatk/Somatic-SNVs-Indels-GATK4/workflows/help-gatk/2-Mutect2-GATK4

Entire log file for the failed task is below 

many thanks

`

2020/07/24 00:17:40 Starting container setup.
2020/07/24 00:17:43 Done container setup.
2020/07/24 00:17:44 Starting localization.
2020/07/24 00:17:50 Localization script execution started...
2020/07/24 00:17:50 Localizing input gs://gatk-test-data/mutect2/Homo_sapiens_assembly38.index_bundle -> /cromwell_root/gatk-test-data/mutect2/Homo_sapiens_assembly38.index_bundle
2020/07/24 00:18:29 Localizing input gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-FilterAlignmentArtifacts/attempt-3/script -> /cromwell_root/script
2020/07/24 00:18:33 Localization script execution complete.
2020/07/24 00:18:46 Done localization.
2020/07/24 00:18:47 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint= us.gcr.io/broad-gatk/gatk@sha256:18146e79d06787483310e5de666502090a480e10ac0fad06a36a5e7a5c9bb1dc /bin/bash /cromwell_root/script
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.4be06a03
00:18:51.090 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
00:18:51.108 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/gatk/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
00:18:51.110 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
00:18:51.328 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
00:18:51.578 INFO  FilterAlignmentArtifacts - ------------------------------------------------------------
00:18:51.578 INFO  FilterAlignmentArtifacts - The Genome Analysis Toolkit (GATK) v4.1.8.0
00:18:51.578 INFO  FilterAlignmentArtifacts - For support and documentation go to https://software.broadinstitute.org/gatk/
00:18:51.579 INFO  FilterAlignmentArtifacts - Executing as root@3c67022d2450 on Linux v4.19.112+ amd64
00:18:51.579 INFO  FilterAlignmentArtifacts - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
00:18:51.579 INFO  FilterAlignmentArtifacts - Start Date/Time: July 24, 2020 12:18:51 AM GMT
00:18:51.579 INFO  FilterAlignmentArtifacts - ------------------------------------------------------------
00:18:51.579 INFO  FilterAlignmentArtifacts - ------------------------------------------------------------
00:18:51.580 INFO  FilterAlignmentArtifacts - HTSJDK Version: 2.22.0
00:18:51.580 INFO  FilterAlignmentArtifacts - Picard Version: 2.22.8
00:18:51.580 INFO  FilterAlignmentArtifacts - HTSJDK Defaults.COMPRESSION_LEVEL : 2
00:18:51.580 INFO  FilterAlignmentArtifacts - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
00:18:51.580 INFO  FilterAlignmentArtifacts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
00:18:51.580 INFO  FilterAlignmentArtifacts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
00:18:51.581 INFO  FilterAlignmentArtifacts - Deflater: IntelDeflater
00:18:51.581 INFO  FilterAlignmentArtifacts - Inflater: IntelInflater
00:18:51.581 INFO  FilterAlignmentArtifacts - GCS max retries/reopens: 20
00:18:51.581 INFO  FilterAlignmentArtifacts - Requester pays: disabled
00:18:51.581 WARN  FilterAlignmentArtifacts - 

[1m[31m   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: FilterAlignmentArtifacts is an EXPERIMENTAL tool and should not be used for production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!![0m


00:18:51.581 INFO  FilterAlignmentArtifacts - Initializing engine
00:18:55.898 INFO  FeatureManager - Using codec VCFCodec to read file gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-Filter/22.hg38-filtered.vcf
00:18:56.977 INFO  FilterAlignmentArtifacts - Done initializing engine
00:18:57.854 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
00:18:57.903 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
00:18:57.904 INFO  IntelPairHmm - Available threads: 4
00:18:57.904 INFO  IntelPairHmm - Requested threads: 4
00:18:57.905 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
00:18:57.905 INFO  ProgressMeter - Starting traversal
00:18:57.905 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
munmap_chunk(): invalid pointer
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 -Xmx11500m -jar /root/gatk.jar FilterAlignmentArtifacts -R gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -V gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-Filter/22.hg38-filtered.vcf -I gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/209d1183-ed9a-4755-a4b3-d595797640ea/PreProcessingForVariantDiscovery_GATK4/9f7c0ab6-b61b-4797-92f1-7929bbf677d8/call-GatherBamFiles/22.hg38.bam --bwa-mem-index-image /cromwell_root/gatk-test-data/mutect2/Homo_sapiens_assembly38.index_bundle -O 22.hg38-filtered.vcf
2020/07/24 00:27:25 Starting delocalization.
2020/07/24 00:27:26 Delocalization script execution started...
2020/07/24 00:27:26 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-FilterAlignmentArtifacts/attempt-3/memory_retry_rc
2020/07/24 00:27:27 Delocalizing output /cromwell_root/rc -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-FilterAlignmentArtifacts/attempt-3/rc
2020/07/24 00:27:28 Delocalizing output /cromwell_root/stdout -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-FilterAlignmentArtifacts/attempt-3/stdout
2020/07/24 00:27:29 Delocalizing output /cromwell_root/stderr -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-FilterAlignmentArtifacts/attempt-3/stderr
2020/07/24 00:27:31 Delocalizing output /cromwell_root/22.hg38-filtered.vcf -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-FilterAlignmentArtifacts/attempt-3/22.hg38-filtered.vcf
2020/07/24 00:27:32 Delocalizing output /cromwell_root/22.hg38-filtered.vcf.idx -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/5219ad90-3cbc-4ce6-9f1a-a6ed9791996f/Mutect2/ceafe1f6-0671-4bd9-bbf1-a24cc38033b8/call-FilterAlignmentArtifacts/attempt-3/22.hg38-filtered.vcf.idx
Required file output '/cromwell_root/22.hg38-filtered.vcf.idx' does not exist.

`