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Mutect2 in GATK 4.1.4 not producing stats file?

I'm trying to use the Following Best Practices guide on Mutect2 using the Dockerized GATK on GCP (so all steps are happening "within" the docker without exiting the docker instance at any point). (I'm moving the question from that page's discussion to its own question.)

Where does Mutect2 in GATK 4.1.4 put the .stats file? I can't find it to delocalize for next steps like filtering. I expected it to be at (in my example) unfiltered.vcf.stats, but that file isn't produced.

Command line:

/gatk/gatk --java-options "-Xmx${RAM}G" \
    Mutect2 \
    --input ${cram} \
    --reference ${REFERENCE_FASTA} \
    --output unfiltered.vcf

Mutect2 run info:

10:06:22.798 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:06:24.107 INFO  Mutect2 - ------------------------------------------------------------
10:06:24.108 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.4.0
10:06:24.108 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
10:06:24.109 INFO  Mutect2 - Executing as [email protected] on Linux v4.19.80+ amd64
10:06:24.114 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
10:06:24.114 INFO  Mutect2 - Start Date/Time: November 9, 2019 10:06:22 AM UTC
10:06:24.114 INFO  Mutect2 - ------------------------------------------------------------
10:06:24.115 INFO  Mutect2 - ------------------------------------------------------------
10:06:24.115 INFO  Mutect2 - HTSJDK Version: 2.20.3
10:06:24.116 INFO  Mutect2 - Picard Version: 2.21.1
10:06:24.116 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:06:24.116 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:06:24.116 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:06:24.116 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

...

12:16:20.925 INFO  ProgressMeter - Un_KN707838v1_decoy:901            129.9              10752010          82766.9
12:16:30.929 INFO  ProgressMeter - Un_KN707896v1_decoy:301            130.1              10752790          82666.8
12:16:40.934 INFO  ProgressMeter - Un_KN707906v1_decoy:996            130.2              10753100          82563.4
12:16:51.217 INFO  ProgressMeter - Un_KN707951v1_decoy:1060            130.4              10753580          82458.5
12:17:01.258 INFO  ProgressMeter - Un_JTFH01000012v1_decoy:1801            130.6              10754880          82362.8
Using GATK jar /gatk/gatk-package-4.1.4.0-local.jar

But then after the run completes, only the unfiltered.vcf file is present, no unfiltered.vcf.stats file is seen:

#List files in current path:
/bin/ls

./unfiltered.vcf

Answers

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