If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:4.1.1.0
b) Exact command used:

gatk FilterMutectCalls -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta \

                       -V EGAR00001120416_ccRCC-1-tumor-EGAR00001120522_ccRCC-1-normal.somatic.vcf.gz \

                       --tumor-segmentation segments.table \

                       --contamination-table calculatecontamination.table \

                       --ob-priors EGAR00001120416_ccRCC-1-tumor-read-orientation-model.tar.gz \

                       -O EGAR00001120416_ccRCC-1-tumor-EGAR00001120522_ccRCC-1-normal.somatic.filtered.vcf.gz

c) Entire error log:

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 -Xms512M -Xmx5G -jar /sw/bioinfo/GATK/4.1.1.0/rackham/gatk-package-4.1.1.0-local.jar FilterMutectCalls -R r$

11:30:30.928 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/sw/bioinfo/GATK/4.1.1.0/rackham/gatk-package-4.1.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

Feb 28, 2021 11:30:32 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

11:30:32.783 INFO  FilterMutectCalls - ------------------------------------------------------------

11:30:32.784 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.1.0

11:30:32.784 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/

11:30:32.785 INFO  FilterMutectCalls - Executing as xiyasoso@r248.uppmax.uu.se on Linux v3.10.0-1160.11.1.el7.x86_64 amd64

11:30:32.786 INFO  FilterMutectCalls - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_151-b12

11:30:32.786 INFO  FilterMutectCalls - Start Date/Time: February 28, 2021 11:30:30 AM CET

11:30:32.786 INFO  FilterMutectCalls - ------------------------------------------------------------

11:30:32.786 INFO  FilterMutectCalls - ------------------------------------------------------------

11:30:32.787 INFO  FilterMutectCalls - HTSJDK Version: 2.19.0

11:30:32.787 INFO  FilterMutectCalls - Picard Version: 2.19.0

11:30:32.787 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2

11:30:32.787 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

11:30:32.787 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

11:30:32.787 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

11:30:32.788 INFO  FilterMutectCalls - Deflater: IntelDeflater

11:30:32.788 INFO  FilterMutectCalls - Inflater: IntelInflater

11:30:32.788 INFO  FilterMutectCalls - GCS max retries/reopens: 20

11:30:32.788 INFO  FilterMutectCalls - Requester pays: disabled

11:30:32.788 INFO  FilterMutectCalls - Initializing engine

11:30:33.422 INFO  FeatureManager - Using codec VCFCodec to read file file:///crex/proj/sllstore2017024/nobackup/xiya/DNA-seq/EGAR00001120416_ccRCC-1-tumor-EGAR00001120522_ccRCC-1-normal.somatic.vcf.gz

11:30:33.681 INFO  FilterMutectCalls - Done initializing engine

11:30:33.982 INFO  IOUtils - Extracting data from archive: file:///crex/proj/sllstore2017024/nobackup/xiya/DNA-seq/EGAR00001120416_ccRCC-1-tumor-read-orientation-model.tar.gz

11:30:34.006 INFO  IOUtils - Extracting file: ./EGAR00001120416_ccRCC-1-tumor.orientation_priors

11:30:34.088 INFO  ProgressMeter - Starting traversal

11:30:34.088 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

11:30:34.089 INFO  FilterMutectCalls - Starting pass 0 through the variants

11:30:43.519 INFO  FilterMutectCalls - Finished pass 0 through the variants

11:30:43.634 INFO  FilterMutectCalls - Starting pass 1 through the variants

11:30:44.567 INFO  ProgressMeter -        chr7:67297203              0.2                  5000          28628.7

11:30:46.259 INFO  FilterMutectCalls - Finished pass 1 through the variants

11:30:46.363 INFO  FilterMutectCalls - Starting pass 2 through the variants

11:30:49.141 INFO  FilterMutectCalls - Finished pass 2 through the variants

11:30:49.149 INFO  FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter

11:30:49.149 INFO  FilterMutectCalls - No reads filtered by: AllowAllReadsReadFilter

11:30:49.150 INFO  ProgressMeter - chr11_KI270902v1_alt:85649              0.3                 11469          45687.2

11:30:49.150 INFO  ProgressMeter - Traversal complete. Processed 11469 total variants in 0.3 minutes.

11:30:49.193 INFO  FilterMutectCalls - Shutting down engine

[February 28, 2021 11:30:49 AM CET] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.31 minutes.

Runtime.totalMemory()=1256718336

Hi! As the log showed, the filter process didn't filter any variants for me, and the generated filtered vcf is the same as unfiltered vcf. Is that the right situation? I generated a contamination table and read-orientation-model.tar.gz following  https://gatk.broadinstitute.org/hc/en-us/articles/360035531132.

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