Hi,
I want to predict all the possible peptides that could be present in a sample. For this reason we run both mutect2 and haplotypecaller on RNA-seq data. Our goal is to create a union of those 2 vcf files for further analysis. However:

• GenotypeGVCFs only accepts gvcfs.
• FitlerMutectCalls throws an error when processing mutect2 output made with:

--emit-ref-confidence GVCF

I am using gatk 4.2.2.0 from the latest offical (and unaltered) docker image)

According the stdout log messages the first scanning pass of the VCF seems to finish:

13:00:00.588 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Sep 23, 2021 1:00:00 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:00:00.868 INFO  FilterMutectCalls - ------------------------------------------------------------
13:00:00.868 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.2.2.0
13:00:00.868 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
13:00:00.868 INFO  FilterMutectCalls - Executing as root@8aa2f993ccf8 on Linux v5.3.18-lp152.57-default amd64
13:00:00.869 INFO  FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
13:00:00.869 INFO  FilterMutectCalls - Start Date/Time: September 23, 2021 1:00:00 PM GMT
13:00:00.869 INFO  FilterMutectCalls - ------------------------------------------------------------
13:00:00.869 INFO  FilterMutectCalls - ------------------------------------------------------------
13:00:00.869 INFO  FilterMutectCalls - HTSJDK Version: 2.24.1
13:00:00.869 INFO  FilterMutectCalls - Picard Version: 2.25.4
13:00:00.869 INFO  FilterMutectCalls - Built for Spark Version: 2.4.5
13:00:00.869 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:00:00.869 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:00:00.869 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:00:00.870 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:00:00.870 INFO  FilterMutectCalls - Deflater: IntelDeflater
13:00:00.870 INFO  FilterMutectCalls - Inflater: IntelInflater
13:00:00.870 INFO  FilterMutectCalls - GCS max retries/reopens: 20
13:00:00.870 INFO  FilterMutectCalls - Requester pays: disabled
13:00:00.870 INFO  FilterMutectCalls - Initializing engine
13:00:01.522 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/path/to/sample/SampleName.called.g.vcf.gz
13:00:02.097 INFO  FilterMutectCalls - Done initializing engine
13:00:02.293 INFO  IOUtils - Extracting data from archive: file:///home/path/to/sample/read-orientation-model.tar.gz
13:00:02.348 INFO  IOUtils - Extracting file: ./SampleName.orientation_priors
13:00:02.385 INFO  ProgressMeter - Starting traversal
13:00:02.385 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:00:02.386 INFO  FilterMutectCalls - Starting pass 0 through the variants
13:00:12.401 INFO  ProgressMeter -           1:15882556              0.2                352000        2109047.3
13:00:22.405 INFO  ProgressMeter -           1:56553721              0.3               1248000        3740633.4
13:00:32.405 INFO  ProgressMeter -          1:153762932              0.5               2166000        4329258.1
13:00:42.409 INFO  ProgressMeter -          1:224423507              0.7               3191000        4783749.3
13:00:52.411 INFO  ProgressMeter -          10:44371946              0.8               4039000        4844377.8
13:01:02.416 INFO  ProgressMeter -         10:110510369              1.0               4945000        4942528.7
13:01:12.418 INFO  ProgressMeter -          11:46397314              1.2               5824000        4989719.0
13:01:22.420 INFO  ProgressMeter -         11:114256138              1.3               6798000        5096334.1
13:01:32.423 INFO  ProgressMeter -          12:44002822              1.5               7702000        5132613.6
13:01:42.424 INFO  ProgressMeter -         12:116210604              1.7               8709000        5223415.1
13:01:52.425 INFO  ProgressMeter -          13:99548149              1.8               9621000        5245958.3
13:02:02.428 INFO  ProgressMeter -          14:77287162              2.0              10547000        5271654.9
13:02:12.433 INFO  ProgressMeter -          15:55359021              2.2              11457000        5285935.1
13:02:22.444 INFO  ProgressMeter -           16:1792430              2.3              12368000        5298376.4
13:02:32.452 INFO  ProgressMeter -          16:68121250              2.5              13311000        5322058.3
13:02:42.456 INFO  ProgressMeter -          17:18681513              2.7              14218000        5329418.4
13:02:52.463 INFO  ProgressMeter -          17:64911885              2.8              15148000        5343932.5
13:03:02.464 INFO  ProgressMeter -          18:55303785              3.0              16075000        5356042.1
13:03:12.475 INFO  ProgressMeter -          19:19603794              3.2              17019000        5371904.7
13:03:22.481 INFO  ProgressMeter -             2:277916              3.3              17909000        5370149.2
13:03:32.486 INFO  ProgressMeter -           2:74092473              3.5              18817000        5373726.8
13:03:42.491 INFO  ProgressMeter -          2:168876729              3.7              19697000        5369346.4
13:03:52.495 INFO  ProgressMeter -            20:361613              3.8              20697000        5396659.8
13:04:02.505 INFO  ProgressMeter -           21:9097727              4.0              21644000        5408318.4
13:04:12.506 INFO  ProgressMeter -          22:39793603              4.2              22577000        5415880.4
13:04:22.511 INFO  ProgressMeter -           3:47122775              4.3              23481000        5416088.4
13:04:32.514 INFO  ProgressMeter -          3:125002012              4.5              24396000        5418764.4
13:04:42.522 INFO  ProgressMeter -            4:2508511              4.7              25367000        5433146.8
13:04:52.526 INFO  ProgressMeter -          4:106041565              4.8              26287000        5436065.3
13:05:02.540 INFO  ProgressMeter -           5:53056131              5.0              27239000        5445004.9
13:05:12.545 INFO  ProgressMeter -          5:143268322              5.2              28186000        5452558.2
13:05:22.546 INFO  ProgressMeter -           6:31627330              5.3              29092000        5452024.0
13:05:32.550 INFO  ProgressMeter -          6:125459062              5.5              30051000        5461104.2
13:05:42.551 INFO  ProgressMeter -           7:30028818              5.7              30973000        5463172.3
13:05:52.555 INFO  ProgressMeter -          7:104938114              5.8              31844000        5456336.8
13:06:02.560 INFO  ProgressMeter -           8:22066737              6.0              32712000        5449366.1
13:06:12.563 INFO  ProgressMeter -          8:125357902              6.2              33655000        5454958.0
13:06:22.568 INFO  ProgressMeter -           9:92242342              6.3              34572000        5456123.6
13:06:32.592 INFO  ProgressMeter -          9:134780930              6.5              35317000        5430794.5
13:06:42.577 INFO  ProgressMeter -          X:149925594              6.7              36347000        5449447.9
13:06:44.681 WARN  IntelInflater - Zero Bytes Written : 0
13:06:44.748 INFO  FilterMutectCalls - Finished pass 0 through the variants
13:06:49.201 INFO  FilterMutectCalls - Shutting down engine
[September 23, 2021 1:06:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 6.81 minutes.
Runtime.totalMemory()=810942464

Followed by the stacktrace below:

java.lang.IllegalArgumentException: log10p: Log10-probability must be 0 or less
	at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:798)
	at org.broadinstitute.hellbender.utils.MathUtils.log10BinomialProbability(MathUtils.java:646)
	at org.broadinstitute.hellbender.utils.MathUtils.binomialProbability(MathUtils.java:639)
	at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.lambda$calculateQuantileBackgroundResponsibilities$10(SomaticClusteringModel.java:271)
	at org.broadinstitute.hellbender.utils.MathUtils.applyToArray(MathUtils.java:1047)
	at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.calculateQuantileBackgroundResponsibilities(SomaticClusteringModel.java:271)
	at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.initializeClusters(SomaticClusteringModel.java:165)
	at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.learnAndClearAccumulatedData(SomaticClusteringModel.java:325)
	at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.learnParameters(Mutect2FilteringEngine.java:153)
	at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.afterNthPass(FilterMutectCalls.java:165)
	at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /gatk/gatk-package-4.2.2.0-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 -Xmx800M -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /gatk/gatk-package-4.2.2.0-local.jar FilterMutectCalls --reference homo_sapiens_genome.fa --variant SampleName.called.g.vcf.gz --stats merged_mutect.stats --output output_dir/SampleName.mutect2.filtered.vcf.gz --filtering-stats output_dir/SampleName.mutect_filtering.stats --tumor-segmentation segments.table --contamination-table calculatecontamination.table --ob-priors read-orientation-model.tar.gz

I did notice the problem seems to occur after the entire file was scanned 1 time, so I therefore assume the problem is not with any particular variant.

All preceding steps/tools according to the best practices for RNA variant calling complete without errors. So I have performed the splitNcigarReads as recommended.

My reference is based on the Ensembl contig names. but I have converted all the GRCh38 input vcf files such as the known variant arguments to this naming convention as well. (and haplotypeCaller and other steps run just fine with these files)

I think the 2 relevant commands that I run are:

gatk \
  --java-options "-Xmx${memory_limit}M -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \
  FilterMutectCalls \
  --reference "${genome_fasta}" \
  --variant "${mutect_vcf}" \
  --stats "${mutect_vcf_stats}" \
  --output "${filtered_vcf}" \
  --filtering-stats "${filtering_stats}" \
  --tumor-segmentation "${tumor_segmentation_table}" \
  --contamination-table "${contamination_table}" \
  --ob-priors "${read_orientation_model}" \
;

and:

gatk \
  --java-options "-Xmx${memory_limit}M" \
  Mutect2 \
  --reference "${ref_path}/genome/${genome}" \
  --smith-waterman FASTEST_AVAILABLE \
  --pair-hmm-implementation FASTEST_AVAILABLE \
  --native-pair-hmm-threads ${native_hmm_threads} \
  --native-pair-hmm-use-double-precision \
  --recover-all-dangling-branches \
  --max-mnp-distance 0 \
  --f1r2-tar-gz "${output_f1r2}" \
  --output "${output_file}" \
  --input "${aligned_reads}" \
  --panel-of-normals "${panel_of_normals_vcf}" \
  --germline-resource "${allele_frequency_vcf}" \
  --intervals "${interval_list}" \
  --emit-ref-confidence GVCF \
  --soft-clip-low-quality-ends \
  --dragstr-params-path "${dragstr_params_path}" \
;

When googling for:

log10p: Log10-probability must be 0 or less

I found old issues (2019 or 2020 if memory serves) which seem to have been solved shortly after, so I assume this is an unrelated issue?Thanks in advance.