Bug in FilterAlignmentArtifacts

[gevro]

GATK version: 4.4.0.0

Crashing in FilterAlignmentArtifacts. Not clear why

Command

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 -Xmx30g -jar /gpfs/data/lab/bin/gatk/gatk-package-4.4.0.0-local.jar FilterAlignmentArtifacts -R /gpfs/data/lab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta -V 60603-bulk.filtered.vcf.gz -I /gpfs/data/lab/projects/Mini/analysis/STR/60603-bulk_results/60603-bulk.cram --bwa-mem-index-image /gpfs/data/lab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta.img -O 60603-bulk.filtered.FAA.vcf.gz

Error:

11:02:16.087 INFO  ProgressMeter -       chrX:144247387            619.0                145000            234.3
11:05:08.297 WARN  IntelInflater - Zero Bytes Written : 0
12:29:39.297 INFO  FilterAlignmentArtifacts - Shutting down engine
[August 15, 2023 at 12:29:39 PM EDT] org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts done. Elapsed time: 710.24 minutes.
Runtime.totalMemory()=4345298944
java.lang.IllegalStateException: Padded span must contain active span.
        at org.broadinstitute.hellbender.utils.Utils.validate(Utils.java:814)
        at org.broadinstitute.hellbender.engine.AssemblyRegion.<init>(AssemblyRegion.java:109)
        at org.broadinstitute.hellbender.engine.AssemblyRegion.<init>(AssemblyRegion.java:85)
        at org.broadinstitute.hellbender.engine.AssemblyRegion.<init>(AssemblyRegion.java:120)
        at org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts.makeAssemblyRegionFromVariantReads(FilterAlignmentArtifacts.java:280)
        at org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts.apply(FilterAlignmentArtifacts.java:212)
        at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:133)
        at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.afterTraverse(MultiVariantWalkerGroupedOnStart.java:193)
        at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:166)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
        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 /gpfs/data/lab/bin/gatk/gatk-package-4.4.0.0-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 -Xmx30g -jar /gpfs/data/lab/bin/gatk/gatk-package-4.4.0.0-local.jar FilterAlignmentArtifacts -R /gpfs/data/lab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta -V 60603-bulk.filtered.vcf.gz -I /gpfs/data/lab/projects/Mini/analysis/STR/60603-bulk_results/60603-bulk.cram --bwa-mem-index-image /gpfs/data/lab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta.img -O 60603-bulk.filtered.FAA.vcf.gz