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FilterMutectCalls BUG

sabaferdoussabaferdous Cancer Research UK Member

Dear GATK Team,

I am writing you to discuss a an error while using FilterMutectCalls program and it seems a poential bug.
I wanted to change the default value of **--normal-p-value-threshold **. It looks like the tool doesnt accept this parameter at all. I tried using it with the default value of 0.001 as well.

The program works fine when this parameter is removed. Moreover, the error message also states that BUG: couldn't set field value .

please see the attached command and the error message.

** gatk FilterMutectCalls -V TAR-158_unfiltered.vcf.gz --normal-p-value-threshold 0.0001 -R ../data/hg_ref/genome.fa --contamination-table TAR-158_tumor_calculatecontamination.table -O TAR-158_artifact_0.01.vcf.gz**

Using GATK jar /mnt/gpfs1/lmod/apps/gatk/4.1.1.0/gatk-package-4.1.1.0-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 -jar /mnt/gpfs1/lmod/apps/gatk/4.1.1.0/gatk-package-4.1.1.0-local.jar FilterMutectCalls -V TAR-158_unfiltered.vcf.gz --normal-p-value-threshold 0.0001 -R ../data/hg_ref/genome.fa --contamination-table TAR-158_tumor_calculatecontamination.table -O TAR-158_artifact_0.01.vcf.gz
org.broadinstitute.barclay.argparser.CommandLineException$ShouldNeverReachHereException: BUG: couldn't set field value. For normalPileupPValueThreshold in org.broadinstitute.hellbe[email protected]69d45cca with value 1.0E-4 This shouldn't happen since we setAccessible(true)
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser$ArgumentDefinition.setFieldValue(CommandLineArgumentParser.java:1248)
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.setArgument(CommandLineArgumentParser.java:710)
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:427)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:232)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: java.lang.IllegalAccessException: Can not set static final double field org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection.normalPileupPValueThreshold to java.lang.Double
at sun.reflect.UnsafeFieldAccessorImpl.throwFinalFieldIllegalAccessException(UnsafeFieldAccessorImpl.java:76)
at sun.reflect.UnsafeFieldAccessorImpl.throwFinalFieldIllegalAccessException(UnsafeFieldAccessorImpl.java:80)
at sun.reflect.UnsafeQualifiedStaticDoubleFieldAccessorImpl.set(UnsafeQualifiedStaticDoubleFieldAccessorImpl.java:77)
at java.lang.reflect.Field.set(Field.java:764)
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser$ArgumentDefinition.setFieldValue(CommandLineArgumentParser.java:1245)
... 7 more

Best regards,

Issue · Github
by bhanuGandham

Issue Number
5978
State
open
Last Updated
Assignee
Array

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