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GATK 4.0.5.0 Module help command does not work?

SkyWarriorSkyWarrior TurkeyMember ✭✭✭

Hi

As usual I like checking the help blobs from the original application itself but it seems to be broken for GATK 4.0.5.0.

gatk HaplotypeCaller -h throws exception.

Gokalps-Mac-mini:~ sky$ gatk HaplotypeCaller -h
Using GATK jar /Users/sky/scripts/gatk-package-4.0.5.0-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 /Users/sky/scripts/gatk-package-4.0.5.0-local.jar HaplotypeCaller -h
java.lang.IllegalArgumentException: Allowed values request for unrecognized string argument: input
    at org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor.getAllowedValuesForDescriptorHelp(GATKAnnotationPluginDescriptor.java:246)
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.usageForPluginDescriptorArgumentIfApplicable(CommandLineArgumentParser.java:870)
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.makeArgumentDescription(CommandLineArgumentParser.java:847)
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.printArgumentUsage(CommandLineArgumentParser.java:791)
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.lambda$printArgumentUsageBlock$2(CommandLineArgumentParser.java:276)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    at java.util.stream.SortedOps$SizedRefSortingSink.end(SortedOps.java:352)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.printArgumentUsageBlock(CommandLineArgumentParser.java:276)
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.usage(CommandLineArgumentParser.java:308)
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:417)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:221)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:195)
    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)

And this is what happens in 4.0.4.0

Using GATK jar /gatk/build/libs/gatk-package-4.0.4.0-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 /gatk/build/libs/gatk-package-4.0.4.0-local.jar HaplotypeCaller -h
USAGE: HaplotypeCaller [arguments]

Call germline SNPs and indels via local re-assembly of haplotypes
Version:4.0.4.0


Required Arguments:

--input,-I:String             BAM/SAM/CRAM file containing reads  This argument must be specified at least once.
                              Required.

--output,-O:String            File to which variants should be written  Required.

--reference,-R:String         Reference sequence file  Required.


Optional Arguments:

--activity-profile-out:String Output the raw activity profile results in IGV format  Default value: null.

--add-output-sam-program-record,-add-output-sam-program-record:Boolean
                              If true, adds a PG tag to created SAM/BAM/CRAM files.  Default value: true. Possible
                              values: {true, false}

--add-output-vcf-command-line,-add-output-vcf-command-line:Boolean
                              If true, adds a command line header line to created VCF files.  Default value: true.
                              Possible values: {true, false}

--alleles:FeatureInput        The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES
                              Default value: null.

--annotate-with-num-discovered-alleles:Boolean
                              If provided, we will annotate records with the number of alternate alleles that were
                              discovered (but not necessarily genotyped) at a given site  Default value: false. Possible
                              values: {true, false}

Same problem persists in docker version as well.

Thanks.

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