Funcotator returns a nullpointer exception when trying to output compressed VCF
open | Created 2019-02-15 | Last updated 2019-07-01| Posted by fpbarthel | See in Github


Engine Funcotator bug


Bug Report

Affected tool(s) or class(es)

Funcotator

Affected version(s)

GATK 4.1.0.0 release

Description

Funcotator returns a NullPointerException when trying to output compressed VCF:

15:35:26.085 INFO  Funcotator - Creating a VCF file for output: XXXX
15:35:26.125 INFO  ProgressMeter - Starting traversal
15:35:26.125 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
15:35:26.328 INFO  Funcotator - Shutting down engine
[February 15, 2019 3:35:26 PM EST] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.18 minutes.
Runtime.totalMemory()=3391094784
java.lang.NullPointerException
        at htsjdk.tribble.index.tabix.TabixIndexCreator.finalizeFeature(TabixIndexCreator.java:106)
        at htsjdk.tribble.index.tabix.TabixIndexCreator.finalizeIndex(TabixIndexCreator.java:129)
        at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.close(IndexingVariantContextWriter.java:177)
        at htsjdk.variant.variantcontext.writer.VCFWriter.close(VCFWriter.java:231)
        at org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer.close(VcfOutputRenderer.java:137)
        at org.broadinstitute.hellbender.tools.funcotator.Funcotator.closeTool(Funcotator.java:883)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:970)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
        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)

Steps to reproduce

Does not work

gatk Funcotator --variant input.vcf.gz --reference /path/to/human_g1k_v37_decoy.fasta --ref-version hg19 --data-sources-path /path/to/funcotator_dataSources.v1.6.20190124s/ --output output.vcf.gz --output-file-format VCF

Works

gatk Funcotator --variant input.vcf.gz --reference /path/to/human_g1k_v37_decoy.fasta --ref-version hg19 --data-sources-path /path/to/funcotator_dataSources.v1.6.20190124s/ --output output.vcf --output-file-format VCF

(note that the --output parameter is different)

Expected behavior

It should either give an error/warning saying outputting compressed VCF output is not supported, or output a compressed VCF like other GATK tools

Actual behavior

See examples above


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