htsjdk.tribble.TribbleException$MalformedFeatureFile

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    • htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /project/ibilab/projects/Devraj_Basu_HNSCC_Devraj_2016_3/large_data/bcbio-result5/work/mutect2/chr17/720-chr17_78458800_81195210.vcf.gz at htsjdk.tribble.TabixFeatureReader.readHeader(TabixFeatureReader.java:90) at htsjdk.tribble.TabixFeatureReader.<init>(TabixFeatureReader.java:74) at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:85) at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:66) at org.broadinstitute.gatk.tools.CatVariants.getFeatureReader(CatVariants.java:188) at org.broadinstitute.gatk.tools.CatVariants.execute(CatVariants.java:280) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.tools.CatVariants.main(CatVariants.java:312) Caused by: htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:119) at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:88) at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:41) at htsjdk.tribble.TabixFeatureReader.readHeader(TabixFeatureReader.java:88) ... 8 more
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