htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: For input string: "R", for input source: /media/sf_BigShare/SCID_recall/batch3/work/gemini/batch3-gatk-haplotype.vcf.gz

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    • htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: For input string: "R", for input source: /media/sf_BigShare/SCID_recall/batch3/work/gemini/batch3-gatk-haplotype.vcf.gz at htsjdk.tribble.TabixFeatureReader.readHeader(TabixFeatureReader.java:75) at htsjdk.tribble.TabixFeatureReader.<init>(TabixFeatureReader.java:59) at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:85) at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:66) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:93) at clojure.lang.Reflector.invokeStaticMethod(Reflector.java:207) at bcbio.variation.variantcontext$get_vcf_header.invoke(variantcontext.clj:144) at bcbio.variation.variantcontext$get_samples.invoke(variantcontext.clj:150) at bcbio.variation.vcfsample$consistent_order.invoke(vcfsample.clj:108) at bcbio.variation.ensemble$consensus_calls.invoke(ensemble.clj:109) at bcbio.variation.ensemble$_main.doInvoke(ensemble.clj:132) at clojure.lang.RestFn.applyTo(RestFn.java:137) at clojure.core$apply.invoke(core.clj:630) at bcbio.variation.core$_main.doInvoke(core.clj:35) at clojure.lang.RestFn.applyTo(RestFn.java:137) at bcbio.variation.core.main(Unknown Source) Caused by: java.lang.NumberFormatException: For input string: "R" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.valueOf(Integer.java:766) at htsjdk.variant.vcf.VCFCompoundHeaderLine.<init>(VCFCompoundHeaderLine.java:171) at htsjdk.variant.vcf.VCFFormatHeaderLine.<init>(VCFFormatHeaderLine.java:49) at htsjdk.variant.vcf.AbstractVCFCodec.parseHeaderFromLines(AbstractVCFCodec.java:211) at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:111) at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:88) at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:41) at htsjdk.tribble.TabixFeatureReader.readHeader(TabixFeatureReader.java:73) ... 19 more

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