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    This is a bug in Wise, updating to v4.10 seems to solve the problem.

Solutions on the web

via GitHub by rjsicko
, 1 year ago
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
via GitHub by hyong2000
, 1 year ago
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
via GitHub by parlar
, 1 year ago
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: /home/genetik/irina/myeloid_fastq_run/calling/work/mutect/chr7/16-0206-chr7_50367205_101459534.vcf.gz
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.(VCFCompoundHeaderLine.java:171)	at htsjdk.variant.vcf.VCFFormatHeaderLine.(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)	at htsjdk.tribble.TabixFeatureReader.(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)