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

GitHub | rjsicko | 7 months ago
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    GitHub | 7 months ago | rjsicko
    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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Root Cause Analysis

  1. java.lang.NumberFormatException

    For input string: "R"

    at java.lang.NumberFormatException.forInputString()
  2. Java RT
    Integer.valueOf
    1. java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    2. java.lang.Integer.parseInt(Integer.java:580)
    3. java.lang.Integer.valueOf(Integer.java:766)
    3 frames
  3. HTS JDK
    AbstractFeatureReader.getFeatureReader
    1. htsjdk.variant.vcf.VCFCompoundHeaderLine.<init>(VCFCompoundHeaderLine.java:171)
    2. htsjdk.variant.vcf.VCFFormatHeaderLine.<init>(VCFFormatHeaderLine.java:49)
    3. htsjdk.variant.vcf.AbstractVCFCodec.parseHeaderFromLines(AbstractVCFCodec.java:211)
    4. htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:111)
    5. htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:88)
    6. htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:41)
    7. htsjdk.tribble.TabixFeatureReader.readHeader(TabixFeatureReader.java:73)
    8. htsjdk.tribble.TabixFeatureReader.<init>(TabixFeatureReader.java:59)
    9. htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:85)
    10. htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:66)
    10 frames
  4. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:498)
    4 frames
  5. Clojure
    Reflector.invokeStaticMethod
    1. clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:93)
    2. clojure.lang.Reflector.invokeStaticMethod(Reflector.java:207)
    2 frames
  6. bcbio.variation
    ensemble$_main.doInvoke
    1. bcbio.variation.variantcontext$get_vcf_header.invoke(variantcontext.clj:144)
    2. bcbio.variation.variantcontext$get_samples.invoke(variantcontext.clj:150)
    3. bcbio.variation.vcfsample$consistent_order.invoke(vcfsample.clj:108)
    4. bcbio.variation.ensemble$consensus_calls.invoke(ensemble.clj:109)
    5. bcbio.variation.ensemble$_main.doInvoke(ensemble.clj:132)
    5 frames
  7. Clojure
    core$apply.invoke
    1. clojure.lang.RestFn.applyTo(RestFn.java:137)
    2. clojure.core$apply.invoke(core.clj:630)
    2 frames
  8. bcbio.variation
    core$_main.doInvoke
    1. bcbio.variation.core$_main.doInvoke(core.clj:35)
    1 frame
  9. Clojure
    RestFn.applyTo
    1. clojure.lang.RestFn.applyTo(RestFn.java:137)
    1 frame
  10. bcbio.variation
    core.main
    1. bcbio.variation.core.main(Unknown Source)
    1 frame