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

Searched on Google with the first line of a JAVA stack trace?

We can recommend more relevant solutions and speed up debugging when you paste your entire stack trace with the exception message. Try a sample exception.

Recommended solutions based on your search

Samebug tips

,

Java does not handle IPv6 nameservers before 1.8.0_60. Upgrade to the latest JVM.

,

Is thrown when you try to convert a String to a numeric value, like an int, float, double, long, etc.

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
htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: For input string: "R", for input source: /media/sf_BigShare/SCID_recall/batch3/work/gemini/batch3-gatk-haplotype.vcf.gz
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.valueOf(Integer.java:766)
at htsjdk.variant.vcf.VCFCompoundHeaderLine.(VCFCompoundHeaderLine.java:171)
at htsjdk.variant.vcf.VCFFormatHeaderLine.(VCFFormatHeaderLine.java:49)
at htsjdk.variant.vcf.AbstractVCFCodec.parseHeaderFromLines(AbstractVCFCodec.java:211)
at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:111)
at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:88)
at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:41)
at htsjdk.tribble.TabixFeatureReader.readHeader(TabixFeatureReader.java:73)
at htsjdk.tribble.TabixFeatureReader.(TabixFeatureReader.java:59)
at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:85)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:93)
at bcbio.variation.variantcontext$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)

Users with the same issue

Samebug visitor profile picture
Unknown user
Once, 3 weeks ago
2 times, 1 month ago
2 times, 2 months ago
2 times, 2 months ago
Once, 4 months ago
232 more bugmates

Know the solutions? Share your knowledge to help other developers to debug faster.