java.lang.NullPointerException

GitHub | nh13 | 1 year ago
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  1. 0

    FilterVcf blows up with an IAE

    GitHub | 11 months ago | akiezun
    picard.PicardException: The input vcf must have a sequence dictionary in order to create indexed vcf or bcfs.
  2. 0

    Errors about contigs in BAM or VCF files not being properly ordered or sorted — GATK-Forum

    broadinstitute.org | 3 days ago
    java.lang.IllegalArgumentException: java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected.
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  4. 0

    GitHub comment 734#273598983

    GitHub | 2 months ago | nh13
    htsjdk.samtools.SAMException: Cannot figure out type of file /dev/stdin from extension. Current implementation understands the following types: [FASTA: [.fa.gz, .fna.gz, .txt, .fasta.gz, .fa, .fasta, .fna, .txt.gz], DICTIONARY: [.dict], SAM: [.bam, .sam], VCF: [.bcf, .vcf.gz, .vcf], INTERVAL_LIST: [.interval_list]]
  5. 0

    FilterVcf blows up with NPE

    GitHub | 11 months ago | akiezun
    java.lang.NullPointerException

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    Root Cause Analysis

    1. java.lang.NullPointerException

      No message provided

      at picard.vcf.processor.VcfFileSegmentGenerator$ByWholeContig.readSequences()
    2. picard.vcf.processor
      VariantProcessor$Builder.build
      1. picard.vcf.processor.VcfFileSegmentGenerator$ByWholeContig.readSequences(VcfFileSegmentGenerator.java:112)
      2. picard.vcf.processor.VcfFileSegmentGenerator$ByWholeContig.forVcf(VcfFileSegmentGenerator.java:98)
      3. picard.vcf.processor.VcfFileSegmentGenerator$WidthLimitingDecorator.forVcf(VcfFileSegmentGenerator.java:194)
      4. picard.vcf.processor.VcfFileSegmentGenerator$1.forVcf(VcfFileSegmentGenerator.java:64)
      5. picard.vcf.processor.VariantIteratorProducer$Threadsafe.<init>(VariantIteratorProducer.java:140)
      6. picard.vcf.processor.VariantIteratorProducer.byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(VariantIteratorProducer.java:72)
      7. picard.vcf.processor.VariantProcessor$Builder.composeVcfIteratorProducerFromBuilderArguments(VariantProcessor.java:166)
      8. picard.vcf.processor.VariantProcessor$Builder.build(VariantProcessor.java:149)
      8 frames
    3. picard.vcf
      CollectVariantCallingMetrics.doWork
      1. picard.vcf.CollectVariantCallingMetrics.doWork(CollectVariantCallingMetrics.java:128)
      1 frame
    4. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames