htsjdk.samtools.SAMException: Error opening file: Homo_sapiens_assembly19.fasta.gz

GitHub | arahuja | 4 months ago
  1. 0

    Allow reference file to be loaded from HDFS or GS

    GitHub | 4 months ago | arahuja
    htsjdk.samtools.SAMException: Error opening file: Homo_sapiens_assembly19.fasta.gz
  2. 0

    BuildBamIndex - scary exception on cram input

    GitHub | 7 months ago | akiezun
    htsjdk.samtools.SAMException: Input file must be bam file, not sam file.
  3. 0

    GATK | GATK | Tagged #markduplicates

    broadinstitute.org | 7 months ago
    htsjdk.samtools.SAMException: Cannot read non-existent file: /home/anandie/BWA/home/anandie/BWA/7DLAetAln.bam
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  5. 0

    Hisat v2.0.1 reports identical alignments and does not mark either as secondary.

    GitHub | 7 months ago | MatthewRalston
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 3: null:NB501257:32:HWCMVBGXX:1:212$ 9:5229:14102
  6. 0

    GitHub comment 339#150378100

    GitHub | 1 year ago | droazen
    htsjdk.samtools.util.RuntimeEOFException: htsjdk.samtools.SAMException: Attribute type class java.lang.Long not supported. Tag: I9

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    Root Cause Analysis

    1. htsjdk.samtools.SAMException

      Error opening file: Homo_sapiens_assembly19.fasta.gz

      at htsjdk.samtools.util.IOUtil.openGzipFileForReading()
    2. HTS JDK
      FastaSequenceFile.<init>
      1. htsjdk.samtools.util.IOUtil.openGzipFileForReading(IOUtil.java:518)
      2. htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:494)
      3. htsjdk.samtools.reference.FastaSequenceFile.<init>(FastaSequenceFile.java:53)
      3 frames