htsjdk.samtools.SAMFormatException: Invalid GZIP header

GitHub | tpoterba | 5 months ago
  1. 0

    BGZIP bug

    GitHub | 5 months ago | tpoterba
    htsjdk.samtools.SAMFormatException: Invalid GZIP header
  2. 0

    @PG ID:bwa line containing @RG ID:... causes SAMFormatException

    GitHub | 5 months ago | jblachly
    htsjdk.samtools.SAMFormatException: Error parsing SAM header. Problem parsing @PG key:value pair ID:redacted clashes with ID:bwa. Line: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:/export/local/tools/bwa/bwa mem -t 32 -R @RG ID:redacted SM:redacted LB:1 PL:Illumina PM:Miseq PU:MiseqSN.1 CN:OSU /export/local/ref/indices/bwa/grch37/grch37 cutadapt/redacted_R1.fastq cutadapt/redacted_R2.fastq; File /home/x/capture/aligned_grch37/redacted.bam; Line number 88
  3. 0

    GitHub comment 2#174816922

    GitHub | 12 months ago | brentp
    htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Tag of type i should have signed decimal value; File /dev/stdin; Line 247729 Line: HISEQ:318:H25NKADXY:1:2210:5526:37163 675 chr1 11167510 60 107M13S = 11167604 220 AAAAAACGTGATGGGCACATCTGGGCCTCCAGTTACCAGAAAGGGCACCTAAGAAGGCAGAAGGAAAAGGAATATTTTAATATTTTGAGCTCCTTCAAAGGTTTACAAGGAAACCTGGAA<)?77<AA5?A***5A>1?===<0=ABA############################################################################################ NM:i:3 MD:Z:62A19A8T15 AS:i:92 XS:i:20 RG:Z:769P_AH25NKADXY_L001 BC:Z:AGGGGG OP:i:11167510 XI:i:None XO:Z:AAAAAACGTGATGGGCACATCTGGGCCTCCAGTTACCAGAAAGGGCACCTAAGAAGGCAGAAGGAAAAGGAATATTTTAATATTTTGAGCTCCTTCAAAGGTTTACAAGGAAACCTGGAA OC:Z:107M13S
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  5. 0

    VcfBreakendToReadPair writes SAMRecords extending outside of chromosome boundries

    GitHub | 3 months ago | ayhand
    htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Read name gridss57046, Read CIGAR M operator maps off end of reference
  6. 0

    MAPQ should be 0

    GitHub | 2 years ago | apelin20
    htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 9505, Read name HWI-D00104:87:D1GYYACXX:5:1112:13918:71031, MAPQ should be 0 for unmapped read.

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    Root Cause Analysis

    1. htsjdk.samtools.SAMFormatException

      Invalid GZIP header

      at htsjdk.samtools.util.BlockGunzipper.unzipBlock()
    2. HTS JDK
      BlockCompressedInputStream.available
      1. htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:72)
      2. htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:410)
      3. htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:392)
      4. htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)
      4 frames
    3. org.seqdoop.hadoop_bam
      BGZFSplitCompressionInputStream.read
      1. org.seqdoop.hadoop_bam.util.BGZFSplitCompressionInputStream.readWithinBlock(BGZFSplitCompressionInputStream.java:81)
      2. org.seqdoop.hadoop_bam.util.BGZFSplitCompressionInputStream.read(BGZFSplitCompressionInputStream.java:48)
      2 frames
    4. Java RT
      InputStream.read
      1. java.io.InputStream.read(InputStream.java:101)
      1 frame
    5. Hadoop
      CompressedSplitLineReader.fillBuffer
      1. org.apache.hadoop.mapreduce.lib.input.CompressedSplitLineReader.fillBuffer(CompressedSplitLineReader.java:130)
      1 frame
    6. Hadoop
      LineReader.readLine
      1. org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:216)
      2. org.apache.hadoop.util.LineReader.readLine(LineReader.java:174)
      2 frames
    7. Hadoop
      TextInputFormat.getRecordReader
      1. org.apache.hadoop.mapreduce.lib.input.CompressedSplitLineReader.readLine(CompressedSplitLineReader.java:159)
      2. org.apache.hadoop.mapred.LineRecordReader.<init>(LineRecordReader.java:134)
      3. org.apache.hadoop.mapred.TextInputFormat.getRecordReader(TextInputFormat.java:67)
      3 frames
    8. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.rdd.HadoopRDD$$anon$1.<init>(HadoopRDD.scala:239)
      2. org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:216)
      3. org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:101)
      4. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
      5. org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
      6. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      7. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
      8. org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
      9. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      10. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
      11. org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
      12. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      13. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
      14. org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
      15. org.apache.spark.rdd.UnionRDD.compute(UnionRDD.scala:87)
      16. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
      17. org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
      18. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      19. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
      20. org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
      21. org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
      22. org.apache.spark.scheduler.Task.run(Task.scala:88)
      23. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
      23 frames
    9. Java RT
      Thread.run
      1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
      2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
      3. java.lang.Thread.run(Thread.java:745)
      3 frames