htsjdk.samtools.SAMFormatException: Invalid GZIP header

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, 1 year ago
Invalid GZIP header
htsjdk.samtools.SAMFormatException: Invalid GZIP header
at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:72)
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:410)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:392)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)
at org.seqdoop.hadoop_bam.util.BGZFSplitCompressionInputStream.readWithinBlock(BGZFSplitCompressionInputStream.java:81)
at org.seqdoop.hadoop_bam.util.BGZFSplitCompressionInputStream.read(BGZFSplitCompressionInputStream.java:48)
at java.io.InputStream.read(InputStream.java:101)
at org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:216)
at org.apache.hadoop.mapreduce.lib.input.CompressedSplitLineReader.readLine(CompressedSplitLineReader.java:159)
at org.apache.hadoop.mapred.LineRecordReader.(LineRecordReader.java:134)
at org.apache.spark.rdd.HadoopRDD$$anon$1.(HadoopRDD.scala:239)
at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:216)
at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:101)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.UnionRDD.compute(UnionRDD.scala:87)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

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