Off topic:Error using Hadoop BAM

Question

[shalini.ravishankar]

Hello Everyone,

I am new to Hadoop BAM and bio world. I tried to use hadoop bam as :

$ hadoop jar \
  /usr/local/hadoop/share/hadoop/tools/lib/hadoop-streaming-2.5.1.jar \
  -libjars hadoop-bam-7.0.0.jar,picard-1.86.0.jar \
  -inputformat org.seqdoop.hadoop_bam.BAMInputFormat$1 \
  -file ./methratio.py \
  -file '../fadata/Genome.fa' \
  -mapper methratio.py \
  -input ./wgEncodeSydhRnaSeqK562Ifna6hPolyaAln.bam \
  -output ./outfile

but when I run this I am getting error as:

Exception in thread "main" java.lang.NoClassDefFoundError: htsjdk/samtools/seekablestream/SeekableStream

        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:270)
        at org.apache.hadoop.conf.Configuration.getClassByNameOrNull(Configuration.java:1986)
        at org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:1951)
        at org.apache.hadoop.streaming.StreamUtil.goodClassOrNull(StreamUtil.java:51)
        at org.apache.hadoop.streaming.StreamJob.setJobConf(StreamJob.java:784)
        at org.apache.hadoop.streaming.StreamJob.run(StreamJob.java:128)
        at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:70)
        at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:84)
        at org.apache.hadoop.streaming.HadoopStreaming.main(HadoopStreaming.java:50)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.hadoop.util.RunJar.main(RunJar.java:212)
Caused by: java.lang.ClassNotFoundException: htsjdk.samtools.seekablestream.SeekableStream
        at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
        ... 15 more

I am trying to process a bam file on hadoop. Can someone please let me know what is wrong here?