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Error using Hadoop BAM

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?

hdfs hadoop genome hadoopbam bam
• 2,557 views • link
updated by Ram Ram • written by shalini.ravishankar • shalini.ravishankar

Hey hi,

I tried with

hadoop jar \
  /usr/local/hadoop/share/hadoop/tools/lib/hadoop-streaming-2.5.1.jar \
  -libjars hadoop-bam-7.0.0.jar,htsjdk-1.118.jar \
  -inputformat org.seqdoop.hadoop_bam.BAMInputFormat$1 \
  -file ./methratio.py \
  -file '../fadata/Genome.fa' \
  -mapper methratio.py \
  -input ./wgEncodeSydhRnaSeqK562Ifna6hPolyaAln.bam \
  -output ./outfile

Still having same issue

• 0 views • link
updated by Ram Ram • written by shalini.ravishankar • shalini.ravishankar

Hello shalini.ravishankar!

We believe that this post does not fit the main topic of this site.

Closing this post as OP has not been on Biostars for over 2.5 years.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by Ram Ram

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