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  • pagarwal
    Junior Member
    • Jun 2009
    • 1

    Myrna on Hadoop

    Hello,

    I have been trying to run Myrna on a 5 node hadoop cluster with CentOS following the directions at:


    Myrna was installed on the master node on NFS, so all the slave nodes can also access the application. I set all the environment variables in my .bash_profile file and checked to make sure they are available on all nodes. SSH is passwordless. Here is the command that I used:

    $MYRNA_HOME/myrna_hadoop \
    --preprocess \
    --input=hdfs://myrna_pa/example/yeast/small.manifest \
    --output=hdfs://myrna_pa/example/yeast/output_small \
    --reference=hdfs://myrna_refs_pa/yeast_ensembl_67.jar \
    --streaming=/usr/lib/hadoop-mapreduce/hadoop-streaming.jar

    But I get the following error:

    Myrna expects 'bowtie' to be at path /home/thad/myrna_pa/myrna-1.2.0/bin/linux64/bowtie on the workers
    Myrna expects 'Rscript' to be at path /home/thad/myrna_pa/myrna-1.2.0/R/bin/Rscript on the workers
    Myrna expects 'fastq-dump' to be at path /home/thad/myrna_pa/sratoolkit.2.1.16-centos_linux64/bin/fastq-dump on the workers
    Could not parse Hadoop version: "mapreduce/hadoop"

    Strangely, when I did not the set up right such as env vars in .bash_profile etc, I was getting this same error. Nothing seems to fix it. Any help will be appreciated.

    Other potentially useful information is that I have installed Cloudera Distribution for Hadoop (CDH), version 4. One reason for the problem might be that Myrna does not work with this version. The last error message (red) suggests that the version string was not parsable by Myrna code (MyrnaIface.pm) so it died.


    Thanks,

    - Pankaj
    Last edited by pagarwal; 09-26-2012, 01:23 PM. Reason: New understanding of the cause or error
  • 9000revs
    Member
    • Jun 2013
    • 15

    #2
    I had similar issues with Crossbow on CDH4. It worked on CDH3 (which is the 0.02x ver of Hadoop as mentioned as pre-req for this).

    Comment

    • sudheer1414
      Junior Member
      • Sep 2013
      • 2

      #3
      Thanks for sahring for this valuble information and it is useful for hadoop learners.hadoop online trainings also provides besthttp://hadooponlinetrainings.com/hadoop-online-traininghadoop online training

      Comment

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