I am new to hadoop infrastructure. I have setup one-node hadoop cluster using Cloudera manager 4.7.1. Now I am trying to use an application DistMap, a bioinformatics application which is designed to work on hadoop. I am getting the following error.
Exception in thread "main" java.lang.
How are you running your client application? Note that it should be run like the following:
hadoop jar <jar filename> <ClassName>
That is a first place to start.
Thanks for getting back to me.
I am following DistMap Manual run the application.
This is how I am running DistMap
DistMap_v1.0/distmap --reference-fasta datasets/WholeGenome/genome.fa --reference-index-archive datasets/indexed_genome/refarch.tgz --input "datasets/synthetic_sample1.fq.gz,datasets/synthetic_sample2.fq.gz" --mapper bwa --mapper-path bwa-0.5.8c/bwa --picard-mergesamfiles-jar picard-tools-1.99/MergeSamFiles.jar --picard-sortsam-jar picard-tools-1.99/SortSam.jar --mapper-args "-o 1 -n 0.01 -l 200 -e 12 -dd 12" --output-format sam --output /home/ashwin/distmap_output/ --hadoop-home /usr/lib/hadoop-0.20-mapreduce/
@ash I have moved this thread to the MapReduce board in hopes someone here can assist you further. This could very well be a configuration problem related to the MR framework, since it's a MR job you're trying to run.