Hello,
I am trying to run Crossbow via EMR command line. I managed to complete all the crossbow steps- Alignment with Bowtie, Calling SNPS and Postprocess. I am getting an error in the final step Get Counters. Can anyone please help me fix this?
controller
2013-10-08T03:39:40.661Z INFO Fetching jar file.
2013-10-08T03:39:42.169Z INFO Working dir /mnt/var/lib/hadoop/steps/5
2013-10-08T03:39:42.169Z INFO Executing /usr/lib/jvm/java-6-sun/bin/java -cp /home/hadoop/conf:/usr/lib/jvm/java-6-sun/lib/tools.jar:/home/hadoop:/home/hadoop/hadoop-tools.jar:/home/hadoop/hadoop-core.jar:/home/hadoop/hadoop-core-0.20.205.jar:/home/hadoop/hadoop-tools-0.20.205.jar:/home/hadoop/lib/*:/home/hadoop/lib/jetty-ext/* -Xmx1000m -Dhadoop.log.dir=/mnt/var/log/hadoop/steps/5 -Dhadoop.log.file=syslog -Dhadoop.home.dir=/home/hadoop -Dhadoop.id.str=hadoop -Dhadoop.root.logger=INFO,DRFA -Djava.io.tmpdir=/mnt/var/lib/hadoop/steps/5/tmp -Djava.library.path=/home/hadoop/native/Linux-amd64-64 org.apache.hadoop.util.RunJar /home/hadoop/contrib/streaming/hadoop-streaming-0.20.205.jar -D mapred.reduce.tasks=1 -input s3n://crossbow-emr/dummy-input -output s3n://ashwin-test/crossbow-emr-cli_crossbow_counters/ignoreme1 -mapper cat -reducer s3n://crossbow-emr/1.2.1/Counters.pl --output=S3N://ashwin-test/crossbow-emr-cli_crossbow_counters -cacheFile s3n://crossbow-emr/1.2.1/Get.pm#Get.pm -cacheFile s3n://crossbow-emr/1.2.1/Counters.pm#Counters.pm -cacheFile s3n://crossbow-emr/1.2.1/Util.pm#Util.pm -cacheFi ...