I am trying to parallelize some very long RNA sequence for the sake of
predicting their RNA 2D structures. I am using a binary executable c
program called pknotsRG as my mapper. I tried the following bin/hadoop
command:
HADOOP_HOME$ bin/hadoop
jar /data/yehdego/hadoop-0.20.2/hadoop-0.20.2-streaming.jar
-mapper /data/yehdego/hadoop-0.20.2/pknotsRG
-file /data/yehdego/hadoop-0.20.2/pknotsRG
-input /user/yehdego/RF00028_B.bpseqL3G5_seg_Centered_Method.txt
-output /user/yehdego/RF-out -reducer NONE -verbose
but i keep getting the following error message:
java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess
failed with code 1
at
org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:311)
at
org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:545)
at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:132)
at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:57)
at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:36)
at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:358)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:307)
at org.apache.hadoop.mapred.Child.main(Child.java:170)
FYI: my input file is RF00028_B.bpseqL3G5_seg_Centered_Method.txt which
is a chunk of RNA sequences and the mapper is expected to get the input
and execute the input file line by line and out put the predicted
structure for each line of sequence for a specified number of maps. Any
help on this problem is really appreciated. Thanks.
