What steps will reproduce the problem?
Run this pipeline:
DATA="file.txt"
@Filter("count")
count = {
exec """
wc -l $DATA > $output
"""
}
Bpipe.run {
count
}
What is the expected output? What do you see instead?
I get a long, but cryptic error message involving a division by zero:
====================================================================================================
| Starting Pipeline at 2013-05-03 11:15 |
====================================================================================================
=========================================== Stage count ============================================
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:106)
at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:128)
Caused by: java.lang.ArithmeticException: / by zero
at org.codehaus.groovy.runtime.typehandling.IntegerMath.modImpl(IntegerMath.java:72)
at org.codehaus.groovy.runtime.typehandling.NumberMath.mod(NumberMath.java:89)
What version of the product are you using? On what operating system?
Linux 3.2.0-39-generic
jdk 1.6.0
bpipe 0.9.8
Please provide any additional information below.
Removing the @Filter() statement solves the issue.
Original issue reported on code.google.com by florent....@gmail.com on 3 May 2013 at 1:22
Original issue reported on code.google.com by
florent....@gmail.com
on 3 May 2013 at 1:22