pallassgj / bpipe

Automatically exported from code.google.com/p/bpipe
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Filter cryptic error message #75

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago
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