I have a perl program that needs to call a java program called 'getseq.java'. The perl program and the java program are in different directories.

If I cd to the directory containing getseq.java on the command line, then run the perl program from here, then the following code works fine ('getseq.java' needs 3 arguments - a number like BC000898 and the names of 2 output files to write to).

system "java getseq BC000898 C:/testjava/DNA2.txt C:/testjava/protein2.txt";

However, if I try to run the perl program from outside this directory, it doesn't work; I get the "exception in thread main..." error. Why??

In reply to system call to a java program by Becky

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