[svtoolkit-help] Java Library Path

[Fritz, E. R [AN S] <er...@ia...>]

Hello,

I am getting the following error when trying to run the ComputeGenomeMask portion of the SVToolkit.

INFO  17:32:10,456 HelpFormatter - ---------------------------------------------------------- 
INFO  17:32:10,459 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGenomeMask 
INFO  17:32:10,460 HelpFormatter - Program Args: -R Chr12.fa -O Chr12.mask.fa -readLength 83 
INFO  17:32:10,460 HelpFormatter - Date/Time: 2011/03/28 17:32:10 
INFO  17:32:10,460 HelpFormatter - ---------------------------------------------------------- 
INFO  17:32:10,461 HelpFormatter - ---------------------------------------------------------- 
INFO  17:32:10,525 GenomeMaskAlgorithm - Initializing bwa ... 
Exception in thread "main" java.lang.UnsatisfiedLinkError: no bwa in java.library.path
	at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1754)
	at java.lang.Runtime.loadLibrary0(Runtime.java:823)
	at java.lang.System.loadLibrary(System.java:1045)
	at org.broadinstitute.sting.alignment.bwa.c.BWACAligner.<clinit>(BWACAligner.java:21)
	at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.getAligner(GenomeMaskAlgorithm.java:206)
	at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.getAlignmentCode(GenomeMaskAlgorithm.java:119)
	at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.generateMaskForSequence(GenomeMaskAlgorithm.java:93)
	at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.generateMask(GenomeMaskAlgorithm.java:75)
	at org.broadinstitute.sv.apps.ComputeGenomeMask.run(ComputeGenomeMask.java:63)
	at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:33)
	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
	at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:23)
	at org.broadinstitute.sv.apps.ComputeGenomeMask.main(ComputeGenomeMask.java:49)


If anyone could tell me how to solve this issue that would be great.

-Eric


Eric Fritz
Assistant Scientist II
Iowa State University
2255G Kildee Hall
Ames, IA 50014