Re: [svtoolkit-help] Java Library Path

[Bob H. <han...@br...>]

Hi, Eric,
The ${SV_DIR}/bwa directory is not on your LD_LIBRARY_PATH.
I.e. you need to do something like:

export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}


If you were following the script here:
http://sourceforge.net/mailarchive/forum.php?thread_name=4D700372.9060201%40broadinstitute.org&forum_name=svtoolkit-help
the location of libbwa.so changed since that was posted.  I will put a 
cleaned up script in the FAQ.

Also note that the correct way to create a mask for one chromosome is to 
use the entire reference genome and the -sequence argument.
Otherwise, you will fail to mask locations that unique on chr12 but not 
unique across the whole genome.

-Bob

On 3/28/11 6:32 PM, Fritz, Eric R [AN S] wrote:
> 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
> ------------------------------------------------------------------------------
> Create and publish websites with WebMatrix
> Use the most popular FREE web apps or write code yourself;
> WebMatrix provides all the features you need to develop and publish
> your website. http://p.sf.net/sfu/ms-webmatrix-sf
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help