svtoolkit-help

[svtoolkit-help] no bwa in java.library.path

[Mira H. <mir...@du...>]

Hi,
I just asked this question at the GSA support website,
but maybe it would be more appropriate for you.
thanks in advance for your help.
I'm trying to test my installation of svtoolkit using the test scripts provided, but it fails and complains that it cannot find the bwa library.
I am using Mac OS X Lion.
I have the libbwa.so copied into /usr/lib/java/ as well as /Library/Java/Extensions/.
I have tried booting into both 64bit and 32bit mode and both failed.
Would you have any clue why it's not finding the library?
I know this question is not exactly about your software, but I'm hoping maybe someone will have knowledge about this problem.
thank you

Miras-air:installtest mirahan$ java -Xmx1g -Djava.io.tmpdir=/usr/local/src/svtoolkit/svtoolkit/installtest/tmpdir -Djava.library.path=/usr/lib/java/ -cp /usr/local/src/svtoolkit/svtoolkit/lib/SVToolkit.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam -O /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
INFO 11:36:26,878 HelpFormatter - ---------------------------------------------------------------------------
INFO 11:36:26,880 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5039M, Compiled 2011/01/20 22:58:34
INFO 11:36:26,880 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:36:26,880 HelpFormatter - Please view our documentation athttp://www.broadinstitute.org/gsa/wiki
INFO 11:36:26,881 HelpFormatter - For support, please view our support site athttp://getsatisfaction.com/gsa
INFO 11:36:26,881 HelpFormatter - Program Args: -T SVAltAligner -R /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam -O /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
INFO 11:36:26,881 HelpFormatter - Date/Time: 2011/11/22 11:36:26
INFO 11:36:26,881 HelpFormatter - ---------------------------------------------------------------------------
INFO 11:36:26,881 HelpFormatter - ---------------------------------------------------------------------------
INFO 11:36:26,885 GenomeAnalysisEngine - Strictness is SILENT
Exception in thread "main" java.lang.UnsatisfiedLinkError: no bwa in java.library.path
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1758)
at java.lang.Runtime.loadLibrary0(Runtime.java:823)
at java.lang.System.loadLibrary(System.java:1045)
at org.broadinstitute.sting.alignment.bwa.c.BWACAligner.(BWACAligner.java:21)
at org.broadinstitute.sv.breakpoint.BreakpointAligner.initialize(BreakpointAligner.java:46)
at org.broadinstitute.sv.breakpoint.SVAltAlignerWalker.initialize(SVAltAlignerWalker.java:86)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)
Miras-air:installtest mirahan$ ls /usr/lib/java/
libbwa.so libjdns_sd.jnilib
Miras-air:installtest mirahan$ ls /Library/Java/Extensions/
libbwa.so

Re: [svtoolkit-help] no bwa in java.library.path

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

I think it's a fair question!
I currently don't support running any of the genome strip functions that 
require bwa (e.g. genome masking or alt allele alignments) on non-linux 
platforms.
You could try to build libbwa for macos and see if that works for you, 
but the binary in the distribution is a linux binary.
-Bob

On 11/22/11 12:01 PM, Mira Han wrote:
>
> Hi,
> I just asked this question at the GSA support website,
> but maybe it would be more appropriate for you.
> thanks in advance for your help.
> I'm trying to test my installation of svtoolkit using the test scripts 
> provided, but it fails and complains that it cannot find the bwa library.
> I am using Mac OS X Lion.
> I have the libbwa.so copied into /usr/lib/java/ as well as 
> /Library/Java/Extensions/.
> I have tried booting into both 64bit and 32bit mode and both failed.
> Would you have any clue why it's not finding the library?
> I know this question is not exactly about your software, but I'm 
> hoping maybe someone will have knowledge about this problem.
> thank you
>
> Miras-air:installtest mirahan$ java -Xmx1g 
> -Djava.io.tmpdir=/usr/local/src/svtoolkit/svtoolkit/installtest/tmpdir 
> -Djava.library.path=/usr/lib/java/ -cp 
> /usr/local/src/svtoolkit/svtoolkit/lib/SVToolkit.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R 
> /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam 
> -O 
> /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam 
> -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference 
> test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
> INFO 11:36:26,878 HelpFormatter - 
> --------------------------------------------------------------------------- 
>
> INFO 11:36:26,880 HelpFormatter - The Genome Analysis Toolkit (GATK) 
> v1.0.5039M, Compiled 2011/01/20 22:58:34
> INFO 11:36:26,880 HelpFormatter - Copyright (c) 2010 The Broad Institute
> INFO 11:36:26,880 HelpFormatter - Please view our documentation 
> athttp://www.broadinstitute.org/gsa/wiki
> INFO 11:36:26,881 HelpFormatter - For support, please view our support 
> site athttp://getsatisfaction.com/gsa
> INFO 11:36:26,881 HelpFormatter - Program Args: -T SVAltAligner -R 
> /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam 
> -O 
> /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam 
> -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference 
> test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
> INFO 11:36:26,881 HelpFormatter - Date/Time: 2011/11/22 11:36:26
> INFO 11:36:26,881 HelpFormatter - 
> --------------------------------------------------------------------------- 
>
> INFO 11:36:26,881 HelpFormatter - 
> --------------------------------------------------------------------------- 
>
> INFO 11:36:26,885 GenomeAnalysisEngine - Strictness is SILENT
> Exception in thread "main" java.lang.UnsatisfiedLinkError: no bwa in 
> java.library.path
> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1758)
> at java.lang.Runtime.loadLibrary0(Runtime.java:823)
> at java.lang.System.loadLibrary(System.java:1045)
> at 
> org.broadinstitute.sting.alignment.bwa.c.BWACAligner.(BWACAligner.java:21) 
>
> at 
> org.broadinstitute.sv.breakpoint.BreakpointAligner.initialize(BreakpointAligner.java:46) 
>
> at 
> org.broadinstitute.sv.breakpoint.SVAltAlignerWalker.initialize(SVAltAlignerWalker.java:86) 
>
> at 
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) 
>
> at 
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) 
>
> at 
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) 
>
> at 
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) 
>
> at 
> org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) 
>
> Miras-air:installtest mirahan$ ls /usr/lib/java/
> libbwa.so libjdns_sd.jnilib
> Miras-air:installtest mirahan$ ls /Library/Java/Extensions/
> libbwa.so
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help