Re: [svtoolkit-help] SVDiscovery error for installation test

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

Glad you solved the R problem.
For the benefit of others, can you post what was wrong with the 
environment to cause these symptoms?

Regarding the fasta indexing, I suspect you have a blank line in your 
fasta file.  Could you check that?
I'll fix the code to generate a better error message.

-Bob

On 9/13/11 12:36 PM, Ashish Kumar wrote:
>
> Hi Bob,
>
> I could resolve the problem. It was R environment related.
>
> As a next step, I am now creating a Genome mask file for my reference 
> genome. For this, when I try to index my fasta file, I keep getting 
> the following error:
>
> Exception in thread "main" java.lang.RuntimeException: String index 
> out of range: 0
>
>         at 
> org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:36)
>
>         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.IndexFastaFile.main(IndexFastaFile.java:39)
>
> Caused by: java.lang.StringIndexOutOfBoundsException: String index out 
> of range: 0
>
>         at 
> java.lang.AbstractStringBuilder.charAt(AbstractStringBuilder.java:191)
>
>         at java.lang.StringBuilder.charAt(StringBuilder.java:72)
>
>         at 
> org.broadinstitute.sv.util.fasta.FastaIndexer.indexFastaFile(FastaIndexer.java:48)
>
>         at 
> org.broadinstitute.sv.apps.IndexFastaFile.run(IndexFastaFile.java:49)
>
>         at 
> org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:33)
>
>         ... 3 more
>
> Would you be able to provide some clues please? Perhaps if you could 
> explain - what type of values/how many characters does the program 
> expect in the first column of the "<ref.fasta>.fai" file?
>
> Thanks,
>
> Ashish
>
> *From:*Bob Handsaker [mailto:han...@br...]
> *Sent:* 08 September 2011 23:45
> *To:* svt...@li...
> *Subject:* Re: [svtoolkit-help] SVDiscovery error for installation test
>
> Hi, Ashish,
> I don't know the exact problem, but it seems like something with your 
> R environment.
> You can try running the following short R script:
>
> require("coin")
> df = data.frame(COVERAGE=1:10)
> df$DELETED = as.factor(df$COVERAGE > 5)
> wilcox_test(COVERAGE ~ DELETED, df, alternative="l")
>
> which will hopefully reproduce the problem so that you can diagnose it.
> Something approximating this isn't running when R is invoked from java.
>
> -Bob
>
> On 9/8/11 3:05 PM, Ashish Kumar wrote:
>
> Hi Bob,
>
> While running the installation test, it seems that the SVDiscovery 
> step complains about an R function. I have the "coin package" is 
> installed on my server.
>
> I am pasting the error below, please advice.
>
> Best,
>
> Ashish
>
> ##### ERROR 
> ------------------------------------------------------------------------------------------
>
> ##### ERROR stack trace
>
> java.lang.RuntimeException: Error running script 
> /ib/users/ashish/genostrip/svtoolkit/R/discovery/compute_ranksum_pvalue.R: 
> Error in function (classes, fdef, mtable)  :
>
>   unable to find an inherited method for function "pvalue", for 
> signature "htest"
>
> Calls: main ... compute.ranksum.pvalue.coin -> pvalue -> <Anonymous>
>
> Execution halted
>
>         at 
> org.broadinstitute.sv.discovery.ClusterDepthModule.computeRankSumPValue(ClusterDepthModule.java:284)
>
>         at 
> org.broadinstitute.sv.discovery.ClusterDepthModule.computeDepth(ClusterDepthModule.java:195)
>
>         at 
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:395)
>
>         at 
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303)
>
>         at 
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163)
>
>         at 
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
>
>         at 
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
>
>         at 
> org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
>
>         at 
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75)
>
>         at 
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
>
>         at 
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
>
>         at 
> org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
>
>         at 
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
>
>         at 
> org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
>
>         at 
> org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
>
> ##### ERROR 
> ------------------------------------------------------------------------------------------
>
> ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
>
>
>
>
> ------------------------------------------------------------------------------
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