[svtoolkit-help] discovery ERROR: there is no package called 'coin'
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[svtoolkit-help] discovery ERROR: there is no package called 'coin'
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From: Sophia D. <sd...@pc...> - 2012-02-14 15:14:57
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Dear colleagues, when running the discovery.sh script (adjusted to my folder structure, see attached) from installtest, I get the following output; basically the problem seems to be that there is a package called coin missing. What is this package and where should it be? I am also attaching the log output from this run. SVToolkit version 1.03 (build 619) Build date: 2011/02/12 17:23:22 Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP INFO 13:52:12,832 QScriptManager - Compiling 2 QScripts INFO 13:52:17,314 QScriptManager - Compilation complete INFO 13:52:19,653 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,653 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 13:52:19,653 HelpFormatter - Program Args: -S /apps/SVTOOLKIT/qscript/SVPreprocess.q -S /apps/SVTOOLKIT/qscript/SVQScript.q -gatk /apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -tempDir /home/production/sderdak/temp -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -runDirectory /home/production/sderdak/svtoolkit_test -md /home/production/sderdak/svtoolkit_test/metadata -jobLogDir /home/production/sderdak/svtoolkit_test/logs -I /apps/SVTOOLKIT/installtest/data/installtest.bam -run INFO 13:52:19,653 HelpFormatter - Date/Time: 2012/02/14 13:52:19 INFO 13:52:19,653 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,654 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,655 QCommandLine - Scripting SVPreprocess INFO 13:52:19,723 QCommandLine - Added 7 functions INFO 13:52:19,723 QGraph - Generating graph. INFO 13:52:19,743 QGraph - Running jobs. INFO 13:52:19,749 QGraph - Deleting intermediate files. INFO 13:52:19,750 QCommandLine - Done INFO 13:52:21,688 QScriptManager - Compiling 2 QScripts INFO 13:52:26,150 QScriptManager - Compilation complete INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,466 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 13:52:28,466 HelpFormatter - Program Args: -S /apps/SVTOOLKIT/qscript/SVDiscovery.q -S /apps/SVTOOLKIT/qscript/SVQScript.q -gatk /apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -tempDir /home/production/sderdak/temp -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -runDirectory /home/production/sderdak/svtoolkit_test -md /home/production/sderdak/svtoolkit_test/metadata -jobLogDir /home/production/sderdak/svtoolkit_test/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /apps/SVTOOLKIT/installtest/benchmark/test1.discovery.vcf -run INFO 13:52:28,466 HelpFormatter - Date/Time: 2012/02/14 13:52:28 INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,468 QCommandLine - Scripting SVDiscovery INFO 13:52:28,534 QCommandLine - Added 2 functions INFO 13:52:28,534 QGraph - Generating graph. INFO 13:52:28,544 QGraph - Running jobs. WARN 13:52:28,554 IOUtils - Unable to delete /apps/SVTOOLKIT/installtest/benchmark/test1.discovery.vcf INFO 13:52:28,572 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:28,572 ShellJobRunner - Output written to /home/production/sderdak/svtoolkit_test/logs/Q-4407@n8-1.out ERROR 13:52:42,426 ShellJobRunner - Error: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 ERROR 13:52:42,426 ShellJobRunner - [GC 3072K->480K(8896K), 0.0017910 secs] [GC 3552K->827K(11968K), 0.0011520 secs] [GC 6971K->4376K(11968K), 0.0247150 secs] [Full GC 4376K->4374K(18816K), 0.0166730 secs] [GC 10518K->6887K(22784K), 0.0032890 secs] [GC 16999K->12435K(24960K), 0.0076720 secs] [Full GC 12435K->12428K(37440K), 0.0285140 secs] [GC 24447K->12639K(48320K), 0.0205120 secs] [GC 29791K->12895K(48320K), 0.0026380 secs] [GC 30047K->13216K(52736K), 0.0015270 secs] [GC 36448K->13151K(53888K), 0.0012050 secs] [GC 36383K->13391K(56192K), 0.0014730 secs] [GC 40271K->13599K(57024K), 0.0013080 secs] [GC 40479K->13823K(58944K), 0.0018550 secs] [GC 43903K->13999K(59648K), 0.0045090 secs] [GC 44079K->14271K(62144K), 0.0022270 secs] [GC 47743K->14575K(62592K), 0.0047930 secs] [GC 48047K->14720K(66112K), 0.0030170 secs] [GC 51968K->15280K(66304K), 0.0025500 secs] [GC 52528K->15620K(68864K), 0.0027080 secs] [GC 55236K->15712K(69120K), 0.0036740 secs] [GC 55328K->16144K(71808K), 0.0031310 secs] [GC 58192K->16556K(72128K), 0.0031330 secs] [GC 58604K->16888K(75008K), 0.0034090 secs] [GC 61560K->17360K(75264K), 0.0034490 secs] [GC 62032K->17744K(78400K), 0.0033960 secs] [GC 65296K->18164K(78656K), 0.0030270 secs] [GC 65716K->18411K(81152K), 0.0034330 secs] [GC 68203K->18827K(81344K), 0.0028290 secs] [GC 68619K->19341K(83776K), 0.0036700 secs] [GC 71309K->19430K(84032K), 0.0116790 secs] [GC 71398K->19867K(87616K), 0.0073410 secs] INFO 13:52:31,530 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5039M, Compiled 2011/01/20 22:58:34 INFO 13:52:31,532 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:52:31,532 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 13:52:31,532 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 13:52:31,532 HelpFormatter - Program Args: -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:31,532 HelpFormatter - Date/Time: 2012/02/14 13:52:31 INFO 13:52:31,533 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,533 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,549 GenomeAnalysisEngine - Strictness is SILENT INFO 13:52:31,627 SVDiscovery - Initializing SVDiscovery ... INFO 13:52:31,631 SVDiscovery - Opening reference sequence ... INFO 13:52:31,631 SVDiscovery - Opened reference sequence. INFO 13:52:31,631 SVDiscovery - Opening genome mask ... INFO 13:52:31,631 SVDiscovery - Opened genome mask. INFO 13:52:31,631 SVDiscovery - Initializing input data set ... [GC 75291K->23286K(87744K), 0.0053900 secs] INFO 13:52:31,779 SVDiscovery - Initialized data set: 1 file, 900 read groups, 45 samples. INFO 13:52:31,779 SVDiscovery - Opening metadata from /home/production/sderdak/svtoolkit_test/metadata ... INFO 13:52:31,782 SVDiscovery - Opened metadata. INFO 13:52:31,783 SVDiscovery - Initializing discovery algorithm ... INFO 13:52:31,784 SVDiscovery - Loading insert size histograms ... INFO 13:52:31,832 SVDiscovery - Loaded 47 histograms. INFO 13:52:31,927 SVDiscovery - Processing locus: 1:0-0:100-1000000 INFO 13:52:31,927 SVDiscovery - Locus search window: 1:0-0 INFO 13:52:31,927 SVDiscovery - Selecting read pairs ... INFO 13:52:31,928 SVDiscovery - Reading input file /apps/SVTOOLKIT/installtest/data/installtest.bam ... [GC 78710K->30853K(88960K), 0.0225700 secs] [Full GC 30853K->18529K(96064K), 0.0494600 secs] [GC 73825K->18689K(99584K), 0.0120350 secs] [GC 73985K->18849K(103424K), 0.0115620 secs] [GC 77793K->19009K(103488K), 0.0145240 secs] [GC 77953K->19009K(108928K), 0.0152100 secs] [GC 83521K->19105K(108672K), 0.0009450 secs] [GC 83617K->19169K(111296K), 0.0008710 secs] [GC 88225K->19329K(112512K), 0.0007470 secs] [GC 88385K->19361K(113792K), 0.0010330 secs] [GC 91745K->19713K(114944K), 0.0010300 secs] [GC 92097K->19777K(115200K), 0.0012700 secs] [GC 92444K->23278K(116096K), 0.0024210 secs] INFO 13:52:34,179 SVDiscovery - Processing clusters ... [GC 97902K->20577K(116672K), 0.0022160 secs] INFO 13:52:34,276 SVDiscovery - Clustering: Generating clusters for 6 read pairs. INFO 13:52:34,276 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 13:52:34,276 SVDiscovery - Processing cluster 1:61722491-61722556 1:61723000-61723144 LR 6 [GC 97121K->60120K(137472K), 6.3453430 secs] [Full GC 60120K->49911K(161216K), 0.0665450 secs] [GC 126455K->52056K(185216K), 0.0193480 secs] [GC 140376K->52024K(185856K), 0.0169610 secs] [GC 140344K->52056K(194624K), 0.0167830 secs] #DBG: RC Cache fill 1:61712557-61812556 100000 45 7.307225 sec [GC 152600K->51960K(196224K), 0.0151720 secs] Error: Exception processing cluster: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : could not find function "wilcox_test" Calls: main -> compute.ranksum.pvalue.coin In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'coin' Execution halted Cluster: 1:61722491-61722556 1:61723000-61723144 LR 6 INFO 13:52:42,238 GATKRunReport - Aggregating data for run report [GC 58947K->52088K(205888K), 0.0118240 secs] [Full GC 52088K->13053K(205888K), 0.0492310 secs] ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.RuntimeException: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : could not find function "wilcox_test" Calls: main -> compute.ranksum.pvalue.coin In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'coin' 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): ##### ERROR ##### ERROR Please visit to wiki to see if this is a known problem ##### ERROR If not, please post the error, with stack trace, to the GATK forum ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : ##### ERROR could not find function "wilcox_test" ##### ERROR Calls: main -> compute.ranksum.pvalue.coin ##### ERROR In addition: Warning message: ##### ERROR In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : ##### ERROR there is no package called 'coin' ##### ERROR Execution halted ##### ERROR ------------------------------------------------------------------------------------------ INFO 13:52:42,427 QCommandLine - Done with errors INFO 13:52:42,429 QGraph - ------- INFO 13:52:42,433 QGraph - Failed: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:42,433 QGraph - Log: /home/production/sderdak/svtoolkit_test/logs/Q-4407@n8-1.out thanks for any suggestions, cheers, Sophia -- Sophia Derdak, PhD Data Analysis Group National Center for Genomic Analysis (CNAG) Parc Cientific de Barcelona Torre I, 2a planta Baldiri Reixac, 4 08028 Barcelona, SPAIN http://www.cnag.cat Tel: +34 9340 20846 Email: sd...@pc... |
