svtoolkit-help Mailing List for Structural Variation Toolkit (Page 5)
Status: Beta
Brought to you by:
bhandsaker
Menu
▾
▴
svtoolkit-help — bug reports and trouble shooting
You can subscribe to this list here.
| 2011 |
Jan
|
Feb
(2) |
Mar
(7) |
Apr
(3) |
May
|
Jun
(9) |
Jul
(2) |
Aug
(2) |
Sep
(15) |
Oct
(13) |
Nov
(11) |
Dec
(8) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2012 |
Jan
(14) |
Feb
(5) |
Mar
(4) |
Apr
(8) |
May
(2) |
Jun
(8) |
Jul
(6) |
Aug
(4) |
Sep
(8) |
Oct
(5) |
Nov
(2) |
Dec
(4) |
| 2013 |
Jan
(4) |
Feb
|
Mar
(4) |
Apr
|
May
(8) |
Jun
(3) |
Jul
|
Aug
(1) |
Sep
|
Oct
(4) |
Nov
|
Dec
(3) |
| 2014 |
Jan
|
Feb
|
Mar
(3) |
Apr
(5) |
May
|
Jun
|
Jul
|
Aug
|
Sep
(1) |
Oct
|
Nov
|
Dec
|
| 2015 |
Jan
(2) |
Feb
(9) |
Mar
(2) |
Apr
(6) |
May
|
Jun
(7) |
Jul
|
Aug
(2) |
Sep
(4) |
Oct
(4) |
Nov
(1) |
Dec
(1) |
| 2016 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
(2) |
Aug
(3) |
Sep
(3) |
Oct
(1) |
Nov
|
Dec
|
| 2017 |
Jan
|
Feb
(2) |
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
(3) |
Oct
(3) |
Nov
(1) |
Dec
|
| 2018 |
Jan
(2) |
Feb
|
Mar
|
Apr
|
May
(3) |
Jun
(6) |
Jul
|
Aug
(4) |
Sep
|
Oct
(1) |
Nov
|
Dec
|
|
From: lishiyong <lis...@bg...> - 2013-03-07 08:16:43
|
Hi: I have 22 samples(11 tumour samples and 11 matched adjacent non-tumour samples). Each sample has been sequenced almost 50X whole genome. I want to use the genome-strip to detect the SV. But it would take too much time to merge into one bam,and too much memory to storage the bam. Could it get a list of each sample's bam as the input? or is There another way to solve this problem? Best wishes to you. Shiyong li |
|
From: Bob H. <han...@br...> - 2013-03-03 20:24:47
|
This exception is coming from Queue, which is the load management software from the GATK. It seems to be trying to resolve the name of the local machine, which is maybe set to something non-standard on your system. Could you try posting this to the GATK forums on VanillaForum and see if you get some help there? I assume you have already googled to see if someone else has had this problem with Queue. It is not something I have run into before. -Bob On 3/3/13 6:18 AM, ÖìÕþÁØ wrote: > > Dear Doctor, > > I am sorry to botter you. > When I am installing Genome Strip, I run ./discovery.sh. met bugs below: > > SVToolkit version 1.04 (build 1068) > Build date: 2013/01/14 19:34:19 > Web site: http://www.broadinstitute.org/software/genomestrip > Exception in thread "main" java.lang.ExceptionInInitializerError > at > org.broadinstitute.sting.queue.engine.QGraphSettings.<init>(QGraphSettings.scala:64) > at > org.broadinstitute.sting.queue.QCommandLine.<init>(QCommandLine.scala:85) > at > org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:49) > at > org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) > Caused by: java.net.UnknownHostException: core 7: core 7 > at java.net.InetAddress.getLocalHost(InetAddress.java:1426) > at > org.broadinstitute.sting.queue.util.SystemUtils$.<init>(SystemUtils.scala:35) > at > org.broadinstitute.sting.queue.util.SystemUtils$.<clinit>(SystemUtils.scala) > ... 4 more > > my java version is > java version "1.6.0_24" > OpenJDK Runtime Environment (IcedTea6 1.11.5) (Gentoo build 1.6.0_24-b24) > OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode) > > Would you mind helping me to figure out this problem? > > Thank you very much. > > best wishes, > > Zhenglin Zhu > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Bob H. <han...@br...> - 2013-01-21 14:30:45
|
Hi, The root of the problem is in your data: There are two reads with the same ID (read name) but two different read groups. I don't know if this is the problem, but Genome STRiP does require read names to be unique across all of the bams you are analyzing together. The read IDs are: 588658 The read groups are: 561924SRR063635,998169SRR063658 -Bob On 1/20/13 3:18 AM, Wen Yao wrote: > > Hi Bob, > I have been using genome-strip these days. I have fixed several > errors with your kindly help. I encountered a new error recently. Here > is the error messages: > java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir > -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R > /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta > -I /home/wbxie/wild_rice/bwa_map/100.bam -I > /home/wbxie/wild_rice/bwa_map/101.bam -I > /home/wbxie/wild_rice/bwa_map/102.bam -I > /home/wbxie/wild_rice/bwa_map/103.bam > .........<truncated>.......... > -I /home/wbxie/bam_file_MSUv7/W321.bam -I > /home/wbxie/bam_file_MSUv7/W322.bam -I > /home/wbxie/bam_file_MSUv7/W323.bam -I > /home/wbxie/bam_file_MSUv7/W324.bam -I > /home/wbxie/bam_file_MSUv7/W325.bam -I > /home/wbxie/bam_file_MSUv7/W326.bam -I > /home/wbxie/bam_file_MSUv7/W327.bam -I > /home/wbxie/bam_file_MSUv7/W328.bam -I > /home/wbxie/bam_file_MSUv7/W329.bam -I > /home/wbxie/bam_file_MSUv7/W330.bam -O > /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/P0008.discovery.vcf > -md wild_rice_test2/metadata -disableGATKTraversal -configFile > conf/genstrip_installtest_parameters.txt -runDirectory wild_rice_test2 > -genomeMaskFile data/rice_all_genomes_v7.mask.fasta -partitionName > P0008 -filePrefix P0008 -L chr06:1-31248787 -searchLocus > chr06:1-31248787 -searchWindow chr06:1-31248787 -searchMinimumSize 100 > -searchMaximumSize 1000000 > org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. > Command line: > sh > /home/wbxie/software/svtoolkit/installtest/all_tmpdir/.exec1738692847535129737 > Exit code: 1 > Standard error contained: > [GC 524288K->72586K(2009792K), 0.7542970 secs] > INFO 15:53:17,194 HelpFormatter - > ----------------------------------------------------------------------------------- > > INFO 15:53:17,215 HelpFormatter - The Genome Analysis Toolkit (GATK) > v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 > INFO 15:53:17,217 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 15:53:17,218 HelpFormatter - Please view our documentation at > http://www.broadinstitute.org/gsa/wiki > INFO 15:53:17,219 HelpFormatter - For support, please view our > support site at http://getsatisfaction.com/gsa > INFO 15:53:17,221 HelpFormatter - Program Args: -T SVDiscovery -R > /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta > -O > /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/P0008.discovery.vcf > -md wild_rice_test2/metadata -disableGATKTraversal -configFile > conf/genstrip_installtest_parameters.txt -runDirectory wild_rice_test2 > -genomeMaskFile data/rice_all_genomes_v7.mask.fasta -partitionName > P0008 -filePrefix P0008 -L chr06:1-31248787 -searchLocus > chr06:1-31248787 -searchWindow chr06:1-31248787 -searchMinimumSize 100 > -searchMaximumSize 1000000 > INFO 15:53:17,223 HelpFormatter - Date/Time: 2012/11/10 15:53:17 > INFO 15:53:17,224 HelpFormatter - > ----------------------------------------------------------------------------------- > > INFO 15:53:17,225 HelpFormatter - > ----------------------------------------------------------------------------------- > > INFO 15:53:17,414 GenomeAnalysisEngine - Strictness is SILENT > INFO 15:53:19,702 SVDiscovery - Initializing SVDiscovery ... > INFO 15:53:19,764 SVDiscovery - Opening reference sequence ... > INFO 15:53:19,772 SVDiscovery - Opened reference sequence. > INFO 15:53:19,773 SVDiscovery - Opening genome mask ... > INFO 15:53:19,781 SVDiscovery - Opened genome mask. > INFO 15:53:19,782 SVDiscovery - Initializing input data set ... > [GC 596874K->78691K(2534080K), 0.8322460 secs] > INFO 15:53:27,431 SVDiscovery - Initialized data set: 713 files, 811 > read groups, 713 samples. > INFO 15:53:27,432 SVDiscovery - Opening metadata from > wild_rice_test2/metadata ... > INFO 15:53:27,437 SVDiscovery - Opened metadata. > INFO 15:53:27,444 SVDiscovery - Initializing discovery algorithm ... > INFO 15:53:27,451 SVDiscovery - Loading insert size histograms ... > [GC 1127267K->98598K(2534080K), 0.9073720 secs] > [GC 1147174K->24483K(2708864K), 0.1410060 secs] > [GC 1247843K->26795K(2637056K), 0.1760810 secs] > INFO 15:54:32,991 SVDiscovery - Loaded 713 histograms. > INFO 15:54:33,011 SVDiscovery - Discovery alt home filtering is > disabled. > INFO 15:54:38,649 SVDiscovery - Processing locus: > chr06:1-31248787:100-1000000 > INFO 15:54:38,650 SVDiscovery - Locus search window: chr06:1-31248787 > INFO 15:54:38,651 SVDiscovery - Selecting read pairs ... > INFO 15:54:38,665 SVDiscovery - Reading input file > /home/wbxie/wild_rice/bwa_map/100.bam ... > [GC 1250155K->122384K(2632768K), 0.3954950 secs] > [GC 1234768K->38536K(2653376K), 0.2583210 secs] > INFO 15:55:02,373 SVDiscovery - Reading input file > /home/wbxie/wild_rice/bwa_map/101.bam ... > [GC 1150920K->55080K(2641856K), 0.2100770 secs] > [GC 1168232K->62044K(2648000K), 0.2142580 secs] > [GC 1175196K->68624K(2655360K), 0.2988430 secs] > INFO 15:55:35,214 SVDiscovery - Reading input file > /home/wbxie/wild_rice/bwa_map/102.bam ... > [GC 1197840K->79312K(2658240K), 0.2794220 secs] > [GC 1208528K->86788K(2660160K), 0.1888030 secs] > INFO 15:56:05,021 SVDiscovery - Reading input file > /home/wbxie/wild_rice/bwa_map/103.bam ... > [GC 1224900K->104476K(2663296K), 0.1776500 secs] > [GC 1242588K->112492K(2664448K), 0.1901910 secs] > ........<truncated>............ > > INFO 20:37:59,770 SVDiscovery - Reading input file > /home/wbxie/bam_file_MSUv7/W329.bam ... > [GC 2485525K->1119669K(2798528K), 0.2848940 secs] > INFO 20:38:13,593 SVDiscovery - Reading input file > /home/wbxie/bam_file_MSUv7/W330.bam ... > [GC 2494325K->1125669K(2798528K), 0.0883570 secs] > [GC 437423K->181927K(1772288K), 0.0068700 secs] > #DBG: RC Cache fill chr06:1-110000 110000 713 124.640302 sec > INFO 20:51:51,800 SVDiscovery - Clustering: Generating clusters for 3 > read pairs. > INFO 20:51:51,857 SVDiscovery - Clustering: Generating clusters for 2 > read pairs. > INFO 20:51:51,863 SVDiscovery - Clustering: Generating clusters for > 27 read pairs. > INFO 20:51:51,865 SVDiscovery - Clustering: Generating clusters for 2 > read pairs. > INFO 20:51:51,902 SVDiscovery - Clustering: Generating clusters for 3 > read pairs. > INFO 20:51:51,919 SVDiscovery - Clustering: Generating clusters for 2 > read pairs. > INFO 20:51:51,919 SVDiscovery - Processing cluster chr06:19014-19110 > chr06:96702-96800 LR 3 > [GC 435751K->182805K(1771008K), 0.0077180 secs] > INFO 20:51:54,382 SVDiscovery - Clustering: Generating clusters for 7 > read pairs. > INFO 20:51:54,383 SVDiscovery - Clustering: LR split size 7 / 7 > maximal clique size 4 clique count 1 > ........<truncated>............ > > #DBG: RC Cache miss chr06:19217935-19684171 466237 713 93.022620 sec > INFO 17:56:41,850 SVDiscovery - Clustering: Generating clusters for 7 > read pairs. > INFO 17:56:41,850 SVDiscovery - Processing cluster > chr06:19220034-19220159 chr06:19221402-19221547 LR 8 > INFO 17:56:43,322 SVDiscovery - Clustering: Generating clusters for > 56 read pairs. > INFO 17:56:43,322 SVDiscovery - Clustering: LR split size 56 / 56 > maximal clique size 49 clique count 1 > INFO 17:56:43,323 SVDiscovery - Clustering: LR split size 7 / 56 > maximal clique size 2 clique count 4 > INFO 17:56:43,323 SVDiscovery - Clustering: LR split size 5 / 56 > maximal clique size 2 clique count 2 > INFO 17:56:43,323 SVDiscovery - Clustering: LR split size 3 / 56 > maximal clique size 2 clique count 1 > INFO 17:56:43,330 SVDiscovery - Clustering: Generating clusters for 7 > read pairs. > INFO 17:56:43,332 SVDiscovery - Clustering: Generating clusters for > 16 read pairs. > INFO 17:56:43,332 SVDiscovery - Processing cluster > chr06:19231617-19231729 chr06:19234427-19234538 LR 7 > INFO 17:56:44,579 SVDiscovery - Clustering: Generating clusters for > 47 read pairs. > INFO 17:56:44,580 SVDiscovery - Processing cluster > chr06:19241754-19242136 chr06:19242646-19243023 LR 16 > INFO 17:56:45,946 SVDiscovery - Clustering: Generating clusters for 6 > read pairs. > INFO 17:56:45,946 SVDiscovery - Processing cluster > chr06:19246397-19246741 chr06:19257339-19257677 LR 47 > INFO 17:56:48,264 SVDiscovery - Clustering: Generating clusters for > 61 read pairs. > INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 61 / 61 > maximal clique size 24 clique count 2 > INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 37 / 61 > maximal clique size 8 clique count 1 > INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 29 / 61 > maximal clique size 6 clique count 1 > INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 23 / 61 > maximal clique size 4 clique count 12 > INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 19 / 61 > maximal clique size 4 clique count 1 > INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 15 / 61 > maximal clique size 3 clique count 1 > INFO 17:56:48,266 SVDiscovery - Clustering: LR split size 12 / 61 > maximal clique size 2 clique count 5 > INFO 17:56:48,266 SVDiscovery - Clustering: LR split size 10 / 61 > maximal clique size 2 clique count 3 > INFO 17:56:48,266 SVDiscovery - Clustering: LR split size 8 / 61 > maximal clique size 2 clique count 1 > INFO 17:56:48,266 SVDiscovery - Clustering: LR split size 6 / 61 > maximal clique size 1 clique count 7 > INFO 17:56:48,266 SVDiscovery - Processing cluster > chr06:19251412-19251521 chr06:19251687-19251798 LR 6 > [GC 2142252K->1436452K(2264448K), 0.0112090 secs] > ........<truncated>............ > > [GC 1890370K->1480970K(1981440K), 0.0178220 secs] > #DBG: RC Cache fill chr06:19469143-19579142 110000 713 40.510878 sec > INFO 18:03:09,242 SVDiscovery - Clustering: Generating clusters for > 71 read pairs. > INFO 18:03:09,252 SVDiscovery - Clustering: Generating clusters for > 29 read pairs. > INFO 18:03:09,253 SVDiscovery - Processing cluster > chr06:19487235-19487648 chr06:19487750-19488179 LR 71 > [GC 1885898K->1481505K(1976960K), 0.0271590 secs] > INFO 18:03:11,443 SVDiscovery - Clustering: Generating clusters for > 2242 read pairs. > INFO 18:03:11,447 SVDiscovery - Processing cluster > chr06:19491405-19491795 chr06:19491950-19492233 LR 29 > INFO 18:03:14,039 SVDiscovery - Clustering: Generating clusters for > 38 read pairs. > INFO 18:03:14,039 SVDiscovery - Processing cluster > chr06:19494543-19494998 chr06:19495229-19495651 LR 2242 > INFO 18:03:21,277 SVDiscovery - Clustering: Generating clusters for > 18 read pairs. > INFO 18:03:21,278 SVDiscovery - Processing cluster > chr06:19496317-19496648 chr06:19497509-19497827 LR 38 > INFO 18:03:23,408 SVDiscovery - Clustering: Generating clusters for > 55 read pairs. > INFO 18:03:23,408 SVDiscovery - Processing cluster > chr06:19498084-19498232 chr06:19498470-19498540 LR 18 > INFO 18:03:26,501 SVDiscovery - Clustering: Generating clusters for > 26 read pairs. > INFO 18:03:26,501 SVDiscovery - Processing cluster > chr06:19498190-19498545 chr06:19499094-19499431 LR 55 > INFO 18:03:28,669 SVDiscovery - Clustering: Generating clusters for > 37 read pairs. > INFO 18:03:28,670 SVDiscovery - Clustering: LR split size 37 / 37 > maximal clique size 35 clique count 1 > INFO 18:03:28,670 SVDiscovery - Processing cluster > chr06:19498703-19499092 chr06:19555751-19556165 LR 26 > INFO 18:03:31,080 SVDiscovery - Clustering: Generating clusters for > 448 read pairs. > INFO 18:03:31,081 SVDiscovery - Processing cluster > chr06:19499200-19499561 chr06:19500107-19500495 LR 35 > INFO 18:03:33,336 SVDiscovery - Clustering: Generating clusters for 6 > read pairs. > INFO 18:03:33,336 SVDiscovery - Processing cluster > chr06:19503888-19504073 chr06:19504474-19504672 LR 448 > [GC 1858707K->1476197K(1971200K), 0.0162020 secs] > [Full GC 1476197K->235694K(1971200K), 0.1011760 secs] > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.IllegalArgumentException: Read pair records have different > read groups: 588658: 561924SRR063635,998169SRR063658 > at org.broadinstitute.sv.util.ReadPair.create(ReadPair.java:120) > at > org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm.createReadPair(ReadPairClusteringAlgorithm.java:318) > at > org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm.loadReadPairs(ReadPairClusteringAlgorithm.java:572) > at > org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm.access$600(ReadPairClusteringAlgorithm.java:45) > at > org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm$ClusterIterator.advance(ReadPairClusteringAlgorithm.java:1170) > at > org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm$ClusterIterator.next(ReadPairClusteringAlgorithm.java:1123) > at > org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm$ClusterIterator.next(ReadPairClusteringAlgorithm.java:1096) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:337) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:192) > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:174) > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45) > at > org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:76) > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234) > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) > at > org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67) > at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): > ##### ERROR > ##### ERROR Please visit the 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: Read pair records have different read groups: > 588658: 561924SRR063635,998169SRR063658 > ##### ERROR > ------------------------------------------------------------------------------------------ > at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) > at > org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) > at > org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) > at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) > at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) > at > org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at > org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) > at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) > > > ------------------------------------------------------------------------------ > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. SALE $99.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122412 > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Wen Y. <yw...@gm...> - 2013-01-20 08:17:35
|
Hi Bob, I have been using genome-strip these days. I have fixed several errors with your kindly help. I encountered a new error recently. Here is the error messages: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I /home/wbxie/wild_rice/bwa_map/100.bam -I /home/wbxie/wild_rice/bwa_map/101.bam -I /home/wbxie/wild_rice/bwa_map/102.bam -I /home/wbxie/wild_rice/bwa_map/103.bam .........<truncated>.......... -I /home/wbxie/bam_file_MSUv7/W321.bam -I /home/wbxie/bam_file_MSUv7/W322.bam -I /home/wbxie/bam_file_MSUv7/W323.bam -I /home/wbxie/bam_file_MSUv7/W324.bam -I /home/wbxie/bam_file_MSUv7/W325.bam -I /home/wbxie/bam_file_MSUv7/W326.bam -I /home/wbxie/bam_file_MSUv7/W327.bam -I /home/wbxie/bam_file_MSUv7/W328.bam -I /home/wbxie/bam_file_MSUv7/W329.bam -I /home/wbxie/bam_file_MSUv7/W330.bam -O /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/P0008.discovery.vcf -md wild_rice_test2/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory wild_rice_test2 -genomeMaskFile data/rice_all_genomes_v7.mask.fasta -partitionName P0008 -filePrefix P0008 -L chr06:1-31248787 -searchLocus chr06:1-31248787 -searchWindow chr06:1-31248787 -searchMinimumSize 100 -searchMaximumSize 1000000 org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. Command line: sh /home/wbxie/software/svtoolkit/installtest/all_tmpdir/.exec1738692847535129737 Exit code: 1 Standard error contained: [GC 524288K->72586K(2009792K), 0.7542970 secs] INFO 15:53:17,194 HelpFormatter - ----------------------------------------------------------------------------------- INFO 15:53:17,215 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 INFO 15:53:17,217 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 15:53:17,218 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 15:53:17,219 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 15:53:17,221 HelpFormatter - Program Args: -T SVDiscovery -R /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -O /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/P0008.discovery.vcf -md wild_rice_test2/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory wild_rice_test2 -genomeMaskFile data/rice_all_genomes_v7.mask.fasta -partitionName P0008 -filePrefix P0008 -L chr06:1-31248787 -searchLocus chr06:1-31248787 -searchWindow chr06:1-31248787 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 15:53:17,223 HelpFormatter - Date/Time: 2012/11/10 15:53:17 INFO 15:53:17,224 HelpFormatter - ----------------------------------------------------------------------------------- INFO 15:53:17,225 HelpFormatter - ----------------------------------------------------------------------------------- INFO 15:53:17,414 GenomeAnalysisEngine - Strictness is SILENT INFO 15:53:19,702 SVDiscovery - Initializing SVDiscovery ... INFO 15:53:19,764 SVDiscovery - Opening reference sequence ... INFO 15:53:19,772 SVDiscovery - Opened reference sequence. INFO 15:53:19,773 SVDiscovery - Opening genome mask ... INFO 15:53:19,781 SVDiscovery - Opened genome mask. INFO 15:53:19,782 SVDiscovery - Initializing input data set ... [GC 596874K->78691K(2534080K), 0.8322460 secs] INFO 15:53:27,431 SVDiscovery - Initialized data set: 713 files, 811 read groups, 713 samples. INFO 15:53:27,432 SVDiscovery - Opening metadata from wild_rice_test2/metadata ... INFO 15:53:27,437 SVDiscovery - Opened metadata. INFO 15:53:27,444 SVDiscovery - Initializing discovery algorithm ... INFO 15:53:27,451 SVDiscovery - Loading insert size histograms ... [GC 1127267K->98598K(2534080K), 0.9073720 secs] [GC 1147174K->24483K(2708864K), 0.1410060 secs] [GC 1247843K->26795K(2637056K), 0.1760810 secs] INFO 15:54:32,991 SVDiscovery - Loaded 713 histograms. INFO 15:54:33,011 SVDiscovery - Discovery alt home filtering is disabled. INFO 15:54:38,649 SVDiscovery - Processing locus: chr06:1-31248787:100-1000000 INFO 15:54:38,650 SVDiscovery - Locus search window: chr06:1-31248787 INFO 15:54:38,651 SVDiscovery - Selecting read pairs ... INFO 15:54:38,665 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/100.bam ... [GC 1250155K->122384K(2632768K), 0.3954950 secs] [GC 1234768K->38536K(2653376K), 0.2583210 secs] INFO 15:55:02,373 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/101.bam ... [GC 1150920K->55080K(2641856K), 0.2100770 secs] [GC 1168232K->62044K(2648000K), 0.2142580 secs] [GC 1175196K->68624K(2655360K), 0.2988430 secs] INFO 15:55:35,214 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/102.bam ... [GC 1197840K->79312K(2658240K), 0.2794220 secs] [GC 1208528K->86788K(2660160K), 0.1888030 secs] INFO 15:56:05,021 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/103.bam ... [GC 1224900K->104476K(2663296K), 0.1776500 secs] [GC 1242588K->112492K(2664448K), 0.1901910 secs] ........<truncated>............ INFO 20:37:59,770 SVDiscovery - Reading input file /home/wbxie/bam_file_MSUv7/W329.bam ... [GC 2485525K->1119669K(2798528K), 0.2848940 secs] INFO 20:38:13,593 SVDiscovery - Reading input file /home/wbxie/bam_file_MSUv7/W330.bam ... [GC 2494325K->1125669K(2798528K), 0.0883570 secs] [GC 437423K->181927K(1772288K), 0.0068700 secs] #DBG: RC Cache fill chr06:1-110000 110000 713 124.640302 sec INFO 20:51:51,800 SVDiscovery - Clustering: Generating clusters for 3 read pairs. INFO 20:51:51,857 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 20:51:51,863 SVDiscovery - Clustering: Generating clusters for 27 read pairs. INFO 20:51:51,865 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 20:51:51,902 SVDiscovery - Clustering: Generating clusters for 3 read pairs. INFO 20:51:51,919 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 20:51:51,919 SVDiscovery - Processing cluster chr06:19014-19110 chr06:96702-96800 LR 3 [GC 435751K->182805K(1771008K), 0.0077180 secs] INFO 20:51:54,382 SVDiscovery - Clustering: Generating clusters for 7 read pairs. INFO 20:51:54,383 SVDiscovery - Clustering: LR split size 7 / 7 maximal clique size 4 clique count 1 ........<truncated>............ #DBG: RC Cache miss chr06:19217935-19684171 466237 713 93.022620 sec INFO 17:56:41,850 SVDiscovery - Clustering: Generating clusters for 7 read pairs. INFO 17:56:41,850 SVDiscovery - Processing cluster chr06:19220034-19220159 chr06:19221402-19221547 LR 8 INFO 17:56:43,322 SVDiscovery - Clustering: Generating clusters for 56 read pairs. INFO 17:56:43,322 SVDiscovery - Clustering: LR split size 56 / 56 maximal clique size 49 clique count 1 INFO 17:56:43,323 SVDiscovery - Clustering: LR split size 7 / 56 maximal clique size 2 clique count 4 INFO 17:56:43,323 SVDiscovery - Clustering: LR split size 5 / 56 maximal clique size 2 clique count 2 INFO 17:56:43,323 SVDiscovery - Clustering: LR split size 3 / 56 maximal clique size 2 clique count 1 INFO 17:56:43,330 SVDiscovery - Clustering: Generating clusters for 7 read pairs. INFO 17:56:43,332 SVDiscovery - Clustering: Generating clusters for 16 read pairs. INFO 17:56:43,332 SVDiscovery - Processing cluster chr06:19231617-19231729 chr06:19234427-19234538 LR 7 INFO 17:56:44,579 SVDiscovery - Clustering: Generating clusters for 47 read pairs. INFO 17:56:44,580 SVDiscovery - Processing cluster chr06:19241754-19242136 chr06:19242646-19243023 LR 16 INFO 17:56:45,946 SVDiscovery - Clustering: Generating clusters for 6 read pairs. INFO 17:56:45,946 SVDiscovery - Processing cluster chr06:19246397-19246741 chr06:19257339-19257677 LR 47 INFO 17:56:48,264 SVDiscovery - Clustering: Generating clusters for 61 read pairs. INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 61 / 61 maximal clique size 24 clique count 2 INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 37 / 61 maximal clique size 8 clique count 1 INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 29 / 61 maximal clique size 6 clique count 1 INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 23 / 61 maximal clique size 4 clique count 12 INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 19 / 61 maximal clique size 4 clique count 1 INFO 17:56:48,265 SVDiscovery - Clustering: LR split size 15 / 61 maximal clique size 3 clique count 1 INFO 17:56:48,266 SVDiscovery - Clustering: LR split size 12 / 61 maximal clique size 2 clique count 5 INFO 17:56:48,266 SVDiscovery - Clustering: LR split size 10 / 61 maximal clique size 2 clique count 3 INFO 17:56:48,266 SVDiscovery - Clustering: LR split size 8 / 61 maximal clique size 2 clique count 1 INFO 17:56:48,266 SVDiscovery - Clustering: LR split size 6 / 61 maximal clique size 1 clique count 7 INFO 17:56:48,266 SVDiscovery - Processing cluster chr06:19251412-19251521 chr06:19251687-19251798 LR 6 [GC 2142252K->1436452K(2264448K), 0.0112090 secs] ........<truncated>............ [GC 1890370K->1480970K(1981440K), 0.0178220 secs] #DBG: RC Cache fill chr06:19469143-19579142 110000 713 40.510878 sec INFO 18:03:09,242 SVDiscovery - Clustering: Generating clusters for 71 read pairs. INFO 18:03:09,252 SVDiscovery - Clustering: Generating clusters for 29 read pairs. INFO 18:03:09,253 SVDiscovery - Processing cluster chr06:19487235-19487648 chr06:19487750-19488179 LR 71 [GC 1885898K->1481505K(1976960K), 0.0271590 secs] INFO 18:03:11,443 SVDiscovery - Clustering: Generating clusters for 2242 read pairs. INFO 18:03:11,447 SVDiscovery - Processing cluster chr06:19491405-19491795 chr06:19491950-19492233 LR 29 INFO 18:03:14,039 SVDiscovery - Clustering: Generating clusters for 38 read pairs. INFO 18:03:14,039 SVDiscovery - Processing cluster chr06:19494543-19494998 chr06:19495229-19495651 LR 2242 INFO 18:03:21,277 SVDiscovery - Clustering: Generating clusters for 18 read pairs. INFO 18:03:21,278 SVDiscovery - Processing cluster chr06:19496317-19496648 chr06:19497509-19497827 LR 38 INFO 18:03:23,408 SVDiscovery - Clustering: Generating clusters for 55 read pairs. INFO 18:03:23,408 SVDiscovery - Processing cluster chr06:19498084-19498232 chr06:19498470-19498540 LR 18 INFO 18:03:26,501 SVDiscovery - Clustering: Generating clusters for 26 read pairs. INFO 18:03:26,501 SVDiscovery - Processing cluster chr06:19498190-19498545 chr06:19499094-19499431 LR 55 INFO 18:03:28,669 SVDiscovery - Clustering: Generating clusters for 37 read pairs. INFO 18:03:28,670 SVDiscovery - Clustering: LR split size 37 / 37 maximal clique size 35 clique count 1 INFO 18:03:28,670 SVDiscovery - Processing cluster chr06:19498703-19499092 chr06:19555751-19556165 LR 26 INFO 18:03:31,080 SVDiscovery - Clustering: Generating clusters for 448 read pairs. INFO 18:03:31,081 SVDiscovery - Processing cluster chr06:19499200-19499561 chr06:19500107-19500495 LR 35 INFO 18:03:33,336 SVDiscovery - Clustering: Generating clusters for 6 read pairs. INFO 18:03:33,336 SVDiscovery - Processing cluster chr06:19503888-19504073 chr06:19504474-19504672 LR 448 [GC 1858707K->1476197K(1971200K), 0.0162020 secs] [Full GC 1476197K->235694K(1971200K), 0.1011760 secs] ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.IllegalArgumentException: Read pair records have different read groups: 588658: 561924SRR063635,998169SRR063658 at org.broadinstitute.sv.util.ReadPair.create(ReadPair.java:120) at org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm.createReadPair(ReadPairClusteringAlgorithm.java:318) at org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm.loadReadPairs(ReadPairClusteringAlgorithm.java:572) at org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm.access$600(ReadPairClusteringAlgorithm.java:45) at org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm$ClusterIterator.advance(ReadPairClusteringAlgorithm.java:1170) at org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm$ClusterIterator.next(ReadPairClusteringAlgorithm.java:1123) at org.broadinstitute.sv.discovery.ReadPairClusteringAlgorithm$ClusterIterator.next(ReadPairClusteringAlgorithm.java:1096) at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:337) at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:192) at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:174) at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45) at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:76) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67) at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): ##### ERROR ##### ERROR Please visit the 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: Read pair records have different read groups: 588658: 561924SRR063635,998169SRR063658 ##### ERROR ------------------------------------------------------------------------------------------ at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) |
|
From: Bob H. <han...@br...> - 2013-01-09 18:43:25
|
It has been used with some success on non-human diploid organisms. But am I right that p. falciparum is haploid? That might actually be ok for the most part, but would require you to change some settings and look carefully at the results. If you're motivated and have good informatics skills I think it should be doable. I think you could set the diploid and haploid genome sizes in the configuration file to the same values, as a first step. You would also want to override the default filtering. In discovery, you would want to not use the membership test, since that assumes a diploid organism, but this filter is not very important. In genotyping, you would want to not use the inbreeding coefficient filter for the same reason. To do GC-bias correction, which is very useful, we currently use a mask to remove regions that may not be fixed ploidy in all samples. This doesn't have to be perfect, but it is good to remove known copy-number-polymorphic regions. Worst case, I might suggest masking nothing and doing gc-bias correction anyway (or trying with and without and seeing which way gives you tighter clusters in genotyping). So, it might be a bit of an adventure. But if you run into places where the code is assuming diploid, I can look into fixes for you. The good news is that it's a small genome, so the computational burden won't be so large, and homozygous deletions are much easier to detect. -Bob On 1/9/13 1:11 PM, Harold Ocholla wrote: > Hello, > > Can I use GenomeSTRIP to analyse non human data, for example plasmodium falciparum? > > Regards, Harold. > ------------------------------------------------------------------------------ > Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery > and much more. Keep your Java skills current with LearnJavaNow - > 200+ hours of step-by-step video tutorials by Java experts. > SALE $49.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122612 > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Harold O. <har...@gm...> - 2013-01-09 18:11:10
|
Hello, Can I use GenomeSTRIP to analyse non human data, for example plasmodium falciparum? Regards, Harold. |
|
From: Bob H. <han...@br...> - 2012-12-29 02:07:02
|
Hi, I think the root cause is not included in the listing below. It would be somewhere around the line that says <truncated>. I suggest looking in the log file which is /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/logs/Q-25077@cbsuwrkst3-1.out Hopefully a more informative error message will be present in the file. If you are running all of chr10 in one job, this may take a very long time, especially if you have many bam files. It would be better to run in smaller windows, say 3Mb with 10Kb overlap. -Bob On 12/28/12 8:44 AM, Margarida Cardoso Moreira wrote: > Dear Bob, > > I have tried to run SVDiscovery (builds 939 and 982) a few times unsuccessfully and from the ouput I cannot understand where the problem lies. I hope you can point me in the right direction. > > Thank you, > > Margarida > > NFO 18:09:51,476 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 18:09:51,476 FunctionEdge - Output written to /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/logs/Q-25077@cbsuwrkst3-1.out > ERROR 02:39:28,674 FunctionEdge - Error: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 > org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. > Command line: > sh /local/workdir/mmc256/TMPDIR/.exec1516894392817500268 > Exit code: 1 > Standard error contained: > [GC 96128K->13273K(368448K), 0.0192090 secs] > [GC 109401K->13738K(464576K), 0.0208630 secs] > [GC 205994K->14937K(464576K), 0.0188690 secs] > [GC 207193K->16321K(656832K), 0.0193450 secs] > [GC 400833K->6968K(656832K), 0.0083910 secs] > INFO 18:09:54,786 HelpFormatter - ----------------------------------------------------------------------------------- > INFO 18:09:54,788 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 > INFO 18:09:54,788 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 18:09:54,788 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki > INFO 18:09:54,788 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa > INFO 18:09:54,788 HelpFormatter - Program Args: -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 18:09:54,789 HelpFormatter - Date/Time: 2012/12/26 18:09:54 > INFO 18:09:54,789 HelpFormatter - ----------------------------------------------------------------------------------- > INFO 18:09:54,789 HelpFormatter - ----------------------------------------------------------------------------------- > INFO 18:09:54,808 GenomeAnalysisEngine - Strictness is SILENT > INFO 18:09:55,012 SVDiscovery - Initializing SVDiscovery ... > INFO 18:09:55,030 SVDiscovery - Opening reference sequence ... > INFO 18:09:55,031 SVDiscovery - Opened reference sequence. > INFO 18:09:55,031 SVDiscovery - Opening genome mask ... > INFO 18:09:55,031 SVDiscovery - Opened genome mask. > INFO 18:09:55,031 SVDiscovery - Initializing input data set ... > [GC 391480K->67565K(1014208K), 0.0361670 secs] > INFO 18:10:03,292 SVDiscovery - Initialized data set: 989 files, 1016 read groups, 989 samples. > INFO 18:10:03,292 SVDiscovery - Opening metadata from GenomeStrip/SVPreprocess.chr10.reheader/metadata ... > INFO 18:10:03,293 SVDiscovery - Opened metadata. > INFO 18:10:03,294 SVDiscovery - Initializing discovery algorithm ... > INFO 18:10:03,296 SVDiscovery - Loading insert size distributions ... > INFO 18:10:03,825 SVDiscovery - Loaded 1007 distributions. > INFO 18:10:03,827 SVDiscovery - Discovery alt home filtering is disabled. > [GC 806893K->217491K(1043904K), 0.0831660 secs] > INFO 18:10:05,154 SVDiscovery - Processing locus: 10:0-0:100-1000000 > INFO 18:10:05,155 SVDiscovery - Locus search window: 10:0-0 > INFO 18:10:05,155 SVDiscovery - Selecting read pairs ... > INFO 18:10:05,156 SVDiscovery - Reading input file chr10/A00120_D0DM2ACXX-1-ID03.10.bam ... > [GC 956819K->312712K(1466048K), 0.0679270 secs] > [Full GC 312712K->148645K(1547456K), 0.1027800 secs] > > > Then it goes through the 990 bams and then the following output: > > [GC 2155745K->1482913K(3462144K), 0.0066560 secs] > INFO 06:07:21,812 SVDiscovery - Processing clusters ... > INFO 06:07:22,189 SVDiscovery - Initializing memory-mapped read count caching > INFO 06:07:22,193 SVDiscovery - No hapmap snp genotype directory specified > INFO 06:07:22,194 SVDiscovery - No array intensity data specified > [GC 2148769K->1486917K(3455296K), 0.0150400 secs] > [GC 2145925K->1487797K(3448576K), 0.0082620 secs] > [GC 2140085K->1488453K(3443584K), 0.0124010 secs] > > ... > > [GC 2392741K->1630997K(3551424K), 0.0155810 secs] > INFO 06:21:53,398 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 06:21:53,427 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 06:21:53,427 SVDiscovery - Processing cluster 10:61557-61673 10:62417-62541 LR 2 > [GC 2384853K->1641320K(3543168K), 0.0100730 secs] > [GC 2386600K->1650590K(3533504K), 0.0068270 secs] > [GC 2387486K->1661004K(3530304K), 0.0066540 secs] > [GC 2389708K->1666093K(3521920K), 0.0093920 secs] > [GC 2386733K->1671487K(3515904K), 0.0189450 secs] > [GC 2384255K->1674895K(3503168K), 0.0155220 secs] > [GC 2379919K->1682929K(3501376K), 0.0104000 secs] > [GC 2380337K->1685314K(3492096K), 0.0103700 secs] > [GC 2375298K->1689139K(3488256K), 0.0108180 secs] > [GC 2371827K->1689491K(3475264K), 0.0102240 secs] > [GC 2365011K->1695845K(3474560K), 0.0104230 secs] > [GC 2364325K->1696679K(3465216K), 0.0121330 secs] > [GC 2358247K->1698277K(3460032K), 0.0158710 secs] > [GC 2353061K->1699349K(3452160K), 0.0100870 secs] > #DBG: RC Cache fill 10:51674-161673 110000 989 210.149950 sec > INFO 06:25:32,081 SVDiscovery - Clustering: Generating clusters for 4 read pairs. > INFO 06:25:32,081 SVDiscovery - Processing cluster 10:95107-95253 10:95944-96119 LR 2 > INFO 06:25:34,182 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 06:25:34,182 SVDiscovery - Processing cluster 10:95824-96088 10:96537-96746 LR 4 > [GC 2347477K->1699105K(3445312K), 0.0178790 secs] > > ... > > [GC 2785507K->2065539K(3522944K), 0.0182860 secs] > INFO 10:42:07,666 SVDiscovery - Clustering: Generating clusters for 4 read pairs. > INFO 10:42:07,666 SVDiscovery - Clustering: LR split size 4 / 4 maximal clique size 1 clique count 9 > INFO 10:42:07,699 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 10:42:07,699 SVDiscovery - Processing cluster 10:4740080-4740244 10:4740705-4740871 LR 2 > INFO 10:42:09,696 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 10:42:09,696 SVDiscovery - Processing cluster 10:4741548-4741760 10:4742231-4742493 LR 2 > INFO 10:42:11,686 SVDiscovery - Clustering: Generating clusters for 5 read pairs. > INFO 10:42:11,686 SVDiscovery - Processing cluster 10:4742734-4742838 10:4743410-4743518 LR 2 > INFO 10:42:13,690 SVDiscovery - Clustering: Generating clusters for 3 read pairs. > INFO 10:42:13,6 > > <truncated> > at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) > at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) > at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) > at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) > at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) > at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) > at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) > at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) > INFO 02:39:37,731 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done > INFO 02:39:38,253 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done > INFO 02:39:38,264 QCommandLine - Done with errors > INFO 02:39:38,406 QGraph - ------- > INFO 02:39:38,653 QGraph - Failed: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 02:39:38,653 QGraph - Log: /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/logs/Q-25077@cbsuwrkst3-1.out > > > > ------------------------------------------------------------------------------ > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and > much more. Get web development skills now with LearnDevNow - > 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. > SALE $99.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122812 > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Margarida C. M. <mm...@co...> - 2012-12-28 16:45:09
|
Dear Bob, I have tried to run SVDiscovery (builds 939 and 982) a few times unsuccessfully and from the ouput I cannot understand where the problem lies. I hope you can point me in the right direction. Thank you, Margarida NFO 18:09:51,476 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 18:09:51,476 FunctionEdge - Output written to /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/logs/Q-25077@cbsuwrkst3-1.out ERROR 02:39:28,674 FunctionEdge - Error: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. Command line: sh /local/workdir/mmc256/TMPDIR/.exec1516894392817500268 Exit code: 1 Standard error contained: [GC 96128K->13273K(368448K), 0.0192090 secs] [GC 109401K->13738K(464576K), 0.0208630 secs] [GC 205994K->14937K(464576K), 0.0188690 secs] [GC 207193K->16321K(656832K), 0.0193450 secs] [GC 400833K->6968K(656832K), 0.0083910 secs] INFO 18:09:54,786 HelpFormatter - ----------------------------------------------------------------------------------- INFO 18:09:54,788 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 INFO 18:09:54,788 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 18:09:54,788 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 18:09:54,788 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 18:09:54,788 HelpFormatter - Program Args: -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 18:09:54,789 HelpFormatter - Date/Time: 2012/12/26 18:09:54 INFO 18:09:54,789 HelpFormatter - ----------------------------------------------------------------------------------- INFO 18:09:54,789 HelpFormatter - ----------------------------------------------------------------------------------- INFO 18:09:54,808 GenomeAnalysisEngine - Strictness is SILENT INFO 18:09:55,012 SVDiscovery - Initializing SVDiscovery ... INFO 18:09:55,030 SVDiscovery - Opening reference sequence ... INFO 18:09:55,031 SVDiscovery - Opened reference sequence. INFO 18:09:55,031 SVDiscovery - Opening genome mask ... INFO 18:09:55,031 SVDiscovery - Opened genome mask. INFO 18:09:55,031 SVDiscovery - Initializing input data set ... [GC 391480K->67565K(1014208K), 0.0361670 secs] INFO 18:10:03,292 SVDiscovery - Initialized data set: 989 files, 1016 read groups, 989 samples. INFO 18:10:03,292 SVDiscovery - Opening metadata from GenomeStrip/SVPreprocess.chr10.reheader/metadata ... INFO 18:10:03,293 SVDiscovery - Opened metadata. INFO 18:10:03,294 SVDiscovery - Initializing discovery algorithm ... INFO 18:10:03,296 SVDiscovery - Loading insert size distributions ... INFO 18:10:03,825 SVDiscovery - Loaded 1007 distributions. INFO 18:10:03,827 SVDiscovery - Discovery alt home filtering is disabled. [GC 806893K->217491K(1043904K), 0.0831660 secs] INFO 18:10:05,154 SVDiscovery - Processing locus: 10:0-0:100-1000000 INFO 18:10:05,155 SVDiscovery - Locus search window: 10:0-0 INFO 18:10:05,155 SVDiscovery - Selecting read pairs ... INFO 18:10:05,156 SVDiscovery - Reading input file chr10/A00120_D0DM2ACXX-1-ID03.10.bam ... [GC 956819K->312712K(1466048K), 0.0679270 secs] [Full GC 312712K->148645K(1547456K), 0.1027800 secs] Then it goes through the 990 bams and then the following output: [GC 2155745K->1482913K(3462144K), 0.0066560 secs] INFO 06:07:21,812 SVDiscovery - Processing clusters ... INFO 06:07:22,189 SVDiscovery - Initializing memory-mapped read count caching INFO 06:07:22,193 SVDiscovery - No hapmap snp genotype directory specified INFO 06:07:22,194 SVDiscovery - No array intensity data specified [GC 2148769K->1486917K(3455296K), 0.0150400 secs] [GC 2145925K->1487797K(3448576K), 0.0082620 secs] [GC 2140085K->1488453K(3443584K), 0.0124010 secs] ... [GC 2392741K->1630997K(3551424K), 0.0155810 secs] INFO 06:21:53,398 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 06:21:53,427 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 06:21:53,427 SVDiscovery - Processing cluster 10:61557-61673 10:62417-62541 LR 2 [GC 2384853K->1641320K(3543168K), 0.0100730 secs] [GC 2386600K->1650590K(3533504K), 0.0068270 secs] [GC 2387486K->1661004K(3530304K), 0.0066540 secs] [GC 2389708K->1666093K(3521920K), 0.0093920 secs] [GC 2386733K->1671487K(3515904K), 0.0189450 secs] [GC 2384255K->1674895K(3503168K), 0.0155220 secs] [GC 2379919K->1682929K(3501376K), 0.0104000 secs] [GC 2380337K->1685314K(3492096K), 0.0103700 secs] [GC 2375298K->1689139K(3488256K), 0.0108180 secs] [GC 2371827K->1689491K(3475264K), 0.0102240 secs] [GC 2365011K->1695845K(3474560K), 0.0104230 secs] [GC 2364325K->1696679K(3465216K), 0.0121330 secs] [GC 2358247K->1698277K(3460032K), 0.0158710 secs] [GC 2353061K->1699349K(3452160K), 0.0100870 secs] #DBG: RC Cache fill 10:51674-161673 110000 989 210.149950 sec INFO 06:25:32,081 SVDiscovery - Clustering: Generating clusters for 4 read pairs. INFO 06:25:32,081 SVDiscovery - Processing cluster 10:95107-95253 10:95944-96119 LR 2 INFO 06:25:34,182 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 06:25:34,182 SVDiscovery - Processing cluster 10:95824-96088 10:96537-96746 LR 4 [GC 2347477K->1699105K(3445312K), 0.0178790 secs] ... [GC 2785507K->2065539K(3522944K), 0.0182860 secs] INFO 10:42:07,666 SVDiscovery - Clustering: Generating clusters for 4 read pairs. INFO 10:42:07,666 SVDiscovery - Clustering: LR split size 4 / 4 maximal clique size 1 clique count 9 INFO 10:42:07,699 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 10:42:07,699 SVDiscovery - Processing cluster 10:4740080-4740244 10:4740705-4740871 LR 2 INFO 10:42:09,696 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 10:42:09,696 SVDiscovery - Processing cluster 10:4741548-4741760 10:4742231-4742493 LR 2 INFO 10:42:11,686 SVDiscovery - Clustering: Generating clusters for 5 read pairs. INFO 10:42:11,686 SVDiscovery - Processing cluster 10:4742734-4742838 10:4743410-4743518 LR 2 INFO 10:42:13,690 SVDiscovery - Clustering: Generating clusters for 3 read pairs. INFO 10:42:13,6 <truncated> at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) INFO 02:39:37,731 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done INFO 02:39:38,253 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done INFO 02:39:38,264 QCommandLine - Done with errors INFO 02:39:38,406 QGraph - ------- INFO 02:39:38,653 QGraph - Failed: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 02:39:38,653 QGraph - Log: /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/logs/Q-25077@cbsuwrkst3-1.out |
|
From: Bob H. <han...@br...> - 2012-12-21 16:08:38
|
I don't know if this is the only problem, but it looks like you are using hg19 as the reference but using a genome mask built for the g1k_v37 reference. References must match exactly but this isn't always checked in the code. You need to make sure that (a) your bams are aligned against the reference you specify (b) the genome mask you are using is built for the same reference (c) you update your config file with the appropriate genome sizes based on your reference and mask (for more details, see notes in this presentation: http://www.broadinstitute.org/files/shared/mpg/nextgen2011/nextgen2011_handsaker.pdf) -Bob On 12/21/12 3:22 AM, Shu Mei Teo wrote: > I ran this with no ERROR message: > java -Xmx2g -cp Queue.jar:SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.queue.QCommandLine -S > /hpctmp/svtoolkit/qscript/SVPreprocess.q -S > /hpctmp/svtoolkit/qscript/SVQScript.q -gatk GenomeAnalysisTK.jar -cp > SVToolkit.jar:GenomeAnalysisTK.jar -configFile > /hpctmp/svtoolkit/conf/conf/genstrip_parameters.txt -tempDir > /hpctmp/shumei/tempdir -md /hpctmp/shumei/svprocess_out -R > /hpctmp/shumei/refhg19/ucsc.hg19.fasta -genomeMaskFile > /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -genderMapFile > /home/svu/ephtsm/sample.map -I > /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -I > /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -run -bsub -jobQueue > atlas7_parallel -jobProject lsf_project -jobLogDir /hpctmp/shumei/logs > INFO 16:32:28,661 QScriptManager - Compiling 2 QScripts INFO > 16:32:34,003 QScriptManager - Compilation complete INFO 16:32:36,690 > HelpFormatter - > --------------------------------------------------------- INFO > 16:32:36,691 HelpFormatter - Program Name: > org.broadinstitute.sting.queue.QCommandLine INFO 16:32:36,691 > HelpFormatter - Program Args: -S > /hpctmp/svtoolkit/qscript/SVPreprocess.q -S > /hpctmp/svtoolkit/qscript/SVQScript.q -gatk GenomeAnalysisTK.jar -cp > SVToolkit.jar:GenomeAnalysisTK.jar -configFile > /hpctmp/svtoolkit/conf/conf/genstrip_parameters.txt -tempDir > /hpctmp/shumei/tempdir -md /hpctmp/shumei/svprocess_out -R > /hpctmp/shumei/refhg19/ucsc.hg19.fasta -genomeMaskFile > /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -genderMapFile > /home/svu/ephtsm/sample.map -I > /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -I > /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -run -bsub -jobQueue > atlas7_parallel -jobProject lsf_project -jobLogDir /hpctmp/shumei/logs > INFO 16:32:36,692 HelpFormatter - Date/Time: 2012/12/20 16:32:36 INFO > 16:32:36,692 HelpFormatter - > --------------------------------------------------------- INFO > 16:32:36,693 HelpFormatter - ------------------------- > -------------------------------- INFO 16:32:36,695 QCommandLine - > Scripting SVPreprocess INFO 16:32:36,824 QCommandLine - Added 10 > functions INFO 16:32:36,825 QGraph - Generating graph. INFO > 16:32:36,861 QGraph - Generating scatter gather jobs. INFO > 16:32:36,863 QGraph - Removing original jobs. INFO 16:32:36,865 QGraph > - Adding scatter gather jobs. INFO 16:32:36,865 QGraph - Regenerating > graph. INFO 16:32:36,887 QGraph - Running jobs. INFO 16:32:37,077 > Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeInsertSizeDistributions -R > /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -md > /hpctmp/shumei/svprocess_out -createEmpty > INFO 16:32:37,263 Lsf706JobRunner - Submitted LSF job id: 9048 INFO > 16:32:37,306 Lsf706Jo bRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeInsertSizeDistributions -R > /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -md > /hpctmp/shumei/svprocess_out -createEmpty > INFO 16:32:37,467 Lsf706JobRunner - Submitted LSF job id: 9049 INFO > 16:32:37,495 Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt > -md /hpctmp/shumei/svprocess_out -genomeMaskFile > /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16 > :32:37,611 Lsf706JobRunner - Submitted LSF job id: 9050 INFO > 16:32:37,640 Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt > -md /hpctmp/shumei/svprocess_out -genomeMaskFile > /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO > 16:32:37,801 Lsf706JobRunner - Submitted LSF job id: 9051 INFO > 16:39:11,177 Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.de > dup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile > /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO > 16:39:41,314 Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeInsertSizeDistributions -R > /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -md > /hpctmp/shumei/svprocess_out -createEmpty > INFO 16:39:41,386 Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeInsertSizeDistributions -R > /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -md > /hpctmp/shumei/svprocess_ou t -createEmpty > INFO 16:39:41,448 Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt > -md /hpctmp/shumei/svprocess_out -genomeMaskFile > /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO > 16:39:41,453 Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I > /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -I > /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -O > /hpctmp/shumei/svprocess_out/isd.hist.bin INFO 16:39:41,676 > Lsf706JobRunner - Submitted LSF job id: 9064 INFO 16:39:41,7 06 > Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sv.apps.MergeReadDepthCoverage -I > /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt > -I > /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt > -O /hpctmp/shumei/svprocess_out/depth.dat INFO 16:39:41,927 > Lsf706JobRunner - Submitted LSF job id: 9065 INFO 16:40:12,185 > Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I > /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -I > /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -O > /hpctmp/shumei/svprocess_out/isd.hist.bin INFO 16:40:12,215 > Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv > .apps.MergeReadDepthCoverage -I > /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt > -I > /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt > -O /hpctmp/shumei/svprocess_out/depth.dat INFO 16:40:12,219 > Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sv.apps.ComputeInsertStatistics -I > /hpctmp/shumei/svprocess_out/isd.hist.bin -O > /hpctmp/shumei/svprocess_out/isd.stats.dat INFO 16:40:13,471 > Lsf706JobRunner - Submitted LSF job id: 9066 INFO 16:40:13,552 > Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt > -md /hpctmp/shumei/svp rocess_out -maxInsertSizeStandardDeviations 3 > INFO 16:40:13,702 Lsf706JobRunner - Submitted LSF job id: 9067 INFO > 16:40:13,732 Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt > -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 > INFO 16:40:13,856 Lsf706JobRunner - Submitted LSF job id: 9068 INFO > 16:41:14,669 Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sv.apps.ComputeInsertStatistics -I > /hpctmp/shumei/svprocess_out/isd.hist.bin -O > /hpctmp/shumei/svprocess_out/isd.stats.dat INFO 16:45:46,258 > Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmp > dir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt > -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 > INFO 16:46:16,342 Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I > /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O > /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt > -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 > INFO 16:46:16,346 Lsf706JobRunner - Starting: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar org.broadinst > itute.sv.apps.MergeReadSpanCoverage -I > /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt > -I > /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt > -O /hpctmp/shumei/svprocess_out/spans.dat INFO 16:46:17,273 > Lsf706JobRunner - Submitted LSF job id: 9074 INFO 16:46:47,967 > Lsf706JobRunner - Done: bsub java -Xmx4g > -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp > SVToolkit.jar:GenomeAnalysisTK.jar > org.broadinstitute.sv.apps.MergeReadSpanCoverage -I > /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt > -I > /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt > -O /hpctmp/shumei/svprocess_out/spans.dat INFO 16:46:47,971 QGraph - > Deleting intermediate files. INFO 16:46:47,977 QCommandLine - Done > > But yet depth.dat has no output > more depth.dat > SAMPLE LIBRARY READGROUP COUNT > > What could be the reason? The bam files have been indexed and > recalibrated following GATK best practices. Because there is no error > message, I am not sure how to start troubleshooting what could have > gone wrong. > Hope to receive some help here! > > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Shu M. T. <shu...@ho...> - 2012-12-21 08:22:24
|
I ran this with no ERROR message: java -Xmx2g -cp Queue.jar:SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.queue.QCommandLine -S /hpctmp/svtoolkit/qscript/SVPreprocess.q -S /hpctmp/svtoolkit/qscript/SVQScript.q -gatk GenomeAnalysisTK.jar -cp SVToolkit.jar:GenomeAnalysisTK.jar -configFile /hpctmp/svtoolkit/conf/conf/genstrip_parameters.txt -tempDir /hpctmp/shumei/tempdir -md /hpctmp/shumei/svprocess_out -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -genderMapFile /home/svu/ephtsm/sample.map -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -run -bsub -jobQueue atlas7_parallel -jobProject lsf_project -jobLogDir /hpctmp/shumei/logs INFO 16:32:28,661 QScriptManager - Compiling 2 QScripts INFO 16:32:34,003 QScriptManager - Compilation complete INFO 16:32:36,690 HelpFormatter - --------------------------------------------------------- INFO 16:32:36,691 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 16:32:36,691 HelpFormatter - Program Args: -S /hpctmp/svtoolkit/qscript/SVPreprocess.q -S /hpctmp/svtoolkit/qscript/SVQScript.q -gatk GenomeAnalysisTK.jar -cp SVToolkit.jar:GenomeAnalysisTK.jar -configFile /hpctmp/svtoolkit/conf/conf/genstrip_parameters.txt -tempDir /hpctmp/shumei/tempdir -md /hpctmp/shumei/svprocess_out -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -genderMapFile /home/svu/ephtsm/sample.map -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -run -bsub -jobQueue atlas7_parallel -jobProject lsf_project -jobLogDir /hpctmp/shumei/logs INFO 16:32:36,692 HelpFormatter - Date/Time: 2012/12/20 16:32:36 INFO 16:32:36,692 HelpFormatter - --------------------------------------------------------- INFO 16:32:36,693 HelpFormatter - --------------------------------------------------------- INFO 16:32:36,695 QCommandLine - Scripting SVPreprocess INFO 16:32:36,824 QCommandLine - Added 10 functions INFO 16:32:36,825 QGraph - Generating graph. INFO 16:32:36,861 QGraph - Generating scatter gather jobs. INFO 16:32:36,863 QGraph - Removing original jobs. INFO 16:32:36,865 QGraph - Adding scatter gather jobs. INFO 16:32:36,865 QGraph - Regenerating graph. INFO 16:32:36,887 QGraph - Running jobs. INFO 16:32:37,077 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -md /hpctmp/shumei/svprocess_out -createEmpty INFO 16:32:37,263 Lsf706JobRunner - Submitted LSF job id: 9048 INFO 16:32:37,306 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -md /hpctmp/shumei/svprocess_out -createEmpty INFO 16:32:37,467 Lsf706JobRunner - Submitted LSF job id: 9049 INFO 16:32:37,495 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16:32:37,611 Lsf706JobRunner - Submitted LSF job id: 9050 INFO 16:32:37,640 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16:32:37,801 Lsf706JobRunner - Submitted LSF job id: 9051 INFO 16:39:11,177 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16:39:41,314 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -md /hpctmp/shumei/svprocess_out -createEmpty INFO 16:39:41,386 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -md /hpctmp/shumei/svprocess_out -createEmpty INFO 16:39:41,448 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16:39:41,453 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -I /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -O /hpctmp/shumei/svprocess_out/isd.hist.bin INFO 16:39:41,676 Lsf706JobRunner - Submitted LSF job id: 9064 INFO 16:39:41,706 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeReadDepthCoverage -I /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt -I /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt -O /hpctmp/shumei/svprocess_out/depth.dat INFO 16:39:41,927 Lsf706JobRunner - Submitted LSF job id: 9065 INFO 16:40:12,185 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -I /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -O /hpctmp/shumei/svprocess_out/isd.hist.bin INFO 16:40:12,215 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeReadDepthCoverage -I /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt -I /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt -O /hpctmp/shumei/svprocess_out/depth.dat INFO 16:40:12,219 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.ComputeInsertStatistics -I /hpctmp/shumei/svprocess_out/isd.hist.bin -O /hpctmp/shumei/svprocess_out/isd.stats.dat INFO 16:40:13,471 Lsf706JobRunner - Submitted LSF job id: 9066 INFO 16:40:13,552 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 INFO 16:40:13,702 Lsf706JobRunner - Submitted LSF job id: 9067 INFO 16:40:13,732 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 INFO 16:40:13,856 Lsf706JobRunner - Submitted LSF job id: 9068 INFO 16:41:14,669 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.ComputeInsertStatistics -I /hpctmp/shumei/svprocess_out/isd.hist.bin -O /hpctmp/shumei/svprocess_out/isd.stats.dat INFO 16:45:46,258 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 INFO 16:46:16,342 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 INFO 16:46:16,346 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeReadSpanCoverage -I /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt -I /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt -O /hpctmp/shumei/svprocess_out/spans.dat INFO 16:46:17,273 Lsf706JobRunner - Submitted LSF job id: 9074 INFO 16:46:47,967 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeReadSpanCoverage -I /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt -I /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt -O /hpctmp/shumei/svprocess_out/spans.dat INFO 16:46:47,971 QGraph - Deleting intermediate files. INFO 16:46:47,977 QCommandLine - Done But yet depth.dat has no output more depth.dat SAMPLE LIBRARY READGROUP COUNT What could be the reason? The bam files have been indexed and recalibrated following GATK best practices. Because there is no error message, I am not sure how to start troubleshooting what could have gone wrong.Hope to receive some help here! |
|
From: Bob H. <han...@br...> - 2012-11-03 21:44:41
|
It looks like you included bam 100.bam twice in the input list. This is then (I suspect) detected as two read pairs with the same read name, which is not supported. -Bob On 11/1/12 8:30 PM, yw wrote: > Hi there, > I have been tried to run Genome-STRIP with my data these days. I believe > I have successfully installed the software. The install test was okay. > And I tried with 30 BAM files and got the results. However, When I came > to more BAM files, something went wrong. > I can't figure out what is wrong with my BAM files. Anyone has any > suggestions? Thx. > > Here is the error message: > > java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir > -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R > /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I > /home/wbxie/wild_rice/bwa_map/100.bam -I > /home/wbxie/wild_rice/bwa_map/100.bam -I > /home/wbxie/wild_rice/bwa_map/101.bam -I > [snip] |
|
From: yw <yw...@gm...> - 2012-11-02 03:30:06
|
Hi there, I have been tried to run Genome-STRIP with my data these days. I believe I have successfully installed the software. The install test was okay. And I tried with 30 BAM files and got the results. However, When I came to more BAM files, something went wrong. I can't figure out what is wrong with my BAM files. Anyone has any suggestions? Thx. Here is the error message: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I /home/wbxie/wild_rice/bwa_map/100.bam -I /home/wbxie/wild_rice/bwa_map/100.bam -I /home/wbxie/wild_rice/bwa_map/101.bam -I /home/wbxie/wild_rice/bwa_map/102.bam -I /home/wbxie/wild_rice/bwa_map/103.bam -I /home/wbxie/wild_rice/bwa_map/104.bam -I /home/wbxie/wild_rice/bwa_map/105.bam -I /home/wbxie/wild_rice/bwa_map/106.bam -I /home/wbxie/wild_rice/bwa_map/107.bam -I /home/wbxie/wild_rice/bwa_map/108.bam -I /home/wbxie/wild_rice/bwa_map/109.bam -I /home/wbxie/wild_rice/bwa_map/10.bam -I /home/wbxie/wild_rice/bwa_map/110.bam -I /home/wbxie/wild_rice/bwa_map/111.bam -I /home/wbxie/wild_rice/bwa_map/112.bam -I /home/wbxie/wild_rice/bwa_map/113.bam -I /home/wbxie/wild_rice/bwa_map/114.bam -I /home/wbxie/wild_rice/bwa_map/115.bam -I /home/wbxie/wild_rice/bwa_map/116.bam -I /home/wbxie/wild_rice/bwa_map/117.bam -I /home/wbxie/wild_rice/bwa_map/118.bam -I /home/wbxie/wild_rice/bwa_map/119.bam -I /home/wbxie/wild_rice/bwa_map/11.bam -I /home/wbxie/wild_rice/bwa_map/120.bam -I /home/wbxie/wild_rice/bwa_map/121.bam -I /home/wbxie/wild_rice/bwa_map/122.bam -I /home/wbxie/wild_rice/bwa_map/123.bam -I /home/wbxie/wild_rice/bwa_map/124.bam -I /home/wbxie/wild_rice/bwa_map/125.bam -I /home/wbxie/wild_rice/bwa_map/126.bam -I /home/wbxie/wild_rice/bwa_map/127.bam -I /home/wbxie/wild_rice/bwa_map/128.bam -I /home/wbxie/wild_rice/bwa_map/129.bam -I /home/wbxie/wild_rice/bwa_map/12.bam -I /home/wbxie/wild_rice/bwa_map/130.bam -I /home/wbxie/wild_rice/bwa_map/132.bam -I /home/wbxie/wild_rice/bwa_map/133.bam -I /home/wbxie/wild_rice/bwa_map/134.bam -I /home/wbxie/wild_rice/bwa_map/135.bam -I /home/wbxie/wild_rice/bwa_map/13.bam -I /home/wbxie/wild_rice/bwa_map/14.bam -I /home/wbxie/wild_rice/bwa_map/15.bam -I /home/wbxie/wild_rice/bwa_map/16.bam -I /home/wbxie/wild_rice/bwa_map/17.bam -I /home/wbxie/wild_rice/bwa_map/18.bam -I /home/wbxie/wild_rice/bwa_map/19.bam -I /home/wbxie/wild_rice/bwa_map/1.bam -I /home/wbxie/wild_rice/bwa_map/20.bam -I /home/wbxie/wild_rice/bwa_map/21.bam -I /home/wbxie/wild_rice/bwa_map/22.bam -I /home/wbxie/wild_rice/bwa_map/23.bam -I /home/wbxie/wild_rice/bwa_map/24.bam -I /home/wbxie/wild_rice/bwa_map/25.bam -I /home/wbxie/wild_rice/bwa_map/26.bam -I /home/wbxie/wild_rice/bwa_map/27.bam -I /home/wbxie/wild_rice/bwa_map/28.bam -I /home/wbxie/wild_rice/bwa_map/29.bam -I /home/wbxie/wild_rice/bwa_map/2.bam -I /home/wbxie/wild_rice/bwa_map/30.bam -I /home/wbxie/wild_rice/bwa_map/31.bam -I /home/wbxie/wild_rice/bwa_map/32.bam -I /home/wbxie/wild_rice/bwa_map/33.bam -I /home/wbxie/wild_rice/bwa_map/34.bam -I /home/wbxie/wild_rice/bwa_map/35.bam -I /home/wbxie/wild_rice/bwa_map/36.bam -I /home/wbxie/wild_rice/bwa_map/37.bam -I /home/wbxie/wild_rice/bwa_map/38.bam -I /home/wbxie/wild_rice/bwa_map/39.bam -I /home/wbxie/wild_rice/bwa_map/3.bam -I /home/wbxie/wild_rice/bwa_map/40.bam -I /home/wbxie/wild_rice/bwa_map/41.bam -I /home/wbxie/wild_rice/bwa_map/42.bam -I /home/wbxie/wild_rice/bwa_map/43.bam -I /home/wbxie/wild_rice/bwa_map/44.bam -I /home/wbxie/wild_rice/bwa_map/45.bam -I /home/wbxie/wild_rice/bwa_map/46.bam -I /home/wbxie/wild_rice/bwa_map/47.bam -I /home/wbxie/wild_rice/bwa_map/48.bam -I /home/wbxie/wild_rice/bwa_map/49.bam -I /home/wbxie/wild_rice/bwa_map/4.bam -I /home/wbxie/wild_rice/bwa_map/50.bam -I /home/wbxie/wild_rice/bwa_map/51.bam -I /home/wbxie/wild_rice/bwa_map/52.bam -I /home/wbxie/wild_rice/bwa_map/53.bam -I /home/wbxie/wild_rice/bwa_map/54.bam -I /home/wbxie/wild_rice/bwa_map/55.bam -I /home/wbxie/wild_rice/bwa_map/56.bam -I /home/wbxie/wild_rice/bwa_map/57.bam -I /home/wbxie/wild_rice/bwa_map/58.bam -I /home/wbxie/wild_rice/bwa_map/59.bam -I /home/wbxie/wild_rice/bwa_map/5.bam -I /home/wbxie/wild_rice/bwa_map/60.bam -I /home/wbxie/wild_rice/bwa_map/61.bam -I /home/wbxie/wild_rice/bwa_map/62.bam -I /home/wbxie/wild_rice/bwa_map/63.bam -I /home/wbxie/wild_rice/bwa_map/64.bam -I /home/wbxie/wild_rice/bwa_map/65.bam -I /home/wbxie/wild_rice/bwa_map/66.bam -I /home/wbxie/wild_rice/bwa_map/67.bam -I /home/wbxie/wild_rice/bwa_map/68.bam -I /home/wbxie/wild_rice/bwa_map/69.bam -I /home/wbxie/wild_rice/bwa_map/6.bam -I /home/wbxie/wild_rice/bwa_map/70.bam -I /home/wbxie/wild_rice/bwa_map/71.bam -I /home/wbxie/wild_rice/bwa_map/72.bam -I /home/wbxie/wild_rice/bwa_map/73.bam -I /home/wbxie/wild_rice/bwa_map/74.bam -I /home/wbxie/wild_rice/bwa_map/75.bam -I /home/wbxie/wild_rice/bwa_map/76.bam -I /home/wbxie/wild_rice/bwa_map/77.bam -I /home/wbxie/wild_rice/bwa_map/78.bam -I /home/wbxie/wild_rice/bwa_map/79.bam -I /home/wbxie/wild_rice/bwa_map/7.bam -I /home/wbxie/wild_rice/bwa_map/80.bam -I /home/wbxie/wild_rice/bwa_map/81.bam -I /home/wbxie/wild_rice/bwa_map/83.bam -I /home/wbxie/wild_rice/bwa_map/84.bam -I /home/wbxie/wild_rice/bwa_map/85.bam -I /home/wbxie/wild_rice/bwa_map/86.bam -I /home/wbxie/wild_rice/bwa_map/87.bam -I /home/wbxie/wild_rice/bwa_map/88.bam -I /home/wbxie/wild_rice/bwa_map/89.bam -I /home/wbxie/wild_rice/bwa_map/8.bam -I /home/wbxie/wild_rice/bwa_map/90.bam -I /home/wbxie/wild_rice/bwa_map/91.bam -I /home/wbxie/wild_rice/bwa_map/92.bam -I /home/wbxie/wild_rice/bwa_map/93.bam -I /home/wbxie/wild_rice/bwa_map/94.bam -I /home/wbxie/wild_rice/bwa_map/95.bam -I /home/wbxie/wild_rice/bwa_map/96.bam -I /home/wbxie/wild_rice/bwa_map/97.bam -I /home/wbxie/wild_rice/bwa_map/98.bam -I /home/wbxie/wild_rice/bwa_map/99.bam -I /home/wbxie/wild_rice/bwa_map/9.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W01.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W02.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W03.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W04.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W05.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W06.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W07.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W08.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W09.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W10.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W11.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W12.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W13.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W14.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W15.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W16.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W17.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W18.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W19.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W20.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W21.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W22.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W23.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W24.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W25.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W26.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W27.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W28.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W29.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W30.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W31.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W32.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W33.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W34.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W35.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W36.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W37.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W38.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W39.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W40.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W41.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W42.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W43.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W44.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W45.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W46.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W47.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W48.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W49.bam -I /home/wbxie/wild_rice/wangwen/bwa_map/W50.bam -I /home/wbxie/bam_file_MSUv7/C001.bam -I /home/wbxie/bam_file_MSUv7/C002.bam -I /home/wbxie/bam_file_MSUv7/C003.bam -I /home/wbxie/bam_file_MSUv7/C004.bam -I /home/wbxie/bam_file_MSUv7/C005.bam -I /home/wbxie/bam_file_MSUv7/C006.bam -I /home/wbxie/bam_file_MSUv7/C007.bam -I /home/wbxie/bam_file_MSUv7/C008.bam -I /home/wbxie/bam_file_MSUv7/C009.bam -I /home/wbxie/bam_file_MSUv7/C010.bam -I /home/wbxie/bam_file_MSUv7/C011.bam -I /home/wbxie/bam_file_MSUv7/C012.bam -I /home/wbxie/bam_file_MSUv7/C013.bam -I /home/wbxie/bam_file_MSUv7/C014.bam -I /home/wbxie/bam_file_MSUv7/C015.bam -I /home/wbxie/bam_file_MSUv7/C016.bam -I /home/wbxie/bam_file_MSUv7/C017.bam -I /home/wbxie/bam_file_MSUv7/C018.bam -I /home/wbxie/bam_file_MSUv7/C019.bam -I /home/wbxie/bam_file_MSUv7/C020.bam -I /home/wbxie/bam_file_MSUv7/C021.bam -I /home/wbxie/bam_file_MSUv7/C022.bam -I /home/wbxie/bam_file_MSUv7/C023.bam -I /home/wbxie/bam_file_MSUv7/C024.bam -I /home/wbxie/bam_file_MSUv7/C025.bam -I /home/wbxie/bam_file_MSUv7/C026.bam -I /home/wbxie/bam_file_MSUv7/C027.bam -I /home/wbxie/bam_file_MSUv7/C028.bam -I /home/wbxie/bam_file_MSUv7/C029.bam -I /home/wbxie/bam_file_MSUv7/C030.bam -I /home/wbxie/bam_file_MSUv7/C031.bam -I /home/wbxie/bam_file_MSUv7/C032.bam -I /home/wbxie/bam_file_MSUv7/C033.bam -I /home/wbxie/bam_file_MSUv7/C034.bam -I /home/wbxie/bam_file_MSUv7/C035.bam -I /home/wbxie/bam_file_MSUv7/C036.bam -I /home/wbxie/bam_file_MSUv7/C037.bam -I /home/wbxie/bam_file_MSUv7/C038.bam -I /home/wbxie/bam_file_MSUv7/C039.bam -I /home/wbxie/bam_file_MSUv7/C040.bam -I /home/wbxie/bam_file_MSUv7/C041.bam -I /home/wbxie/bam_file_MSUv7/C042.bam -I /home/wbxie/bam_file_MSUv7/C043.bam -I /home/wbxie/bam_file_MSUv7/C044.bam -I /home/wbxie/bam_file_MSUv7/C045.bam -I /home/wbxie/bam_file_MSUv7/C046.bam -I /home/wbxie/bam_file_MSUv7/C047.bam -I /home/wbxie/bam_file_MSUv7/C048.bam -I /home/wbxie/bam_file_MSUv7/C049.bam -I /home/wbxie/bam_file_MSUv7/C050.bam -I /home/wbxie/bam_file_MSUv7/C051.bam -I /home/wbxie/bam_file_MSUv7/C052.bam -I /home/wbxie/bam_file_MSUv7/C053.bam -I /home/wbxie/bam_file_MSUv7/C054.bam -I /home/wbxie/bam_file_MSUv7/C055.bam -I /home/wbxie/bam_file_MSUv7/C056.bam -I /home/wbxie/bam_file_MSUv7/C057.bam -I /home/wbxie/bam_file_MSUv7/C058.bam -I /home/wbxie/bam_file_MSUv7/C059.bam -I /home/wbxie/bam_file_MSUv7/C060.bam -I /home/wbxie/bam_file_MSUv7/C061.bam -I /home/wbxie/bam_file_MSUv7/C062.bam -I /home/wbxie/bam_file_MSUv7/C063.bam -I /home/wbxie/bam_file_MSUv7/C064.bam -I /home/wbxie/bam_file_MSUv7/C065.bam -I /home/wbxie/bam_file_MSUv7/C066.bam -I /home/wbxie/bam_file_MSUv7/C067.bam -I /home/wbxie/bam_file_MSUv7/C068.bam -I /home/wbxie/bam_file_MSUv7/C069.bam -I /home/wbxie/bam_file_MSUv7/C070.bam -I /home/wbxie/bam_file_MSUv7/C071.bam -I /home/wbxie/bam_file_MSUv7/C072.bam -I /home/wbxie/bam_file_MSUv7/C073.bam -I /home/wbxie/bam_file_MSUv7/C074.bam -I /home/wbxie/bam_file_MSUv7/C075.bam -I /home/wbxie/bam_file_MSUv7/C076.bam -I /home/wbxie/bam_file_MSUv7/C077.bam -I /home/wbxie/bam_file_MSUv7/C078.bam -I /home/wbxie/bam_file_MSUv7/C079.bam -I /home/wbxie/bam_file_MSUv7/C080.bam -I /home/wbxie/bam_file_MSUv7/C081.bam -I /home/wbxie/bam_file_MSUv7/C082.bam -I /home/wbxie/bam_file_MSUv7/C083.bam -I /home/wbxie/bam_file_MSUv7/C084.bam -I /home/wbxie/bam_file_MSUv7/C085.bam -I /home/wbxie/bam_file_MSUv7/C086.bam -I /home/wbxie/bam_file_MSUv7/C087.bam -I /home/wbxie/bam_file_MSUv7/C088.bam -I /home/wbxie/bam_file_MSUv7/C089.bam -I /home/wbxie/bam_file_MSUv7/C090.bam -I /home/wbxie/bam_file_MSUv7/C091.bam -I /home/wbxie/bam_file_MSUv7/C092.bam -I /home/wbxie/bam_file_MSUv7/C093.bam -I /home/wbxie/bam_file_MSUv7/C094.bam -I /home/wbxie/bam_file_MSUv7/C095.bam -I /home/wbxie/bam_file_MSUv7/C096.bam -I /home/wbxie/bam_file_MSUv7/C097.bam -I /home/wbxie/bam_file_MSUv7/C098.bam -I /home/wbxie/bam_file_MSUv7/C099.bam -I /home/wbxie/bam_file_MSUv7/C100.bam -I /home/wbxie/bam_file_MSUv7/C101.bam -I /home/wbxie/bam_file_MSUv7/C102.bam -I /home/wbxie/bam_file_MSUv7/C103.bam -I /home/wbxie/bam_file_MSUv7/C104.bam -I /home/wbxie/bam_file_MSUv7/C105.bam -I /home/wbxie/bam_file_MSUv7/C106.bam -I /home/wbxie/bam_file_MSUv7/C107.bam -I /home/wbxie/bam_file_MSUv7/C108.bam -I /home/wbxie/bam_file_MSUv7/C109.bam -I /home/wbxie/bam_file_MSUv7/C110.bam -I /home/wbxie/bam_file_MSUv7/C111.bam -I /home/wbxie/bam_file_MSUv7/C112.bam -I /home/wbxie/bam_file_MSUv7/C113.bam -I /home/wbxie/bam_file_MSUv7/C114.bam -I /home/wbxie/bam_file_MSUv7/C115.bam -I /home/wbxie/bam_file_MSUv7/C116.bam -I /home/wbxie/bam_file_MSUv7/C117.bam -I /home/wbxie/bam_file_MSUv7/C118.bam -I /home/wbxie/bam_file_MSUv7/C119.bam -I /home/wbxie/bam_file_MSUv7/C120.bam -I /home/wbxie/bam_file_MSUv7/C121.bam -I /home/wbxie/bam_file_MSUv7/C122.bam -I /home/wbxie/bam_file_MSUv7/C123.bam -I /home/wbxie/bam_file_MSUv7/C124.bam -I /home/wbxie/bam_file_MSUv7/C125.bam -I /home/wbxie/bam_file_MSUv7/C127.bam -I /home/wbxie/bam_file_MSUv7/C128.bam -I /home/wbxie/bam_file_MSUv7/C129.bam -I /home/wbxie/bam_file_MSUv7/C130.bam -I /home/wbxie/bam_file_MSUv7/C131.bam -I /home/wbxie/bam_file_MSUv7/C132.bam -I /home/wbxie/bam_file_MSUv7/C133.bam -I /home/wbxie/bam_file_MSUv7/C134.bam -I /home/wbxie/bam_file_MSUv7/C135.bam -I /home/wbxie/bam_file_MSUv7/C136.bam -I /home/wbxie/bam_file_MSUv7/C137.bam -I /home/wbxie/bam_file_MSUv7/C138.bam -I /home/wbxie/bam_file_MSUv7/C139.bam -I /home/wbxie/bam_file_MSUv7/C140.bam -I /home/wbxie/bam_file_MSUv7/C141.bam -I /home/wbxie/bam_file_MSUv7/C142.bam -I /home/wbxie/bam_file_MSUv7/C143.bam -I /home/wbxie/bam_file_MSUv7/C144.bam -I /home/wbxie/bam_file_MSUv7/C145.bam -I /home/wbxie/bam_file_MSUv7/C146.bam -I /home/wbxie/bam_file_MSUv7/C147.bam -I /home/wbxie/bam_file_MSUv7/C148.bam -I /home/wbxie/bam_file_MSUv7/C149.bam -I /home/wbxie/bam_file_MSUv7/C150.bam -I /home/wbxie/bam_file_MSUv7/C151.bam -I /home/wbxie/bam_file_MSUv7/C152.bam -I /home/wbxie/bam_file_MSUv7/C153.bam -I /home/wbxie/bam_file_MSUv7/C154.bam -I /home/wbxie/bam_file_MSUv7/C155.bam -I /home/wbxie/bam_file_MSUv7/C156.bam -I /home/wbxie/bam_file_MSUv7/C157.bam -I /home/wbxie/bam_file_MSUv7/C158.bam -I /home/wbxie/bam_file_MSUv7/C159.bam -I /home/wbxie/bam_file_MSUv7/C160.bam -I /home/wbxie/bam_file_MSUv7/C161.bam -I /home/wbxie/bam_file_MSUv7/C162.bam -I /home/wbxie/bam_file_MSUv7/C163.bam -I /home/wbxie/bam_file_MSUv7/C164.bam -I /home/wbxie/bam_file_MSUv7/C165.bam -I /home/wbxie/bam_file_MSUv7/C166.bam -I /home/wbxie/bam_file_MSUv7/C167.bam -I /home/wbxie/bam_file_MSUv7/C168.bam -I /home/wbxie/bam_file_MSUv7/C169.bam -I /home/wbxie/bam_file_MSUv7/C170.bam -I /home/wbxie/bam_file_MSUv7/C171.bam -I /home/wbxie/bam_file_MSUv7/C172.bam -I /home/wbxie/bam_file_MSUv7/C173.bam -I /home/wbxie/bam_file_MSUv7/C174.bam -I /home/wbxie/bam_file_MSUv7/C175.bam -I /home/wbxie/bam_file_MSUv7/C176.bam -I /home/wbxie/bam_file_MSUv7/C177.bam -I /home/wbxie/bam_file_MSUv7/C178.bam -I /home/wbxie/bam_file_MSUv7/C179.bam -I /home/wbxie/bam_file_MSUv7/C180.bam -I /home/wbxie/bam_file_MSUv7/C181.bam -I /home/wbxie/bam_file_MSUv7/C182.bam -I /home/wbxie/bam_file_MSUv7/C183.bam -I /home/wbxie/bam_file_MSUv7/C184.bam -I /home/wbxie/bam_file_MSUv7/C185.bam -I /home/wbxie/bam_file_MSUv7/C186.bam -I /home/wbxie/bam_file_MSUv7/C187.bam -I /home/wbxie/bam_file_MSUv7/C188.bam -I /home/wbxie/bam_file_MSUv7/C189.bam -I /home/wbxie/bam_file_MSUv7/C190.bam -I /home/wbxie/bam_file_MSUv7/C191.bam -I /home/wbxie/bam_file_MSUv7/C192.bam -I /home/wbxie/bam_file_MSUv7/C193.bam -I /home/wbxie/bam_file_MSUv7/C194.bam -I /home/wbxie/bam_file_MSUv7/C195.bam -I /home/wbxie/bam_file_MSUv7/C196.bam -I /home/wbxie/bam_file_MSUv7/C197.bam -I /home/wbxie/bam_file_MSUv7/C198.bam -I /home/wbxie/bam_file_MSUv7/C199.bam -I /home/wbxie/bam_file_MSUv7/C200.bam -I /home/wbxie/bam_file_MSUv7/C201.bam -I /home/wbxie/bam_file_MSUv7/C202.bam -I /home/wbxie/bam_file_MSUv7/C203.bam -I /home/wbxie/bam_file_MSUv7/W001.bam -I /home/wbxie/bam_file_MSUv7/W002.bam -I /home/wbxie/bam_file_MSUv7/W003.bam -I /home/wbxie/bam_file_MSUv7/W004.bam -I /home/wbxie/bam_file_MSUv7/W005.bam -I /home/wbxie/bam_file_MSUv7/W006.bam -I /home/wbxie/bam_file_MSUv7/W007.bam -I /home/wbxie/bam_file_MSUv7/W008.bam -I /home/wbxie/bam_file_MSUv7/W009.bam -I /home/wbxie/bam_file_MSUv7/W010.bam -I /home/wbxie/bam_file_MSUv7/W011.bam -I /home/wbxie/bam_file_MSUv7/W012.bam -I /home/wbxie/bam_file_MSUv7/W013.bam -I /home/wbxie/bam_file_MSUv7/W014.bam -I /home/wbxie/bam_file_MSUv7/W015.bam -I /home/wbxie/bam_file_MSUv7/W016.bam -I /home/wbxie/bam_file_MSUv7/W017.bam -I /home/wbxie/bam_file_MSUv7/W018.bam -I /home/wbxie/bam_file_MSUv7/W019.bam -I /home/wbxie/bam_file_MSUv7/W020.bam -I /home/wbxie/bam_file_MSUv7/W021.bam -I /home/wbxie/bam_file_MSUv7/W022.bam -I /home/wbxie/bam_file_MSUv7/W023.bam -I /home/wbxie/bam_file_MSUv7/W024.bam -I /home/wbxie/bam_file_MSUv7/W025.bam -I /home/wbxie/bam_file_MSUv7/W026.bam -I /home/wbxie/bam_file_MSUv7/W027.bam -I /home/wbxie/bam_file_MSUv7/W028.bam -I /home/wbxie/bam_file_MSUv7/W029.bam -I /home/wbxie/bam_file_MSUv7/W030.bam -I /home/wbxie/bam_file_MSUv7/W031.bam -I /home/wbxie/bam_file_MSUv7/W032.bam -I /home/wbxie/bam_file_MSUv7/W033.bam -I /home/wbxie/bam_file_MSUv7/W034.bam -I /home/wbxie/bam_file_MSUv7/W035.bam -I /home/wbxie/bam_file_MSUv7/W036.bam -I /home/wbxie/bam_file_MSUv7/W037.bam -I /home/wbxie/bam_file_MSUv7/W038.bam -I /home/wbxie/bam_file_MSUv7/W039.bam -I /home/wbxie/bam_file_MSUv7/W040.bam -I /home/wbxie/bam_file_MSUv7/W041.bam -I /home/wbxie/bam_file_MSUv7/W042.bam -I /home/wbxie/bam_file_MSUv7/W043.bam -I /home/wbxie/bam_file_MSUv7/W044.bam -I /home/wbxie/bam_file_MSUv7/W045.bam -I /home/wbxie/bam_file_MSUv7/W046.bam -I /home/wbxie/bam_file_MSUv7/W047.bam -I /home/wbxie/bam_file_MSUv7/W048.bam -I /home/wbxie/bam_file_MSUv7/W049.bam -I /home/wbxie/bam_file_MSUv7/W050.bam -I /home/wbxie/bam_file_MSUv7/W051.bam -I /home/wbxie/bam_file_MSUv7/W052.bam -I /home/wbxie/bam_file_MSUv7/W053.bam -I /home/wbxie/bam_file_MSUv7/W054.bam -I /home/wbxie/bam_file_MSUv7/W055.bam -I /home/wbxie/bam_file_MSUv7/W056.bam -I /home/wbxie/bam_file_MSUv7/W057.bam -I /home/wbxie/bam_file_MSUv7/W058.bam -I /home/wbxie/bam_file_MSUv7/W059.bam -I /home/wbxie/bam_file_MSUv7/W060.bam -I /home/wbxie/bam_file_MSUv7/W061.bam -I /home/wbxie/bam_file_MSUv7/W062.bam -I /home/wbxie/bam_file_MSUv7/W063.bam -I /home/wbxie/bam_file_MSUv7/W064.bam -I /home/wbxie/bam_file_MSUv7/W065.bam -I /home/wbxie/bam_file_MSUv7/W066.bam -I /home/wbxie/bam_file_MSUv7/W067.bam -I /home/wbxie/bam_file_MSUv7/W068.bam -I /home/wbxie/bam_file_MSUv7/W069.bam -I /home/wbxie/bam_file_MSUv7/W070.bam -I /home/wbxie/bam_file_MSUv7/W071.bam -I /home/wbxie/bam_file_MSUv7/W072.bam -I /home/wbxie/bam_file_MSUv7/W073.bam -I /home/wbxie/bam_file_MSUv7/W074.bam -I /home/wbxie/bam_file_MSUv7/W075.bam -I /home/wbxie/bam_file_MSUv7/W076.bam -I /home/wbxie/bam_file_MSUv7/W077.bam -I /home/wbxie/bam_file_MSUv7/W078.bam -I /home/wbxie/bam_file_MSUv7/W079.bam -I /home/wbxie/bam_file_MSUv7/W080.bam -I /home/wbxie/bam_file_MSUv7/W081.bam -I /home/wbxie/bam_file_MSUv7/W082.bam -I /home/wbxie/bam_file_MSUv7/W083.bam -I /home/wbxie/bam_file_MSUv7/W084.bam -I /home/wbxie/bam_file_MSUv7/W085.bam -I /home/wbxie/bam_file_MSUv7/W086.bam -I /home/wbxie/bam_file_MSUv7/W087.bam -I /home/wbxie/bam_file_MSUv7/W088.bam -I /home/wbxie/bam_file_MSUv7/W089.bam -I /home/wbxie/bam_file_MSUv7/W090.bam -I /home/wbxie/bam_file_MSUv7/W091.bam -I /home/wbxie/bam_file_MSUv7/W092.bam -I /home/wbxie/bam_file_MSUv7/W093.bam -I /home/wbxie/bam_file_MSUv7/W094.bam -I /home/wbxie/bam_file_MSUv7/W095.bam -I /home/wbxie/bam_file_MSUv7/W096.bam -I /home/wbxie/bam_file_MSUv7/W097.bam -I /home/wbxie/bam_file_MSUv7/W098.bam -I /home/wbxie/bam_file_MSUv7/W099.bam -I /home/wbxie/bam_file_MSUv7/W100.bam -I /home/wbxie/bam_file_MSUv7/W101.bam -I /home/wbxie/bam_file_MSUv7/W102.bam -I /home/wbxie/bam_file_MSUv7/W103.bam -I /home/wbxie/bam_file_MSUv7/W104.bam -I /home/wbxie/bam_file_MSUv7/W105.bam -I /home/wbxie/bam_file_MSUv7/W106.bam -I /home/wbxie/bam_file_MSUv7/W107.bam -I /home/wbxie/bam_file_MSUv7/W108.bam -I /home/wbxie/bam_file_MSUv7/W109.bam -I /home/wbxie/bam_file_MSUv7/W110.bam -I /home/wbxie/bam_file_MSUv7/W111.bam -I /home/wbxie/bam_file_MSUv7/W112.bam -I /home/wbxie/bam_file_MSUv7/W113.bam -I /home/wbxie/bam_file_MSUv7/W114.bam -I /home/wbxie/bam_file_MSUv7/W115.bam -I /home/wbxie/bam_file_MSUv7/W116.bam -I /home/wbxie/bam_file_MSUv7/W117.bam -I /home/wbxie/bam_file_MSUv7/W118.bam -I /home/wbxie/bam_file_MSUv7/W119.bam -I /home/wbxie/bam_file_MSUv7/W120.bam -I /home/wbxie/bam_file_MSUv7/W121.bam -I /home/wbxie/bam_file_MSUv7/W122.bam -I /home/wbxie/bam_file_MSUv7/W123.bam -I /home/wbxie/bam_file_MSUv7/W124.bam -I /home/wbxie/bam_file_MSUv7/W125.bam -I /home/wbxie/bam_file_MSUv7/W126.bam -I /home/wbxie/bam_file_MSUv7/W127.bam -I /home/wbxie/bam_file_MSUv7/W128.bam -I /home/wbxie/bam_file_MSUv7/W129.bam -I /home/wbxie/bam_file_MSUv7/W130.bam -I /home/wbxie/bam_file_MSUv7/W131.bam -I /home/wbxie/bam_file_MSUv7/W132.bam -I /home/wbxie/bam_file_MSUv7/W133.bam -I /home/wbxie/bam_file_MSUv7/W134.bam -I /home/wbxie/bam_file_MSUv7/W135.bam -I /home/wbxie/bam_file_MSUv7/W136.bam -I /home/wbxie/bam_file_MSUv7/W137.bam -I /home/wbxie/bam_file_MSUv7/W138.bam -I /home/wbxie/bam_file_MSUv7/W139.bam -I /home/wbxie/bam_file_MSUv7/W140.bam -I /home/wbxie/bam_file_MSUv7/W141.bam -I /home/wbxie/bam_file_MSUv7/W142.bam -I /home/wbxie/bam_file_MSUv7/W143.bam -I /home/wbxie/bam_file_MSUv7/W144.bam -I /home/wbxie/bam_file_MSUv7/W145.bam -I /home/wbxie/bam_file_MSUv7/W146.bam -I /home/wbxie/bam_file_MSUv7/W147.bam -I /home/wbxie/bam_file_MSUv7/W148.bam -I /home/wbxie/bam_file_MSUv7/W149.bam -I /home/wbxie/bam_file_MSUv7/W150.bam -I /home/wbxie/bam_file_MSUv7/W151.bam -I /home/wbxie/bam_file_MSUv7/W152.bam -I /home/wbxie/bam_file_MSUv7/W153.bam -I /home/wbxie/bam_file_MSUv7/W154.bam -I /home/wbxie/bam_file_MSUv7/W155.bam -I /home/wbxie/bam_file_MSUv7/W156.bam -I /home/wbxie/bam_file_MSUv7/W157.bam -I /home/wbxie/bam_file_MSUv7/W158.bam -I /home/wbxie/bam_file_MSUv7/W159.bam -I /home/wbxie/bam_file_MSUv7/W160.bam -I /home/wbxie/bam_file_MSUv7/W161.bam -I /home/wbxie/bam_file_MSUv7/W162.bam -I /home/wbxie/bam_file_MSUv7/W163.bam -I /home/wbxie/bam_file_MSUv7/W164.bam -I /home/wbxie/bam_file_MSUv7/W165.bam -I /home/wbxie/bam_file_MSUv7/W166.bam -I /home/wbxie/bam_file_MSUv7/W167.bam -I /home/wbxie/bam_file_MSUv7/W168.bam -I /home/wbxie/bam_file_MSUv7/W169.bam -I /home/wbxie/bam_file_MSUv7/W170.bam -I /home/wbxie/bam_file_MSUv7/W171.bam -I /home/wbxie/bam_file_MSUv7/W172.bam -I /home/wbxie/bam_file_MSUv7/W173.bam -I /home/wbxie/bam_file_MSUv7/W174.bam -I /home/wbxie/bam_file_MSUv7/W175.bam -I /home/wbxie/bam_file_MSUv7/W176.bam -I /home/wbxie/bam_file_MSUv7/W177.bam -I /home/wbxie/bam_file_MSUv7/W178.bam -I /home/wbxie/bam_file_MSUv7/W179.bam -I /home/wbxie/bam_file_MSUv7/W180.bam -I /home/wbxie/bam_file_MSUv7/W181.bam -I /home/wbxie/bam_file_MSUv7/W182.bam -I /home/wbxie/bam_file_MSUv7/W183.bam -I /home/wbxie/bam_file_MSUv7/W184.bam -I /home/wbxie/bam_file_MSUv7/W185.bam -I /home/wbxie/bam_file_MSUv7/W186.bam -I /home/wbxie/bam_file_MSUv7/W187.bam -I /home/wbxie/bam_file_MSUv7/W188.bam -I /home/wbxie/bam_file_MSUv7/W189.bam -I /home/wbxie/bam_file_MSUv7/W190.bam -I /home/wbxie/bam_file_MSUv7/W191.bam -I /home/wbxie/bam_file_MSUv7/W192.bam -I /home/wbxie/bam_file_MSUv7/W193.bam -I /home/wbxie/bam_file_MSUv7/W194.bam -I /home/wbxie/bam_file_MSUv7/W195.bam -I /home/wbxie/bam_file_MSUv7/W197.bam -I /home/wbxie/bam_file_MSUv7/W198.bam -I /home/wbxie/bam_file_MSUv7/W199.bam -I /home/wbxie/bam_file_MSUv7/W200.bam -I /home/wbxie/bam_file_MSUv7/W201.bam -I /home/wbxie/bam_file_MSUv7/W202.bam -I /home/wbxie/bam_file_MSUv7/W203.bam -I /home/wbxie/bam_file_MSUv7/W204.bam -I /home/wbxie/bam_file_MSUv7/W205.bam -I /home/wbxie/bam_file_MSUv7/W206.bam -I /home/wbxie/bam_file_MSUv7/W207.bam -I /home/wbxie/bam_file_MSUv7/W208.bam -I /home/wbxie/bam_file_MSUv7/W209.bam -I /home/wbxie/bam_file_MSUv7/W210.bam -I /home/wbxie/bam_file_MSUv7/W211.bam -I /home/wbxie/bam_file_MSUv7/W212.bam -I /home/wbxie/bam_file_MSUv7/W213.bam -I /home/wbxie/bam_file_MSUv7/W214.bam -I /home/wbxie/bam_file_MSUv7/W215.bam -I /home/wbxie/bam_file_MSUv7/W216.bam -I /home/wbxie/bam_file_MSUv7/W217.bam -I /home/wbxie/bam_file_MSUv7/W218.bam -I /home/wbxie/bam_file_MSUv7/W219.bam -I /home/wbxie/bam_file_MSUv7/W220.bam -I /home/wbxie/bam_file_MSUv7/W221.bam -I /home/wbxie/bam_file_MSUv7/W222.bam -I /home/wbxie/bam_file_MSUv7/W223.bam -I /home/wbxie/bam_file_MSUv7/W224.bam -I /home/wbxie/bam_file_MSUv7/W225.bam -I /home/wbxie/bam_file_MSUv7/W226.bam -I /home/wbxie/bam_file_MSUv7/W227.bam -I /home/wbxie/bam_file_MSUv7/W228.bam -I /home/wbxie/bam_file_MSUv7/W229.bam -I /home/wbxie/bam_file_MSUv7/W230.bam -I /home/wbxie/bam_file_MSUv7/W231.bam -I /home/wbxie/bam_file_MSUv7/W233.bam -I /home/wbxie/bam_file_MSUv7/W234.bam -I /home/wbxie/bam_file_MSUv7/W235.bam -I /home/wbxie/bam_file_MSUv7/W236.bam -I /home/wbxie/bam_file_MSUv7/W237.bam -I /home/wbxie/bam_file_MSUv7/W238.bam -I /home/wbxie/bam_file_MSUv7/W239.bam -I /home/wbxie/bam_file_MSUv7/W240.bam -I /home/wbxie/bam_file_MSUv7/W241.bam -I /home/wbxie/bam_file_MSUv7/W242.bam -I /home/wbxie/bam_file_MSUv7/W243.bam -I /home/wbxie/bam_file_MSUv7/W244.bam -I /home/wbxie/bam_file_MSUv7/W245.bam -I /home/wbxie/bam_file_MSUv7/W246.bam -I /home/wbxie/bam_file_MSUv7/W247.bam -I /home/wbxie/bam_file_MSUv7/W248.bam -I /home/wbxie/bam_file_MSUv7/W249.bam -I /home/wbxie/bam_file_MSUv7/W250.bam -I /home/wbxie/bam_file_MSUv7/W251.bam -I /home/wbxie/bam_file_MSUv7/W252.bam -I /home/wbxie/bam_file_MSUv7/W253.bam -I /home/wbxie/bam_file_MSUv7/W254.bam -I /home/wbxie/bam_file_MSUv7/W255.bam -I /home/wbxie/bam_file_MSUv7/W256.bam -I /home/wbxie/bam_file_MSUv7/W257.bam -I /home/wbxie/bam_file_MSUv7/W258.bam -I /home/wbxie/bam_file_MSUv7/W259.bam -I /home/wbxie/bam_file_MSUv7/W260.bam -I /home/wbxie/bam_file_MSUv7/W261.bam -I /home/wbxie/bam_file_MSUv7/W262.bam -I /home/wbxie/bam_file_MSUv7/W263.bam -I /home/wbxie/bam_file_MSUv7/W264.bam -I /home/wbxie/bam_file_MSUv7/W265.bam -I /home/wbxie/bam_file_MSUv7/W266.bam -I /home/wbxie/bam_file_MSUv7/W267.bam -I /home/wbxie/bam_file_MSUv7/W268.bam -I /home/wbxie/bam_file_MSUv7/W269.bam -I /home/wbxie/bam_file_MSUv7/W270.bam -I /home/wbxie/bam_file_MSUv7/W271.bam -I /home/wbxie/bam_file_MSUv7/W272.bam -I /home/wbxie/bam_file_MSUv7/W273.bam -I /home/wbxie/bam_file_MSUv7/W274.bam -I /home/wbxie/bam_file_MSUv7/W275.bam -I /home/wbxie/bam_file_MSUv7/W276.bam -I /home/wbxie/bam_file_MSUv7/W277.bam -I /home/wbxie/bam_file_MSUv7/W278.bam -I /home/wbxie/bam_file_MSUv7/W279.bam -I /home/wbxie/bam_file_MSUv7/W280.bam -I /home/wbxie/bam_file_MSUv7/W281.bam -I /home/wbxie/bam_file_MSUv7/W282.bam -I /home/wbxie/bam_file_MSUv7/W283.bam -I /home/wbxie/bam_file_MSUv7/W284.bam -I /home/wbxie/bam_file_MSUv7/W285.bam -I /home/wbxie/bam_file_MSUv7/W286.bam -I /home/wbxie/bam_file_MSUv7/W287.bam -I /home/wbxie/bam_file_MSUv7/W288.bam -I /home/wbxie/bam_file_MSUv7/W289.bam -I /home/wbxie/bam_file_MSUv7/W290.bam -I /home/wbxie/bam_file_MSUv7/W291.bam -I /home/wbxie/bam_file_MSUv7/W292.bam -I /home/wbxie/bam_file_MSUv7/W293.bam -I /home/wbxie/bam_file_MSUv7/W294.bam -I /home/wbxie/bam_file_MSUv7/W295.bam -I /home/wbxie/bam_file_MSUv7/W296.bam -I /home/wbxie/bam_file_MSUv7/W297.bam -I /home/wbxie/bam_file_MSUv7/W298.bam -I /home/wbxie/bam_file_MSUv7/W299.bam -I /home/wbxie/bam_file_MSUv7/W300.bam -I /home/wbxie/bam_file_MSUv7/W301.bam -I /home/wbxie/bam_file_MSUv7/W302.bam -I /home/wbxie/bam_file_MSUv7/W303.bam -I /home/wbxie/bam_file_MSUv7/W304.bam -I /home/wbxie/bam_file_MSUv7/W305.bam -I /home/wbxie/bam_file_MSUv7/W306.bam -I /home/wbxie/bam_file_MSUv7/W307.bam -I /home/wbxie/bam_file_MSUv7/W308.bam -I /home/wbxie/bam_file_MSUv7/W309.bam -I /home/wbxie/bam_file_MSUv7/W310.bam -I /home/wbxie/bam_file_MSUv7/W311.bam -I /home/wbxie/bam_file_MSUv7/W312.bam -I /home/wbxie/bam_file_MSUv7/W313.bam -I /home/wbxie/bam_file_MSUv7/W314.bam -I /home/wbxie/bam_file_MSUv7/W315.bam -I /home/wbxie/bam_file_MSUv7/W316.bam -I /home/wbxie/bam_file_MSUv7/W317.bam -I /home/wbxie/bam_file_MSUv7/W318.bam -I /home/wbxie/bam_file_MSUv7/W319.bam -I /home/wbxie/bam_file_MSUv7/W320.bam -I /home/wbxie/bam_file_MSUv7/W321.bam -I /home/wbxie/bam_file_MSUv7/W322.bam -I /home/wbxie/bam_file_MSUv7/W323.bam -I /home/wbxie/bam_file_MSUv7/W324.bam -I /home/wbxie/bam_file_MSUv7/W325.bam -I /home/wbxie/bam_file_MSUv7/W326.bam -I /home/wbxie/bam_file_MSUv7/W327.bam -I /home/wbxie/bam_file_MSUv7/W328.bam -I /home/wbxie/bam_file_MSUv7/W329.bam -I /home/wbxie/bam_file_MSUv7/W330.bam -O /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/P0001.discovery.vcf -md wild_rice_test2/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory wild_rice_test2 -genomeMaskFile data/rice_all_genomes_v7.mask.fasta -partitionName P0001 -filePrefix P0001 -L chr13:1-490520 -searchLocus chr13:1-490520 -searchWindow chr13:1-490520 -searchMinimumSize 100 -searchMaximumSize 1000000 org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. Command line: sh /home/wbxie/software/svtoolkit/installtest/all_tmpdir/.exec5645035130960711054 Exit code: 1 Standard error contained: [GC 524288K->73003K(2009792K), 0.1090360 secs] INFO 18:49:12,251 HelpFormatter - ----------------------------------------------------------------------------------- INFO 18:49:12,255 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 INFO 18:49:12,255 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 18:49:12,255 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 18:49:12,256 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 18:49:12,256 HelpFormatter - Program Args: -T SVDiscovery -R /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -O /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/P0001.discovery.vcf -md wild_rice_test2/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory wild_rice_test2 -genomeMaskFile data/rice_all_genomes_v7.mask.fasta -partitionName P0001 -filePrefix P0001 -L chr13:1-490520 -searchLocus chr13:1-490520 -searchWindow chr13:1-490520 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 18:49:12,256 HelpFormatter - Date/Time: 2012/10/31 18:49:12 INFO 18:49:12,256 HelpFormatter - ----------------------------------------------------------------------------------- INFO 18:49:12,257 HelpFormatter - ----------------------------------------------------------------------------------- INFO 18:49:12,295 GenomeAnalysisEngine - Strictness is SILENT INFO 18:49:24,911 SVDiscovery - Initializing SVDiscovery ... INFO 18:49:25,602 SVDiscovery - Opening reference sequence ... INFO 18:49:25,604 SVDiscovery - Opened reference sequence. INFO 18:49:25,604 SVDiscovery - Opening genome mask ... INFO 18:49:25,605 SVDiscovery - Opened genome mask. INFO 18:49:25,605 SVDiscovery - Initializing input data set ... [GC 597291K->77188K(2534080K), 0.1140310 secs] INFO 18:50:10,322 SVDiscovery - Initialized data set: 714 files, 811 read groups, 713 samples. INFO 18:50:10,322 SVDiscovery - Opening metadata from wild_rice_test2/metadata ... INFO 18:50:10,324 SVDiscovery - Opened metadata. INFO 18:50:10,327 SVDiscovery - Initializing discovery algorithm ... INFO 18:50:10,329 SVDiscovery - Loading insert size histograms ... [GC 1125764K->95799K(2534080K), 0.0965770 secs] [GC 1144375K->25378K(2708864K), 0.0264040 secs] [GC 1248738K->22178K(2592448K), 0.0159070 secs] INFO 18:50:28,991 SVDiscovery - Loaded 713 histograms. INFO 18:50:29,246 SVDiscovery - Discovery alt home filtering is disabled. INFO 18:50:34,300 SVDiscovery - Processing locus: chr13:1-490520:100-1000000 INFO 18:50:34,300 SVDiscovery - Locus search window: chr13:1-490520 INFO 18:50:34,300 SVDiscovery - Selecting read pairs ... INFO 18:50:34,302 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/100.bam ... [GC 1202722K->116136K(2642176K), 0.0972580 secs] INFO 18:50:35,591 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/100.bam ... INFO 18:50:36,210 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/101.bam ... INFO 18:50:36,755 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/102.bam ... INFO 18:50:37,831 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/103.bam ... INFO 18:50:38,497 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/104.bam ... INFO 18:50:39,044 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/105.bam ... INFO 18:50:39,569 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/106.bam ... [GC 1248488K->29382K(2503680K), 0.0308620 secs] INFO 18:50:40,746 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/107.bam ... INFO 18:50:41,388 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/108.bam ... INFO 18:50:42,944 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/109.bam ... [GC 1123078K->30510K(2550080K), 0.0262990 secs] INFO 18:50:43,447 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/10.bam ... INFO 18:50:44,718 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/110.bam ... INFO 18:50:45,521 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/111.bam ... INFO 18:50:46,216 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/112.bam ... INFO 18:50:46,579 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/113.bam ... INFO 18:50:46,991 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/114.bam ... INFO 18:50:47,443 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/115.bam ... [GC 1087278K->33903K(2429184K), 0.0333420 secs] INFO 18:50:47,826 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/116.bam ... INFO 18:50:48,614 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/117.bam ... INFO 18:50:49,366 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/118.bam ... INFO 18:50:49,807 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/119.bam ... INFO 18:50:50,898 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/11.bam ... [GC 1055407K->37127K(2479552K), 0.0348190 secs] INFO 18:50:51,539 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/120.bam ... INFO 18:50:52,165 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/121.bam ... INFO 18:50:52,542 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/122.bam ... INFO 18:50:53,271 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/123.bam ... INFO 18:50:54,482 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/124.bam ... [GC 1024903K->40183K(2358016K), 0.0309840 secs] INFO 18:50:55,152 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/125.bam ... INFO 18:50:55,815 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/126.bam ... INFO 18:50:56,251 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/127.bam ... INFO 18:50:57,213 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/128.bam ... [GC 995703K->42367K(2412928K), 0.0230370 secs] INFO 18:50:58,763 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/129.bam ... INFO 18:51:00,579 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/12.bam ... INFO 18:51:02,881 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/130.bam ... INFO 18:51:05,376 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/132.bam ... [GC 967039K->44807K(2297024K), 0.0225620 secs] INFO 18:51:07,376 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/133.bam ... INFO 18:51:09,755 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/134.bam ... INFO 18:51:10,440 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/135.bam ... INFO 18:51:11,409 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/13.bam ... [GC 939975K->47447K(2348800K), 0.0217250 secs] INFO 18:51:11,748 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/14.bam ... INFO 18:51:12,472 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/15.bam ... INFO 18:51:13,077 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/16.bam ... INFO 18:51:13,996 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/17.bam ... INFO 18:51:14,685 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/18.bam ... INFO 18:51:15,072 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/19.bam ... [GC 914391K->50271K(2242112K), 0.0236740 secs] INFO 18:51:15,506 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/1.bam ... INFO 18:51:16,303 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/20.bam ... INFO 18:51:17,061 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/21.bam ... INFO 18:51:17,511 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/22.bam ... INFO 18:51:17,880 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/23.bam ... [GC 890207K->52655K(2288448K), 0.0215040 secs] INFO 18:51:18,447 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/24.bam ... INFO 18:51:19,278 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/25.bam ... INFO 18:51:19,718 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/26.bam ... INFO 18:51:20,365 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/27.bam ... INFO 18:51:21,014 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/28.bam ... [GC 866735K->54951K(2191168K), 0.0215550 secs] INFO 18:51:21,776 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/29.bam ... INFO 18:51:22,405 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/2.bam ... INFO 18:51:22,916 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/30.bam ... INFO 18:51:23,825 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/31.bam ... [GC 844327K->57087K(2232448K), 0.0223550 secs] INFO 18:51:24,258 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/32.bam ... INFO 18:51:24,620 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/33.bam ... INFO 18:51:25,221 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/34.bam ... INFO 18:51:27,655 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/35.bam ... INFO 18:51:29,777 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/36.bam ... INFO 18:51:31,625 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/37.bam ... INFO 18:51:33,937 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/38.bam ... [GC 822783K->60055K(2145280K), 0.0198480 secs] INFO 18:51:36,299 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/39.bam ... INFO 18:51:38,042 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/3.bam ... INFO 18:51:38,595 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/40.bam ... [GC 803031K->62319K(2180032K), 0.0218570 secs] INFO 18:51:39,032 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/41.bam ... INFO 18:51:39,434 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/42.bam ... INFO 18:51:40,512 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/43.bam ... INFO 18:51:40,980 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/44.bam ... [GC 783535K->63991K(2101376K), 0.0191640 secs] INFO 18:51:41,738 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/45.bam ... INFO 18:51:41,999 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/46.bam ... INFO 18:51:42,588 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/47.bam ... INFO 18:51:43,510 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/48.bam ... [GC 764343K->66415K(2131904K), 0.0176510 secs] INFO 18:51:44,043 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/49.bam ... INFO 18:51:44,662 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/4.bam ... INFO 18:51:45,430 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/50.bam ... INFO 18:51:46,094 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/51.bam ... [GC 746799K->69015K(2063168K), 0.0198660 secs] INFO 18:51:46,805 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/52.bam ... INFO 18:51:47,480 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/53.bam ... INFO 18:51:48,326 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/54.bam ... [GC 730199K->71767K(2087232K), 0.0255990 secs] INFO 18:51:49,781 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/55.bam ... INFO 18:51:50,476 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/56.bam ... INFO 18:51:50,996 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/57.bam ... INFO 18:51:51,746 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/58.bam ... INFO 18:51:52,313 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/59.bam ... INFO 18:51:52,633 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/5.bam ... [GC 714519K->75007K(2027520K), 0.0200360 secs] INFO 18:51:53,613 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/60.bam ... INFO 18:51:54,009 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/61.bam ... INFO 18:51:54,334 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/62.bam ... INFO 18:51:54,620 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/63.bam ... INFO 18:51:54,958 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/64.bam ... INFO 18:51:55,525 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/65.bam ... [GC 700095K->77551K(2046016K), 0.0227850 secs] INFO 18:51:56,376 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/66.bam ... INFO 18:51:58,199 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/67.bam ... [GC 685679K->78439K(1992384K), 0.0184230 secs] INFO 18:51:59,867 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/68.bam ... INFO 18:52:01,613 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/69.bam ... INFO 18:52:04,087 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/6.bam ... INFO 18:52:06,793 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/70.bam ... INFO 18:52:08,640 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/71.bam ... INFO 18:52:08,878 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/72.bam ... INFO 18:52:09,110 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/73.bam ... INFO 18:52:09,286 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/74.bam ... INFO 18:52:09,462 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/75.bam ... INFO 18:52:09,662 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/76.bam ... [GC 670247K->82111K(2008256K), 0.0173290 secs] INFO 18:52:09,787 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/77.bam ... INFO 18:52:09,909 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/78.bam ... INFO 18:52:10,160 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/79.bam ... INFO 18:52:10,365 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/7.bam ... INFO 18:52:10,806 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/80.bam ... INFO 18:52:10,981 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/81.bam ... INFO 18:52:11,188 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/83.bam ... INFO 18:52:11,778 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/84.bam ... INFO 18:52:13,377 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/85.bam ... [GC 658239K->83943K(1963136K), 0.0213960 secs] INFO 18:52:13,975 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/86.bam ... INFO 18:52:14,539 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/87.bam ... INFO 18:52:15,016 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/88.bam ... INFO 18:52:15,953 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/89.bam ... [GC 645031K->85199K(1974016K), 0.0175260 secs] INFO 18:52:16,641 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/8.bam ... INFO 18:52:18,498 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/90.bam ... INFO 18:52:19,025 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/91.bam ... [GC 631823K->86495K(1933248K), 0.0156370 secs] INFO 18:52:20,446 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/92.bam ... INFO 18:52:21,345 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/93.bam ... [GC 619231K->88839K(1942272K), 0.0189790 secs] INFO 18:52:22,029 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/94.bam ... INFO 18:52:23,056 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/95.bam ... INFO 18:52:23,844 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/96.bam ... [GC 608199K->91399K(1908224K), 0.0195950 secs] INFO 18:52:24,434 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/97.bam ... INFO 18:52:25,537 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/98.bam ... INFO 18:52:26,093 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/99.bam ... [GC 597895K->92807K(1913280K), 0.0195380 secs] INFO 18:52:26,842 SVDiscovery - Reading input file /home/wbxie/wild_rice/bwa_map/9.bam ... INFO 18:52:27,546 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W01.bam ... [GC 586887K->94023K(1882304K), 0.0151020 secs] [GC 576135K->95615K(1886848K), 0.0141770 secs] INFO 18:52:32,415 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W02.bam ... [GC 566207K->97127K(1859520K), 0.0161000 secs] [GC 556647K->98523K(1862272K), 0.0137530 secs] INFO 18:52:36,124 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W03.bam ... [GC 547355K->99171K(1838272K), 0.0115450 secs] [GC 537699K->99659K(1839616K), 0.0117330 secs] INFO 18:52:40,179 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W04.bam ... [GC 528203K->100363K(1818624K), 0.0099520 secs] [GC 519307K->100739K(1818496K), 0.0117450 secs] INFO 18:52:42,661 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W05.bam ... [GC 510403K->101891K(1800512K), 0.0096000 secs] [GC 502595K->102099K(1797888K), 0.0104900 secs] [GC 494163K->102451K(1783040K), 0.0106100 secs] INFO 18:52:48,203 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W06.bam ... [GC 486131K->102859K(1777728K), 0.0093240 secs] INFO 18:52:50,169 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W07.bam ... [GC 478475K->103851K(1767744K), 0.0113390 secs] [GC 471659K->104819K(1759936K), 0.0115180 secs] [GC 465075K->105355K(1752512K), 0.0084150 secs] INFO 18:52:54,024 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W08.bam ... [GC 458315K->105947K(1745600K), 0.0108320 secs] [GC 451867K->107763K(1739712K), 0.0148410 secs] [GC 446835K->108827K(1732224K), 0.0133290 secs] INFO 18:52:58,657 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W09.bam ... [GC 441243K->109427K(1725824K), 0.0099850 secs] [GC 435443K->110123K(1719552K), 0.0125140 secs] [GC 429931K->111403K(1713728K), 0.0132940 secs] [GC 425195K->112755K(1707776K), 0.0126480 secs] INFO 18:53:03,392 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W10.bam ... [GC 420723K->113411K(1702080K), 0.0116380 secs] [GC 415683K->115003K(1697152K), 0.0144650 secs] [GC 411771K->115963K(1691200K), 0.0118830 secs] [GC 407419K->116899K(1685888K), 0.0140450 secs] INFO 18:53:07,985 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W11.bam ... [GC 403171K->117723K(1681024K), 0.0091770 secs] [GC 399003K->118555K(1675968K), 0.0090400 secs] INFO 18:53:10,884 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W12.bam ... [GC 394971K->119403K(1671552K), 0.0109490 secs] [GC 391083K->119803K(1666560K), 0.0125700 secs] [GC 386875K->120619K(1662208K), 0.0103530 secs] [GC 383211K->121315K(1657792K), 0.0087830 secs] [GC 379555K->121003K(1652928K), 0.0070150 secs] INFO 18:53:15,392 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W13.bam ... [GC 375019K->121907K(1649344K), 0.0075980 secs] [GC 371827K->121587K(1644672K), 0.0083340 secs] [GC 367475K->122051K(1641088K), 0.0085640 secs] [GC 364035K->122659K(1637504K), 0.0106830 secs] [GC 360867K->122451K(1633344K), 0.0078820 secs] [GC 356947K->122499K(1629632K), 0.0085530 secs] [GC 353411K->122579K(1626048K), 0.0074810 secs] [GC 349971K->122667K(1622656K), 0.0092880 secs] INFO 18:53:23,301 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W14.bam ... [GC 346667K->122843K(1619456K), 0.0069360 secs] [GC 343515K->123171K(1616128K), 0.0086260 secs] [GC 340579K->123147K(1612864K), 0.0101090 secs] [GC 337419K->123387K(1609920K), 0.0091570 secs] [GC 334587K->123555K(1606976K), 0.0083170 secs] [GC 331747K->123611K(1603968K), 0.0059730 secs] [GC 328859K->123419K(1600832K), 0.0110960 secs] INFO 18:53:28,636 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W15.bam ... [GC 325787K->123867K(1598400K), 0.0076520 secs] [GC 323419K->124083K(1595648K), 0.0094950 secs] [GC 320947K->123923K(1592768K), 0.0073860 secs] INFO 18:53:31,667 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W16.bam ... [GC 318163K->124355K(1590464K), 0.0098310 secs] [GC 315971K->124495K(1587776K), 0.0061800 secs] [GC 313551K->124343K(1584960K), 0.0093670 secs] [GC 310903K->124687K(1582720K), 0.0069470 secs] [GC 308815K->124839K(1580480K), 0.0090590 secs] [GC 306599K->125007K(1578240K), 0.0102340 secs] [GC 304463K->125039K(1575872K), 0.0065920 secs] [GC 302255K->125111K(1573632K), 0.0078390 secs] INFO 18:53:38,514 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W17.bam ... [GC 300151K->125255K(1571520K), 0.0067460 secs] [GC 298119K->125543K(1569472K), 0.0068200 secs] [GC 296295K->125623K(1567360K), 0.0073280 secs] [GC 294327K->125887K(1565440K), 0.0082320 secs] [GC 292543K->125919K(1563328K), 0.0097040 secs] [GC 290591K->125831K(1596096K), 0.0093780 secs] INFO 18:53:42,258 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W18.bam ... [GC 323463K->126335K(1593792K), 0.0075270 secs] [GC 321279K->126479K(1591040K), 0.0058870 secs] [GC 318799K->126600K(1588480K), 0.0087120 secs] [GC 316360K->127015K(1586240K), 0.0071740 secs] [GC 314279K->126751K(1583424K), 0.0072950 secs] [GC 311583K->127095K(1581248K), 0.0068910 secs] [GC 309559K->126991K(1578752K), 0.0081580 secs] [GC 307151K->127247K(1576576K), 0.0061810 secs] [GC 305167K->127408K(1574464K), 0.0083500 secs] [GC 303088K->127415K(1572160K), 0.0084700 secs] [GC 300919K->127471K(1569984K), 0.0074520 secs] [GC 298863K->127544K(1567872K), 0.0073890 secs] INFO 18:53:51,206 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W19.bam ... [GC 296888K->127975K(1566144K), 0.0083840 secs] [GC 295271K->127751K(1563776K), 0.0071630 secs] [GC 293063K->127999K(1561984K), 0.0073520 secs] [GC 291391K->127840K(1559872K), 0.0069980 secs] [GC 289312K->128023K(1558144K), 0.0069980 secs] [GC 287639K->128063K(1556288K), 0.0090880 secs] INFO 18:53:55,175 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W20.bam ... [GC 285823K->128639K(1554944K), 0.0083390 secs] [GC 284607K->128400K(1552768K), 0.0067610 secs] [GC 282640K->128623K(1551168K), 0.0066380 secs] [GC 281135K->129087K(1581952K), 0.0086330 secs] [GC 312127K->128999K(1618304K), 0.0095790 secs] [GC 348647K->129792K(1615488K), 0.0079140 secs] INFO 18:53:59,287 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W21.bam ... [GC 346240K->130239K(1611904K), 0.0061660 secs] [GC 343551K->130647K(1608960K), 0.0077450 secs] [GC 340887K->130616K(1605824K), 0.0078470 secs] [GC 337848K->130664K(1602880K), 0.0081610 secs] [GC 335016K->130864K(1600192K), 0.0072030 secs] [GC 332400K->131128K(1597632K), 0.0074790 secs] [GC 329912K->131079K(1594752K), 0.0093360 secs] INFO 18:54:04,595 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W22.bam ... [GC 327175K->131456K(1592384K), 0.0100230 secs] [GC 324928K->131656K(1589632K), 0.0079420 secs] [GC 322568K->132040K(1587328K), 0.0072980 secs] [GC 320456K->131944K(1584576K), 0.0078480 secs] INFO 18:54:07,694 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W23.bam ... [GC 317928K->132880K(1582784K), 0.0070040 secs] [GC 316432K->133136K(1580032K), 0.0059220 secs] [GC 314320K->133672K(1577920K), 0.0107030 secs] [GC 312552K->133840K(1575680K), 0.0062960 secs] [GC 310480K->134096K(1573440K), 0.0103420 secs] [GC 308560K->134952K(1608832K), 0.0077280 secs] [GC 344360K->135104K(1650560K), 0.0100510 secs] INFO 18:54:12,690 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W24.bam ... [GC 386432K->135544K(1646464K), 0.0079440 secs] [GC 382840K->136144K(1642624K), 0.0081930 secs] [GC 379536K->137216K(1639360K), 0.0104640 secs] [GC 376768K->138488K(1635584K), 0.0121570 secs] [GC 374328K->139056K(1631488K), 0.0088540 secs] [GC 371248K->139008K(1627648K), 0.0077950 secs] [GC 367680K->139832K(1648256K), 0.0138530 secs] INFO 18:54:18,704 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W25.bam ... [GC 387512K->140224K(1643200K), 0.0107090 secs] [GC 383936K->140088K(1638784K), 0.0064150 secs] [GC 379960K->140280K(1635072K), 0.0106940 secs] [GC 376440K->140800K(1631616K), 0.0076590 secs] [GC 373312K->140712K(1627776K), 0.0075550 secs] [GC 369704K->141160K(1624576K), 0.0069120 secs] INFO 18:54:24,299 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W26.bam ... [GC 366696K->141264K(1621184K), 0.0069660 secs] [GC 363472K->140984K(1617408K), 0.0094210 secs] [GC 359928K->141456K(1614592K), 0.0063290 secs] [GC 357200K->141552K(1611392K), 0.0085470 secs] [GC 354160K->141560K(1608256K), 0.0073180 secs] INFO 18:54:28,874 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W27.bam ... [GC 351160K->142160K(1605760K), 0.0064920 secs] [GC 348816K->142360K(1602752K), 0.0064730 secs] [GC 346136K->142808K(1600064K), 0.0117680 secs] [GC 343768K->142632K(1596928K), 0.0066200 secs] [GC 340840K->142784K(1594176K), 0.0066150 secs] [GC 338304K->142968K(1591616K), 0.0068720 secs] INFO 18:54:33,196 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W28.bam ... [GC 335864K->144032K(1589888K), 0.0061670 secs] [GC 334368K->144648K(1587456K), 0.0105730 secs] [GC 332488K->145240K(1584192K), 0.0073870 secs] [GC 330648K->145920K(1582208K), 0.0072970 secs] [GC 328960K->146184K(1579840K), 0.0083820 secs] INFO 18:54:36,364 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W29.bam ... [GC 326856K->147008K(1578048K), 0.0074540 secs] [GC 325376K->146768K(1575040K), 0.0065350 secs] [GC 322896K->146792K(1572736K), 0.0063310 secs] [GC 320744K->146856K(1570496K), 0.0071200 secs] [GC 318696K->147152K(1568512K), 0.0057730 secs] [GC 316880K->147064K(1566272K), 0.0069300 secs] INFO 18:54:39,808 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W30.bam ... [GC 314744K->147800K(1564800K), 0.0087250 secs] [GC 313496K->147760K(1597568K), 0.0075950 secs] [GC 346608K->147840K(1621440K), 0.0080710 secs] [GC 369344K->148240K(1638720K), 0.0084380 secs] INFO 18:54:42,569 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W31.bam ... [GC 387024K->148944K(1634432K), 0.0084980 secs] [GC 384016K->148888K(1630144K), 0.0075110 secs] [GC 380376K->149360K(1626944K), 0.0063560 secs] [GC 377328K->149760K(1623680K), 0.0087050 secs] [GC 374336K->150528K(1620736K), 0.0077600 secs] [GC 371776K->150608K(1617216K), 0.0070980 secs] INFO 18:54:46,624 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W32.bam ... [GC 368592K->151104K(1614208K), 0.0087490 secs] [GC 365888K->150952K(1610624K), 0.0069070 secs] [GC 362664K->151592K(1608000K), 0.0077210 secs] [GC 360296K->151512K(1604736K), 0.0067860 secs] [GC 357272K->151864K(1601984K), 0.0085240 secs] INFO 18:54:50,386 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W33.bam ... [GC 354744K->152024K(1599104K), 0.0073760 secs] [GC 352088K->152816K(1596736K), 0.0082600 secs] [GC 350128K->152528K(1593536K), 0.0069810 secs] [GC 347152K->152688K(1590848K), 0.0079070 secs] [GC 344688K->152568K(1588096K), 0.0072750 secs] [GC 342008K->152944K(1585792K), 0.0064030 secs] INFO 18:54:54,281 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W34.bam ... [GC 339888K->153344K(1583616K), 0.0092000 secs] [GC 337856K->153352K(1580864K), 0.0073660 secs] [GC 335496K->153968K(1579008K), 0.0070450 secs] [GC 333808K->153872K(1576448K), 0.0064200 secs] [GC 331472K->154232K(1574400K), 0.0089140 secs] INFO 18:54:57,250 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W35.bam ... [GC 329592K->154344K(1572160K), 0.0093050 secs] [GC 327528K->154672K(1570048K), 0.0065730 secs] [GC 325744K->154968K(1568064K), 0.0073720 secs] [GC 323992K->154648K(1565568K), 0.0063200 secs] [GC 321624K->154896K(1563648K), 0.0064870 secs] [GC 319888K->155320K(1561984K), 0.0058860 secs] INFO 18:55:01,935 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W36.bam ... [GC 318392K->155872K(1560448K), 0.0079720 secs] [GC 317024K->155816K(1558144K), 0.0066430 secs] [GC 315112K->156088K(1556416K), 0.0090630 secs] [GC 313528K->156136K(1554432K), 0.0077650 secs] [GC 311784K->156288K(1552768K), 0.0079960 secs] [GC 310208K->156376K(1550912K), 0.0065270 secs] INFO 18:55:05,767 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W37.bam ... [GC 308568K->156952K(1549696K), 0.0063830 secs] [GC 307480K->156896K(1579456K), 0.0091980 secs] [GC 337568K->157432K(1577472K), 0.0078280 secs] [GC 335800K->157544K(1613056K), 0.0097640 secs] [GC 371624K->158192K(1615104K), 0.0086260 secs] INFO 18:55:08,556 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W38.bam ... [GC 373936K->158528K(1612096K), 0.0062680 secs] [GC 371136K->158176K(1608384K), 0.0079830 secs] [GC 367776K->158224K(1605376K), 0.0076110 secs] [GC 364880K->158424K(1602560K), 0.0060240 secs] [GC 362200K->158568K(1599744K), 0.0069180 secs] [GC 359528K->158488K(1596800K), 0.0072610 secs] [GC 356696K->158664K(1594176K), 0.0061180 secs] INFO 18:55:13,788 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W39.bam ... [GC 354184K->159408K(1592128K), 0.0071710 secs] [GC 352304K->159336K(1589184K), 0.0068170 secs] [GC 349672K->159632K(1586752K), 0.0097900 secs] [GC 347472K->159936K(1584384K), 0.0078110 secs] [GC 345344K->160288K(1582080K), 0.0074270 secs] [GC 343328K->160656K(1579776K), 0.0075370 secs] [GC 341328K->160568K(1577088K), 0.0091460 secs] INFO 18:55:18,008 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W40.bam ... [GC 338936K->161224K(1575360K), 0.0062590 secs] [GC 337352K->161744K(1610496K), 0.0119870 secs] [GC 373136K->161816K(1646400K), 0.0085430 secs] [GC 409368K->163008K(1643072K), 0.0083250 secs] [GC 406592K->162616K(1637952K), 0.0055480 secs] INFO 18:55:21,998 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W41.bam ... [GC 402360K->163880K(1635392K), 0.0082890 secs] [GC 399912K->164808K(1631936K), 0.0086170 secs] [GC 397192K->164968K(1628160K), 0.0073300 secs] [GC 393832K->165032K(1624384K), 0.0050900 secs] INFO 18:55:24,964 SVDiscovery - Reading input file /home/wbxie/wild_rice/wangwen/bwa_map/W42.bam ... [GC 390440K->166320K(1621888K), 0.0080250 secs] [GC 388400K->166304K(1617856K), 0.0068710 secs] [GC 385120K... [truncated message content] |
|
From: Bob H. <han...@br...> - 2012-10-31 17:04:11
|
If you are using the pre-computed Homo_sapiens_assembly19 mask, the mitochondrial contig is "MT", not "chrM". > $ grep M Homo_sapiens_assembly19.mask.101.fasta.stats > SEQUENCE UNMASKED MASKED > MT 15057 1512 The reference sequence you align to has to match the reference used to build the genome mask you use exactly, in every respect. -Bob On 10/31/12 11:44 AM, Jinlu Cai wrote: > Dear Team members: > > When I run the SVTK with our 6 sample whole genome data, we get the > following error in ComputeReadDepthCoverage step : > > Standard error contained: > INFO 03:35:39,889 HelpFormatter - > --------------------------------------------- > -------------------------------------- > INFO 03:35:39,891 HelpFormatter - The Genome Analysis Toolkit (GATK) > v1.0-6121- > g40e3165, Compiled 2011/09/04 20:57:29 > INFO 03:35:39,891 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 03:35:39,891 HelpFormatter - Please view our documentation at > http://www.b > roadinstitute.org/gsa/wiki > INFO 03:35:39,891 HelpFormatter - For support, please view our > support site at > http://getsatisfaction.com/gsa > INFO 03:35:39,892 HelpFormatter - Program Args: -T > ComputeReadDepthCoverage -R > /rio1/indexes/ucsc/hg19/fasta/ucsc.hg19.fasta -I > /cork/jcai/bernice2/MZH12024_HU > MzbjR/SVTK_result/merged.bam -O > /cork/jcai/bernice2/MZH12024_HUMzbjR/SVTK_result > /metadata/depth/merged.depth.txt -md > /cork/jcai/bernice2/MZH12024_HUMzbjR/SVTK_r > esult/metadata -genomeMaskFile > /cork/jcai/SVTK/mask/Homo_sapiens_assembly19.mask > .101.fasta -minMapQ 10 > INFO 03:35:39,892 HelpFormatter - Date/Time: 2012/10/31 03:35:39 > INFO 03:35:39,892 HelpFormatter - > --------------------------------------------- > -------------------------------------- > INFO 03:35:39,892 HelpFormatter - > --------------------------------------------- > -------------------------------------- > INFO 03:35:39,897 GenomeAnalysisEngine - Strictness is SILENT > INFO 03:35:40,866 ComputeReadDepthCoverageWalker - Using genome mask > /cork/jcai > /SVTK/mask/Homo_sapiens_assembly19.mask.101.fasta > ##### ERROR > -------------------------------------------------------------------- > ---------------------- > ##### ERROR stack trace > java.lang.IllegalArgumentException: Invalid sequence position: chrM:45 > at org.broadinstitute.sv.mask.GenomeMaskFastaFile.getMaskBit(GenomeMaskF > astaFile.java:80) > at org.broadinstitute.sv.common.ReadCountAlgorithm.shouldCountRecord(Rea > dCountAlgorithm.java:260) > at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.m > ap(ComputeReadDepthCoverageWalker.java:72) > at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.m > ap(ComputeReadDepthCoverageWalker.java:38) > at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(Trave > rseReads.java:101) > at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(Trave > rseReads.java:49) > at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute( > LinearMicroScheduler.java:70) > at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnal > ysisEngine.java:234) > at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLi > neExecutable.java:113) > at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command > LineProgram.java:221) > at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.ja > va:87) > ##### ERROR > -------------------------------------------------------------------- > ---------------------- > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): > ##### ERROR > ##### ERROR Please visit the 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://g > etsatisfaction.com/gsa > ##### ERROR > ##### ERROR MESSAGE: Invalid sequence position: chrM:45 > ##### ERROR > -------------------------------------------------------------------- > ---------------------- > > Thanks. > > Jinlu Cai > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_sfd2d_oct > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Jinlu C. <jin...@ei...> - 2012-10-31 15:44:54
|
Dear Team members: When I run the SVTK with our 6 sample whole genome data, we get the following error in ComputeReadDepthCoverage step : Standard error contained: INFO 03:35:39,889 HelpFormatter - --------------------------------------------- -------------------------------------- INFO 03:35:39,891 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121- g40e3165, Compiled 2011/09/04 20:57:29 INFO 03:35:39,891 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 03:35:39,891 HelpFormatter - Please view our documentation at http://www.b roadinstitute.org/gsa/wiki INFO 03:35:39,891 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 03:35:39,892 HelpFormatter - Program Args: -T ComputeReadDepthCoverage -R /rio1/indexes/ucsc/hg19/fasta/ucsc.hg19.fasta -I /cork/jcai/bernice2/MZH12024_HU MzbjR/SVTK_result/merged.bam -O /cork/jcai/bernice2/MZH12024_HUMzbjR/SVTK_result /metadata/depth/merged.depth.txt -md /cork/jcai/bernice2/MZH12024_HUMzbjR/SVTK_r esult/metadata -genomeMaskFile /cork/jcai/SVTK/mask/Homo_sapiens_assembly19.mask .101.fasta -minMapQ 10 INFO 03:35:39,892 HelpFormatter - Date/Time: 2012/10/31 03:35:39 INFO 03:35:39,892 HelpFormatter - --------------------------------------------- -------------------------------------- INFO 03:35:39,892 HelpFormatter - --------------------------------------------- -------------------------------------- INFO 03:35:39,897 GenomeAnalysisEngine - Strictness is SILENT INFO 03:35:40,866 ComputeReadDepthCoverageWalker - Using genome mask /cork/jcai /SVTK/mask/Homo_sapiens_assembly19.mask.101.fasta ##### ERROR -------------------------------------------------------------------- ---------------------- ##### ERROR stack trace java.lang.IllegalArgumentException: Invalid sequence position: chrM:45 at org.broadinstitute.sv.mask.GenomeMaskFastaFile.getMaskBit(GenomeMaskF astaFile.java:80) at org.broadinstitute.sv.common.ReadCountAlgorithm.shouldCountRecord(Rea dCountAlgorithm.java:260) at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.m ap(ComputeReadDepthCoverageWalker.java:72) at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.m ap(ComputeReadDepthCoverageWalker.java:38) at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(Trave rseReads.java:101) at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(Trave rseReads.java:49) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute( LinearMicroScheduler.java:70) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnal ysisEngine.java:234) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLi neExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:221) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.ja va:87) ##### ERROR -------------------------------------------------------------------- ---------------------- ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): ##### ERROR ##### ERROR Please visit the 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://g etsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Invalid sequence position: chrM:45 ##### ERROR -------------------------------------------------------------------- ---------------------- Thanks. Jinlu Cai |
|
From: yw <yw...@gm...> - 2012-10-08 06:26:38
|
Hi Bob, I reindex the BAM file, but the problem still existed. I tried to "samtools view", it was okay. I remapped the sequences using BWA, then the problem was solved. Sorry for starting a new thread. I don't know how to put all of this in the same thread. Andrew |
|
From: Bob H. <han...@br...> - 2012-10-06 22:30:16
|
It is likely that your bam file or bam index file is corrupted. I would try reindexing the file with "samtools index C046.bam" If this doesn't fix the problem, I would try "samtools view" to see if samtools can read the file successfully. -Bob On 10/6/12 3:33 AM, yw wrote: > Hi all, > I used Genome-STRIP recently. I believe I have successfully installed > the software. The install test was okay. And I tried with 30 BAM files > and got the results. However, When I came to more BAM files, some of the > BAM files went wrong. Here is the error message: > > java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir > -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeInsertSizeHistograms -R > /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I > /home/wbxie/bam_file_MSUv7/C046.bam -O > /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/metadata/isd/C046.hist.bin > -md wild_rice_test2/metadata -createEmpty > INFO 15:19:52,903 HelpFormatter - > ----------------------------------------------------------------------------------- > > INFO 15:19:52,908 HelpFormatter - The Genome Analysis Toolkit (GATK) > v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 > INFO 15:19:52,909 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 15:19:52,909 HelpFormatter - Please view our documentation at > http://www.broadinstitute.org/gsa/wiki > INFO 15:19:52,910 HelpFormatter - For support, please view our support > site at http://getsatisfaction.com/gsa > INFO 15:19:52,910 HelpFormatter - Program Args: -T > ComputeInsertSizeHistograms -R > /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I > /home/wbxie/bam_file_MSUv7/C046.bam -O > /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/metadata/isd/C046.hist.bin > -md wild_rice_test2/metadata -createEmpty > INFO 15:19:52,911 HelpFormatter - Date/Time: 2012/10/06 15:19:52 > INFO 15:19:52,911 HelpFormatter - > ----------------------------------------------------------------------------------- > > INFO 15:19:52,912 HelpFormatter - > ----------------------------------------------------------------------------------- > > INFO 15:19:52,922 GenomeAnalysisEngine - Strictness is SILENT > INFO 15:19:54,579 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL > STARTING] > INFO 15:19:54,579 TraversalEngine - Location processed.reads runtime > per.1M.reads completed total.runtime remaining > INFO 15:20:04,247 TraversalEngine - chr01:24865802 1.24e+06 10.0 s 8.1 s > 6.8% 2.5 m 2.3 m > INFO 15:20:14,247 TraversalEngine - chr02:31101998 2.69e+06 20.0 s 7.4 s > 20.0% 100.0 s 80.0 s > INFO 15:20:24,291 TraversalEngine - chr04:9103726 4.11e+06 30.0 s 7.3 s > 33.4% 89.9 s 59.9 s > INFO 15:20:34,292 TraversalEngine - chr05:15404145 5.53e+06 40.0 s 7.2 s > 44.6% 89.9 s 49.8 s > INFO 15:20:44,293 TraversalEngine - chr07:4981864 6.98e+06 50.1 s 7.2 s > 58.1% 86.1 s 36.1 s > INFO 15:20:54,303 TraversalEngine - chr08:24859331 8.42e+06 60.1 s 7.1 s > 71.3% 84.2 s 24.2 s > INFO 15:21:04,347 TraversalEngine - chr10:12704502 9.76e+06 70.1 s 7.2 s > 81.8% 85.7 s 15.6 s > INFO 15:21:14,387 TraversalEngine - chr12:14627327 1.12e+07 80.1 s 7.1 s > 96.2% 83.3 s 3.1 s > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.RuntimeException: Invalid file pointer: 71767958683648 > at > net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:477) > at > net.sf.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:577) > at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:243) > at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:314) > at > org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.getIterator(SAMDataSource.java:557) > at > org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.fillShard(SAMDataSource.java:482) > at > org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.advance(ReadShardStrategy.java:176) > at > org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.next(ReadShardStrategy.java:126) > at > org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.next(ReadShardStrategy.java:41) > at > org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator$1.doBody(GenomeLocProcessingTracker.java:261) > at > org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator$1.doBody(GenomeLocProcessingTracker.java:253) > at > org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$WithLock.run(GenomeLocProcessingTracker.java:426) > at > org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:253) > at > org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:216) > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:53) > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234) > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at > org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) > Caused by: java.io.IOException: Invalid file pointer: 71767958683648 > at > net.sf.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:220) > at > net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:590) > at > net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:460) > ... 18 more > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): > ##### ERROR > ##### ERROR Please visit the 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: Invalid file pointer: 71767958683648 > ##### ERROR > ------------------------------------------------------------------------------------------ > > Could anyone please help? Thank you in advance. > > Andrew > > ------------------------------------------------------------------------------ > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: yw <yw...@gm...> - 2012-10-06 07:33:08
|
Hi all, I used Genome-STRIP recently. I believe I have successfully installed the software. The install test was okay. And I tried with 30 BAM files and got the results. However, When I came to more BAM files, some of the BAM files went wrong. Here is the error message: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeHistograms -R /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I /home/wbxie/bam_file_MSUv7/C046.bam -O /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/metadata/isd/C046.hist.bin -md wild_rice_test2/metadata -createEmpty INFO 15:19:52,903 HelpFormatter - ----------------------------------------------------------------------------------- INFO 15:19:52,908 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 INFO 15:19:52,909 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 15:19:52,909 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 15:19:52,910 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 15:19:52,910 HelpFormatter - Program Args: -T ComputeInsertSizeHistograms -R /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I /home/wbxie/bam_file_MSUv7/C046.bam -O /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/metadata/isd/C046.hist.bin -md wild_rice_test2/metadata -createEmpty INFO 15:19:52,911 HelpFormatter - Date/Time: 2012/10/06 15:19:52 INFO 15:19:52,911 HelpFormatter - ----------------------------------------------------------------------------------- INFO 15:19:52,912 HelpFormatter - ----------------------------------------------------------------------------------- INFO 15:19:52,922 GenomeAnalysisEngine - Strictness is SILENT INFO 15:19:54,579 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] INFO 15:19:54,579 TraversalEngine - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 15:20:04,247 TraversalEngine - chr01:24865802 1.24e+06 10.0 s 8.1 s 6.8% 2.5 m 2.3 m INFO 15:20:14,247 TraversalEngine - chr02:31101998 2.69e+06 20.0 s 7.4 s 20.0% 100.0 s 80.0 s INFO 15:20:24,291 TraversalEngine - chr04:9103726 4.11e+06 30.0 s 7.3 s 33.4% 89.9 s 59.9 s INFO 15:20:34,292 TraversalEngine - chr05:15404145 5.53e+06 40.0 s 7.2 s 44.6% 89.9 s 49.8 s INFO 15:20:44,293 TraversalEngine - chr07:4981864 6.98e+06 50.1 s 7.2 s 58.1% 86.1 s 36.1 s INFO 15:20:54,303 TraversalEngine - chr08:24859331 8.42e+06 60.1 s 7.1 s 71.3% 84.2 s 24.2 s INFO 15:21:04,347 TraversalEngine - chr10:12704502 9.76e+06 70.1 s 7.2 s 81.8% 85.7 s 15.6 s INFO 15:21:14,387 TraversalEngine - chr12:14627327 1.12e+07 80.1 s 7.1 s 96.2% 83.3 s 3.1 s ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.RuntimeException: Invalid file pointer: 71767958683648 at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:477) at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:577) at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:243) at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:314) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.getIterator(SAMDataSource.java:557) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.fillShard(SAMDataSource.java:482) at org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.advance(ReadShardStrategy.java:176) at org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.next(ReadShardStrategy.java:126) at org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.next(ReadShardStrategy.java:41) at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator$1.doBody(GenomeLocProcessingTracker.java:261) at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator$1.doBody(GenomeLocProcessingTracker.java:253) at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$WithLock.run(GenomeLocProcessingTracker.java:426) at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:253) at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:216) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:53) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) Caused by: java.io.IOException: Invalid file pointer: 71767958683648 at net.sf.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:220) at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:590) at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:460) ... 18 more ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): ##### ERROR ##### ERROR Please visit the 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: Invalid file pointer: 71767958683648 ##### ERROR ------------------------------------------------------------------------------------------ Could anyone please help? Thank you in advance. Andrew |
|
From: yw <yw...@gm...> - 2012-09-26 02:29:25
|
Hi Bob, I changed the version of bwa. That worked. Thx. Andrew |
|
From: Bob H. <han...@br...> - 2012-09-25 03:22:40
|
The problem is that the previous job (bwa index test2/altalign/installtest.sites.alt.fasta) failed. And I am guessing it didn't return a non-zero exit status or it didn't create the bwt index files. There is a similar report here http://gatkforums.broadinstitute.org/discussion/1338/genome-strip-test-installation-error where they say they had an newer version of bwa installed, so this may be similar. -Bob On 9/23/12 9:12 AM, yw wrote: > Hi, > I am trying to configure GenomeSTRiP. Till now, I have run > discovery.sh without error. When I came to genotyping.sh. It went > wrong. All the output information is shown below: > > SVToolkit version 1.04 (build 982) > Build date: 2012/08/10 18:30:21 > Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP > INFO 15:58:10,295 QScriptManager - Compiling 2 QScripts > INFO 15:58:20,855 QScriptManager - Compilation complete > INFO 15:58:20,987 HelpFormatter - > --------------------------------------------------------- > INFO 15:58:20,987 HelpFormatter - Program Name: > org.broadinstitute.sting.queue.QCommandLine > INFO 15:58:20,988 HelpFormatter - Program Args: -S > /home/wbxie/software/svtoolkit/qscript/SVPreprocess.q -S > /home/wbxie/software/svtoolkit/qscript/SVQScript.q -gatk > /home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir > -R data/human_b36_chr1.fasta -genomeMaskFile > data/human_b36_chr1.mask.fasta -genderMapFile > data/installtest_gender.map -copyNumberMaskFile > data/cn2_mask_g1k_b36_chr1.fasta -runDirectory test2 -md > test2/metadata -computeGCProfiles -jobLogDir test2/logs -I > data/installtest.bam -run > INFO 15:58:20,988 HelpFormatter - Date/Time: 2012/09/23 15:58:20 > INFO 15:58:20,989 HelpFormatter - > --------------------------------------------------------- > INFO 15:58:20,989 HelpFormatter - > --------------------------------------------------------- > INFO 15:58:20,995 QCommandLine - Scripting SVPreprocess > INFO 15:58:21,326 QCommandLine - Added 10 functions > INFO 15:58:21,326 QGraph - Generating graph. > INFO 15:58:21,371 QGraph - Generating scatter gather jobs. > INFO 15:58:21,373 QGraph - Removing original jobs. > INFO 15:58:21,375 QGraph - Adding scatter gather jobs. > INFO 15:58:21,376 QGraph - Regenerating graph. > INFO 15:58:21,388 QGraph - Running jobs. > INFO 15:58:21,479 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeInsertSizeHistograms -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin > -md test2/metadata -createEmpty > INFO 15:58:21,480 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-1.out > INFO 15:59:14,762 QGraph - 9 Pend, 1 Run, 0 Fail, 0 Done > INFO 15:59:14,773 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeInsertSizeHistograms -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin > -md test2/metadata -createEmpty > INFO 15:59:14,778 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin > -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin > INFO 15:59:14,778 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-2.out > INFO 15:59:15,234 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadDepthCoverage -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt > -md test2/metadata -genomeMaskFile data/human_b36_chr1.mask.fasta > -minMapQ 10 > INFO 15:59:15,235 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-4.out > INFO 16:00:08,246 QGraph - 7 Pend, 2 Run, 0 Fail, 1 Done > INFO 16:00:08,249 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin > -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin > INFO 16:00:08,252 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadDepthCoverage -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt > -md test2/metadata -genomeMaskFile data/human_b36_chr1.mask.fasta > -minMapQ 10 > INFO 16:00:08,255 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.ComputeInsertStatistics -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin > -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.stats.dat > INFO 16:00:08,255 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-3.out > INFO 16:00:09,077 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadSpanCoverage -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt > -md test2/metadata -maxInsertSizeStandardDeviations 3 > INFO 16:00:09,077 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-6.out > INFO 16:01:02,106 QGraph - 5 Pend, 2 Run, 0 Fail, 3 Done > INFO 16:01:02,110 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.ComputeInsertStatistics -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin > -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.stats.dat > INFO 16:01:02,113 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T > ComputeReadSpanCoverage -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt > -md test2/metadata -maxInsertSizeStandardDeviations 3 > INFO 16:01:02,116 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.MergeReadSpanCoverage -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt > -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans.dat > INFO 16:01:02,116 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-7.out > INFO 16:01:02,840 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.MergeReadDepthCoverage -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt > -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth.dat > INFO 16:01:02,840 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-5.out > INFO 16:01:03,514 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.ComputeGCProfiles -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/reference.gcprof.zip > -R data/human_b36_chr1.fasta -md test2/metadata -writeReferenceProfile > true -genomeMaskFile data/human_b36_chr1.mask.fasta > -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta > INFO 16:01:03,515 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-8.out > INFO 16:01:52,913 QGraph - 2 Pend, 3 Run, 0 Fail, 5 Done > INFO 16:01:52,921 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.MergeReadSpanCoverage -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt > -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans.dat > INFO 16:01:52,923 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.MergeReadDepthCoverage -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt > -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth.dat > INFO 16:01:52,925 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.ComputeGCProfiles -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/reference.gcprof.zip > -R data/human_b36_chr1.fasta -md test2/metadata -writeReferenceProfile > true -genomeMaskFile data/human_b36_chr1.mask.fasta > -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta > INFO 16:01:52,927 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.ComputeGCProfiles -I > /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip > -R data/human_b36_chr1.fasta -md test2/metadata -referenceProfile > test2/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile > data/human_b36_chr1.mask.fasta -copyNumberMaskFile > data/cn2_mask_g1k_b36_chr1.fasta > INFO 16:01:52,928 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-9.out > INFO 16:02:00,425 QGraph - 1 Pend, 1 Run, 0 Fail, 8 Done > INFO 16:02:22,924 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.ComputeGCProfiles -I > /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip > -R data/human_b36_chr1.fasta -md test2/metadata -referenceProfile > test2/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile > data/human_b36_chr1.mask.fasta -copyNumberMaskFile > data/cn2_mask_g1k_b36_chr1.fasta > INFO 16:02:22,926 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.MergeGCProfiles -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip > -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofiles.zip > INFO 16:02:22,927 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-10.out > INFO 16:02:23,629 QGraph - 0 Pend, 1 Run, 0 Fail, 9 Done > INFO 16:02:52,932 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.MergeGCProfiles -I > /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip > -O > /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofiles.zip > INFO 16:02:52,933 QGraph - 0 Pend, 0 Run, 0 Fail, 10 Done > INFO 16:02:52,935 QCommandLine - Done > INFO 16:03:01,726 QScriptManager - Compiling 2 QScripts > INFO 16:03:12,978 QScriptManager - Compilation complete > INFO 16:03:13,101 HelpFormatter - > --------------------------------------------------------- > INFO 16:03:13,102 HelpFormatter - Program Name: > org.broadinstitute.sting.queue.QCommandLine > INFO 16:03:13,103 HelpFormatter - Program Args: -S > /home/wbxie/software/svtoolkit/qscript/SVAltAlign.q -S > /home/wbxie/software/svtoolkit/qscript/SVQScript.q -gatk > /home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir > -R data/human_b36_chr1.fasta -genomeMaskFile > data/human_b36_chr1.mask.fasta -runDirectory test2 -md test2/metadata > -jobLogDir test2/logs -vcf data/installtest.sites.vcf -I > data/installtest.bam -O test2/installtest.alt.bam -run > INFO 16:03:13,103 HelpFormatter - Date/Time: 2012/09/23 16:03:13 > INFO 16:03:13,104 HelpFormatter - > --------------------------------------------------------- > INFO 16:03:13,104 HelpFormatter - > --------------------------------------------------------- > INFO 16:03:13,110 QCommandLine - Scripting SVAltAlign > INFO 16:03:13,365 QCommandLine - Added 7 functions > INFO 16:03:13,366 QGraph - Generating graph. > INFO 16:03:13,407 QGraph - Generating scatter gather jobs. > INFO 16:03:13,409 QGraph - Removing original jobs. > INFO 16:03:13,411 QGraph - Adding scatter gather jobs. > INFO 16:03:13,412 QGraph - Regenerating graph. > INFO 16:03:13,419 QGraph - Running jobs. > INFO 16:03:13,484 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.GenerateAltAlleleFasta -I > /home/wbxie/software/svtoolkit/installtest/data/installtest.sites.vcf > -O > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta > -R data/human_b36_chr1.fasta > INFO 16:03:13,484 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-1.out > INFO 16:03:14,183 QGraph - 6 Pend, 1 Run, 0 Fail, 0 Done > INFO 16:03:43,481 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.GenerateAltAlleleFasta -I > /home/wbxie/software/svtoolkit/installtest/data/installtest.sites.vcf > -O > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta > -R data/human_b36_chr1.fasta > INFO 16:03:43,484 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > net.sf.picard.sam.CreateSequenceDictionary > O=/home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.dict > R=test2/altalign/installtest.sites.alt.fasta > TRUNCATE_NAMES_AT_WHITESPACE=TRUE > INFO 16:03:43,485 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-2.out > INFO 16:03:43,986 FunctionEdge - Starting: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.IndexFastaFile -I > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta > -O > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta.fai > INFO 16:03:43,987 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-3.out > INFO 16:03:44,572 FunctionEdge - Starting: bwa index > test2/altalign/installtest.sites.alt.fasta > INFO 16:03:44,572 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-4.out > INFO 16:03:44,680 QGraph - 3 Pend, 3 Run, 0 Fail, 1 Done > INFO 16:04:13,485 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > net.sf.picard.sam.CreateSequenceDictionary > O=/home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.dict > R=test2/altalign/installtest.sites.alt.fasta > TRUNCATE_NAMES_AT_WHITESPACE=TRUE > INFO 16:04:13,487 FunctionEdge - Done: java -Xmx4g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -cp > "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" > org.broadinstitute.sv.apps.IndexFastaFile -I > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta > -O > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta.fai > INFO 16:04:13,489 FunctionEdge - Done: bwa index > test2/altalign/installtest.sites.alt.fasta > INFO 16:04:13,514 FunctionEdge - Starting: java -Xmx1g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 16:04:13,514 FunctionEdge - Output written to > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-5.out > ERROR 16:05:01,564 FunctionEdge - Error: java -Xmx1g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. > Command line: > sh > /home/wbxie/software/svtoolkit/installtest/tmpdir/.exec5518112783651967939 > Exit code: 1 > Standard error contained: > INFO 16:04:19,251 HelpFormatter - > ----------------------------------------------------------------------------------- > INFO 16:04:19,256 HelpFormatter - The Genome Analysis Toolkit (GATK) > v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 > INFO 16:04:19,256 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 16:04:19,257 HelpFormatter - Please view our documentation at > http://www.broadinstitute.org/gsa/wiki > INFO 16:04:19,257 HelpFormatter - For support, please view our > support site at http://getsatisfaction.com/gsa > INFO 16:04:19,258 HelpFormatter - Program Args: -T SVAltAligner -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 16:04:19,258 HelpFormatter - Date/Time: 2012/09/23 16:04:19 > INFO 16:04:19,259 HelpFormatter - > ----------------------------------------------------------------------------------- > INFO 16:04:19,259 HelpFormatter - > ----------------------------------------------------------------------------------- > INFO 16:04:19,271 GenomeAnalysisEngine - Strictness is SILENT > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > org.broadinstitute.sting.utils.exceptions.ReviewedStingException: > Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it. > at > org.broadinstitute.sting.alignment.bwa.c.BWACAligner.<init>(BWACAligner.java:39) > 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:234) > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at > org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): > ##### ERROR > ##### ERROR Please visit the 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: Reverse BWT file is missing; please rerun 'bwa > aln' to regenerate it. > ##### ERROR > ------------------------------------------------------------------------------------------ > > at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) > at > org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) > at > org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) > at > org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) > at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) > at > org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at > org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) > at > org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) > INFO 16:05:01,566 QGraph - 2 Pend, 1 Run, 0 Fail, 4 Done > INFO 16:05:01,567 QGraph - 2 Pend, 0 Run, 1 Fail, 4 Done > INFO 16:05:01,567 QCommandLine - Done with errors > INFO 16:05:01,569 QGraph - ------- > INFO 16:05:01,575 QGraph - Failed: java -Xmx1g > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O > /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 16:05:01,576 QGraph - Log: > /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-5.out > > Any advices? Thank you in advance. > > Andrew > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: yw <yw...@gm...> - 2012-09-23 13:15:50
|
Hi, I am trying to configure GenomeSTRiP. Till now, I have run discovery.sh without error. When I came to genotyping.sh. It went wrong. All the output information is shown below: SVToolkit version 1.04 (build 982) Build date: 2012/08/10 18:30:21 Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP INFO 15:58:10,295 QScriptManager - Compiling 2 QScripts INFO 15:58:20,855 QScriptManager - Compilation complete INFO 15:58:20,987 HelpFormatter - --------------------------------------------------------- INFO 15:58:20,987 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 15:58:20,988 HelpFormatter - Program Args: -S /home/wbxie/software/svtoolkit/qscript/SVPreprocess.q -S /home/wbxie/software/svtoolkit/qscript/SVQScript.q -gatk /home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta -runDirectory test2 -md test2/metadata -computeGCProfiles -jobLogDir test2/logs -I data/installtest.bam -run INFO 15:58:20,988 HelpFormatter - Date/Time: 2012/09/23 15:58:20 INFO 15:58:20,989 HelpFormatter - --------------------------------------------------------- INFO 15:58:20,989 HelpFormatter - --------------------------------------------------------- INFO 15:58:20,995 QCommandLine - Scripting SVPreprocess INFO 15:58:21,326 QCommandLine - Added 10 functions INFO 15:58:21,326 QGraph - Generating graph. INFO 15:58:21,371 QGraph - Generating scatter gather jobs. INFO 15:58:21,373 QGraph - Removing original jobs. INFO 15:58:21,375 QGraph - Adding scatter gather jobs. INFO 15:58:21,376 QGraph - Regenerating graph. INFO 15:58:21,388 QGraph - Running jobs. INFO 15:58:21,479 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeHistograms -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin -md test2/metadata -createEmpty INFO 15:58:21,480 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-1.out INFO 15:59:14,762 QGraph - 9 Pend, 1 Run, 0 Fail, 0 Done INFO 15:59:14,773 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeHistograms -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin -md test2/metadata -createEmpty INFO 15:59:14,778 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin INFO 15:59:14,778 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-2.out INFO 15:59:15,234 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt -md test2/metadata -genomeMaskFile data/human_b36_chr1.mask.fasta -minMapQ 10 INFO 15:59:15,235 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-4.out INFO 16:00:08,246 QGraph - 7 Pend, 2 Run, 0 Fail, 1 Done INFO 16:00:08,249 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin INFO 16:00:08,252 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt -md test2/metadata -genomeMaskFile data/human_b36_chr1.mask.fasta -minMapQ 10 INFO 16:00:08,255 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeInsertStatistics -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.stats.dat INFO 16:00:08,255 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-3.out INFO 16:00:09,077 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt -md test2/metadata -maxInsertSizeStandardDeviations 3 INFO 16:00:09,077 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-6.out INFO 16:01:02,106 QGraph - 5 Pend, 2 Run, 0 Fail, 3 Done INFO 16:01:02,110 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeInsertStatistics -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.stats.dat INFO 16:01:02,113 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt -md test2/metadata -maxInsertSizeStandardDeviations 3 INFO 16:01:02,116 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeReadSpanCoverage -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans.dat INFO 16:01:02,116 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-7.out INFO 16:01:02,840 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeReadDepthCoverage -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth.dat INFO 16:01:02,840 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-5.out INFO 16:01:03,514 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeGCProfiles -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/reference.gcprof.zip -R data/human_b36_chr1.fasta -md test2/metadata -writeReferenceProfile true -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta INFO 16:01:03,515 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-8.out INFO 16:01:52,913 QGraph - 2 Pend, 3 Run, 0 Fail, 5 Done INFO 16:01:52,921 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeReadSpanCoverage -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans.dat INFO 16:01:52,923 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeReadDepthCoverage -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth.dat INFO 16:01:52,925 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeGCProfiles -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/reference.gcprof.zip -R data/human_b36_chr1.fasta -md test2/metadata -writeReferenceProfile true -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta INFO 16:01:52,927 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeGCProfiles -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip -R data/human_b36_chr1.fasta -md test2/metadata -referenceProfile test2/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta INFO 16:01:52,928 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-9.out INFO 16:02:00,425 QGraph - 1 Pend, 1 Run, 0 Fail, 8 Done INFO 16:02:22,924 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeGCProfiles -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip -R data/human_b36_chr1.fasta -md test2/metadata -referenceProfile test2/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta INFO 16:02:22,926 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeGCProfiles -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofiles.zip INFO 16:02:22,927 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-10.out INFO 16:02:23,629 QGraph - 0 Pend, 1 Run, 0 Fail, 9 Done INFO 16:02:52,932 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeGCProfiles -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofiles.zip INFO 16:02:52,933 QGraph - 0 Pend, 0 Run, 0 Fail, 10 Done INFO 16:02:52,935 QCommandLine - Done INFO 16:03:01,726 QScriptManager - Compiling 2 QScripts INFO 16:03:12,978 QScriptManager - Compilation complete INFO 16:03:13,101 HelpFormatter - --------------------------------------------------------- INFO 16:03:13,102 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 16:03:13,103 HelpFormatter - Program Args: -S /home/wbxie/software/svtoolkit/qscript/SVAltAlign.q -S /home/wbxie/software/svtoolkit/qscript/SVQScript.q -gatk /home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -runDirectory test2 -md test2/metadata -jobLogDir test2/logs -vcf data/installtest.sites.vcf -I data/installtest.bam -O test2/installtest.alt.bam -run INFO 16:03:13,103 HelpFormatter - Date/Time: 2012/09/23 16:03:13 INFO 16:03:13,104 HelpFormatter - --------------------------------------------------------- INFO 16:03:13,104 HelpFormatter - --------------------------------------------------------- INFO 16:03:13,110 QCommandLine - Scripting SVAltAlign INFO 16:03:13,365 QCommandLine - Added 7 functions INFO 16:03:13,366 QGraph - Generating graph. INFO 16:03:13,407 QGraph - Generating scatter gather jobs. INFO 16:03:13,409 QGraph - Removing original jobs. INFO 16:03:13,411 QGraph - Adding scatter gather jobs. INFO 16:03:13,412 QGraph - Regenerating graph. INFO 16:03:13,419 QGraph - Running jobs. INFO 16:03:13,484 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.GenerateAltAlleleFasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.sites.vcf -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta -R data/human_b36_chr1.fasta INFO 16:03:13,484 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-1.out INFO 16:03:14,183 QGraph - 6 Pend, 1 Run, 0 Fail, 0 Done INFO 16:03:43,481 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.GenerateAltAlleleFasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.sites.vcf -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta -R data/human_b36_chr1.fasta INFO 16:03:43,484 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" net.sf.picard.sam.CreateSequenceDictionary O=/home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.dict R=test2/altalign/installtest.sites.alt.fasta TRUNCATE_NAMES_AT_WHITESPACE=TRUE INFO 16:03:43,485 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-2.out INFO 16:03:43,986 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.IndexFastaFile -I /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta.fai INFO 16:03:43,987 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-3.out INFO 16:03:44,572 FunctionEdge - Starting: bwa index test2/altalign/installtest.sites.alt.fasta INFO 16:03:44,572 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-4.out INFO 16:03:44,680 QGraph - 3 Pend, 3 Run, 0 Fail, 1 Done INFO 16:04:13,485 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" net.sf.picard.sam.CreateSequenceDictionary O=/home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.dict R=test2/altalign/installtest.sites.alt.fasta TRUNCATE_NAMES_AT_WHITESPACE=TRUE INFO 16:04:13,487 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.IndexFastaFile -I /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta.fai INFO 16:04:13,489 FunctionEdge - Done: bwa index test2/altalign/installtest.sites.alt.fasta INFO 16:04:13,514 FunctionEdge - Starting: java -Xmx1g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 16:04:13,514 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-5.out ERROR 16:05:01,564 FunctionEdge - Error: java -Xmx1g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. Command line: sh /home/wbxie/software/svtoolkit/installtest/tmpdir/.exec5518112783651967939 Exit code: 1 Standard error contained: INFO 16:04:19,251 HelpFormatter - ----------------------------------------------------------------------------------- INFO 16:04:19,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 INFO 16:04:19,256 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 16:04:19,257 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 16:04:19,257 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 16:04:19,258 HelpFormatter - Program Args: -T SVAltAligner -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 16:04:19,258 HelpFormatter - Date/Time: 2012/09/23 16:04:19 INFO 16:04:19,259 HelpFormatter - ----------------------------------------------------------------------------------- INFO 16:04:19,259 HelpFormatter - ----------------------------------------------------------------------------------- INFO 16:04:19,271 GenomeAnalysisEngine - Strictness is SILENT ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it. at org.broadinstitute.sting.alignment.bwa.c.BWACAligner.<init>(BWACAligner.java:39) 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:234) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): ##### ERROR ##### ERROR Please visit the 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: Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it. ##### ERROR ------------------------------------------------------------------------------------------ at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) INFO 16:05:01,566 QGraph - 2 Pend, 1 Run, 0 Fail, 4 Done INFO 16:05:01,567 QGraph - 2 Pend, 0 Run, 1 Fail, 4 Done INFO 16:05:01,567 QCommandLine - Done with errors INFO 16:05:01,569 QGraph - ------- INFO 16:05:01,575 QGraph - Failed: java -Xmx1g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 16:05:01,576 QGraph - Log: /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-5.out Any advices? Thank you in advance. Andrew |
|
From: Bob H. <han...@br...> - 2012-09-14 13:03:56
|
On 9/14/12 8:36 AM, Ankita igib wrote: > Hi Bob, > > I have few more issues, i am trying to use plotgenotyping module using > command as follows > command - > java -cp > /data1/home/ankita/1000G_Data/svtoolkit/lib/SVToolkit.jar:/data1/home/1000G_Data/svtoolkit/lib/gatk/GenomeAnalysisTK.jar > org.broadinstitute.sv.apps.PlotGenotypingResults -site DEL_147 -o > test.pdf -rundirectory . > > Error - Exception in thread "main" java.lang.NoClassDefFoundError: > org/broadinstitute/sv/apps/PlotGenotypingResults > Caused by: java.lang.ClassNotFoundException: > org.broadinstitute.sv.apps.PlotGenotypingResults > at java.net.URLClassLoader$1.run(URLClassLoader.java:217) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:205) > at java.lang.ClassLoader.loadClass(ClassLoader.java:319) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) > at java.lang.ClassLoader.loadClass(ClassLoader.java:264) > at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:332) > > I tried to find, but couldn't find the answer. This is newer functionality only available in more recent interim releases. If you want to use this, you should download the latest interim release. > > (ii) for tigra_sv installation - i got cmake file, main.cpp samtools.h > file for installation but unable to install it, Can you guide ? No, you'll have to contact someone at WashU. > > (iii) While using alt_alignment, we have to provide unmapped bam > files separately or tool can identify the flags for unmapped reads in > a bam file (supposed downloaded from 1000 Genomes), how to use > tigra_sv in alt_alignment steps, as output of tigra_sv is a text file > of breakpoints. If you have sequencing data with longer paired reads (75-100bp) there is very little value in using completely unmapped read pairs and the alt alignment steps. It is more important if you have short 36 bp reads or unpaired data. Unmapped mates (stored in your bam files at the same POS as the mapped mate) will be used for split-read genotyping by default. I don't have a tool to convert the tigra_sv output into a well-formed vcf, which is what you will need to do to use breakpoints in genotyping. -Bob > > -- > ------------ > Regards > Ankita > DST Inspire Fellow (Graduate Student) > Lab no 604A > G.N. Ramachandran Knowledge Center for Genome Informatics > Institute of Genomics and Integrative Biology (CSIR) > North Campus DU, Near Jubliee Hall > Delhi - 110007 > > > http://igvbrowser.igib.res.in > > > > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Ankita i. <an...@ig...> - 2012-09-14 12:36:24
|
Hi Bob, I have few more issues, i am trying to use plotgenotyping module using command as follows command - java -cp /data1/home/ankita/1000G_Data/svtoolkit/lib/SVToolkit.jar:/data1/home/1000G_Data/svtoolkit/lib/gatk/GenomeAnalysisTK.jar org.broadinstitute.sv.apps.PlotGenotypingResults -site DEL_147 -o test.pdf -rundirectory . Error - Exception in thread "main" java.lang.NoClassDefFoundError: org/broadinstitute/sv/apps/PlotGenotypingResults Caused by: java.lang.ClassNotFoundException: org.broadinstitute.sv.apps.PlotGenotypingResults at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:319) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:264) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:332) I tried to find, but couldn't find the answer. (ii) for tigra_sv installation - i got cmake file, main.cpp samtools.h file for installation but unable to install it, Can you guide ? (iii) While using alt_alignment, we have to provide unmapped bam files separately or tool can identify the flags for unmapped reads in a bam file (supposed downloaded from 1000 Genomes), how to use tigra_sv in alt_alignment steps, as output of tigra_sv is a text file of breakpoints. -- ------------ Regards Ankita DST Inspire Fellow (Graduate Student) Lab no 604A G.N. Ramachandran Knowledge Center for Genome Informatics Institute of Genomics and Integrative Biology (CSIR) North Campus DU, Near Jubliee Hall Delhi - 110007 http://igvbrowser.igib.res.in |
|
From: Bob H. <han...@br...> - 2012-09-14 11:58:01
|
On 9/14/12 1:42 AM, Ankita igib wrote: > > Hi > > My queries are - > > (i) I don't understand what are benchmark datasets in svtoolkit folder > ? In benchmark folder they have test vcf files. But i have used it for > another set of samples, what is benchmark data for them? That's why > everytime on running discovery.sh script i got error for differing > with benchmark dataset. The discovery.sh and genotyping.sh scripts are part of the "installation test", which does a small test run of the main workflows in Genome STRiP, just to make sure the installation is correct. The benchmark data is part of the installation test (i.e. the correct answer). You can use discovery.sh and genotyping.sh as guides to using Genome STRiP, but you should also look at the underlying Q scripts as well to understand the steps involved. And you should be aware of the two most common mistakes: The -L 1 argument is restricting the analysis to chromosome 1. In any production use, you should include -reduceInsertSizeDistributions in SVPreprocess (you can do this in the installtest too, but it makes the test take longer to run; it is a net performance gain on larger data sets). > > (ii) How can i find/discover duplications even without genotyping them > using Genome STRip (as i far i understand Genome STRip also works for > genotytping deletions), is there any script available to find > duplications using Genome STRip? Genome STRiP currently does not have a duplication discovery module, although we are doing research in this area. Genotyping duplication sites is also not officially supported. You might consider CNVnator for duplication discovery based on read depth. Regards, -Bob > > > > - > Regards > Ankita > DST Inspire Fellow (Graduate Student) > Lab no 604A > G.N. Ramachandran Knowledge Center for Genome Informatics > Institute of Genomics and Integrative Biology (CSIR) > North Campus DU, Near Jubliee Hall > Delhi - 110007 > > > http://igvbrowser.igib.res.in > > > > > > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Ankita i. <an...@ig...> - 2012-09-14 06:11:54
|
Hi My queries are - (i) I don't understand what are benchmark datasets in svtoolkit folder ? In benchmark folder they have test vcf files. But i have used it for another set of samples, what is benchmark data for them? That's why everytime on running discovery.sh script i got error for differing with benchmark dataset. (ii) How can i find/discover duplications even without genotyping them using Genome STRip (as i far i understand Genome STRip also works for genotytping deletions), is there any script available to find duplications using Genome STRip? - Regards Ankita DST Inspire Fellow (Graduate Student) Lab no 604A G.N. Ramachandran Knowledge Center for Genome Informatics Institute of Genomics and Integrative Biology (CSIR) North Campus DU, Near Jubliee Hall Delhi - 110007 http://igvbrowser.igib.res.in |
|
From: Ankita i. <an...@ig...> - 2012-09-14 06:06:33
|
My queries are - (i) I don't understand what are benchmark datasets in svtoolkit folder ? In benchmark folder they have test vcf files. But i have used it for another set of samples, what is benchmark data for them? That's why everytime on running discovery.sh script i got error for differing with benchmark dataset. (ii) How can i find/discover duplications even without genotyping them using Genome STRip (as i far i understand Genome STRip also works for genotytping deletions), is there any script available to find duplications using Genome STRip? - Regards Ankita DST Inspire Fellow (Graduate Student) Lab no 604A G.N. Ramachandran Knowledge Center for Genome Informatics Institute of Genomics and Integrative Biology (CSIR) North Campus DU, Near Jubliee Hall Delhi - 110007 http://igvbrowser.igib.res.in |
3 messages has been excluded from this view by a project administrator.
