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From: Yue X. <inu...@gm...> - 2016-10-04 05:49:01
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Hi, I am using Genome Strip CNV pipeline with 13 bam files, each with a coverage of 35-45x (there are two of them with a coverage of about 80x). The size of the bam files range from 20 Gb to 40 Gb. The supercomputer I use in my university has both space and file number limitations. This application generates a huge quantity of temporary files and uses huge space (seems like the temporary files are generated at GATK steps). I requested increases of space and file number limit several times, but they were never enough. Thus I was wondering if you could estimate the number of the temporary files that will be generated in the CNV pipeline for my 13 bam files, and the space required, so I can know if it is possible for me to run the CNV pipeline. I really appreciate any of your help! Best regards, Yue Xing |
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From: Joshua R. <jos...@sa...> - 2016-09-03 16:47:08
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I got a fatal exception from SVDepthScanner while in the process of doing a trial run of CNV Discovery using GenomeStrip. The error message was: java.lang.IllegalArgumentException: Illegal base [Y] seen in the allele This exception is thrown by htsjdk (https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/variant/variantcontext/Allele.java#L231) when attempting to build a variant context with an Allele that contains bases other than 'A', 'C', 'G', 'T', 'N', '*', or '.' - I didn't find anyone else encountering this error using GenomeStrip, although there was a GATK forum post about it happening in HaplotypeCaller. By doing an strace on the SVDepthScanner process (it is otherwise tricky to debug without source), I was able to determine that the exception occurred just after reading a section of the fasta reference within the "hs37d5" contig (i.e. the decoy sequences). Those sequences do indeed contain sequence ambiguity characters, including 'Y', but I'm not sure why SVDepthScanner is attempting to create a variant context within the decoy sequences, as the input files for the test run are all limited to chromosome 20. I was able to workaround the issue by adding the `-intervalList` argument with an interval of "20" to limit processing to chromosome 20 only, but I wanted to post here in case anyone else encounters this issue. Cheers, Josh. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
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From: Bob H. <han...@br...> - 2016-09-01 14:05:20
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Hi, Kumar, This is a problem with the Broad web server (which was upgraded recently). We are working with Broad IT to address it. In the meantime, there are a couple of workarounds: a) If you have an account already, log in to the account using the email address for the account and enter the same email address in the password field. This may give you an error message, but it will have logged you in successfully. Navigate to the download page and it should work. b) If you don't have an account already, create a new one. This will give you an error message, but it will successfully create the account. Then follow (a) above. Sorry about the difficulty, but the fix is out of our control and we're waiting for help with the Broad public-facing web server. -Bob On 9/1/16 7:29 AM, Singh, Kumar Saurabh wrote: > > Hi, > > I am trying to install Genome Strip, but I guess the registration page > is not working properly. Is there any other way of downloading Genome > Strip? > > Many thanks. > > Kumar > > *------- > Kumar Saurabh Singh, PhD* > Research Fellow > <http://biosciences.exeter.ac.uk/staff/index.php?web_id=Kumar_Saurabh_Singh> > > College of Life and Environmental Sciences > University of Exeter > Cornwall campus > Penryn TR10 9FE UK > Ext: 01326253702 > _K....@ex... > www.exeter.ac.uk_ > > http://www.exeter.ac.uk/codebox/email-sig/staff-sig.gif > > This email and any attachment may contain information that is > confidential, privileged, or subject to copyright, and which may be > exempt from disclosure under applicable legislation. It is intended > for the addressee only. If you received this message in error, please > let me know and delete the email and any attachments immediately. The > University will not accept responsibility for the > accuracy/completeness of this email and its attachments. > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Singh, K. S. <K.S...@ex...> - 2016-09-01 11:29:47
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Hi, I am trying to install Genome Strip, but I guess the registration page is not working properly. Is there any other way of downloading Genome Strip? Many thanks. Kumar ------- Kumar Saurabh Singh, PhD Research Fellow<http://biosciences.exeter.ac.uk/staff/index.php?web_id=Kumar_Saurabh_Singh> College of Life and Environmental Sciences University of Exeter Cornwall campus Penryn TR10 9FE UK Ext: 01326253702 K.S...@ex... www.exeter.ac.uk [http://www.exeter.ac.uk/codebox/email-sig/staff-sig.gif] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments. |
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From: Bob H. <han...@br...> - 2016-08-29 12:56:21
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We don't have a reference metadata bundle available for hg38 yet, but we should soon. -Bob On 8/29/16 4:35 AM, weikf wrote: > Hello , > > I am using strip to analysis my sample. > > hg 38 is requested to be reference. > > It is hard for me to get references metadata for hg38, could you please tell me how can I get them ? > > eg: > ploidymap > gcmask.fasta > svmask.fasta > > I am extremely grateful for your help. > > Best wishes, > kangfei > ------------------------------------------------------------------------------ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: weikf <wei...@ge...> - 2016-08-29 08:49:04
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Hello , I am using strip to analysis my sample. hg 38 is requested to be reference. It is hard for me to get references metadata for hg38, could you please tell me how can I get them ? eg: ploidymap gcmask.fasta svmask.fasta I am extremely grateful for your help. Best wishes, kangfei |
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From: Bertolotti, A. C. <r01...@ab...> - 2016-08-22 10:31:01
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Hello,
I am having problems running the installtest in svtoolkit. I am hoping you have some advice for me.
This is the error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sv/apps/SVToolkitInfo : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.security.SecureClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$100(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source)
I have checked my Java versions. I am running Java 7 and the version is 1.7.0.
Have you encountered this problem? Any help would be greatly appreciated.
Thank you for your time.
Best wishes,
Alicia
Alicia Bertolotti
PhD student
Institute of Biological and Environmental Sciences,
University of Aberdeen,
Zoology Building - Room 216,
Aberdeen,
AB24 2TZ.
The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.
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From: Selma B. <bs_...@es...> - 2016-07-28 01:22:52
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Hello, I'm a student from Algeria and i'm preparing a project in bioinformatics using GATK. I need a tool for SV detection and i've chosen GenomeSTRiP. I loged in the website and tried to download this tool; it starts the download normally but always stops and never continues till the end, i tried with different versions and had the same problem. Please help me with this. Thank you |
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From: Wenhua W. <wen...@ot...> - 2016-07-19 06:15:23
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Dear Bob, I have been through the filtering discussions briefly. I have a couple of questions re user intervention/filtering mentioned at your tutorial July 2013. I assume the user filtering is not incorporated in the discovery.sh or genotype.sh in the installtest directory (version 2.00.1611). a) are the user filtering operations still required as described in the tutorial, i.e. site filtering firstly SVAnnotator then GATK VariantFiltration? b) is 'Alternate allele alignment' possibly only when breakpoint assembly is available, e.g. bam files after a TIGRA run? Thanks Wen |
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From: Bob H. <han...@br...> - 2015-12-01 12:23:42
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Did you look on the support forum? It is preferable to get help there. Did you run preprocessing first? -Bob On 11/26/15 3:24 AM, JINGJING JIN wrote: > Dear all, > > I try to use svtoolkit to find the CNV across different samples like this: > > java -Xmx150g -cp > /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.gatk.queue.QCommandLine -S > /gpfs01/home/jingjing/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q > -S /gpfs01/home/jingjing/software/svtoolkit/qscript/SVQScript.q -cp > /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar > -gatk > /gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar > -configFile > /gpfs01/home/jingjing/software/svtoolkit/conf/genstrip_parameters.txt > -R > /gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa > -I input_bam_files.list -tilingWindowSize 1000 -tilingWindowOverlap > 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 > -minimumRefinedLength 500 -run > > > The following is the error message: > > > INFO 16:00:55,482 QScriptManager - Compiling 2 QScripts > INFO 16:01:03,449 QScriptManager - Compilation complete > INFO 16:01:03,516 HelpFormatter - > ---------------------------------------------------------------------- > INFO 16:01:03,516 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled > 2015/10/04 09:18:40 > INFO 16:01:03,516 HelpFormatter - Copyright (c) 2012 The Broad Institute > INFO 16:01:03,517 HelpFormatter - For support and documentation go to > http://www.broadinstitute.org/gatk > INFO 16:01:03,518 HelpFormatter - Program Args: -S > /gpfs01/home/jingjing/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q > -S /gpfs01/home/jingjing/software/svtoolkit/qscript/SVQScript.q -cp > /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar > -gatk > /gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar > -configFile > /gpfs01/home/jingjing/software/svtoolkit/conf/genstrip_parameters.txt > -R > /gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa > -I input_bam_files.list -tilingWindowSize 1000 -tilingWindowOverlap > 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 > -minimumRefinedLength 500 -run > INFO 16:01:03,519 HelpFormatter - Executing as jingjing@node-1-7 on > Linux 2.6.32-431.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM > 1.8.0_60-b27. > INFO 16:01:03,519 HelpFormatter - Date/Time: 2015/11/26 16:01:03 > INFO 16:01:03,520 HelpFormatter - > ---------------------------------------------------------------------- > INFO 16:01:03,520 HelpFormatter - > ---------------------------------------------------------------------- > INFO 16:01:03,528 QCommandLine - Scripting CNVDiscoveryPipeline > INFO 16:01:03,791 QCommandLine - Added 15 functions > INFO 16:01:03,791 QGraph - Generating graph. > INFO 16:01:03,811 QGraph - Running jobs. > INFO 16:01:03,842 FunctionEdge - Starting: 'java' '-Xmx2048m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' > '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/input_bam_files.list' > '-O' > '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/bam_headers/merged_headers.bam' > '-L' 'NONE' > INFO 16:01:03,842 FunctionEdge - Output written to > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-1.out > > INFO 16:01:39,124 QGraph - 14 Pend, 1 Run, 0 Fail, 0 Done > INFO 16:01:39,130 FunctionEdge - Done: 'java' '-Xmx2048m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' > '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/input_bam_files.list' > '-O' > '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/bam_headers/merged_headers.bam' > '-L' 'NONE' > INFO 16:01:39,132 QGraph - Writing incremental jobs reports... > INFO 16:01:39,133 QJobsReporter - Writing JobLogging GATKReport to > file > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt > > INFO 16:01:39,183 FunctionEdge - Starting: samtools index > bam_headers/merged_headers.bam > INFO 16:01:39,184 FunctionEdge - Output written to > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-2.out > > INFO 16:01:39,260 FunctionEdge - Starting: 'java' '-Xmx2048m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' > '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' > '-R' > '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' > '-filterDescriptionFile' > 'gender_gt_filters/gender_gt_filter_descr.txt' > INFO 16:01:39,260 FunctionEdge - Output written to > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out > > INFO 16:01:43,885 QGraph - 12 Pend, 2 Run, 0 Fail, 1 Done > INFO 16:02:09,130 FunctionEdge - Done: samtools index > bam_headers/merged_headers.bam > ERROR 16:02:09,136 FunctionEdge - Error: 'java' '-Xmx2048m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' > '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' > '-R' > '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' > '-filterDescriptionFile' > 'gender_gt_filters/gender_gt_filter_descr.txt' > ERROR 16:02:09,139 FunctionEdge - Contents of > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out: > Exception in thread "main" > org.broadinstitute.gatk.utils.commandline.MissingArgumentException: > Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing. > Argument with name '--genderMapFile' (-genderMapFile) is missing. > at > org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:299) > at > org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:279) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:224) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) > at > org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29) > at > org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25) > at > org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile.main(CreateGenderGenotypeFilterFile.java:59) > > INFO 16:02:09,140 QGraph - Writing incremental jobs reports... > INFO 16:02:09,140 QJobsReporter - Writing JobLogging GATKReport to > file > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt > > INFO 16:02:09,264 QGraph - 12 Pend, 0 Run, 1 Fail, 2 Done > INFO 16:02:09,265 QCommandLine - Writing final jobs report... > INFO 16:02:09,266 QJobsReporter - Writing JobLogging GATKReport to > file > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt > > INFO 16:02:09,271 QJobsReporter - Plotting JobLogging GATKReport to > file > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.pdf > > WARN 16:02:09,810 RScriptExecutor - RScript exited with 1. Run with > -l DEBUG for more info. > INFO 16:02:09,812 QCommandLine - Done with errors > INFO 16:02:09,814 QGraph - ------- > INFO 16:02:09,815 QGraph - Failed: 'java' '-Xmx2048m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' > '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' > '-R' > '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' > '-filterDescriptionFile' > 'gender_gt_filters/gender_gt_filter_descr.txt' > INFO 16:02:09,815 QGraph - Log: > /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out > > INFO 16:02:09,816 QCommandLine - Script failed: 12 Pend, 0 Run, 1 > Fail, 2 Done > > > Can anyone give me some suggestions about how to deal with it? > > Thanks! > > Jingjing > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: JINGJING J. <jjj...@gm...> - 2015-11-26 08:24:25
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Dear all, I try to use svtoolkit to find the CNV across different samples like this: java -Xmx150g -cp /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.gatk.queue.QCommandLine -S /gpfs01/home/jingjing/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q -S /gpfs01/home/jingjing/software/svtoolkit/qscript/SVQScript.q -cp /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar -gatk /gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /gpfs01/home/jingjing/software/svtoolkit/conf/genstrip_parameters.txt -R /gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa -I input_bam_files.list -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500 -run The following is the error message: INFO 16:00:55,482 QScriptManager - Compiling 2 QScripts INFO 16:01:03,449 QScriptManager - Compilation complete INFO 16:01:03,516 HelpFormatter - ---------------------------------------------------------------------- INFO 16:01:03,516 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/10/04 09:18:40 INFO 16:01:03,516 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 16:01:03,517 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 16:01:03,518 HelpFormatter - Program Args: -S /gpfs01/home/jingjing/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q -S /gpfs01/home/jingjing/software/svtoolkit/qscript/SVQScript.q -cp /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar -gatk /gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /gpfs01/home/jingjing/software/svtoolkit/conf/genstrip_parameters.txt -R /gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa -I input_bam_files.list -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500 -run INFO 16:01:03,519 HelpFormatter - Executing as jingjing@node-1-7 on Linux 2.6.32-431.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_60-b27. INFO 16:01:03,519 HelpFormatter - Date/Time: 2015/11/26 16:01:03 INFO 16:01:03,520 HelpFormatter - ---------------------------------------------------------------------- INFO 16:01:03,520 HelpFormatter - ---------------------------------------------------------------------- INFO 16:01:03,528 QCommandLine - Scripting CNVDiscoveryPipeline INFO 16:01:03,791 QCommandLine - Added 15 functions INFO 16:01:03,791 QGraph - Generating graph. INFO 16:01:03,811 QGraph - Running jobs. INFO 16:01:03,842 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/input_bam_files.list' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/bam_headers/merged_headers.bam' '-L' 'NONE' INFO 16:01:03,842 FunctionEdge - Output written to /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-1.out INFO 16:01:39,124 QGraph - 14 Pend, 1 Run, 0 Fail, 0 Done INFO 16:01:39,130 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/input_bam_files.list' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/bam_headers/merged_headers.bam' '-L' 'NONE' INFO 16:01:39,132 QGraph - Writing incremental jobs reports... INFO 16:01:39,133 QJobsReporter - Writing JobLogging GATKReport to file /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt INFO 16:01:39,183 FunctionEdge - Starting: samtools index bam_headers/merged_headers.bam INFO 16:01:39,184 FunctionEdge - Output written to /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-2.out INFO 16:01:39,260 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' '-R' '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' '-filterDescriptionFile' 'gender_gt_filters/gender_gt_filter_descr.txt' INFO 16:01:39,260 FunctionEdge - Output written to /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out INFO 16:01:43,885 QGraph - 12 Pend, 2 Run, 0 Fail, 1 Done INFO 16:02:09,130 FunctionEdge - Done: samtools index bam_headers/merged_headers.bam ERROR 16:02:09,136 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' '-R' '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' '-filterDescriptionFile' 'gender_gt_filters/gender_gt_filter_descr.txt' ERROR 16:02:09,139 FunctionEdge - Contents of /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out: Exception in thread "main" org.broadinstitute.gatk.utils.commandline.MissingArgumentException: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing. Argument with name '--genderMapFile' (-genderMapFile) is missing. at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:299) at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:279) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:224) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29) at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25) at org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile.main(CreateGenderGenotypeFilterFile.java:59) INFO 16:02:09,140 QGraph - Writing incremental jobs reports... INFO 16:02:09,140 QJobsReporter - Writing JobLogging GATKReport to file /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt INFO 16:02:09,264 QGraph - 12 Pend, 0 Run, 1 Fail, 2 Done INFO 16:02:09,265 QCommandLine - Writing final jobs report... INFO 16:02:09,266 QJobsReporter - Writing JobLogging GATKReport to file /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt INFO 16:02:09,271 QJobsReporter - Plotting JobLogging GATKReport to file /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.pdf WARN 16:02:09,810 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. INFO 16:02:09,812 QCommandLine - Done with errors INFO 16:02:09,814 QGraph - ------- INFO 16:02:09,815 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' '-R' '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' '-filterDescriptionFile' 'gender_gt_filters/gender_gt_filter_descr.txt' INFO 16:02:09,815 QGraph - Log: /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out INFO 16:02:09,816 QCommandLine - Script failed: 12 Pend, 0 Run, 1 Fail, 2 Done Can anyone give me some suggestions about how to deal with it? Thanks! Jingjing |
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From: William G. <W....@su...> - 2015-10-15 13:26:38
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Hi, I¹m testing GenomeStrip to run on 230 Drosophila melanogaster females in a Linux Sun Grid Engine cluster. My deletion detection pipeline is Preprocess, Disocovery, Genotyper. The last test run on a 2Mb section of all individuals took 40 minutes. In the final vcf, generated by the genotyper, there are 362 events, of which 17 are PASS. My problem is that I don¹t really know how to interpret the output. A typical genotype entry for a passed deletion is .:LQ:-0.48,-0.48,-0.48:-0.48,-0.48,-0.48:0 although occasionally there is a .:LQ:-2.00,-0.31,-0.31:-2.00,-0.31,-0.31:0 I¹m not able to find this info out anywhere else. Sincerely, William Gilks ________________________________________ Research Fellow School of Life Sciences University of Sussex, United Kingdom Tel +44(0)1273 678 559 FAX +44(0)1273 877586 URL http://www.sussex.ac.uk/lifesci/morrowlab/people |
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From: Ana P. <ana...@gm...> - 2015-10-14 15:00:10
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Hi Bob, Thank you for your detailed replied. I will try to do what you suggested and see how far I get. Will definitely let you know how/if it works or of any other questions I might have. Would love this method to work for our lab so, fingers crossed. Thanks again, Ana > No dia 14/10/2015, às 15:43, Bob Handsaker <han...@br... <mailto:han...@br...>> escreveu: > > Hi, Ana, > > The documentation is reflective of the fact that I haven't tried anything like this and I can't promise that there won't be some gotchas. > But from my brief reading of the ZW system (on Wikipedia), I think you could try using a custom ploidy map (details below) and see how far you get. > I would be interested to learn where things do and don't work. > > First, you should determine if there are pseudo-autosomal regions on Z or W, like in human, and in particular how your reference sequence models these. > This has as much to do with how the reference is built and how the alignments are done as it does the acutal biology. > > The hg19 ploidy map we use looks like this: > X 2699521 154931043 F 2 > X 2699521 154931043 M 1 > Y 1 59373566 F 0 > Y 1 59373566 M 1 > * * * * 2 > > Where we are specifically indicating the non-PAR region on X (as opposed to all of X). > Note that the human reference includes the PARs on X but masks out the PARs on Y. > > If you have no PARs, then you might try something like: > Z 1 nnn M 2 > Z 1 nnn F 1 > W 1 nnn M 0 > W 1 nnn F 1 > * * * * 2 > > Basically, the ploidy map is giving the expected ploidy for a sample with a certain gender in each region of the genome. > You can specify as many regions as you need. The last line is a wild-card saying the rest of the genome is diploid. > > The preprocessing code is hard-wired to do an X/Y sex chromosome analysis and automatically call sample gender. > This may fall over or it may just not produce any output (which would be the more desirable). Please let me know if it falls over. > Since there won't be any automated gender calls, you will have to supply the gender of each of your samples. > The preprocessing code is using read depth across X and Y (with a custom mask that helps clean up the signal) and then calling gender from the gross copy-number estimates. > You could also do something similar, either to call gender or to QC your gender assignments. > > Hope this helps, > -Bob > > On 10/13/15 10:56 AM, Ana Pinharanda wrote: >> Dear Bob, >> >> I have installed and run the test data for svtoolkit_2.00.1602 with no errors. >> >> I work with a non-human female heterogametic (ZW) system and while reading the documentation under >> http://www.broadinstitute.org/software/genomestrip/node_ReferenceMetadata.html <http://www.broadinstitute.org/software/genomestrip/node_ReferenceMetadata.html> >> on how to built a custom reference metadata bundle, I came across the following statement under the reference.ploidymap.txt section >> "Currently, only organisms with a human-like XY sex determination system are fully supported." >> >> >> My question is: what does this actually mean? >> >> Does it mean that they are not supported just simply because there are no examples of any of them under your reference metadata bundles? >> Or does it mean that for my runs to work I need to swap the Z for a X and the W for a Y when I make the ploidymap.txt? >> Or does it mean that beyond swapping the letter (Z->X & W->Y) I also have to label males as females and females as males so that the predictions of a male heterogametic system match up with what I am feeding into it? >> >> Finally, what would your predictions be if I dropped any W linked regions altogether from the analysis? Would a Z0 system be allowed? If so, how would I make the ploidymap be able to reflect this correctly? >> >> Thank you in advance for the time spent, >> >> All the best, >> >> Ana >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> svtoolkit-help mailing list >> svt...@li... <mailto:svt...@li...> >> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help <https://lists.sourceforge.net/lists/listinfo/svtoolkit-help> > > ------------------------------------------------------------------------------ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... <mailto:svt...@li...> > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help <https://lists.sourceforge.net/lists/listinfo/svtoolkit-help> |
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From: Bob H. <han...@br...> - 2015-10-14 14:43:14
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Hi, Ana, The documentation is reflective of the fact that I haven't tried anything like this and I can't promise that there won't be some gotchas. But from my brief reading of the ZW system (on Wikipedia), I think you could try using a custom ploidy map (details below) and see how far you get. I would be interested to learn where things do and don't work. First, you should determine if there are pseudo-autosomal regions on Z or W, like in human, and in particular how your reference sequence models these. This has as much to do with how the reference is built and how the alignments are done as it does the acutal biology. The hg19 ploidy map we use looks like this: X 2699521 154931043 F 2 X 2699521 154931043 M 1 Y 1 59373566 F 0 Y 1 59373566 M 1 * * * * 2 Where we are specifically indicating the non-PAR region on X (as opposed to all of X). Note that the human reference includes the PARs on X but masks out the PARs on Y. If you have no PARs, then you might try something like: Z 1 nnn M 2 Z 1 nnn F 1 W 1 nnn M 0 W 1 nnn F 1 * * * * 2 Basically, the ploidy map is giving the expected ploidy for a sample with a certain gender in each region of the genome. You can specify as many regions as you need. The last line is a wild-card saying the rest of the genome is diploid. The preprocessing code is hard-wired to do an X/Y sex chromosome analysis and automatically call sample gender. This may fall over or it may just not produce any output (which would be the more desirable). Please let me know if it falls over. Since there won't be any automated gender calls, you will have to supply the gender of each of your samples. The preprocessing code is using read depth across X and Y (with a custom mask that helps clean up the signal) and then calling gender from the gross copy-number estimates. You could also do something similar, either to call gender or to QC your gender assignments. Hope this helps, -Bob On 10/13/15 10:56 AM, Ana Pinharanda wrote: > Dear Bob, > > I have installed and run the test data for svtoolkit_2.00.1602 with no > errors. > > I work with a non-human female heterogametic (ZW) system and while > reading the documentation under > _http://www.broadinstitute.org/software/genomestrip/node_ReferenceMetadata.html_ > on how to built a custom reference metadata bundle, I came across the > following statement under the /reference./ploidymap.txt section > "Currently, only organisms with a human-like XY sex determination > system are fully supported." > > > My question is: what does this actually mean? > > Does it mean that they are not supported just simply because there are > no examples of any of them under your reference metadata bundles? > Or does it mean that for my runs to work I need to swap the Z for a X > and the W for a Y when I make the ploidymap.txt? > Or does it mean that beyond swapping the letter (Z->X & W->Y) I also > have to label males as females and females as males so that the > predictions of a male heterogametic system match up with what I am > feeding into it? > > Finally, what would your predictions be if I dropped any W linked > regions altogether from the analysis? Would a Z0 system be allowed? If > so, how would I make the ploidymap be able to reflect this correctly? > > Thank you in advance for the time spent, > > All the best, > > Ana > > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Ana P. <ana...@gm...> - 2015-10-13 14:57:05
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Dear Bob, I have installed and run the test data for svtoolkit_2.00.1602 with no errors. I work with a non-human female heterogametic (ZW) system and while reading the documentation under http://www.broadinstitute.org/software/genomestrip/node_ReferenceMetadata.html on how to built a custom reference metadata bundle, I came across the following statement under the reference.ploidymap.txt section "Currently, only organisms with a human-like XY sex determination system are fully supported." My question is: what does this actually mean? Does it mean that they are not supported just simply because there are no examples of any of them under your reference metadata bundles? Or does it mean that for my runs to work I need to swap the Z for a X and the W for a Y when I make the ploidymap.txt? Or does it mean that beyond swapping the letter (Z->X & W->Y) I also have to label males as females and females as males so that the predictions of a male heterogametic system match up with what I am feeding into it? Finally, what would your predictions be if I dropped any W linked regions altogether from the analysis? Would a Z0 system be allowed? If so, how would I make the ploidymap be able to reflect this correctly? Thank you in advance for the time spent, All the best, Ana |
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From: Bob H. <han...@br...> - 2015-09-23 14:40:56
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That's funny. It is working for me. Try this to test: $ wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam --2015-09-23 10:38:48-- http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam Resolving ftp.1000genomes.ebi.ac.uk... 193.62.192.8 Connecting to ftp.1000genomes.ebi.ac.uk|193.62.192.8|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 13775539379 (13G) [application/octet-stream] Saving to: `HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam' (you can kill it if the download starts successfully) -Bob On 9/23/15 9:55 AM, Yuan Chen wrote: > Hi , > > > I have just installed GenomeStrip and I have successfully run install > test job. when I try to run cookbook example : *Genotyping a novel > site using 1000 Genomes Phase 1 (local) > <http://www.broadinstitute.org/software/genomestrip/cookbook-genotyping-novel-site-1000-genomes-phase-1>* > I only use the first 5 lines in bam list file : test_bam.list : > http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam > http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00100/alignment/HG00100.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam > http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00103/alignment/HG00103.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam > http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00106/alignment/HG00106.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam > http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00108/alignment/HG00108.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam > > But I keep having connection time out error, see error message below, > any idea what could be wrong ? > > yuan > > ERROR 14:01:36,632 FunctionEdge - > Error: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/.queue/tmp' '-cp' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/SVToolkit.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/Queue.jar' > org.broadinstitute.sv.main.SVGenotyper '-T' > 'SVGenotyperWalker' '-R' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.fasta' '-I' 'bamfile_lists/test_bam.list' '-O' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/1000G_MERGED_DEL_2_99615.genotypes.vcf' '-inputFileIndexCache' > '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/bam_indices' '-disableGATKTraversal' 'true' '-md' > '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/metadata' '-configFile' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/conf/genstrip_parameters.txt' '-runDirectory' > 'rundir' '-genderMapFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/dataset/samples_1kg_phase1_illumina.gender.map' '-ploidyMapFile' > '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.ploidy.map' '-genomeMaskFile' > '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/svmasks/human_g1k_v37.mask.36.fasta' '-vcf' 'example/1000G_MERGED_DEL_2_99615.vcf' > > ERROR 14:01:36,661 FunctionEdge - Contents > of /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/logs/SVGenotyper-1.out: > java.net.ConnectException: Connection timed out > at java.net.PlainSocketImpl.socketConnect(Native Method) > at > java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) > at > java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) > at > java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) > at java.net.Socket.connect(Socket.java:579) > at java.net.Socket.connect(Socket.java:528) > at sun.net.NetworkClient.doConnect(NetworkClient.java:180) > at sun.net.www.http.HttpClient.openServer(HttpClient.java:378) > at sun.net.www.http.HttpClient.openServer(HttpClient.java:473) > at sun.net.www.http.HttpClient.<init>(HttpClient.java:203) > at sun.net.www.http.HttpClient.New(HttpClient.java:290) > at sun.net.www.http.HttpClient.New(HttpClient.java:306) > at > sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:995) > at > sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:931) > at > sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:849) > at > sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1299) > at > htsjdk.samtools.seekablestream.SeekableHTTPStream.read(SeekableHTTPStream.java:119) > at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) > at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) > at java.io.BufferedInputStream.read(BufferedInputStream.java:334) > at > org.broadinstitute.sv.dataset.SAMUrlLocation$SeekableBufferedStream.read(SAMUrlLocation.java:195) > at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) > at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) > at java.io.BufferedInputStream.read(BufferedInputStream.java:334) > at > htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:100) > at > htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:421) > at > htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:409) > at > htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:364) > at > htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127) > at > htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252) > at java.io.DataInputStream.read(DataInputStream.java:149) > at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404) > at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380) > at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:366) > at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:493) > at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:183) > at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:148) > at > htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:163) > at > org.broadinstitute.sv.dataset.SAMUrlLocation.createSamFileReader(SAMUrlLocation.java:81) > at org.broadinstitute.sv.dataset.DataSet.initInputFile(DataSet.java:115) > at org.broadinstitute.sv.dataset.DataSet.initialize(DataSet.java:106) > at > org.broadinstitute.sv.genotyping.SVGenotyperWalker.initDataSet(SVGenotyperWalker.java:359) > at > org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:205) > at > org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) > at > org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319) > at > org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) > at > org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) > at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78) > at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21) > INFO 14:00:23,049 23-Sep-2015 ProgressMeter - Starting > 0.0 6.5 m 644.9 w 100.0% 6.5 m 0.0 s > INFO 14:00:53,052 23-Sep-2015 ProgressMeter - Starting > 0.0 7.0 m 694.5 w 100.0% 7.0 m 0.0 s > INFO 14:01:23,054 23-Sep-2015 ProgressMeter - Starting > 0.0 7.5 m 744.1 w 100.0% 7.5 m 0.0 s > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.RuntimeException: Error reading from the URL: offset=0, > length=131072 > at > org.broadinstitute.sv.dataset.SAMUrlLocation$SeekableBufferedStream.read(SAMUrlLocation.java:205) > at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) > at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) > at java.io.BufferedInputStream.read(BufferedInputStream.java:334) > at > htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:100) > at > htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:421) > at > htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:409) > at > htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:364) > at > htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127) > at > htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252) > at java.io.DataInputStream.read(DataInputStream.java:149) > at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404) > at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380) > at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:366) > at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:493) > at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:183) > at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:148) > at > htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:163) > at > org.broadinstitute.sv.dataset.SAMUrlLocation.createSamFileReader(SAMUrlLocation.java:81) > at org.broadinstitute.sv.dataset.DataSet.initInputFile(DataSet.java:115) > at org.broadinstitute.sv.dataset.DataSet.initialize(DataSet.java:106) > at > org.broadinstitute.sv.genotyping.SVGenotyperWalker.initDataSet(SVGenotyperWalker.java:359) > at > org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:205) > at > org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) > at > org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319) > at > org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) > at > org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) > at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78) > at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21) > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>): > ##### ERROR > ##### ERROR This might be a bug. Please check the documentation guide > to see if this is a known problem. > ##### ERROR If not, please post the error message, with stack trace, > to the GATK forum. > ##### ERROR Visit our website and forum for extensive documentation > and answers to > ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk > ##### ERROR > ##### ERROR MESSAGE: Error reading from the URL: offset=0, length=131072 > ##### ERROR > ------------------------------------------------------------------------------------------ > > INFO 14:01:36,663 QGraph - Writing incremental jobs reports... > INFO 14:01:36,663 QJobsReporter - Writing JobLogging GATKReport to > file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.txt > > INFO 14:01:37,157 QGraph - 0 Pend, 0 Run, 1 Fail, 0 Done > INFO 14:01:37,158 QCommandLine - Writing final jobs report... > INFO 14:01:37,159 QJobsReporter - Writing JobLogging GATKReport to > file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.txt > > INFO 14:01:37,169 QJobsReporter - Plotting JobLogging GATKReport to > file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.pdf > > WARN 14:01:39,375 RScriptExecutor - RScript exited with 1. Run with > -l DEBUG for more info. > INFO 14:01:39,377 QCommandLine - Done with errors > INFO 14:01:39,378 QGraph - ------- > INFO 14:01:39,385 QGraph - > Failed: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/.queue/tmp' '-cp' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/SVToolkit.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/Queue.jar' > org.broadinstitute.sv.main.SVGenotyper '-T' > 'SVGenotyperWalker' '-R' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.fasta' '-I' 'bamfile_lists/test_bam.list' '-O' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/1000G_MERGED_DEL_2_99615.genotypes.vcf' '-inputFileIndexCache' > '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/bam_indices' '-disableGATKTraversal' 'true' '-md' > '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/metadata' '-configFile' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/conf/genstrip_parameters.txt' '-runDirectory' > 'rundir' '-genderMapFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/dataset/samples_1kg_phase1_illumina.gender.map' '-ploidyMapFile' > '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.ploidy.map' '-genomeMaskFile' > '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/svmasks/human_g1k_v37.mask.36.fasta' '-vcf' 'example/1000G_MERGED_DEL_2_99615.vcf' > > INFO 14:01:39,386 QGraph - Log: > /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/logs/SVGenotyper-1.out > > INFO 14:01:39,387 QCommandLine - Script failed: 0 Pend, 0 Run, 1 > Fail, 0 Done > > > ------------------------------------------------------------------------------ > Monitor Your Dynamic Infrastructure at Any Scale With Datadog! > Get real-time metrics from all of your servers, apps and tools > in one place. > SourceForge users - Click here to start your Free Trial of Datadog now! > http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Yuan C. <yua...@gm...> - 2015-09-23 13:56:01
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Hi , I have just installed GenomeStrip and I have successfully run install test job. when I try to run cookbook example : Genotyping a novel site using 1000 Genomes Phase 1 (local) I only use the first 5 lines in bam list file : test_bam.list : http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00100/alignment/HG00100.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00103/alignment/HG00103.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00106/alignment/HG00106.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00108/alignment/HG00108.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam But I keep having connection time out error, see error message below, any idea what could be wrong ? yuan ERROR 14:01:36,632 FunctionEdge - Error: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/.queue/tmp' '-cp' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/SVToolkit.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVGenotyper '-T' 'SVGenotyperWalker' '-R' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.fasta' '-I' 'bamfile_lists/test_bam.list' '-O' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/1000G_MERGED_DEL_2_99615.genotypes.vcf' '-inputFileIndexCache' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/bam_indices' '-disableGATKTraversal' 'true' '-md' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/metadata' '-configFile' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/conf/genstrip_parameters.txt' '-runDirectory' 'rundir' '-genderMapFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/dataset/samples_1kg_phase1_illumina.gender.map' '-ploidyMapFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.ploidy.map' '-genomeMaskFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/svmasks/human_g1k_v37.mask.36.fasta' '-vcf' 'example/1000G_MERGED_DEL_2_99615.vcf' ERROR 14:01:36,661 FunctionEdge - Contents of /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/logs/SVGenotyper-1.out: java.net.ConnectException: Connection timed out at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:579) at java.net.Socket.connect(Socket.java:528) at sun.net.NetworkClient.doConnect(NetworkClient.java:180) at sun.net.www.http.HttpClient.openServer(HttpClient.java:378) at sun.net.www.http.HttpClient.openServer(HttpClient.java:473) at sun.net.www.http.HttpClient.<init>(HttpClient.java:203) at sun.net.www.http.HttpClient.New(HttpClient.java:290) at sun.net.www.http.HttpClient.New(HttpClient.java:306) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:995) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:931) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:849) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1299) at htsjdk.samtools.seekablestream.SeekableHTTPStream.read(SeekableHTTPStream.java:119) at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) at java.io.BufferedInputStream.read(BufferedInputStream.java:334) at org.broadinstitute.sv.dataset.SAMUrlLocation$SeekableBufferedStream.read(SAMUrlLocation.java:195) at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) at java.io.BufferedInputStream.read(BufferedInputStream.java:334) at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:100) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:421) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:409) at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:364) at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127) at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252) at java.io.DataInputStream.read(DataInputStream.java:149) at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404) at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380) at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:366) at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:493) at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:183) at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:148) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:163) at org.broadinstitute.sv.dataset.SAMUrlLocation.createSamFileReader(SAMUrlLocation.java:81) at org.broadinstitute.sv.dataset.DataSet.initInputFile(DataSet.java:115) at org.broadinstitute.sv.dataset.DataSet.initialize(DataSet.java:106) at org.broadinstitute.sv.genotyping.SVGenotyperWalker.initDataSet(SVGenotyperWalker.java:359) at org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:205) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78) at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21) INFO 14:00:23,049 23-Sep-2015 ProgressMeter - Starting 0.0 6.5 m 644.9 w 100.0% 6.5 m 0.0 s INFO 14:00:53,052 23-Sep-2015 ProgressMeter - Starting 0.0 7.0 m 694.5 w 100.0% 7.0 m 0.0 s INFO 14:01:23,054 23-Sep-2015 ProgressMeter - Starting 0.0 7.5 m 744.1 w 100.0% 7.5 m 0.0 s ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.RuntimeException: Error reading from the URL: offset=0, length=131072 at org.broadinstitute.sv.dataset.SAMUrlLocation$SeekableBufferedStream.read(SAMUrlLocation.java:205) at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) at java.io.BufferedInputStream.read(BufferedInputStream.java:334) at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:100) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:421) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:409) at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:364) at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127) at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252) at java.io.DataInputStream.read(DataInputStream.java:149) at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404) at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380) at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:366) at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:493) at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:183) at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:148) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:163) at org.broadinstitute.sv.dataset.SAMUrlLocation.createSamFileReader(SAMUrlLocation.java:81) at org.broadinstitute.sv.dataset.DataSet.initInputFile(DataSet.java:115) at org.broadinstitute.sv.dataset.DataSet.initialize(DataSet.java:106) at org.broadinstitute.sv.genotyping.SVGenotyperWalker.initDataSet(SVGenotyperWalker.java:359) at org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:205) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78) at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>): ##### ERROR ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem. ##### ERROR If not, please post the error message, with stack trace, to the GATK forum. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Error reading from the URL: offset=0, length=131072 ##### ERROR ------------------------------------------------------------------------------------------ INFO 14:01:36,663 QGraph - Writing incremental jobs reports... INFO 14:01:36,663 QJobsReporter - Writing JobLogging GATKReport to file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.txt INFO 14:01:37,157 QGraph - 0 Pend, 0 Run, 1 Fail, 0 Done INFO 14:01:37,158 QCommandLine - Writing final jobs report... INFO 14:01:37,159 QJobsReporter - Writing JobLogging GATKReport to file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.txt INFO 14:01:37,169 QJobsReporter - Plotting JobLogging GATKReport to file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.pdf WARN 14:01:39,375 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. INFO 14:01:39,377 QCommandLine - Done with errors INFO 14:01:39,378 QGraph - ------- INFO 14:01:39,385 QGraph - Failed: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/.queue/tmp' '-cp' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/SVToolkit.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVGenotyper '-T' 'SVGenotyperWalker' '-R' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.fasta' '-I' 'bamfile_lists/test_bam.list' '-O' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/1000G_MERGED_DEL_2_99615.genotypes.vcf' '-inputFileIndexCache' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/bam_indices' '-disableGATKTraversal' 'true' '-md' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/metadata' '-configFile' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/conf/genstrip_parameters.txt' '-runDirectory' 'rundir' '-genderMapFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/dataset/samples_1kg_phase1_illumina.gender.map' '-ploidyMapFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.ploidy.map' '-genomeMaskFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/svmasks/human_g1k_v37.mask.36.fasta' '-vcf' 'example/1000G_MERGED_DEL_2_99615.vcf' INFO 14:01:39,386 QGraph - Log: /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/logs/SVGenotyper-1.out INFO 14:01:39,387 QCommandLine - Script failed: 0 Pend, 0 Run, 1 Fail, 0 Done |
|
From: Bob H. <han...@br...> - 2015-09-16 12:55:21
|
Hi, Can,
My first guess is that you have an incompatible version of htsjdk on
your classpath.
GS comes bundled with its own copy of the GATK (usually somewhat out of
date) that the software is compatible with.
If that isn't it, it will require more investigation.
From the stack trace, this is blowing up inside of htsjdk trying to
read one of your bam files.
-Bob
On 9/16/15 8:04 AM, Can Alkan wrote:
> Hi Bob
>
> I'm running the latest version of GenomeSTRiP, and after
> preprocessing, the discovery step exited with an exception. I copied
> the stack below. I didn't do anything fancy, just edited the
> discovery.sh file. here are the cmd lines:
>
>
> java -cp ${classpath} ${mx} \
> org.broadinstitute.gatk.queue.QCommandLine \
> -S ${SV_DIR}/qscript/SVPreprocess.q \
> -S ${SV_DIR}/qscript/SVQScript.q \
> -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
> --disableJobReport \
> -cp ${classpath} \
> -configFile genstrip_installtest_parameters.txt \
> -tempDir ${SV_TMPDIR} \
> -R $BUNDLE_DIR/human_g1k_hs37d5.fasta \
> -genomeMaskFile $BUNDLE_DIR/human_g1k_hs37d5.svmask.fasta \
> -copyNumberMaskFile $BUNDLE_DIR/human_g1k_hs37d5.gcmask.fasta \
> -genderMapFile gender.map \
> -runDirectory ${runDir} \
> -md ${runDir}/metadata \
> -disableGATKTraversal \
> -useMultiStep \
> -reduceInsertSizeDistributions false \
> -computeGCProfiles true \
> -computeReadCounts true \
> -jobLogDir ${runDir}/logs \
> -I ${bam} \
> -run \
> || exit 1
>
> # Run discovery.
> java -cp ${classpath} ${mx} \
> org.broadinstitute.gatk.queue.QCommandLine \
> -S ${SV_DIR}/qscript/SVDiscovery.q \
> -S ${SV_DIR}/qscript/SVQScript.q \
> -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
> --disableJobReport \
> -cp ${classpath} \
> -configFile genstrip_installtest_parameters.txt \
> -tempDir ${SV_TMPDIR} \
> -R $BUNDLE_DIR/human_g1k_hs37d5.fasta \
> -genomeMaskFile $BUNDLE_DIR/human_g1k_hs37d5.svmask.fasta \
> -genderMapFile gender.map \
> -runDirectory ${runDir} \
> -md ${runDir}/metadata \
> -disableGATKTraversal \
> -jobLogDir ${runDir}/logs \
> -minimumSize 100 \
> -maximumSize 1000000 \
> -suppressVCFCommandLines \
> -I ${bam} \
> -O $runDir/${sites} \
> -run \
> || exit 1
>
>
> the error stack:
>
>
> ##### ERROR stack trace
> java.lang.IllegalArgumentException: Invalid reference index -1
> at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
> at
> htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:473)
> at
> htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryContained(SamReader.java:356)
> at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runTraversal(DeletionDiscoveryAlgorithm.java:141)
> at
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:107)
> at
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:42)
> at
> org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
> at
> org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
> at
> org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
> at
> org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
> at
> org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
> at
> org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
> at
> org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
> at
> org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
> at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
> ##### ERROR
> ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
> ##### ERROR
> ##### ERROR This might be a bug. Please check the documentation guide
> to see if this is a known problem.
> ##### ERROR If not, please post the error message, with stack trace,
> to the GATK forum.
> ##### ERROR Visit our website and forum for extensive documentation
> and answers to
> ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
> ##### ERROR
> ##### ERROR MESSAGE: Invalid reference index -1
> ##### ERROR
> ------------------------------------------------------------------------------------------
>
>
>
>
> ------------------------------------------------------------------------------
> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
> Get real-time metrics from all of your servers, apps and tools
> in one place.
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>
>
> _______________________________________________
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> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help
|
|
From: Can A. <ca...@gm...> - 2015-09-16 12:04:45
|
Hi Bob
I'm running the latest version of GenomeSTRiP, and after preprocessing, the
discovery step exited with an exception. I copied the stack below. I
didn't do anything fancy, just edited the discovery.sh file. here are the
cmd lines:
java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-cp ${classpath} \
-configFile genstrip_installtest_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R $BUNDLE_DIR/human_g1k_hs37d5.fasta \
-genomeMaskFile $BUNDLE_DIR/human_g1k_hs37d5.svmask.fasta \
-copyNumberMaskFile $BUNDLE_DIR/human_g1k_hs37d5.gcmask.fasta \
-genderMapFile gender.map \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-disableGATKTraversal \
-useMultiStep \
-reduceInsertSizeDistributions false \
-computeGCProfiles true \
-computeReadCounts true \
-jobLogDir ${runDir}/logs \
-I ${bam} \
-run \
|| exit 1
# Run discovery.
java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVDiscovery.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-cp ${classpath} \
-configFile genstrip_installtest_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R $BUNDLE_DIR/human_g1k_hs37d5.fasta \
-genomeMaskFile $BUNDLE_DIR/human_g1k_hs37d5.svmask.fasta \
-genderMapFile gender.map \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-disableGATKTraversal \
-jobLogDir ${runDir}/logs \
-minimumSize 100 \
-maximumSize 1000000 \
-suppressVCFCommandLines \
-I ${bam} \
-O $runDir/${sites} \
-run \
|| exit 1
the error stack:
##### ERROR stack trace
java.lang.IllegalArgumentException: Invalid reference index -1
at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
at
htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:473)
at
htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryContained(SamReader.java:356)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runTraversal(DeletionDiscoveryAlgorithm.java:141)
at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:107)
at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:42)
at
org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at
org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
at
org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at
org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at
org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to
see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the
GATK forum.
##### ERROR Visit our website and forum for extensive documentation and
answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Invalid reference index -1
##### ERROR
------------------------------------------------------------------------------------------
|
|
From: Jin S. <jin...@me...> - 2015-08-15 02:17:59
|
Please ignore this message below. I have found the cause of this particular error. On 8/14/15, 3:00 PM, Jin Szatkiewicz wrote: > Hi Bob, > > I am using the latest version of GenomeStrip ( July21, 2015) but had > the following error message while running SV Proprocess. > > "Unable to execute QScript: SVPreprocess.script() threw the following > exception: java.lang.RuntimeException: Cannot locate R script: > metadata/plot_chr_vs_chr_readdepth.R (SV_DIR = )" > > I have searched the mailing list but did not find an entry about this. > Could you let me know how to fix it? Many thanks!! > > Jin > > |
|
From: Jin S. <jin...@me...> - 2015-08-14 19:35:05
|
Hi Bob,
I am using the latest version of GenomeStrip ( July21, 2015) but had the
following error message while running SV Proprocess.
"Unable to execute QScript: SVPreprocess.script() threw the following
exception: java.lang.RuntimeException: Cannot locate R script:
metadata/plot_chr_vs_chr_readdepth.R (SV_DIR = )"
I have searched the mailing list but did not find an entry about this.
Could you let me know how to fix it? Many thanks!!
Jin
P.S. My complete error file is below:
++++++++++
Genome indexes for use with BWA are available
in /proj/seq/data on kure.
bwa/bowtie/bowtie2 indexes are located in "Sequence" directory
under the top level genome directory with name in CAPS, e.g.
MM9_UCSC
INFO 14:47:09,833 QScriptManager - Compiling 2 QScripts
INFO 14:47:17,321 QScriptManager - Compilation complete
INFO 14:47:17,438 HelpFormatter -
----------------------------------------------------------------------
INFO 14:47:17,438 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled
2015/05/15 09:12:56
INFO 14:47:17,438 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 14:47:17,439 HelpFormatter - For support and documentation go to
http://www.broadinstitute.org/gatk
INFO 14:47:17,439 HelpFormatter - Program Args: -S
/nas02/home/j/i/jinpengs/tools/svtoolkit//qscript/SVPreprocess.q -S
/nas02/home/j/i/jinpengs/tools/svtoolkit//qscript/SVQScript.q -gatk
/nas02/home/j/i/jinpengs/tools/svtoolkit//lib/gatk/GenomeAnalysisTK
jar --disableJobReport -cp
/nas02/home/j/i/jinpengs/tools/svtoolkit//lib/SVToolkit.jar:/nas02/home/j/i/jinpengs/tools/svtoolkit//lib/gatk/GenomeAnalysisTK.jar:/nas02/home/j/i/jinpengs/tools/svtoolkit//lib/gatk/Queue.jar
-configFile /nas02/home/j/i/jinpeng
/tools/svtoolkit//conf/genstrip_parameters.txt -tempDir
/lustre/scr/j/i/jinpengs/Donor/GS/working//P1890_101/tmpdir -R
/lustre/scr/j/i/jinpengs/GS.rmd/1000G_phase1//human_g1k_v37.fasta
-genomeMaskFile /lustre/scr/j/i/jinpengs/GS.rmd/1000G_phase1//human_g1
_v37.mask.36.fasta -ploidyMapFile
/lustre/scr/j/i/jinpengs/GS.rmd/1000G_phase1//human_g1k_v37.ploidy.map
-copyNumberMaskFile
/lustre/scr/j/i/jinpengs/GS.rmd/1000G_phase1//human_g1k_v37.gcmask.fasta
-genderMapFile /nas/depts/007/sullilab/projects/donor/bam
/donorwgs_gender.map -runDirectory
/lustre/scr/j/i/jinpengs/Donor/GS/working//P1890_101/ -md
/lustre/scr/j/i/jinpengs/Donor/GS/working//P1890_101//metadata
-disableGATKTraversal -useMultiStep -computeGCProfiles true -jobLogDir
/lustre/scr/j/i/jinpengs/Don
r/GS/working//P1890_101//logs -I
/nas/depts/007/sullilab/projects/donor/bam//P1890_101.clean.dedup.recal.bam
-run
INFO 14:47:17,442 HelpFormatter - Executing as
jin...@c-... on Linux 2.6.18-238.12.1.el5 amd64; Java
HotSpot(TM) 64-Bit Server VM 1.8.0_11-b12.
INFO 14:47:17,442 HelpFormatter - Date/Time: 2015/08/14 14:47:17
INFO 14:47:17,442 HelpFormatter -
----------------------------------------------------------------------
INFO 14:47:17,442 HelpFormatter -
----------------------------------------------------------------------
INFO 14:47:17,449 QCommandLine - Scripting SVPreprocess
INFO 14:47:17,769 QCommandLine - Done with errors
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript:
Unable to execute QScript: SVPreprocess.script() threw the following
exception: java.lang.RuntimeException: Cannot locate R script:
metadata/plot_chr_vs_chr_readdepth.R (SV_DIR =
)
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at
org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at
org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused by: java.lang.RuntimeException: Cannot locate R script:
metadata/plot_chr_vs_chr_readdepth.R (SV_DIR = )
at
org.broadinstitute.sv.util.RUtilities.findRScript(RUtilities.java:47)
at SVPreprocess$PlotChrYvsChrX.<init>(SVPreprocess.q:251)
at SVPreprocess.createMakeProfilesCallGenders(SVPreprocess.q:179)
at SVPreprocess.script(SVPreprocess.q:93)
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156)
... 10 more
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to
see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to
the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and
answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to execute QScript: SVPreprocess.script()
threw the following exception: java.lang.RuntimeException: Cannot locate
R script: metadata/plot_chr_vs_chr_readdepth.R (SV_DIR = )
##### ERROR
------------------------------------------------------------------------------------------
INFO 14:47:17,775 QCommandLine - Shutting down jobs. Please wait...
[ji
|
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From: Bob H. <han...@br...> - 2015-06-22 12:58:15
|
I'd have to research this, but my first reaction is that probably we don't support this, because we force people to register with their email address (and it would allow you to skip registration). We do the registration tracking to help us count usage for our funders. -Bob On 6/22/15 5:04 AM, Maimaris, Jesmeen wrote: > Hello, > > I’m having trouble downloading the software on unix using the wget > command. When using this command I use wget and then web link, but > this downloads the html document and not the tar file. > > Do you have a link that downloads just the tar/tar.gx file in binary? > > I have registered under this email. > > Thanks > > Jes Maimaris > > > > ------------------------------------------------------------------------------ > Monitor 25 network devices or servers for free with OpManager! > OpManager is web-based network management software that monitors > network devices and physical & virtual servers, alerts via email & sms > for fault. Monitor 25 devices for free with no restriction. Download now > http://ad.doubleclick.net/ddm/clk/292181274;119417398;o > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Maimaris, J. <j.m...@uc...> - 2015-06-22 09:05:02
|
Hello, I'm having trouble downloading the software on unix using the wget command. When using this command I use wget and then web link, but this downloads the html document and not the tar file. Do you have a link that downloads just the tar/tar.gx file in binary? I have registered under this email. Thanks Jes Maimaris |
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From: Bob H. <han...@br...> - 2015-06-16 12:22:08
|
I corrected the information in that post. That information was correct at the time, but has since changed (the old way caused problems if you tried to merge preprocessing directories with non-disjoint bams). The memory footprint can be controlled if your bams are disjoint (use -bamFilesAreDisjoint true). If they are not disjoint (i.e. you have the same samples/libraries/read groups in multiple input bam files), then the easiest solution is to give more memory to MergeInsertSizeHistograms. Most bams are disjoint, but the default is to be conservative. -Bob On 6/15/15 11:07 PM, Arthur Wuster wrote: > Hi, > > I'm getting an OutOfMemoryError heap space error running SVPreprocess > on 50 BAMs (see attached log file). The error occurs with > MergeInsertSizeHistograms, which, if I understand the following forum > discussion correctly, shouldn't even run if I use > reduceInsertSizeDistributions: > > http://gatkforums.broadinstitute.org/discussion/2167/genomestrip-svpreprocess-q-java-heap-space-error > > Up-adjusting memory doesn't solve the problem. I'm using v 2.00.1592, > and the installtest runs fine. I've pasted my settings below. > > I'd be very grateful for any advice on how to fix this. > > Thank you for your help, > > Art > > java -cp${classpath}${mx}\ > > org.broadinstitute.gatk.queue.QCommandLine \ > > -S${SV_DIR}/qscript/SVPreprocess.q \ > > -S${SV_DIR}/qscript/SVQScript.q \ > > -gatk${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ > > --disableJobReport\ > > -cp${classpath}\ > > -configFile${dataDir}/genstrip_parameters.txt \ > > -tempDir${SV_TMPDIR}\ > > -R${dataDir}/GRCh38.fa \ > > -genomeMaskFile${dataDir}/GRCh38.mask.100.fasta \ > > -copyNumberMaskFile${dataDir}/GRCh38.cn2_mask.fasta \ > > -genderMapFile${dataDir}/oct14_sex.map \ > > -ploidyMapFile${dataDir}/humgen_g1k_v38_ploidy.map \ > > -runDirectory${runDir}\ > > -md${runDir}/metadata \ > > -disableGATKTraversal\ > > -useMultiStep\ > > -reduceInsertSizeDistributionstrue\ > > -computeGCProfilestrue\ > > -computeReadCountstrue\ > > -jobLogDir${runDir}/logs \ > > -I${bam}\ > > -run\ > > -jobRunnerDrmaa \ > > -gatkJobRunnerDrmaa \ > > -jobProjectsv_nov14 \ > > -jobNative"-R rusage[mem=16]"-jobNative"-q long"\ > > -jobQueuelong \ > > || exit1 > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Arthur W. <wus...@ge...> - 2015-06-16 03:26:06
|
Hi, I'm getting an OutOfMemoryError heap space error running SVPreprocess on 50 BAMs (see attached log file). The error occurs with MergeInsertSizeHistograms, which, if I understand the following forum discussion correctly, shouldn't even run if I use reduceInsertSizeDistributions: http://gatkforums.broadinstitute.org/discussion/2167/genomestrip-svpreprocess-q-java-heap-space-error Up-adjusting memory doesn't solve the problem. I'm using v 2.00.1592, and the installtest runs fine. I've pasted my settings below. I'd be very grateful for any advice on how to fix this. Thank you for your help, Art java -cp ${classpath} ${mx} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVPreprocess.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ --disableJobReport \ -cp ${classpath} \ -configFile ${dataDir}/genstrip_parameters.txt \ -tempDir ${SV_TMPDIR} \ -R ${dataDir}/GRCh38.fa \ -genomeMaskFile ${dataDir}/GRCh38.mask.100.fasta \ -copyNumberMaskFile ${dataDir}/GRCh38.cn2_mask.fasta \ -genderMapFile ${dataDir}/oct14_sex.map \ -ploidyMapFile ${dataDir}/humgen_g1k_v38_ploidy.map \ -runDirectory ${runDir} \ -md ${runDir}/metadata \ -disableGATKTraversal \ -useMultiStep \ -reduceInsertSizeDistributions true \ -computeGCProfiles true \ -computeReadCounts true \ -jobLogDir ${runDir}/logs \ -I ${bam} \ -run \ -jobRunner Drmaa \ -gatkJobRunner Drmaa \ -jobProject sv_nov14 \ -jobNative "-R rusage[mem=16]" -jobNative "-q long" \ -jobQueue long \ || exit 1 |
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