Re: [svtoolkit-help] Genome strip - Unrecognized sequence: 1:0-0

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

This is because the example script uses "-L 1" (only process chromosome 
1) to make it faster,
but you likely don't have a sequence named "1" in your reference genome.
To process the whole genome, simply remove the -L argument.
-Bob

On 10/5/11 2:50 PM, Axel Ericsson wrote:
> Hi
> I have get the following error message when I run the Genome strip: I 
> forwarded the modified shell script, hope you could point me in the 
> right direction.
> Best regards Axel
>
> INFO  14:37:52,013 QScriptManager - Compiling 2 QScripts
> INFO  14:37:59,172 QScriptManager - Compilation complete
> INFO  14:38:02,654 HelpFormatter - 
> ---------------------------------------------------------
> INFO  14:38:02,655 HelpFormatter - Program Name: 
> org.broadinstitute.sting.queue.QCommandLine
> INFO  14:38:02,655 HelpFormatter - Program Args: -S 
> /seq/vsag/axel/tools/Genome_strip/svtoolkit/qscript/SVDiscovery.q -S 
> /seq/vsag/axel/tools/Genome_strip/svtoolkit/qscript/SVQScript.q -gatk 
> /seq/vsag/axel/tools/Genome_strip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar 
> -cp 
> /seq/vsag/axel/tools/Genome_strip/svtoolkit/lib/SVToolkit.jar:/seq/vsag/axel/tools/Genome_strip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/seq/vsag/axel/tools/Genome_strip/svtoolkit/lib/gatk/Queue.jar 
> -configFile conf/genstrip_HCSMA_parameters.txt -tempDir ./tmpdir -R 
> /seq/references/Canis_lupus_familiaris_assembly2/v0/Canis_lupus_familiaris_assembly2.fasta 
> -genomeMaskFile 
> /seq/vsag/hyunji/CCD/capture/genomestrip/canFam2_1_index/work/Canis_lupus_familiaris_assembly2.mask.fasta 
> -genderMapFile data/HCSMA_gender.map -runDirectory HCSMA -md 
> HCSMA/metadata -jobLogDir HCSMA/logs -L 1 -minimumSize 100 
> -maximumSize 1000000 -I 
> /seq/vsag/axel/bamfiles/HCSMCRealignment.HCSMA_B90_Homo_1.clean.dedup.recal.bam 
> -O HCSMA.discovery.vcf -run
> INFO  14:38:02,656 HelpFormatter - Date/Time: 2011/10/05 14:38:02
> INFO  14:38:02,656 HelpFormatter - 
> ---------------------------------------------------------
> INFO  14:38:02,657 HelpFormatter - 
> ---------------------------------------------------------
> INFO  14:38:02,661 QCommandLine - Scripting SVDiscovery
> ##### ERROR 
> ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> java.lang.IllegalArgumentException:*Unrecognized sequence: 1:0-0*
> at 
> org.broadinstitute.sv.queue.ComputeDiscoveryPartitions.computePartitions(ComputeDiscoveryPartitions.java:96)
> at 
> org.broadinstitute.sv.qscript.SVQScript.computeDiscoveryPartitions(SVQScript.q:132)
> at SVDiscovery.script(SVDiscovery.q:19)
> at 
> org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$1.apply(QCommandLine.scala:46)
> at 
> org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$1.apply(QCommandLine.scala:43)
> at scala.collection.Iterator$class.foreach(Iterator.scala:631)
> at 
> scala.collection.JavaConversions$JIteratorWrapper.foreach(JavaConversions.scala:549)
> at scala.collection.IterableLike$class.foreach(IterableLike.scala:79)
> at 
> scala.collection.JavaConversions$JListWrapper.foreach(JavaConversions.scala:596)
> at 
> org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:43)
> at 
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
> at 
> org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:117)
> at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
> ##### ERROR 
> ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
> ##### ERROR
> ##### ERROR Please visit to wiki to see if this is a known problem
> ##### ERROR If not, please post the error, with stack trace, to the 
> GATK forum
> ##### ERROR Visit our wiki for extensive documentation 
> http://www.broadinstitute.org/gsa/wiki
> ##### ERROR Visit our forum to view answers to commonly asked 
> questions http://getsatisfaction.com/gsa
> ##### ERROR
> ##### ERROR MESSAGE: Unrecognized sequence: 1:0-0
> ##### ERROR 
> ------------------------------------------------------------------------------------------
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help