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

[Ashish K. <as...@we...>]

Hi Bob,

On the same issue, if we want to use the -L option, would it be safe to presume that we can chunk up the chromosomes.
So, say something like "-L  20:1250000-2500000" would be a valid option, assuming that this sequence exists in my reference genome?

Thanks,
Ashish


From: Bob Handsaker [mailto:han...@br...]
Sent: 06 October 2011 14:40
To: svt...@li...
Subject: Re: [svtoolkit-help] Genome strip - Unrecognized sequence: 1:0-0

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 ------------------------------------------------------------------------------------------





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