Re: [svtoolkit-help] Genome strip - Unrecognized sequence: 1:0-0
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Re: [svtoolkit-help] Genome strip - Unrecognized sequence: 1:0-0
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From: Bob H. <han...@br...> - 2011-10-21 15:48:51
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Yes, you can use -L to process just a specific interval (or can pass a
file with a list of intervals - the file extension must be .list).
Note that the SVDiscovery queue script also does parallelization
internally, based on the -windowSize parameter.
For example, here are typical parameters to process the genome (or just
the intervals selected with -L) in 3Mb windows for events between 100bp
and 100Kb:
-windowSize 3000000
-windowPadding 100000
-minimumSize 100
-maximumSize 100000
You can invoke the queue script without '-run' to preview the chunking.
-Bob
On 10/21/11 11:30 AM, Ashish Kumar wrote:
>
> 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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