Re: [svtoolkit-help] Problem running Genome Strip: Error message : "Unrecognized sequence: 1:0-0

[Per A. E. <eri...@br...>]

Hi
Any ideas?

On Thu, Jun 7, 2012 at 10:10 PM, Per Axel Ericsson
<eri...@br...> wrote:
> Hi
> I've been trying to run Genome Strip on a ~4Mb region, I've run the
> installation test and I have all the dependencies wokring, my target
> is the dog genome a co-worker have created a genome mask file which
> have been previously been validated.
> Can you point me in a direction what this error message mean?
> I included the error message below :
>
> INFO  15:58:04,137 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_installtest_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_test -md
> HCSMA_test/metadata -jobLogDir HCSMA_test/logs -L 1 -minimumSize 100
> -maximumSize 1000000 -I
> /seq/picard_aggregation/G14162/HCSMA_B90_Homo_1/v3/HCSMA_B90_Homo_1.bam
> -O HCSMA.discovery.vcf -run
> INFO  15:58:04,138 HelpFormatter - Date/Time: 2012/06/07 15:58:04
> INFO  15:58:04,138 HelpFormatter -
> ---------------------------------------------------------
> INFO  15:58:04,138 HelpFormatter -
> ---------------------------------------------------------
> INFO  15:58:04,140 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 ------------------------------------------------------------------------------------------
> Best regards Axel