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

[Axel E. <axe...@gm...>]

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