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

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

The -L argument restricts the regions of the genome you want to cover - 
the chromosome name "1" isn't found in your reference sequence.
-Bob

On 6/13/12 9:26 AM, Per Axel Ericsson wrote:
> 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
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