Re: [svtoolkit-help] Unrecognized sequence: 1:0-0 error with ELAND mapped bams

[Verena T. <ver...@em...>]

Hi Bob,

thanks a lot for your quick reply.

Here is the command right before the error stack:

INFO  23:32:06,755 QGraph - Deleting intermediate files.
INFO  23:32:06,764 QCommandLine - Done
INFO  23:32:09,047 QScriptManager - Compiling 2 QScripts
INFO  23:32:13,741 QScriptManager - Compilation complete
INFO  23:32:15,767 HelpFormatter -
---------------------------------------------------------
INFO  23:32:15,767 HelpFormatter - Program Name:
org.broadinstitute.sting.queue.QCommandLine
INFO  23:32:15,768 HelpFormatter - Program Args: -S
/home/tischler/software/svtoolkit/qscript/SVDiscovery.q -S
/home/tischler/software/svtoolkit/qscript/SVQScript.q -gatk
/home/tischler/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp
/home/tischler/software/svtoolkit/lib/SVToolkit.jar:/home/tischler/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/tischler/software/svtoolkit/lib/gatk/Queue.jar
-configFile conf/genstrip_parameters.txt -tempDir  /home/tischler/tmp/ -R
home/tischler/genomes/GenomeSTRiP_ref/test.fa -genomeMaskFile
/home/tischler/genomes/GenomeSTRiP_ref/test.mask.fasta -genderMapFile
gender.map -runDirectory test -md test/metadata -jobLogDir test/logs -L 1
-minimumSize 100 -maximumSize 1000000 -I /home/tischler/test1/test1.bam -I
/home/tischler/test2/test2.bam -I /home/tischler/test3/test3.bam -I
/home/tischler/test4/test4.bam -I /home/tischler/test5/test5.bam -O
/home/tischler/GenomeSTRiP/deletions.discovery.vcf -run
INFO  23:32:15,768 HelpFormatter - Date/Time: 2011/09/29 23:32:15
INFO  23:32:15,768 HelpFormatter -
---------------------------------------------------------
INFO  23:32:15,768 HelpFormatter -
---------------------------------------------------------
INFO  23:32:15,769 QCommandLine - Scripting SVDiscovery


The command from the bash-script (provided in the GenomeSTRiP package) I
only modified according to my paths:

export SV_DIR=`pwd`
SV_TMPDIR=/home/tischler/tmp/
export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}
mx="-Xmx8g"
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
...
...
# Run discovery
java -cp ${classpath} ${mx} \
    org.broadinstitute.sting.queue.QCommandLine \
    -S ${SV_DIR}/qscript/SVDiscovery.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    -cp ${classpath} \
    -configFile conf/genstrip_parameters.txt \
    -tempDir ${SV_TMPDIR} \
    -R /home/tischler/genomes/GenomeSTRiP_ref/test.fa \
    -genomeMaskFile /home/tischler/genomes/GenomeSTRiP_ref/test.mask.fasta \
    -genderMapFile gender.map \
    -runDirectory ${runDir} \
    -md ${runDir}/metadata \
    -jobLogDir ${runDir}/logs \
    -L 1 \
    -minimumSize 100 \
    -maximumSize 1000000 \
    -I ${bam1} \
    -I ${bam2} \
    -I ${bam3} \
    -I ${bam4} \
    -I ${bam5} \
    -O ${sites} \
    -run \
    || exit 1


I hope this helps!


Cheers
Verena



2011/9/27 Verena Tischler <ver...@em...>

> Dear all,
>
> I am using GenomeSTRiP on eland mapped bam files and get the following
> error message:
>
> INFO 04:20:04,705 HelpFormatter - Date/Time: 2011/09/27 04:20:04
> INFO 04:20:04,705 HelpFormatter -
> ---------------------------------------------------------
> INFO 04:20:04,705 HelpFormatter -
> ---------------------------------------------------------
> INFO 04:20:04,706 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 ----------------------
>
> parsing the input bam files for this sequence I only get a hit in the read
> quality string. Here is how a typical line in my bams looks like:
> HWI-ST169_185:3:41:17915:79533 89 chr15.fa 98634059 91 103M * 0 0
> CTACAAAGATAAAAAATTAGCTGAGTCTGTTGTCACAGGCCTGTCGTCCCAGCTACTGGAGAGGCTGAGGCATGAGAATCGCTTGAACCCGGGGGCAGACGTT
> BAD*96)4(17-@<=8+9+8D;>1:0-0@1+)'7(<><38=1).089FFD=FFF@FF=E=EEDD=?DD:EEE888EEF.DFD
> XD:Z:AA1A2GA1A13G1CA2G2A1G2T6AA11T1G32A6G3 SM:i:91 AS:i:0
> RG:Z:test_eland_101PE_1
>
>
> I hope this explains my problem
> Many thanks in advance for your help
> Verena
>
>


-- 
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Korbel Group - Genome Biology Unit
EMBL (European Molecular Biology Laboratories)
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Germany

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ver...@em...


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