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

[Verena T. <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