GenomeStrip for large deletion

ngs_medicinengs_medicine ILMember
edited August 2015 in Ask the GATK team

In my previous posting, I was suggested to use GenomeStrip for detection of large deletion.
(http://gatkforums.broadinstitute.org/discussion/comment/23197#Comment_23197)

I was working with GenomeStrip.. I could sucessfully run the test script (e.g. discovery.sh/ genotyping.sh)

Then, I would like to run with my data. I only have my sorted_bam file and reference fasta file.
When, I just updated the bam file infor and reference file info from the discovery.sh file, and run it, I got the following errors..

.

org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript: Unable to execute QScript: SVPreprocess.script() threw the following exception: org.broadin stitute.sv.commandline.ArgumentException: Invalid genome interval specified - chromosome/contig name not found in reference genome: 1
at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused by: org.broadinstitute.sv.commandline.ArgumentException: Invalid genome interval specified - chromosome/contig name not found in reference genome: 1
at org.broadinstitute.sv.queue.ComputeGenomeLocusPartitions.computePartitions(ComputeGenomeLocusPartitions.java:68)
at org.broadinstitute.sv.qscript.SVQScript.computeLocusPartitions(SVQScript.q:286)
at org.broadinstitute.sv.qscript.SVQScript.mergeReadCountsByLocus(SVQScript.q:820)
at SVPreprocess.createMultiStepScript(SVPreprocess.q:120)
at SVPreprocess.script(SVPreprocess.q:88)
at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156)
... 10 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Unable to execute QScript: SVPreprocess.script() threw the following exception: org.broadinstitute.sv.commandline.ArgumentException: Invalid genome interval specified - chromosome/contig name not found in reference genome: 1

##### ERROR --------------------------------------------------------------------------

I am not sure why it says that contig name is not found in reference genome.. Could you please let me know about this?

Thanks..

Post edited by ngs_medicine on

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