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Genome STRIP SVPreprocess error

Hi I'm running genomestrip and I got this error

I'm testing whole human genome to find out SVs with Genome STRiP.
I used bwa, picard with Homo_sapiens_assembly38.fasta (GATK bundle)
Here's my command and printed error.

1014% [[email protected] SVanalysis]$ java1.8 -Xmx12g -cp ${classpath} org.broadinstitute.gatk.queue.QCommandLine -S /home01/x1477hyk/prg/svtoolkit/qscript/SVPreprocess.q -S /home01/x1477hyk/prg/svtoolkit/qscript/SVQScript.q -cp ${classpath} -gatk /home01/x1477hyk/prg/GenomeAnalysisTK.jar -configFile /home01/x1477hyk/prg/svtoolkit/conf/genstrip_parameters.txt -R Homo_sapiens_assembly38.fasta -genomeMaskFile /scratch2/x1477hyk/SVanalysis/zipun/Homo_sapiens_assembly38/Homo_sapiens_assembly38.gcmask.fasta -I SRR1291026_addrg_sorted_md.bam -minimumSize 100 -maximumSize 1000000 -md output_metadata_directory -jobLogDir logDir -run

INFO 13:17:23,099 QScriptManager - Compiling 2 QScripts
INFO 13:17:42,455 QScriptManager - Compilation complete
INFO 13:17:43,245 HelpFormatter - ----------------------------------------------------------------------
INFO 13:17:43,245 HelpFormatter - Queue v3.7.GS-r1748-0-g74bfe0b, Compiled 2017/08/21 09:41:56
INFO 13:17:43,245 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 13:17:43,246 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 13:17:43,246 HelpFormatter - Program Args: -S /home01/x1477hyk/prg/svtoolkit/qscript/SVPreprocess.q -S /home01/x1477hyk/prg/svtoolkit/qscript/SVQScript.q -cp /home01/x1477hyk/prg/svtoolkit//lib/SVToolkit.jar:/home01/x1477hyk/prg/svtoolkit//lib/gatk/GenomeAnalysisTK.jar:/home01/x1477hyk/prg/svtoolkit//lib/gatk/Queue.jar -gatk /home01/x1477hyk/prg/GenomeAnalysisTK.jar -configFile /home01/x1477hyk/prg/svtoolkit/conf/genstrip_parameters.txt -R Homo_sapiens_assembly38.fasta -genomeMaskFile /scratch2/x1477hyk/SVanalysis/zipun/Homo_sapiens_assembly38/Homo_sapiens_assembly38.gcmask.fasta -I SRR1291026_addrg_sorted_md.bam -minimumSize 100 -maximumSize 1000000 -md output_metadata_directory -jobLogDir logDir -run
INFO 13:17:43,253 HelpFormatter - Executing as [email protected] on Linux 2.6.18-194.17.1.el5_lustre.1.8.6smp amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13.
INFO 13:17:43,253 HelpFormatter - Date/Time: 2017/09/08 13:17:43
INFO 13:17:43,253 HelpFormatter - ----------------------------------------------------------------------
INFO 13:17:43,253 HelpFormatter - ----------------------------------------------------------------------
INFO 13:17:43,259 QCommandLine - Scripting SVPreprocess
INFO 13:17:43,284 QCommandLine - Done with errors

ERROR --
ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript: Unable to execute QScript: SVPreprocess.script() threw the following exception: java.lang.NullPointerException
at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:158)
at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:146)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:146)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused by: java.lang.NullPointerException
at java.io.File.(File.java:277)
at org.broadinstitute.sv.qscript.SVQScript$ReferenceMetadata.rmdLocation$lzycompute(SVQScript.q:518)
at org.broadinstitute.sv.qscript.SVQScript$ReferenceMetadata.rmdLocation(SVQScript.q:516)
at org.broadinstitute.sv.qscript.SVQScript$ReferenceMetadata.getMetadataFile(SVQScript.q:526)
at org.broadinstitute.sv.qscript.SVQScript$ReferenceMetadata.parameterFile$lzycompute(SVQScript.q:550)
at org.broadinstitute.sv.qscript.SVQScript$ReferenceMetadata.parameterFile(SVQScript.q:550)
at org.broadinstitute.sv.qscript.SVQScript.parameterFiles(SVQScript.q:258)
at org.broadinstitute.sv.qscript.SVQScript$CreateMetaDataDirectory.(SVQScript.q:685)
at org.broadinstitute.sv.preprocess.SVPreprocess.script(SVPreprocess.q:80)
at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:155)
... 10 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1748-0-g74bfe0b):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Unable to execute QScript: SVPreprocess.script() threw the following exception: java.lang.NullPointerException
ERROR ------------------------------------------------------------------------------------------

INFO 13:17:43,287 QCommandLine - Shutting down jobs. Please wait...

Do you have any idea about what was wrong?
Please help

Answers

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