Error running analyze_rna_seq.scala

[ecwheele@tscc-login1 mds_splicing_v4]$ bash process_rnaseq.sh 
INFO  09:21:27,273 QScriptManager - Compiling 1 QScript 
INFO  09:21:36,790 QScriptManager - Compilation complete 
INFO  09:21:36,952 HelpFormatter - ---------------------------------------------------------------------- 
INFO  09:21:36,953 HelpFormatter - Queue v2.3-1155-g931452b, Compiled 2016/01/11 23:38:39 
INFO  09:21:36,953 HelpFormatter - Copyright (c) 2012 The Broad Institute 
INFO  09:21:36,953 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  09:21:36,954 HelpFormatter - Program Args: -S /home/ecwheele/gscripts/qscripts/analyze_rna_seq.scala --input manifest.txt --adapter TCGTATGCCGTCTTCTGCTTG --adapter ATCTCGTATGCCGTCTTCTGCTTG --adapter CGACAGGTTCAGAGTTCTACAGTCCGACGATC --adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -qsub -jobQueue home-scrm -log mds_splicing_v4.log --location /oasis/tscc/scratch/ecwheele/mds_splicing_v4/ --strict -keepIntermediates --flipped flip -run 
INFO  09:21:36,954 HelpFormatter - Date/Time: 2016/01/15 09:21:36 
INFO  09:21:36,954 HelpFormatter - ---------------------------------------------------------------------- 
INFO  09:21:36,954 HelpFormatter - ---------------------------------------------------------------------- 
INFO  09:21:36,962 QCommandLine - Scripting AnalyzeRNASeq 
INFO  09:21:37,232 QCommandLine - Done with errors 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
org.broadinstitute.sting.utils.exceptions.UserException$CannotExecuteQScript: Unable to execute QScript: AnalyzeRNASeq.script() threw the following exception: java.lang.NullPointerException
        at org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
        at org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
        at scala.collection.Iterator$class.foreach(Iterator.scala:772)
        at scala.collection.JavaConversions$JIteratorWrapper.foreach(JavaConversions.scala:573)
        at scala.collection.IterableLike$class.foreach(IterableLike.scala:73)
        at scala.collection.JavaConversions$JListWrapper.foreach(JavaConversions.scala:615)
        at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:147)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
Caused by: java.lang.NullPointerException
        at org.broadinstitute.sting.queue.QScript$class.swapExt(QScript.scala:86)
        at org.broadinstitute.sting.queue.qscripts.AnalyzeRNASeq.swapExt(analyze_rna_seq.scala:14)
        at org.broadinstitute.sting.queue.qscripts.AnalyzeRNASeq$$anonfun$script$3$$anonfun$apply$1.apply(analyze_rna_seq.scala:340)
        at org.broadinstitute.sting.queue.qscripts.AnalyzeRNASeq$$anonfun$script$3$$anonfun$apply$1.apply(analyze_rna_seq.scala:319)
        at scala.collection.LinearSeqOptimized$class.foreach(LinearSeqOptimized.scala:59)
        at scala.collection.immutable.List.foreach(List.scala:76)
        at org.broadinstitute.sting.queue.qscripts.AnalyzeRNASeq$$anonfun$script$3.apply(analyze_rna_seq.scala:319)
        at org.broadinstitute.sting.queue.qscripts.AnalyzeRNASeq$$anonfun$script$3.apply(analyze_rna_seq.scala:315)
        at scala.collection.immutable.Map$Map1.foreach(Map.scala:119)
        at org.broadinstitute.sting.queue.qscripts.AnalyzeRNASeq.script(analyze_rna_seq.scala:315)
        at org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156)
        ... 10 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-1155-g931452b):
##### ERROR
##### ERROR Please check the documentation guide 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 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: AnalyzeRNASeq.script() threw the following exception: java.lang.NullPointerException
##### ERROR ------------------------------------------------------------------------------------------
INFO  09:21:37,252 QCommandLine - Shutting down jobs. Please wait...