Error running RNA-Seq pipeline on single-end data

[shassathe]

I get a NullPointerException every time I run the RNA-Seq pipeline:

INFO  17:45:38,942 QScriptManager - Compiling 1 QScript 
INFO  17:45:47,075 QScriptManager - Compilation complete 
INFO  17:45:47,189 HelpFormatter - ---------------------------------------------------------------------- 
INFO  17:45:47,190 HelpFormatter - Queue v2.3-1155-g931452b, Compiled 2016/01/21 14:31:56 
INFO  17:45:47,190 HelpFormatter - Copyright (c) 2012 The Broad Institute 
INFO  17:45:47,190 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  17:45:47,191 HelpFormatter - Program Args: -S /home/shsathe/gscripts/qscripts/analyze_rna_seq.scala --input sebastian_mn_v3.txt --adapter TCGTATGCCGTCTTCTGCTTG --adapter ATCTCGTATGCCGTCTTCTGCTTG --adapter CGACAGGTTCAGAGTTCTACAGTCCGACGATC --adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -qsub -jobQueue home-yeo -runDir /oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I8/V3 -log sebastian_mn_v3.log --location /oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I8/V3 --strict -keepIntermediates --not_stranded -single_end -run 
INFO  17:45:47,191 HelpFormatter - Date/Time: 2016/02/01 17:45:47 
INFO  17:45:47,191 HelpFormatter - ---------------------------------------------------------------------- 
INFO  17:45:47,191 HelpFormatter - ---------------------------------------------------------------------- 
INFO  17:45:47,198 QCommandLine - Scripting AnalyzeRNASeq 
INFO  17:45:47,236 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  17:45:47,244 QCommandLine - Shutting down jobs. Please wait...