RnaSeq Pipeline Fails before compiling jobs

[shassathe]

Hey guys,
The RnaSeq pipeline seems to be failing even before compiling the Qscript:

INFO  07:26:04,996 QScriptManager - Compiling 1 QScript
ERROR 07:26:07,774 QScriptManager - analyze_rna_seq.scala:319: type mismatch;
 found   : ((AnalyzeRNASeq.this.File, String, String, String, String, String)) => Unit
 required: ((java.io.File, String, String, String, String, String, String)) => ?
ERROR 07:26:07,779 QScriptManager -       for (item: Tuple6[File, String, String, String, String, String] <- valueList) {
ERROR 07:26:07,779 QScriptManager -                                                                       ^
ERROR 07:26:08,092 QScriptManager - one error found
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.queue.QException: Compile of /home/shsathe/gscripts/qscripts/analyze_rna_seq.scala failed with 1 error
        at org.broadinstitute.sting.queue.QScriptManager.loadScripts(QScriptManager.scala:71)
        at org.broadinstitute.sting.queue.QCommandLine.org$broadinstitute$sting$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:95)
        at org.broadinstitute.sting.queue.QCommandLine.getArgumentSources(QCommandLine.scala:227)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:202)
        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)
##### 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: Compile of /home/shsathe/gscripts/qscripts/analyze_rna_seq.scala failed with 1 error
##### ERROR ------------------------------------------------------------------------------------------
INFO  07:26:08,215 QCommandLine - Shutting down jobs. Please wait...

[olgabot]

can you show what version of gscripts you have with "git log" in your
gscripts folder?

On Tue, Sep 15, 2015 at 7:28 AM Shashank Sathe notifications@github.com
wrote:

Hey guys,
The RnaSeq pipeline seems to be failing even before compiling the Qscript:

'''INFO 07:26:04,996 QScriptManager - Compiling 1 QScript
ERROR 07:26:07,774 QScriptManager - analyze_rna_seq.scala:319: type
mismatch;
found : ((AnalyzeRNASeq.this.File, String, String, String, String,
String)) => Unit
required: ((java.io.File, String, String, String, String, String, String))
=> ?
ERROR 07:26:07,779 QScriptManager - for (item: Tuple6[File, String,
String, String, String, String] <- valueList) {
ERROR 07:26:07,779 QScriptManager - ^
ERROR 07:26:08,092 QScriptManager - one error found
ERROR
------------------------------------------------------------------------------------------ ERROR
stack trace

org.broadinstitute.sting.queue.QException: Compile of
/home/shsathe/gscripts/qscripts/analyze_rna_seq.scala failed with 1 error
at
org.broadinstitute.sting.queue.QScriptManager.loadScripts(QScriptManager.scala:71)
at org.broadinstitute.sting.queue.QCommandLine.org
$broadinstitute$sting$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:95)
at
org.broadinstitute.sting.queue.QCommandLine.getArgumentSources(QCommandLine.scala:227)
at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:202)
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)
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: Compile of /home/shsathe/gscripts/qscripts/analyze_rna_seq.scala

failed with 1 error ERROR

INFO 07:26:08,215 QCommandLine - Shutting down jobs. Please wait...
'''

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#79.

[shassathe]

Seems I hadn't updated gscripts in a while. Git pull fixed it. Thanks. This is fixed.