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YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
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RnaSeq Pipeline Fails before compiling jobs #79

Closed shassathe closed 8 years ago

shassathe commented 8 years ago

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 commented 8 years ago

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... '''

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/79.

shassathe commented 8 years ago

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