analyze_rna_seq.scala fails while compiling script

[shassathe]

I am running the rna seq pipeline on C.Elegans RNA-Seq datasets. I keep getting an error while the pipeline compiles the QScript:

Compiling 1 QScript 
ERROR 11:04:51,874 QScriptManager - analyze_rna_seq.scala:295: type mismatch;
 found   : ((AnalyzeRNASeq.this.File, String, String)) => Unit
 required: ((java.io.File, String, String, String, String)) => ? 
ERROR 11:04:51,879 QScriptManager -       for (item: Tuple3[File, String, String] <- valueList) { 
ERROR 11:04:51,879 QScriptManager -                                               ^ 
ERROR 11:04:52,267 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 2.3-1084-gd5ca5d0):
##### 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  11:04:52,328 QCommandLine - Shutting down jobs. Please wait...

I am using "ce10" as the reference genome in my manifest. Could that be an issue?

[gpratt]

My bad, I'll fix it after the encode meeting.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Mon, Jun 1, 2015 at 11:20 AM, Shashank Sathe notifications@github.com wrote:

I am running the rna seq pipeline on C.Elegans RNA-Seq datasets. I keep getting an error while the pipeline compiles the QScript:

Compiling 1 QScript ERROR 11:04:51,874 QScriptManager - analyze_rna_seq.scala:295: type mismatch; found : ((AnalyzeRNASeq.this.File, String, String)) => Unit required: ((java.io.File, String, String, String, String)) => ? ERROR 11:04:51,879 QScriptManager - for (item: Tuple3[File, String, String] <- valueList) { ERROR 11:04:51,879 QScriptManager - ^ ERROR 11:04:52,267 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 2.3-1084-gd5ca5d0):

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 11:04:52,328 QCommandLine - Shutting down jobs. Please wait...

I am using "ce10" as the reference genome in my manifest. Could that be an issue?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/73.

[gpratt]

should be fixed following commit /25aac374614e5d0313406c7004428e3d071e51e5

[Wenhao-Jin]

Hi, Gabe, I also meet the same problem. One question, maybe a little stupid: what do you mean by "commit /25aac374614e5d0313406c7004428e3d071e51e5"?

[gpratt]

Still?

Do a git pull to update your gscripts and the issue should go away. If not its a different issue.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Wed, Jun 3, 2015 at 5:50 PM, Wenhao-Jin notifications@github.com wrote:

Hi, Gabe, I also meet the same problem. One question, maybe a little stupid: what do you mean by "commit /25aac374614e5d0313406c7004428e3d071e51e5"?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/73#issuecomment-108661248.

[Wenhao-Jin]

Yes, it works. Thanks Gabe!

Wenhao

2015-06-04 8:51 GMT+08:00 Gabriel Pratt notifications@github.com:

Still?

Do a git pull to update your gscripts and the issue should go away. If not its a different issue.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Wed, Jun 3, 2015 at 5:50 PM, Wenhao-Jin notifications@github.com wrote:

Hi, Gabe, I also meet the same problem. One question, maybe a little stupid: what do you mean by "commit /25aac374614e5d0313406c7004428e3d071e51e5"?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/73#issuecomment-108661248.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/73#issuecomment-108661606.