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analyze_rna_seq.scala fails while compiling script #73

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shassathe opened this issue Jun 1, 2015 · 5 comments
Closed

analyze_rna_seq.scala fails while compiling script #73

shassathe opened this issue Jun 1, 2015 · 5 comments

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@shassathe
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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
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gpratt commented Jun 1, 2015

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
#73.

@gpratt
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gpratt commented Jun 2, 2015

should be fixed following commit /25aac374614e5d0313406c7004428e3d071e51e5

@gpratt gpratt closed this as completed Jun 2, 2015
@Wenhao-Jin
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Hi, Gabe, I also meet the same problem. One question, maybe a little stupid: what do you mean by "commit /25aac374614e5d0313406c7004428e3d071e51e5"?

@gpratt
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gpratt commented Jun 4, 2015

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
#73 (comment).

@Wenhao-Jin
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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
#73 (comment).


Reply to this email directly or view it on GitHub
#73 (comment).

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