The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
Last chance to register for the GATK workshop next week in Basel, Switzerland! http://www.sib.swiss/training/upcoming-training-events/training/gatk-workshop-lecture

an error I confronted when i run the code below

zhangrui9xzhangrui9x ChinaPosts: 8Member
edited December 2013 in Ask the GATK team
import org.broadinstitute.sting.gatk.walkers.variantrecalibration
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode
import org.broadinstitute.sting.queue.extensions.gatk.CountLoci
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.function.JavaCommandLineFunction

class MyScript extends org.broadinstitute.sting.queue.QScript {
  @Input(doc="The reference file.", shortName="R")
  val reference:File= null
  @Input(doc="The left reads.", shortName="lr")
  val leftreads:File= null
  @Input(doc="The right reads.", shortName="rr")
  val rightreads:File= null


 def script ={
   class leftsaiFormationFunction extends CommandLineFunction{
      @Output(doc="leftSai")
      val leftsai:File=new File("leftsai.sai")
      def commandLine=required("bwa")+required("aln")+required(reference)+required(leftreads)+required(">")+
        required(leftsai)
    }
    val leftsaiFormation=new leftsaiFormationFunction()

    class rightsaiFormationFunction extends CommandLineFunction{
      @Output(doc="rightSai")
      val rightsai:File=new File("rightsai.sai")
      def commandLine=required("bwa")+required("aln")+required(reference)+required(rightreads)+required(">")+
        required(rightsai)
    }
    val rightsaiFormation=new rightsaiFormationFunction()

    class combinedSamFormationFunction extends CommandLineFunction{
      @Input(doc="leftSai")
      val leftsai:File=leftsaiFormation.leftsai
      @Input(doc="rightSai")
      val rightsai:File=rightsaiFormation.rightsai
      @Output(doc="combinedSam")
      val combinedSam:File=new File("combined.sam")
      def commandLine=required("bwa")+required("sampe")+required(reference)+required(leftsai)+
        required(rightsai)+required(leftreads)+required(
        rightreads)+required(">")+required(combinedSam)
    }
    val combinedSamFormation=new combinedSamFormationFunction()


    add(leftsaiFormation)
    add(rightsaiFormation)
    add(combinedSamFormation)

  }
}


the error message says as follow:
lxd@lxd-System-Product-Name:~/Documents/queue$ java -jar Queue.jar -S 111111.scala -R human_g1k_v37.fasta -lr C166_Modified_1.fq -rr C166_Modified_2.fq -run -startFromScratch 
INFO  16:05:35,810 QScriptManager - Compiling 1 QScript 
INFO  16:05:39,696 QScriptManager - Compilation complete 
INFO  16:05:39,759 HelpFormatter - ---------------------------------------------------------------------- 
INFO  16:05:39,759 HelpFormatter - Queue v2.7-2-g6bda569, Compiled 2013/08/28 16:33:34 
INFO  16:05:39,759 HelpFormatter - Copyright (c) 2012 The Broad Institute 
INFO  16:05:39,759 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  16:05:39,760 HelpFormatter - Program Args: -S 111111.scala -R human_g1k_v37.fasta -lr C166_Modified_1.fq -rr C166_Modified_2.fq -run -startFromScratch 
INFO  16:05:39,760 HelpFormatter - Date/Time: 2013/12/06 16:05:39 
INFO  16:05:39,760 HelpFormatter - ---------------------------------------------------------------------- 
INFO  16:05:39,760 HelpFormatter - ---------------------------------------------------------------------- 
INFO  16:05:39,766 QCommandLine - Scripting MyScript 
INFO  16:05:39,800 QCommandLine - Added 3 functions 
INFO  16:05:39,801 QGraph - Generating graph. 
INFO  16:05:39,811 QGraph - Running jobs. 
INFO  16:05:39,812 QGraph - Removing outputs from previous runs. 
INFO  16:05:39,840 FunctionEdge - Starting:  'bwa'  'aln'  'human_g1k_v37.fasta'  'C166_Modified_1.fq'  '>'  '/home/lxd/Documents/queue/leftsai.sai'  
INFO  16:05:39,840 FunctionEdge - Output written to /home/lxd/Documents/queue/leftsai.sai.out 
INFO  16:05:39,858 FunctionEdge - Starting:  'bwa'  'aln'  'human_g1k_v37.fasta'  'C166_Modified_2.fq'  '>'  '/home/lxd/Documents/queue/rightsai.sai'  
INFO  16:05:39,858 FunctionEdge - Output written to /home/lxd/Documents/queue/rightsai.sai.out 
INFO  16:05:39,862 QGraph - 1 Pend, 2 Run, 0 Fail, 0 Done 
ERROR 16:06:09,834 FunctionEdge - Error:  'bwa'  'aln'  'human_g1k_v37.fasta'  'C166_Modified_1.fq'  '>'  '/home/lxd/Documents/queue/leftsai.sai'  
ERROR 16:06:09,839 FunctionEdge - Contents of /home/lxd/Documents/queue/leftsai.sai.out:
/home/lxd/Documents/queue/.queue/tmp/.exec6752111377935879956: 2: /home/lxd/Documents/queue/.queue/tmp/.exec6752111377935879956: bwa: not found 
ERROR 16:06:09,842 FunctionEdge - Error:  'bwa'  'aln'  'human_g1k_v37.fasta'  'C166_Modified_2.fq'  '>'  '/home/lxd/Documents/queue/rightsai.sai'  
ERROR 16:06:09,842 FunctionEdge - Contents of /home/lxd/Documents/queue/rightsai.sai.out:
/home/lxd/Documents/queue/.queue/tmp/.exec7253750678399969841: 2: /home/lxd/Documents/queue/.queue/tmp/.exec7253750678399969841: bwa: not found 
INFO  16:06:09,843 QGraph - Writing incremental jobs reports... 
INFO  16:06:09,844 QJobsReporter - Writing JobLogging GATKReport to file /home/lxd/Documents/queue/111111.jobreport.txt 
INFO  16:06:09,869 QGraph - 1 Pend, 0 Run, 2 Fail, 0 Done 
INFO  16:06:09,870 QCommandLine - Writing final jobs report... 
INFO  16:06:09,870 QJobsReporter - Writing JobLogging GATKReport to file /home/lxd/Documents/queue/111111.jobreport.txt 
INFO  16:06:09,876 QJobsReporter - Plotting JobLogging GATKReport to file /home/lxd/Documents/queue/111111.jobreport.pdf 
WARN  16:06:10,262 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. 
INFO  16:06:10,263 QCommandLine - Done with errors 
INFO  16:06:10,264 QGraph - ------- 
INFO  16:06:10,266 QGraph - Failed:   'bwa'  'aln'  'human_g1k_v37.fasta'  'C166_Modified_1.fq'  '>'  '/home/lxd/Documents/queue/leftsai.sai'  
INFO  16:06:10,266 QGraph - Log:     /home/lxd/Documents/queue/leftsai.sai.out 
INFO  16:06:10,266 QGraph - ------- 
INFO  16:06:10,268 QGraph - Failed:   'bwa'  'aln'  'human_g1k_v37.fasta'  'C166_Modified_2.fq'  '>'  '/home/lxd/Documents/queue/rightsai.sai'  
INFO  16:06:10,268 QGraph - Log:     /home/lxd/Documents/queue/rightsai.sai.out 
INFO  16:06:10,269 QCommandLine - Script failed with 3 total jobs 
lxd@lxd-System-Product-Name:~/Documents/queue$ 

It will be really appreciated for your attention and answer!!!!!

Post edited by Geraldine_VdAuwera on
Tagged:

Best Answer

Answers

Sign In or Register to comment.