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an error I confronted when i run the code below

zhangrui9xzhangrui9x ChinaMember Posts: 8
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
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