Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

type not found: type ExternalCommonArgs

Hi,

I am trying to understand how GATK Queue works, and wrote a mini script to do alignment using bwa mem. The test code failed when running.

The error messages:
not found: type not found: type ExternalCommonArgs
ERROR 21:25:34,464 QScriptManager - case class bwa_mem (inFastQ: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs
ERROR 21:25:34,464 QScriptManager - case class bwa_mem (inFastQ: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs

Then I removed ExternalCommonArgs and ran again. The error is:
ERROR MESSAGE: Non-file found. Try removing the annotation, change the annotation to @Argument, or extend File with FileExtension: private int temp.bwaThreads: 1

Any suggestions for debugging? My code is attached below.

Thanks


import org.broadinstitute.sting.queue.QScript

class temp extends QScript {

qscript =>

@Input(doc="input fastq file - or list of fastq files", shortName="I", required=true)
var input: File = _

@Input(doc="Reference fasta file", shortName="R", required=true)
var reference: File = _

@Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false)
var bwaThreads: Int = 1

val queueLogDir: String = ".qlog/" // Gracefully hide Queue's output

def performAlignment(fq: File): File = {
var alignedBam: File = swapExt(fq, ".fq", ".sam")
add(bwa_mem(fq, alignedBam))
alignedBam

}

def script() {
var outBam: File = performAlignment(input)
}

case class bwa_mem (inFastQ: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs{
@Input(doc="fastq file to be aligned") var fq = inFastQ
@Output(doc="output bam file") var bam = outBam
def commandLine = "bwa mem -t " + bwaThreads + " " + reference + " " + fq + " > " + bam
this.analysisName = queueLogDir + outBam + ".bwamem"
this.jobName = queueLogDir + outBam + ".bwamem"
}
}

Tagged:

Answers

Sign In or Register to comment.