running haplotypeCaller using Queue

I wrote my first script in scala to run haplotyperCaller walker of GATK. However, I am running into some errors when I execute the *.scala script. I am unable to figure out the source of error, any help will be appreciated.

package org.broadinstitute.sting.queue.qscripts
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._

class haplotypeCaller extends QScript {

                @Input(doc="Reference file for the bam files",shortName="R")
                var referenceFile: File = _

                @Input(doc="One or more bam files",shortName="I")
                var bamFiles: List[File] = Nil

                @Argument(doc="the interval string",shortName="L")
                var intervalString: String = ""

                @Argument(doc="heterozygosity to be considered",shortName="heterozygosity")
                var het: Double = 0.006

                @Argument(doc="which sites to emit",shortName="output_mode")
                var outmode: String = "EMIT_ALL_SITES"

                @Output(doc="outFile to write snps and indels",shortName="out")
                var outFile: File = _

        def script(){
                val hc = new HaplotypeCaller


command line arguments passed:
java -jar ./Queue-2.7-4-g6f46d11/Queue.jar -S haplotypeCaller.scala -R ./reference/xx.fasta -I x1.realigned.bam / -I x2.realigned.bam -I x3.realigned.bam -I x4.realigned.bam -I x5.realigned.bam -I x6.realigned.bam -I x7.realigned.bam / -I x8.realigned.bam -I x9.realigned.bam -I x10.realigned.bam -I x11.realigned.bam -I x12.realigned.bam / -L chr1 -heterozygosity 0.006 -output_mode EMIT_ALL_SITES -out gatk.hc.chr1.raw.snps.indels.vcf -run

##### ERROR MESSAGE: Walker requires a reference but none was provided.

The reference file exists in the above mentioned path. I even tried running with absolute path for the reference file but was not successful. Any help will be appreciated.

Best Answers


  • I'm trying to get access to index.php/GATK-Queue but the link seems to be missing.

    I'm using Haplotypecaller and it takes too much time and unfortunately/fortunately Ill need to try and parallelize the following command as it is estimated to take atleast 14 days and we are limited to a max of 4 days runtime.

    /mnt/fastdata/md1jale/software/gatk- HaplotypeCaller -R /mnt/fastdata/md1jale/reference/hs37d5.fa -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24811_1#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_
    iPS/24150_1#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24150_2#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24712_5#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24152_1#1.bam -I /mnt/fastdata/md1
    jale/WGS_MShef7_iPS/24152_2#1.bam -O /mnt/fastdata/md1jale/WGS_MShef7_iPS/output/mshef7_raw_variants.vcf

    We are using the sungrid cluster (qsub).

    Please can you point me to a tutorial where I can wrap the above command. I'm afraid I haven't written in scala before.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    We are not supporting Queue any more, but perhaps you might like WDL better.


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