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  • IllegalArgumentException (Scripture.jar)

    Hi all,

    I'm trying to run Scripture.jar which I have downloaded from the Broad institute website: http://www.broadinstitute.org/softwa...ipture/?q=home
    I'm on a Mac and I have java 6 and 7 (I know that by checking /utilites/java preferences). For the sake of practice, I'm trying to run the walkthrough exercise in the tutorial for this software (http://www.broadinstitute.org/softwa...hrough_example)... in step 7 you need to run scripture with the sam file you have generated in the previous steps and afterwards downloading the mouse size file and the mouse chr19 sequence... this is the command line I'm using:
    >>java –jar scripture.jar –alignment all_alignments.sorted.sam –out chr19.scriptureESTest.segments –sizeFile mm9.sizes –chr chr19 –chrSequence chr19.fa
    However, I'm getting this response:
    Exception in thread "main" java.lang.IllegalArgumentException: Argument alignment is mandatory
    Does anyone know what the problem is....
    I appreciate your support
    lj907

  • #2
    Hello,
    I had the same problem but I solved it by using the scripture-beta2.jar program that you can download at ftp://ftp.broadinstitute.org/pub/pap...ture-beta2.jar

    Best,
    Riccardo

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