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  • Excavator Exome CNV ReadPerla.pl

    Is anyone using excavator for cnv analysis of exomes? I am running into an error with the ReadPerla.pl step. I am running a test and control sample in somatic mode. I have been getting the following error and haven't been able to resolve it. I think the error is related to samtools. I have tried both the current and previous releases. Any advice is greatly appreciated:
    command line:
    perl ReadPerla.pl ReadInput.txt /user/Results --mode somatic

    Checking output folders...
    '/user/Results' folder ready!
    Checking output subfolders...
    '/user/Results/Data' folder ready!
    '/user/Results/Results' folder ready!
    '/user/Results/Plots' folder ready!
    Working on sample 791.
    Checking sample '791' folders...
    ...done!
    Now working with SAMtools...
    Error in seq.default(2, length(tt) * 2, by = 2) :
    wrong sign in 'by' argument
    Calls: seq -> seq.default
    Execution halted

    This error repeats over and over until it ultimately fails. Any insight is greatly appreciated. Thank you

  • #2
    Hi wdemos

    Could you solve your problem? I have the same error.
    Last edited by Fatima.Z; 05-04-2016, 01:52 PM.

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