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Hello, I encountered a problem when running (we only have python 3.x in our system, so cannot use My command line is: $ python --minFraglen=150 --maxFragLen=40000 --maxLBrownEst=1500000 --binsize=20000 --removeb2b=True --removeAdjacent=True --rmapfile=./PCHiC_mm10.rmap --baitmapfile=./PCHiC_mm10.baitmap --designDir=./ --outfilePrefix=PCHiC_temp

or $ python --minFraglen 150 --maxFragLen 40000 --maxLBrownEst 1500000 --binsize 20000 --removeb2b True --removeAdjacent True --rmapfile ./PCHiC_mm10.rmap --baitmapfile ./PCHiC_mm10.baitmap --designDir ./ --outfilePrefix ./PCHiC_temp

But it does not run. It gives me this: Usage: python --minFragLen=<n> --maxFragLen=<n> [--maxLBrownEst=1500000] [--binsize=20000] [removeb2b=True] [--removeAdjacent=True] [--rmapfile=<designDir>/.rmap] [--baitmapfile=<designDir>/.baitmap] [--designDir=.] [--outfilePrefix]

minFragLen and maxFragLen no longer have defaults to prevent errors. Our recommended values for these parameters are: HindIII - 150 and 40000; DpnII - 75 and 1200, respectively

If designDir is provided and contains a single <baitmapfile>.baitmap and <rmapfile>.rmap, these will be used unless explicitly specified. Likewise, the output files will be saved in the designDir unless explicitly specified.

Could you tell me what I did wrong in putting in the command line arguments? Thank you very much!

Iris Zhu

Comments (1)

  1. Mike Lloyd

    I just ran into this. Seems like using the full --maxLBrownEst and --binsize doesn’t work. If you use the shortened single letter versions of those calls the command works. -l and -b respectively.

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