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Issue #30 resolved
leajessop created an issue

I'm trying to use the python script to create the needed design files. I'm getting the following error

Creating .npb and .poe files... Looping through baits... Traceback (most recent call last): File "", line 227, in <module> n[d/binsize] += 1 IndexError: list index out of range

Any suggestions are much appreciated. Lea

Comments (7)

  1. leajessop reporter

    calling python --designDir=/CHiC/CHiCago/binSize1300 --rmapfile=/CHiC/CHiCago/binSize1300/MboIhg19.rmap --baitmapfile=/CHiC/CHiCago/binSize1300/baitmap.baitmap --outfilePrefix=/CHiC/CHiCago/bs1300 --minFragLen=150 --maxFragLen=40000 --maxLBrownEst=1500000 --binsize=1300 --removeb2b=True --removeAdjacent=True

  2. Mikhail Spivakov

    Thanks for your report. I've never seen this before, but I suppose the obvious reason would be if d/binsize is zero, where d is the distance between two fragments. Could it be by any chance that it's zero in some cases (e.g., duplicated fragments or something like that)?

  3. Mikhail Spivakov

    If you're not comfortable debugging the python code step by step, feel free to share your rmap and baitmap files with me (via ftp) and I can have a go.

  4. leajessop reporter

    Thank you. It's odd because a few months ago I used the same baitmap and rmap files with slightly different settings and it worked fine. I can share the files with you thru Dropbox. OK to use your babraham e-mail account?


  5. Mikhail Spivakov

    Thanks for reporting this issue, which was caused by a rounding error. We'll post the updated version to the repo soon.

  6. Mikhail Spivakov

    Basically, you've provided the first use example whereby maxLBrownEst is not a multiple of binsize. Previously, there was never the need to perform any rounding, so we didn't spot an issue there. Thanks!

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