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YeoLab / clipper

A tool to identify CLIP-seq peaks
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Runtime of CLIPer? #107

Open mhorlacher opened 2 years ago

mhorlacher commented 2 years ago

Hi,

I'm running CLIPer on a BAM file from one replicate of an ENCODE eCLIP experiment (--FDR 0.10, -s hg38, otherwise default params) using 8 cores. I'm curious what the average runtime of CLIPer is, as it's running for >12h now, occasionally throwing the warning below. Thanks!

The maximal number of iterations maxit (set to 20 by the program)
allowed for finding a smoothing spline with fp=s has been reached: s
too small.
There is an approximation returned but the corresponding weighted sum
of squared residuals does not satisfy the condition abs(fp-s)/s < tol.
  warnings.warn(message)
neurbio commented 1 year ago

Similar situation. May I ask did u finally get the result? How long it cost?

mhorlacher commented 1 year ago

@neurbio I do not recall exactly how long I left it running, but I believe it was in the order of ~20 hours on 8-12 cores.

neurbio commented 1 year ago

@mhorlacher Thank you so much for ur reply and the info. I finally also finished around 14 Hours on 8 cores.