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bootstrap step is too slow #116

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tangerzhang opened this issue Feb 18, 2020 · 0 comments
Open

bootstrap step is too slow #116

tangerzhang opened this issue Feb 18, 2020 · 0 comments

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@tangerzhang
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I am running bootstrap analysis for a net and below are my commands:

using DataFrames
using PhyloNetworks
using Gadfly
using PhyloPlots
import Cairo
using Cairo
addprocs(50)
@everywhere using PhyloNetworks

net7=readTopology("net7_bucky.out")

bootTrees = readBootstrapTrees("BSlistfiles")
bootnet = bootsnaq(net7, bootTrees, hmax=8, nrep=100, runs=50, filename="snaq/bootsnaq7_raxmlboot")

This step has been running on a linux machine with 56 cores for 11 days and only 14 replicates have been finished.
I am wondering is it normal to take so long in this step? Anything I can do to speed up?
Thanks!

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