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beast_runs.md

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author startdate lastdate
Louis du Plessis
2018/08/29
2018/10/21

Summary

Steps to generate XML files for BEAST analyses and to run the files.

Generate XML files

All models use the sampled-ancestors birth-death skyline under an uncorrelated relaxed clock model and only differ in the substitution model and the parameterisation of the birth-death skyline.

HKY+G+F model

    python makeBeastXML.py -q 120 -t 4 -s 127,128,129,130 -n beastruns -i ../results/config/BDSKYSA.HKY+G+F.relaxedclock/
    python makeBeastXML.py -q 120 -t 4 -s 127,128,129,130 -n beastruns -i ../results/config/BDSKYSA.HKY+G+F.relaxedclock.rootcondition/
    python makeBeastXML.py -q 120 -t 4 -s 127,128,129,130 -n beastruns -i ../results/config/BDSKYSA.HKY+G+F.relaxedclock.treeslicer/

bModelTest

    python makeBeastXML.py -q 120 -t 2 -s 127,128,129,130 -n beastruns -i ../results/config/BDSKYSA.BMT.relaxedclock/
    python makeBeastXML.py -q 120 -t 2 -s 127,128,129,130 -n beastruns -i ../results/config/BDSKYSA.BMT.relaxedclock.rootcondition/

Run analyses on Euler

HKY+G+F model

  • Copy to Euler
  • Make scripts executable chmod +x beastruns.euler.sh
  • Run analyses: ./beastruns.euler.sh ../beast2.jar

bModelTest model

  • Copy to euler
  • Make scripts executable chmod +x beastruns.euler.sh
  • Install bModelTest packagemanager -add bModelTest
  • Modify beastruns.euler.sh to use beast script in bin/ instead of the .jar file.
  • Run analyses: ./beastruns.euler.sh ../../BEASTv2.5.0/bin/beast

Wait

At least one week.

Post-processing

Truncate log and trees files

Truncate the two EBOV-SUBBIG runs that did not reach 200 million states in a week down to 100 million states (not necessary, but means all chains are the same length before combining and 100 million states are sufficient for reaching convergence with 25% burnin).

../../../scripts/truncate.sh EBOV-SUBBIG.BDSKYSA.BMT.relaxedclock.R20.SM 100000000
../../../scripts/truncate.sh EBOV-SUBBIG.BDSKYSA.BMT.relaxedclock.R10.SM 100000000

Combine chains

When combining chains resample every 100000 and use 25% burnin on every chain.

Analyse the following runs further:

  • BDSKYSA.BMT.relaxedclock.R10.S10
    • EBOV-EARLY
    • EBOV-SUB
    • LBR
    • SLE-E
    • SLE-SE
    • SLE-W
  • BDSKYSA.BMT.relaxedclock.R10.SM
    • EBOV-SUB
    • EBOV-SUBBIG
  • BDSKYSA.BMT.relaxedclock.R20.SM
    • EBOV-SUBBIG

MCC trees

TreeAnnotator with 0% burn-in for combined runs (burn-in already removed), 10% burn-in for single runs (uncombined), use 0.0 posterior probability limit (default) and median heights (common ancestor heights won't work for sampled-ancestor trees). Use low memory for bigger trees.