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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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how long does joint ancestral reconstruction with pyjar take? #386

Closed lagphase closed 12 months ago

lagphase commented 1 year ago

Hello,

I have 206 sequences whose whole genome alignment is about 653 Mb. The run has been staying at joint ancestral reconstruction step for a day now. I'm wondering whether it is stalled or how long this step usually takes. My code is

run_gubbins.py --first-tree-builder rapidnj --first-model JC --threads 144 -p gubbins clean.full.aln

Thank you.

nickjcroucher commented 1 year ago

It will depend on the number of polymorphic sites - this is the slowest part of the algorithm - did it complete?