These are chat archives for dereneaton/ipyrad

Jun 2017
Jun 19 2017 15:33
@dereneaton Thanks for your suggestion!. Do you mean, using for #16. filter_adapters = 2? Because I am already doing so and I still have that issue.
Jenny Archibald
Jun 19 2017 21:32

@dereneaton @isaacovercast Hi! With tetrad, does the output to screen sometimes lag significantly behind actual progress? I am assessing whether to give up on an analysis given walltime limits and other users' needs. I tried subsampling 10M quartets following your earlier suggestion, but it still seems to be moving very slowly (see below). Any suggestions? I am wondering if I would need to run this on subclades rather than on the full dataset.
This is the run info and output:

[jkarch@m027 tetc]$ tetrad -s /panfs/pfs.local/scratch/bi/jkarch/cam/ch4/m04c90_outfilesorig/m04c90red.snps.phy \
>   -l /panfs/pfs.local/scratch/bi/jkarch/cam/ch4/m04c90_outfilesorig/ \
>   -n ch4tetc -m random -q 10000000 -c 24 -b 10

tetrad [v.0.6.19] (ipyrad.analysis toolkit)
Quartet inference from phylogenetic invariants
loading seq array [283 taxa x 2513283 bp]
max unlinked SNPs per quartet (nloci): 220722
tetrad instance: ch4tetc
host compute node: [24 cores] on m027
inferring 261630670 induced quartet trees
[#                   ]   6%  initial tree | 12 days, 5:46:39 |