simonhmartin
commented
3 years ago Hi Joro,
As the error mentions "AssertionError: Please specify between 4 and 8 unique taxon names."
Twisst currently only allows a maximum of 8 groups to be specified. The reason is that with 9 groups the number of possible taxon topologies becomes far too large. Even 6 groups gives an output with 105 weighting values. One way around this is if you have pre-defined topologies you are specifically interested in, you can specify those using the just --inputTopos option, and only those topology counts will be recorded.
Andrinajoro
Hi Simon, I was following your instruction in general genomics pakage and running sliding wimdow tree inference with phyml. I manage to generate the trees.gz file as an mput for twisst.py. However when running twisst.py using the following command: python twisst.py -t all_rename_filter2_geno0_phased_renammed_chr_phyml_ML.w50.trees.gz -w output_w50.weights.csv.gz -g ang -g Bta -g bux -g der -g eur -g imb -g ory -g scr -g spe -g str -g syl --method complete --groupsFile groups.tsv; I got the following message: Traceback (most recent call last): File "twisst.py", line 576, in topoDict = makeTopoDict(taxonNames, topos, args.outgroup if args.outgroup else None) File "twisst.py", line 325, in makeTopoDict output["topos"] = allTopos(taxonNames, []) if topos is None else topos File "twisst.py", line 478, in allTopos assert 4 <= len(branches) <= 8, "Please specify between 4 and 8 unique taxon names." AssertionError: Please specify between 4 and 8 unique taxon names.
groups.tsv as: ang_A ang ang_B ang Bta_A Bta Bta_B Bta bux_A bux bux_B bux der_A der der_B der eur_A eur eur_B eur imb_A imb imb_B imb ory_A ory ory_B ory scr_A scr scr_B scr spe_A spe spe_B spe str_A str str_B str syl_A syl syl_B syl
Your advice would be much appreciated Joro