search

carolindahms / TreeMix

Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with bootstrap values, drift and residuals and calculates statistics for every migration event, such as migration support, standard error and p-values.
22 stars 1 forks source link

Step1_TreeMix.sh error - bootstrap files not created #9

Closed EveTC closed 1 year ago

EveTC commented 1 year ago

Hi,

Firstly thank you so much for making these scripts - they look exactly what I was after.

I ran the following command:

bash ./Step1_TreeMix.sh ./file.treemix.frq.gz 64 100 Portugal 100 ~/bin/miniconda3/envs/treemix/bin/consense ./blockBoot100 1 10 10

It does run but comes up with this error. Any ideas how to solve it?

TreeMix v. 1.13
$Revision: 231 $

npop:19 nsnp:87649
Estimating covariance matrix in 876 blocks of size 100
SEED: 1693481582
Starting from:
((Greece:0,Romania:0.00111835):0.0185127,Norway:0.0185127);
Reading tree topology from file:

ERROR: Input Newick string with 1 populations. Input file has 19

There are the expected files in test_migrations/ directory but no files in the bootstrap directory? This means that no consensus tree can be made...

The $outname"_logfile_constree_bootrep.log" file has all the information in but nothing is placed into the bootstrap/ directory

Thank you so much in advance

EveTC commented 1 year ago

I realised my error.

When you run the command do not put a full path to your outfile just the name and be in the directory you wnat the results to go in.