populations-STACKS-STRUCTURE format

[Edgar Caballero]

Hello stacks community, I ran a populations with theese parameters:

populations -P /scratch/genomics/caballeroeg/CPrads/clean_rads/edgar_analysis/m3p -M /scratch/genomics/caballeroeg/populati

ons_ana/paired_populations/paired_popmap.txt -O /scratch/genomics/caballeroeg/populations_ana/random_snps_population -p 3 -

r 0.50 --fstats --vcf --genepop --structure --treemix --hwe --write-random-snp

After using the file I tried to run an fastructure analysis to find the best k mean cluster.

 I am using the faststructure software for my analysis which contains 14177 loci in 156 individuals. I am measuring the best K clustering from 1 to 10 here is my code for fastructure:

(I am using an array which varies from k each iteration):

structure.py

-K $SGE_TASK_ID

--input= /scratch/genomics/caballeroeg/populations_ana/post_stacks_/STRUCTURE/example_structure.str

--output= /scratch/genomics/caballeroeg/FasSTRUCTURE/K_$SGE_TASK_ID

--tol= 10-6

--format= str

--full

Then I applie the distruct command to buil the graphs but they seem odd (I provide them below with my code):

distruct.py \

-K $SGE_TASK_ID \

--input=/scratch/genomics/caballeroeg/FasSTRUCTURE/k$SGE_TASK_ID/K_$SGE_TASK_ID \

--output=/scratch/genomics/caballeroeg/FasSTRUCTURE/K$SGE_TASK_ID \

--popfile=/scratch/genomics/caballeroeg/FasSTRUCTURE/popfile.txt

Even my code runs well my pictures are not as expected I attach them, the all look similar with a different colore, I tried with no popmap but it didn't fit the output,

Can somebody to help to understand what I may be missing in my file, I would highly appreciate your assistance,

thanks in advance,

Edgar