There is no curve in the plot of the final summary file

[candyiris]

Dear Professor Liu, Thanks for your useful software. I have run the blueprint file successfully. However, there is no curve in the output plot.

My work flow in like below: First: easySFS –fold vcf to get SFS Run blueprint file prepared as below (31 diploid individuals):

popid: 2snp-sfs_fold # id of the population (no white space) nseq: 62 # number of sequences L: 236385 # total number of observed nucleic sites, including polymorphic and monomorphic whether_folded: true # whethr the SFS is folded (true or false) SFS: 69686.042 23095.553 20586.810 15777.203 15448.518 7330.874 0 0 0 0 0 44330.215 16379.484 18671.211 15265.352 15200.763 7101.975 0 0 0 0 0 54905.062 26756.418 30674.833 23638.351 14080.338 0 0 0 0 # snp frequency spectrum: number of singleton, number of doubleton, etc. (separated by white space) smallest_size_of_SFS_bin_used_for_estimation: 1 # default is 1; to ignore singletons, uncomment this line and change this number to 2 largest_size_of_SFS_bin_used_for_estimation: 31 # default is nseq/2 for folded SFS pct_training: 0.67 # percentage of sites for training nrand: 15 30 45 60 # number of random break points for each try (separated by white space) project_dir: 2snp-sfs_fold # project directory stairway_plot_dir: stairway_plot_es # directory to the stairway plot files ninput: 200 # number of input files to be created for each estimation

random_seed: 6

output setting

mu: 1.2e-8 # assumed mutation rate per site per generation year_per_generation: 24 # assumed generation time (in years)

plot setting

plot_title: 2Ne-change_fold # title of the plot xrange: 0.1,10000 # Time (1k year) range; format: xmin,xmax; "0,0" for default yrange: 0,0 # Ne (1k individual) range; format: xmin,xmax; "0,0" for default xspacing: 2 # X axis spacing yspacing: 2 # Y axis spacing fontsize: 12 # Font size

The final summary file is shown below.

I would like to inquire about the reason for this situation. Is there any problem with the parameter settings in the above blueprint file. I am looking forward for your kind reply.

Sincerely, candyiris

[lpabonv]

I´m having exactly the same issue! I've realized that the software puts the same estimated population size for all the calculated generations/epochs. Haven´t been able to solve it yet. Were you able to fix it?

[candyiris]

I have solve the problem now. The error of the previous blueprint file may be "L: 236385". 236385 is the number of the SNPs. I change the 236385 into 35457750. 35457750=236385150 (L=the number of SNPs the length of each SNP).