Output Files Not Saving in Nemo Simulation

[Mariana Ribeiro]

Dear Frédéric,

I'm reaching out for assistance regarding an issue I've encountered while running simulations in Nemo.

Despite the simulation running smoothly, I've encountered a hiccup where the output files aren't being saved. My aim is to conduct a straightforward simulation with minimal parameters, generating a genotype dataset comprising both Microsatellites and SNPs for comparative analysis. Specifically, I seek to simulate a single population of 50 individuals, producing a dataset of 20 microsatellites, each with 12 alleles. For SNPs, I intend to alter the parameter to set the number of alleles to 2.

Here are the parameters I'm currently employing in the .ini file:

###         SIMULATION       ###

replicates              1  

generations             1

filename                Simulation1

root_dir                Simulation1

run_mode                overwrite

logfile                 Simulation1.log

random_seed             486532

 

###         POPULATION          ###

patch_number            1

patch_capacity          50

 

###      LIFE CYCLE EVENTS      ###

breed                   1

mating_system           1

 

###          TRAITS          ###

## NEUTRAL MARKERS ##

ntrl_loci                20

ntrl_all                 12

ntrl_mutation_rate       0

ntrl_mutation_model      0

# output #

ntrl_save_genotype       fstat

ntrl_save_freq           allele

ntrl_output_dir          ntrl

ntrl_output_logtime      1

As a newcomer to simulation methodologies, I'm struggling to identify the root cause of this fundamental issue. Any guidance or insights you can offer would be greatly appreciated.

 Thank you very much for your time and consideration.

 Warm regards,

Mariana Ribeiro

[Frederic Guillaume]

Dear Mariana,

To generate an output, you need to add the "save_files" LCE to your life cycle (see section 4.15 in the manual). Also note that your life cycle has only one LCE (breed), it needs the "aging" LCE to correctly simulate multiple generations (read Chapter 4, and section 4.1). Have a look at Chapter 6 of the manual for an example of a basic simulation. Also make sure that the parameters of the neutral markers match with the model you have in mind. Currently, no genetic variation would be generated (read section 5.2).

Best,

Fred