Help with fixing input files

[Bushra Shahid]

Hello,

Thank you so much for the great support system online for running fsc. Im hoping you can help me fix my input files. I want to test ancient vs recent gene flow in 3 pops. I have an unfolded sfs generated via angsd and realsfs.

When I specify recent gene flow as below (only till gene flow 100k ya), I keep getting errors for some runs that MRCA is not found and some lineages failed to coalesce even though I have made sure the pops merge after gene flow has stopped backward in time. Im really confused why this could be happening. 

If I reduce the Ne upper limits to 1e4 than my runs look fine but I dont think that is right because that could potentially be affecting my time estimates. Could you please help me fix my script?

My tpl file:
//Parameters for the coalescence simulation program : fsimcoal2.exe
3 samples to simulate :
//Population effective sizes (number of genes)
NPOP0
NPOP1
NPOP2
//Samples sizes and samples age
38
38
38
//Growth rates : negative growth implies population expansion
0
0
0
//Number of migration matrices : 0 implies no migration between demes
2
//migration matrix 0
0.000 0.000 0.000
0.000 0.000 RATE1
0.000 RATE1 0.000
//migration matrix 1
0.000 0.000 0.000
0.000 0.000 0.000
0.000 0.000 0.000
//historical event: time, source, sink, migrants, new deme size, new growth rate, migration matrix index
3 historical event
100000 0 0 0 1 0 1
TDIV1 1 0 1 1 0 1
500000 0 2 1 1 0 1
//Number of independent loci [chromosome]
1 0
//Per chromosome: Number of contiguous linkage Block: a block is a set of contiguous loci
1
//per Block:data type, number of loci, per generation recombination and mutation rates and optional parameters
FREQ  1   0  7.3e-9 OUTEXP

My est file:
// Search ranges and rules file
// ****************************

[PARAMETERS]
//#isInt? #name #dist.#min #max
//all N are in number of haploid individuals
1 NPOP0 logunif 100 1e6 output
1 NPOP1 logunif 100 1e6 output
1 NPOP2 logunif 100 1e6 output
0   RATE1    unif   1e-10 0.9        output bounded
1 TDIV1 logunif 250000 499999 output bounded

[COMPLEX PARAMETERS]