MRCA not found!

[Coleen]

Hello everyone

I encountered the same issue as described below and have already implemented all the recommended modifications. Does anyone know how to fix it?

Simulations did not converge. MRCA not found! (2 lineages remaining)
Num. steps in coalescent process: 1000001
Bad parameters leading to non-convergent coalescent are written in file s7_test2_bad.par

(It repeated about 14400 times.)

Here is the tpl file (the figure shows historical events)

//Number of population samples (demes)
4
//Population effective sizes (Ne)
N0
N1
N2
N3
//Sample sizes
10
10
10
10
//Growth rates: negative growth implies population expansion
0
0
0
0
//Number of migration matrices : 0 means no migration
0
//Historical events: time, source, sink, migrants, new size, new growth rate, migr. matrix
4
t1 1 2 ra 1 0 0
t1 0 2 rb 1 0 0
t2 0 1 1 1 0 0
t3 3 1 1 N5b 0 0
//Number of independent loci [chromosome]
1 0
//Per chromosome: Number of loci, per locus: SFS (SNP) length
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
FREQ 1 0 1.3e-8 OUTEXP

Here is the est file
// Priors and rules
// ****************
[PARAMETERS]
// Population sizes
1 N0 unif 180 6000 output
1 N1 unif 180 6000 output
1 N2 unif 40 6000 output
1 N3 unif 20 2000 output
1 N5b logunif 20 10000 output
// Times of historical events
1 t1 logunif 100 5000000 output
1 t2 logunif t1 5000000 output
1 t3 logunif t2 5000000 output
// Admixture proportion
0 ra unif 0.3 0.7 output
[COMPLEX PARAMETERS]
0 rb = 1-ra output

Here is my command line
~/fsc28_linux64/fsc28 -t s7_test2.tpl -e s7_test2.est -M -m -n 100000 -L 20 -c 8 -C 1

It can't estimate t2 and t3, and there are some strange numbers in bad.par (as below).
//Number of population samples (demes)
4
//Population effective sizes (Ne)
2612
6594
4025
961
//Sample sizes
10
10
10
10
//Growth 4.200216015685959e-01tes: negative growth implies population expansion
0
0
0
0
//Number of mig4.200216015685959e-01tion matrices : 0 means no mig4.200216015685959e-01tion
0
//Historical events: time, source, sink, mig4.200216015685959e-01nts, new size, new growth 4.200216015685959e-01te, migr. matrix
4
619745 1 2 4.200216015685959e-01 1 0 0
619745 0 2 5.799783984314041e-01 1 0 0
-nan 0 1 1 1 0 0
-nan 3 1 1 7867 0 0
//Number of independent loci [chromosome]
1 0
//Per chromosome: Number of loci, per locus: SFS (SNP) length
1
//per Block: data type, num loci, rec. 4.200216015685959e-01te and mut 4.200216015685959e-01te + optional pa4.200216015685959e-01meters
FREQ 1 0 1.3e-8 OUTEXP

I really appreciate any suggestions.
Thank you 

[Laurent Excoffier]

Hi, as it is mentioned on fastsimcoal2 web pages and in the manual

Changes in fsc27 relative to fsc26New features
1. 1. New syntax in the .est files. It is now possible to include previously defined simple parameters as search range delimiters. The keyword paramInRange needs to be specified at the end of lines containing such parameters.

best

laurent

[Coleen]

Hi, Laurent

Thank you very much for your prompt reply.
Even after adding "paramInRange", the number of "MRCA not found" occurrences remains about the same (15,000-17,000 times). I've tried adjusting the scale of the time ranges.

Originally, it was:

1 t1 logunif 100 5000000 output

1 t2 logunif t1 5000000 output paramInRange
1 t3 logunif t2 5000000 output paramInRange

I've continuously narrowed the range down to:

1 t1 logunif 100 2000 output
1 t2 logunif t1 2000 output paramInRange
1 t3 logunif t2 2000 output paramInRange

However, the number of "MRCA not found" occurrences is still persistently high. Could you please advise on how to improve this? Your help is greatly appreciated.

laurent....@gmail.com 在 2025年6月10日 星期二下午3:10:48 [UTC+8] 的信中寫道：