problem with interpreting .tpl file

[Joanna Giemza]

My command:
./fsc25211 -t file.tpl -n 100000 -N 100000 -e file.est -M 0.001 -l 10 -L 40

My .tpl file:
//Number of population samples (demes)
6 samples to simulate :
//Population effective sizes (number of genes)
NCUR0
NCUR1
NCUR2
NCUR3
NCUR4
NCUR5
//Sample sizes
84
89
86
82
93
93
//Growth rates : negative growth implies population expansion
GR
GR
GR
GR
GR
GR
//Number of migration matrices : 0 implies no migration between demes
1
//Migration matrix 0
0 MIG01 MIG02 MIG03 MIG04 MIG05
MIG10 0 MIG12 MIG13 MIG14 MIG15
MIG20 MIG21 0 MIG23 MIG24 MIG25
MIG30 MIG31 MIG32 0 MIG34 MIG35
MIG40 MIG41 MIG42 MIG43 0 MIG45
MIG50 MIG51 MIG52 MIG53 MIG54 0
//historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix
0  historical event
//Number of independent loci [chromosome]
1 0
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
FREQ 1 0 2.5e-8

The output:
Deme sizes
Deme 0    0
Deme 1    0
Deme 2    0
Deme 3    0
Deme 4    0
Deme 5    0


Sample sizes
Deme 0    0
Deme 1    0
Deme 2    0
Deme 3    0
Deme 4    0
Deme 5    0

Sample ages
Deme 0    0
Deme 1    0
Deme 2    0
Deme 3    0
Deme 4    0
Deme 5    0

Growth rates
Deme 0    9.54898e-313
Deme 1    9.54898e-313
Deme 2    9.54898e-313
Deme 3    9.54898e-313
Deme 4    9.54898e-313
Deme 5    9.54898e-313


Historical events
No historical events defined in input file ...


Number of independent loci to simulate : 0
with the same chromosomal structure

Number of linkage blocks to simulate in structure 1: 0
TDemeCollection::create_lineagesNoRec() : Tree is empty

fastsimcoal2 is building 0 genealogies ...
 
Why so many zeros? Why the software didn't correctly read for example the sample sizes or number of independent loci to simulate? Please help.

[Laurent Excoffier]

it looks like a file format problem... (PC format on linux or the reverse). Can you check the format of your tpl file?

laurent

[Joanna Giemza]

it is ASCII text and I created it on linux. I use fsc on linux as well

[Laurent Excoffier]

can you send me the tpl, est and obs files?

L

[Laurent Excoffier]

Hi,

there were several problems:

1)  you did not define the search range of the parameter NCUR0 in your est file.

    You defined parameter NCUR1 to NCUR6, while you should have defined parameters NCUR0 to NCUR5

2) you did not use the -d command line parameter to indicate you wanted to compute the likelihood from the derived SFS

3) you wrongly named your obs files  (read the manual to see how to do that)

best

laurent

[Joanna Giemza]

Hi Laurent,

Thank You very much, I corrected point 1) and 2) and the problem of zeros is solved. However I don't think I wrongly named my files. What did I named wrongly according to you? The current error is "Observed data file ("../FREX_jointDAFpop1_0.obs") does not seem to be present", but I don't have derived allele sfs, but minor allele sfs and I have a file with "M" instead of "D".

Best,
Joanna

[Laurent Excoffier]

if you  have the jointMAF

then the command

./fsc25211 -t file.tpl -n 100000 -N 100000 -e file.est -M 0.001 -l 10 -L 40 -m

should do

L