splatche out of range

[fredjaya]

Simulations run but output the follow splatche errors:

Simulating demography, iteration no. 1... 
    The number of population source is 1
    ID: ori, Initial density: 9179, Lat: -18.9438, Long: 119.777, Initial size: 9179, Long: 119.777, No resize before the expansion: 0, No bottleneck: 0, Only one source, no migration before the expansion.
    Input file has been sucessfully read!
ERROR: {ImportExportUtils::readGeoPopDensity(...)} [the population 'ori' is on water!]
    Recomputing K in generation 250
... Done! (Duration of the SimulateWorld function: 0 sec.)

• is this an *.est issue? Should limits be changed?

Simulating genetics, iteration no. 1... 
Starting Coalescent simulation
 WARNING:  [the population '1' has not been colonised or it's density (0) is smaller than the sample size (2)!]
...

.est still requires specification of parameters i.e. carrying capacities like pika.est

[CornilleAmandine]

Hello, I have the same issue but I have defined my K. Starting Coalescent simulation WARNING: [the population 'GIN_1' has not been colonised or it's density (0) is smaller than the sample size (12)!]

My .est is

// Priors and rules file
// *********************

[PARAMETERS]
//#isInt? #name #dist.#min  #max    
//all N are in number of diploid individuals
0 STR_MUTATION unif 0.0001 0.01 output
0 LOG_MRATE unif -3.6 -2 hide
0 GR unif 0.001 0.05 output
1 ARG unif 1 30 output //rate de la gamma
0 COEFF_P unif 0.1 0.6 output
1 N_ANCESTRAL unif 1000 10000 output
1 LOG_K unif 3.3 4.6 hide
1 oriLat    unif    16  22 output
1 oriLon    unif    47  51 output

[RULES]

//N_ANCESTRAL*MRATE > 10
LOG_K > (1-LOG_MRATE)

[COMPLEX PARAMETERS]
0 MRATE = pow10(LOG_MRATE) output
1 K =  pow10(LOG_K) output

Could you help me please? Thanks!

[fredjaya]

Hi @CornilleAmandine,

I haven't used X-ORIGIN since this error so I'm not sure of any clear fixes.

One approach I considered was to see if restricting the range of oriLat and oriLon to a region without water would still throw ERROR: {ImportExportUtils::readGeoPopDensity(...)} [the population 'ori' is on water!]. If so, it could rule out defining K as a potential cause of the error.

Might be worth opening an issue on the X-ORIGIN repo for this (possibly common) error

[CornilleAmandine]

Hi Fredjaya/Upe-Squelchers, Thanks a lot! I have already tried to restrict the range but my sites are on the map and not the water. About K, I tried many different corrections but cannot figure out the problem... :/ And sometimes some populations are simulated, and some others not... And I really cannot figure why... Any thoughts? Thanks! Cheers Amandine

On Sat, 1 Aug 2020 at 15:40, Fred Jaya notifications@github.com wrote:

Hi @CornilleAmandine https://github.com/CornilleAmandine,

I haven't used X-ORIGIN since this error so I'm not sure of any clear fixes.

One approach I considered was to see if restricting the range of oriLat and oriLon to a region without water would still throw ERROR: {ImportExportUtils::readGeoPopDensity(...)} [the population 'ori' is on water!]. If so, it could rule out defining K as a potential cause of the error.

Might be worth opening an issue on the X-ORIGIN repo https://github.com/KnowlesLab/X-ORGIN/issues for this (possibly common) error

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[fredjaya]

Quite odd. Based on the error, maybe some simulations work (or don't) based on where ori is initialised? Even then I don't think there's a way to specify identical starting sites across simulations i.e. specifying the same seed

[CornilleAmandine]

Indeed but would be weird to use the same seeds ?

I am may be guessing it is because of my layer. I generated another layer than the one provided for Africa as I am working at the European scale and I am wondering whether splatche can not locate the dot on my new map ...Besides I tried to use the user friendly interface to understand the problem, but it always says segmentation fault, and when I try to look at the splatche log file it just gives me the error message I put in my first message ... I am a bit stuck ... if you have any idea, I am interested in :) Thanks !

On Sat 1 Aug 2020 at 16:20, Fred Jaya notifications@github.com wrote:

Quite odd. Based on the error, maybe some simulations work (or don't) based on where ori is initialised? Even then I don't think there's a way to specify identical starting sites across simulations i.e. specifying the same seed http://cmpg.unibe.ch/software/ABCtoolbox/ABCtoolbox_manual.pdf

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

Tout message que j’envoie en dehors des heures de travail réglementaires ne nécessite aucune réponse immédiate