Gui validated scenarios do not work in commandline version.

[PrestonMcDonald]

I appreciate the immense effort that goes into making these packages, but I have to say, the documentation and error message outputs are not terribly helpful. I don't understand why the gui scenario validation process clears header.txt files but the command line diyabc then hangs on a problems with the scenarios. It's especially troublesome that the scenario in question is identical to an example given in the manual. Can anybody give me some insight into how to get this software running? I've been banging my head against this wall for about 3 weeks now.

Additionally, can anyone explain what the heck this header.txt file even says? There is very little helpful information in the documentation about how to even produce these. I was only able to get this by using the partially functional gui. If this software is meant to be mostly commandline only at this point, some clearly spelled out method of producing the header file seems necessary.

cat header.txt
ANF_LSG_AllSnps.sorted_nosex.DIYABC.snp
11 parameters and 1 summary statistics

4 scenarios: 6 7 5 7
scenario 1 [0.25] (7)
N1 N2 N3
0 sample 1
0 sample 2
ta split 3 1 2 r1
td merge 1 2
td varNe 1 Na
scenario 2 [0.25] (6)
N1 N2 N2 N2
0 sample 1
0 sample 2
ta split 2 3 4 r2
ta merge 1 3
td merge 1 4
td varNe 1 Na
scenario 3 [0.25] (3)
Ne Ne
0 sample 1
0 sample 2
td merge 1 2
td varNe 1 NA
scenario 4 [0.25] (6)
N1 N2 N1 N1
0 sample 1
0 sample 2
ta split 3 2 4 r3
ta merge 1 2
td merge 1 4
td varNe 1 Na

historical parameters priors (11,1)
N1 N UN[10,10000,0,0]
N2 N UN[10,10000,0,0]
N3 N UN[10,10000,0,0]
Na N UN[10,10000,0,0]
NA N UN[10,10000,0,0]
Ne N UN[10,10000,0,0]
ta T UN[10,10000,0,0]
td T UN[10,10000,0,0]
r2 A UN[0.01,0.99,0,0]
r1 A UN[0.01,0.99,0,0]
r3 A UN[0.01,0.99,0,0]
td>ta
DRAW UNTIL

loci description (1)
4257 G1 from 1

group summary statistics (1)
group G1 (1)
HWm 1

scenario N1 N2 N3 Na NA Ne ta td r2 r1 r3 HWm_1

../diyabc-RF-linux-v1.1.54 -p ./ -n t:1
debut
Beginning of doinitRNG options : t:1
Maximal number of threads per computer is set to 1
End of doinitRNG options
Beginning of RNGs initializations
End of RNGs initializations
0-th batch of RNGs' states are saved into ./RNG_state_0000.bin

../diyabc-RF-linux-v1.1.54 -p ./ -R "ALL" -n t:1 -r 1000
debut
simulating data sets with all summary statistics
I have read RNGs' states from file ./RNG_state_0000.bin
debut de l'action r
./ANF_LSG_AllSnps.sorted_nosex.DIYABC.snp.bin
insert title here
Fichier ./ANF_LSG_AllSnps.sorted_nosex.DIYABC.snp : SNP

lecture du fichier txt
k0=-1
this->nloc = 4257
recherche du nombre d'échantillons
2 échantillons : LSG ANF
échantillon 1 : 10 individus
échantillon 2 : 10 individus
genotype[0][0][12]=2
genotype[0][1][12]=1
genotype[0][2][12]=0
genotype[1][0][12]=2
genotype[1][1][12]=1
genotype[1][2][12]=1
genotype[0][3][12]=0
genotype[0][4][12]=1
genotype[0][5][12]=0
genotype[0][6][12]=1
genotype[1][3][12]=0
genotype[1][4][12]=2
genotype[1][5][12]=0
genotype[1][6][12]=1
genotype[1][7][12]=1
genotype[1][8][12]=0
genotype[1][9][12]=0
genotype[0][7][12]=2
genotype[0][8][12]=1
genotype[0][9][12]=0

avant les delete
fin de la lecture du fichier txt
fin de la lecture
tous les locus sont polymorphes
fin de la purge des monomorphes
sexratio=0
apres le' traitement' des snp
reecriture dans le fichier binaire ./ANF_LSG_AllSnps.sorted_nosex.DIYABC.snp.bin
ecribin this->ssize[0][0]=20
ecribin this->ssize[0][1]=20
fin de ecribin
ouverture du fichier ./ANF_LSG_AllSnps.sorted_nosex.DIYABC.snpbin.txt OK
apres maf nloc=4257
apres la deuxième ligne
relecture du fichier binaire
smaf=hudson's algorithm
THIS->MAF=0
sexratio=0
nloc=4257
nsample=2
type 0 catexist =1
type 1 catexist =0
type 2 catexist =0
type 3 catexist =0
type 4 catexist =0
type 0
20 20
this->maf=0
dans libin
this->locus[0].haplosnp[0][0]=1
fin de la lecture du fichier binaire
apres le calcul des coefficients de coalescence

avant missingdata
apres missingdata
nparamtot=11
nstat=1
----------------------------------------apres readHeaderDebut
4 scenario(s)
----------------------------------------apres readHeaderScenarios

!!! I have caught an exception which is:
Erreur dans readheaders().
Error when reading header.txt file : in line 4 population 3 does not exist anymore in scenario 1

I will try to save current RNGs' states.
I have saved current RNGs' states into ./RNG_state_0000.bin

[gdurif]

Hi @PrestonMcDonald

Regarding diyabc command line tool, you can open an issue in the dedicated repository : https://github.com/diyabc/diyabc

Regarding the limitations that you mention, parts of the software are very old and we (=the recent developers) were not part of it at the time. We are stuck working with these old parts (e.g. regarding input file format) and we do not have enough human resources to redevelop the whole thing from scratch to improve these parts or even to document/wrap everything nicely.

Thanks in advance,
Best regards