User Warning while running GADMA

[spilornis-ng]

Hi Ekaterina,

I am trying to run GADMA to infer demographic history for 2 populations based on radseq data. While running, I am getting several warnings, and one of them is the following

UserWarning: Failed to optimise: message: The maximum number of function evaluations is exceeded.
success: False
status: 0
fun: 1114677814749395.8
x: [ 5.521e+07 4.338e+07 6.699e+07]
nit: 1000
nfev: 1031
njev: 3969
nhev: 0
cg_niter: 1010
cg_stop_cond: 2
grad: [ 4.928e+04 -9.446e+07 9.441e+07]
lagrangian_grad: [ 4.928e+04 -2.464e+04 -2.464e+04]
constr: [array([ 2.361e+07]), array([ 5.521e+07, 4.338e+07, 6.699e+07])]
jac: [array([[ 0.000e+00, -1.000e+00, 1.000e+00]]), array([[ 1.000e+00, 0.000e+00, 0.000e+00],
[ 0.000e+00, 1.000e+00, 0.000e+00],
[ 0.000e+00, 0.000e+00, 1.000e+00]])]
constr_nfev: [0, 0]
constr_njev: [0, 0]
constr_nhev: [0, 0]
v: [array([-9.443e+07]), array([ 8.172e-10, 4.685e-10, 6.680e-09])]
method: tr_interior_point
optimality: 49283.00610715232
constr_violation: 0.0
execution_time: 2.3059918880462646
tr_radius: 0.006561028271562303
constr_penalty: 6.097705629027081e+17
barrier_parameter: 0.020000000000000004
barrier_tolerance: 0.020000000000000004
niter: 1000

I am using demes engine to plot the model. I was wondering if you could help me out regarding this.

Best,
Naman

[noscode]

Hi Naman,

Sorry for the slow reply. I am happy to help. I am not sure what may cause this error, but I would be glad to figure that out. Could you please let me know if you checked the values of your site frequency spectrum? Have you already built one from VCF file or are you using VCF file directly in GADMA?

Best regards,
Ekaterina

[spilornis-ng]

Hi Ekaterina,

No worries. Thanks for getting back to me. I am still trying to figure out the pipeline with my dataset. I have checked the values of the SFS, and it appears to be okay to me. I generated the folded SFS using easySFS, maximizing the number of segregating sites while down-projecting. There are a couple of things I am a bit uncertain about.

1. This warning is seen only in certain iterations (I have attached the log below)
2. I do get the pipeline to run, but there are several warnings, such as some parameters hitting their lower or upper bounds. I am wondering if this has to do with the default parameter bounds that I am using.

Please let me know what you think may be happening based on the log and if you require any additional information.

Thanks!

GADMA.log