Cannot use frequency list to initialize beginFreq in trajectory

[marina-klemm]

Kia ora Bo Peng, I keep running into the same error when trying to run my simulation using my mtDNA frequencies file inside the beginFreq at my trajectory function. I have the frequency for 100 alleles and I'm running the simulation with 100 loci. However, whenever I try to define the trajectory, it says "Initial frequency should be provided for each locus (nLoci) or each locus at each subpopulation (nLoci * len(N))." Is there a way around it? My code follows attached in txt.

Additionally, is there a limit of generations or individuals that can be input into a trajectory? I verified that I cannot have a simulation with less than 80 generations, since that gives me the error "AttributeError: 'NoneType' object has no attribute 'func'". In my simulation, I start with 30,000 individuals and my population goes through a bottleneck of 40 within 10 generations. I found trajectory does not run with such a large number of individuals and perhaps with a narrow bottleneck like this. traj.func_error.txt

Thank you so very much for your time. Ngā mihi, Marina.

[BoPeng]

I get mtDNA_1.txt not found error when I tried to reproduce your problem.

[marina-klemm]

Hi Bo, Thank you for your reply. The file follows attached here. Thank you! Kind regards

Em seg., 27 de nov. de 2023 às 18:22, Bo @.***> escreveu:

I get mtDNA_1.txt not found error when I tried to reproduce your problem.

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Marina Klemm she/her PhD in Biological Sciences

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[BoPeng]

I notice that your formatted_list is a list of strings like

['0.130066116932049, 0', '0.0365202462650868, 0', '0.0457264089847202, 0', '0.0843284207640962, 0',

where the documentation says

        beginFreq
            The initial allele frequency of involved loci in all subpopulations.
            It can be a number (same frequency for all loci in all
            subpopulations), or a list of frequencies for each locus (same
            frequency in all subpopulations), or a list of frequencies for each
            locus in each subpopulation in the order of ``loc0_sp0``,
            ``loc1_sp0``, ..., ``loc0_sp1``, ``loc1_sp1``, ... and so on.

I am not sure how exactly you would like to initialize this parameter, but

https://github.com/BoPeng/simuPOP/blob/50f4776530cd2904196e56927000357da9a564b4/src/utils.py#L1365-L1377

is the code to process it.