Recapitulation and recombination maps

[qlan...@gmail.com]

Hi,

I'm trying to use the recapitate function with a recombination map that matches what was used for the SLiM simulation. I modified the recombination map to match the Hapmap style and am able to read the recombination map in using msprime.RecombinationMap.read_hapmap(). However when I try to use this to recapitulate my SLiM treeSeq output (using ts.recapitate(recombination_map=recomb_map, Ne=25000)) I receive the following error:

_msprime.InputError: Input error in initialise: The specified recombination map is cannot translate the coordinates for the specified tree sequence. It is either too coarse (num_loci is too small) or contains zero recombination rates. Please either increase the number of loci or recombination rate

In my recombination map there are no zero recombination rates other than the final line and the number of loci seems to be reasonable: recomb_map.get_num_loci() = 4294967295. I am unsure what the underlying issue is that is producing the error and how I can fix it so I can simulate and recapitulate with the same recombination map. Any advice would be helpful.

Thanks!

Quinn

[Peter Ralph]

Ah ha. I can sort this out. Would you mind opening an issue on pyslim's GitHub page? Ideally with a small example?

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