host compute node: [4 cores] on Patricks-MacBook-Pro.local [ ] 0% | 0:00:29 | simulating count matrices Unknown exception encountered: Unable to open file (unable to lock file, errno = 35, error message = 'Resource temporarily unavailable')
Some papers of interest:
"A One-Penny Imputed Genome from Next-Generation Reference Panels"
Why: using a large population sample you can phase SNPs for any given sample. We could hopefully do this with the large Amaranthus data. Maybe even with smaller population data sets in Pedicularis (what is considered large?). They use msprime simulations in the paper to show that it works, which is cool. Another idea: using a phased panel of pollen data to then use to phase diploids.
"Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species"
Why: infer local ancestry tracks for multiple species. This is what I really want to do with data like for the oaks. Problem is you need phased data for it to work well. The method for assigning tracks here is similar to what we want to do in assigning parental alleles to pollen. We could get phase like in the method above...
-f aargument, though, and that you instead need to tell it to do bootstrapping and then tell it to do the full tree search. It's usually easier to just use the PTHREADS version, submit a long
-f ajob and wait. But I guess getting a whole node for multiple days might take a while...