fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output

Question

[lakemonster]

Hi Everyone

I'm using fastPHASE v.1.4.8 to estimate haplotypes on a UNIX cluster. I have provided the -F flag to get haplotype frequencies and the _freqs file is being returned without those frequencies. Does the -F flag need to interact with any other input files or flags for it to produce freqs? I've tried a few different iterations of supplying positive values behind -F, no -F, -F with the default #iterations, etc. No luck.

Does the pop_labels file need to contain both poplabels on a row and sample names? Seems like that's not the case given the description of the pop_labels file in the manual v1.4.

This is my command:

./fastPHASE -T20 -C45 -F5000 -upop_labels -q0.9 -w -Pm -Pp -KU30 -KL5 -Ki5 -o./ input.inp

Which produces this _freqs file:

> estimated sample haplotype frequencies for entire sample
sampled.haplotype
> estimated sample haplotype frequencies for "subpopulation" 1
sampled.haplotype
> estimated sample haplotype frequencies for "subpopulation" 2
sampled.haplotype

pop_labels is 1x89, with 46 1's and 43 2's all in a single row with a space between the lables, like so

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

Can anyone tell me a bit more about the -F and how to get the _freqs file filled with frequencies?

Thanks so much!

[Shicheng Guo]

It seems beagle is more popular in speed and accuracy, right?

[lakemonster]

seems beagle is more popular

Popularity aside, I can't get -F to work

[Shicheng Guo]

Just check whether you are latest fastPHASE. I just run it now and -F works.

[tututuz]

hi！do you know how to use the fasephase,I can't get the freqs in output,can you give me some advises.