Run migrate with SNP data

[aboozar soorni]

I am a new user and would appreciate some help to disentangle a problem with my analysis. 

I have a huge VCF file which contains ~30K SNPs (33 populations and 69 samples). I used PGDSpider to convert VCF file to migrate format. When I run migrate-n, it reads data but is exiting with the following error:

SEVERE ERROR: Segmentation fault

              this results in an non recoverable crash.

              But check the datatype and your infile for errors, too.

              Please report error with as much detail as possible to

              Peter Beerli <bee...@fsu.edu>

input file (infield) is a huge file, so I have attached just a part of it.

Any suggestions as to how to correct this error?

[Peter Beerli]

Dear Aboozar,

with a complete infile, parmfile little help is available because the error seems very generic.

I suggest that you try to use a dataset that has fewer populations (for example 3 [three]) and fewer loci for example 100!

This would allow checking your data file, if it runs then I would do some tests with that and then expand the number of loci and when that works perhaps expand the number of populations. 

Migrate is not equivalent to the PCA programs. It will explore all possible gene trees for each locus and doing this for 30K loci and 33 populations is an extreme task (do you think that your data contains enough information to extract around 1000 parameters? [39*39])

Peter

PS. It also helps if you tell us which version of migrate you use and which operating system you run it on.

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<infile>

[Peter Beerli]

Dear Aboozar,

withOUT a complete infile, parmfile little help is available because the error seems very generic.

[aboozar soorni]

Dear Peter

Thanks so much. Looks it works for a subset. You're right, 30K loci and 33 populations is an extreme task. I will try to run migrate on populations defined by fastSTRUCTRE.