migrate 3.6.11 problem

[张翰超]

Hi all. I am currently using the Windows version of migrate-n to compute a file containing a total of 17,082 SNP sites. I've observed that about 100 sites have been computed in total over three days, but it shows "0.397094 done," and it is estimated to be completed by the 8th. Is this normal?

[Peter Beerli]

You can go to the migrate website and download a recent version. 3.6 is outdated; the current version is 5.0.6 (source). There is a 5.0 version of Windows that should do it, but anyone using Windows for high-end computing is running into challenges. It will take forever on a single CPU machine if you want to run your 17k loci dataset on a cluster computer (and not a plain Windows machine).

Peter

On Apr 1, 2024, at 10:02 PM, 张翰超 <zhc19...@gmail.com> wrote:

Hi all. I am currently using the Windows version of migrate-n to compute a file containing a total of 17,082 SNP sites. I've observed that about 100 sites have been computed in total over three days, but it shows "0.397094 done," and it is estimated to be completed by the 8th. Is this normal?

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[张翰超]

I have also tried to compute on CentOS, but each time I encounter a "SEVERE ERROR: Segmentation fault this results in a non-recoverable crash. But check the datatype and your infile for errors, too. Please report the error with as much detail as possible to Peter Beerli bee...@fsu.edu," and I am unsure where the problem lies.

[张翰超]

The single-threaded and multi-threaded versions of migrate-n-mpi cannot run.

[张翰超]

The same file can run on Windows, but when run on CentOS, the aforementioned error occurs.

[Peter Beerli]

your input file is not correctly formatted! Did you try to run an example in the example directory?

you can send me a small example with your snps (perhaps around 10 snps) and I can give you instructions.

Peter

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[张翰超]

The file contains a total of 15 populations, with each population having 17k SNP sites. The file approximately looks like the one shown in the picture. Thank you very much for your help!

[Peter Beerli]

I said to send a small input file, not a picture of it and I will not have the time to troubleshoot your 17k locus 15 population file.

send a small 5-population 100 snp dataset

With 15 populations 17k loci  you most likely want to use a different program (one that uses the site frequency spectrum)

Peter

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<migrate.png>

[张翰超]

This is a part of my file, thank you for your help!