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dipetkov / eems

Estimating Effective Migration Surfaces
GNU General Public License v2.0
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Problem running bed2diffs: Error opening plink files #7

Closed mcrossley3 closed 8 years ago

mcrossley3 commented 8 years ago

Hi Dr. Petkova, I get an error message when trying to run bed2diffs on my data. Here is the command and error message:

crossley@denali:~/EEMS_analysis/eems-master/bed2diffs/src$ ./bed2diffs_v1 --bfile b33 Set the number of OpenMP threads to 1

Compute the average genetic differences according to: Dij = (1/|Mij|) sum{m in Mij} (z{im} - z_{jm})^2 where Mij is the set of SNPs where both i and j are called

[Data::getsize] Error opening plink files b33.[bed/bim/fam]

I am running EEMS from an Ubuntu terminal, which has bed2diffs compiled/configured. I generated my BED file from PED/MAP files using PLINK. I understand you may need more information from me before you can diagnose the problem, but wondered if it is already apparent to you what the issues are.

Thank you very much for any insight you can give, -Mike

mcrossley3 commented 8 years ago

I was able to figure out what my problem was: I didn't realize I needed to include the b33.bim and b33.fam files with the b33.bed file - until I thought more deeply about why you had files with that extension in your /bed2diffs/test directory. Thank you very much for your comments earlier, and perhaps I'll be asking for your guidance again in the future. -Mike