R aborts when attempting to use snmf function in LEA package
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@reneecatullo-13361
Last seen 4.9 years ago

Hey folks,

I'm trying to run snmf function in the LEA package on a large SNP dataset (99 indviduals, ~11,000 SNPs). I have, as far as I can tell, perfectly formatted lfmm file. I've re-installed the latest version of the LEA package, and am running the latest R and Xquartz versions.

I create my lfmm file using my existing pipeline:

#this creates the lfmm file on my computer, and writes the path to an object called d2l in R
d2l <- dart2lea(d5, RandRbase, species, dataset)

library(LEA)

#When I run the below, R aborts

snmf_all=snmf(d2l, K=1:6, entropy = TRUE, repetitions = 1, CPU = 2, project = "new", ploidy = 2)

at this stage, d2l is "~/Dropbox/Linkage_frogs/08_L_rothii_analysis/rrtools/rothii/popgen/raw_SNPFilt_1SNPperClone/lea/rothii_DLit17-2634_nooutgroup.lfmm"

 

The first 10 individual/25 SNPs in my lfmm file look like this:

2 2 0 1 1 1 0 0 0 1 0 1 1 0 0 1 2 1 0 2 2 2 1 1 0
1 2 2 0 0 0 0 0 2 0 0 1 0 1 0 1 0 2 2 1 2 1 2 1 1
0 9 0 0 0 0 2 0 0 1 1 2 0 0 2 2 1 0 2 2 0 1 1 2 1
2 0 0 0 0 0 0 0 0 2 1 0 0 0 0 1 0 2 0 1 9 2 1 0 0
0 0 2 0 0 0 2 1 1 2 1 2 0 1 2 2 0 1 1 0 1 0 2 1 1
0 2 2 0 2 0 2 0 0 2 2 2 2 0 2 2 1 2 9 2 1 1 1 1 2
1 1 2 0 0 0 2 0 0 1 2 2 0 2 1 2 0 1 0 1 1 1 1 1 1
1 2 1 0 0 0 2 1 0 2 2 2 2 2 2 1 0 0 2 2 0 2 2 1 1
2 2 1 0 1 0 0 0 0 1 0 0 0 0 2 1 1 1 0 2 1 2 1 1 2
0 0 0 2 2 2 0 2 2 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0
0 0 0 2 2 2 0 2 0 0 0 0 0 2 0 9 9 0 2 0 0 0 0 0 0

Any thoughts would be appreciated!

Renee

snmf lea • 882 views
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Entering edit mode
@olivierfrancois-13371
Last seen 4.9 years ago

hi renee,

Could you include the error message returned by R?

The type of error you described happens with Rstudio when the path is incorrect, f you have insufficient rights to write in the result directory, or if a project with the same name (but different data) already exist. 

My suggestion would be to use a local directory (not a Dropbox directory) and then backup the results in the Dropbox folder when the runs are completed.

regards

olivier

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