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Question: R aborts when attempting to use snmf function in LEA package
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gravatar for renee.catullo
4 months ago by
renee.catullo0 wrote:

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

ADD COMMENTlink modified 4 months ago by olivier.francois0 • written 4 months ago by renee.catullo0
0
gravatar for olivier.francois
4 months ago by
olivier.francois0 wrote:

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

ADD COMMENTlink written 4 months ago by olivier.francois0
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