Error: disimilarity matrix is not a full rank matrix

[space-beaver]

Dear Desislava,

I realise this error has been raised before (#12) but I have followed all suggestions and cannot find a solution to this error with my data. My final dataset has 106 individuals and 1294 snps.

From a starting tped file with 106 individuals, from chr19 of squirrel WG shotgun data and 46,490 snps, I have followed this process:

1. Convert tped to ped and remove sites with missing genotypes plink --tfile chr19_all --recode --allow-extra-chr --out chr19_all_noMiss --geno 0

2. Transpose to SNP-major and generate bim, bed, fam files plink --bfile chr19_all_noMiss --transpose --make-bed --out chr19_all_noMiss_trans

3. Recode chromosome names sed -i 's/LR738630.1/19/g' chr19_all_noMiss_trans

4. Calculate diffs matrix with bed2diffs (done with v1 and v2) ./bed2diffs_v1 --bfile chr19_all_noMiss_trans

5. Run eems ./runeems_snps --params squirrels.ini --seed 123

Error: [Graph::initialize] Generate population grid and sample assignment Loaded sample coordinates from chr19_all_noMiss_trans.coord There are 42 observed demes (out of 81 demes) The population grid has 81 demes and 198 edges There are 106 samples assigned to 42 observed demes [Graph::initialize] Done.

[Diffs::initialize] Error: The dissimilarity matrix is not a full-rank distance matrix.

I have run both bed2diffsv1 and bed2diffsv2 and have the same problem with both (they are identical). I have checked the matrix properties in R (same for both matrices) and these are shown below. The eigenvalues have 2 positive values, and the rest are negative. The sum is also non-negative, so this may indicate a problem but I can't find a reason why these matrices don't fulfil the requirement of a full rank matrix for the eems program. If anyone can help find the solve, I'd be very grateful. I have attached .diffs, .ini, .coord, .bim, .bed and .fam files.

isSymmetric(mat_v1, check.attributes = FALSE) TRUE isSymmetric(mat_v1) FALSE

rankMatrix(mat_v1) [1] 105 attr(,"method") [1] "tolNorm2" attr(,"useGrad") [1] FALSE attr(,"tol") [1] 2.353673e-14

#check that matrix is non-negatibve

a <- min(mat_v1 >= 0) 1L

#Check that matrix has a diagonal of 0s by extracting diagonal values

mat_v11[row(mat_v1)==col(mat_v1)] [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [44] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [87] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

##calculate eigenvalues, sum and n pos, n neg

eigenvals <- eigen(mat_v1)$values sum(eigenvals) -1.103423e-13 neg <- sum(eigenvals < -tol) 104L pos <- sum(eigenvals > +tol) 2L

svul_eems.zip