Are Plink MDS plots supposed to complete so quickly?

Question

[devenvyas]

I ran MDS plots on a data set of >620,000 SNPs and 934 individuals using plink.

I followed the advice of a former lab member as well as this tutorial (https://www.staff.ncl.ac.uk/heather.cordell/pak2010MDS.html - mainly just the stuff after "To perform MDS analysis in PLINK, we first calculate a file").

plink --file dataset --genome --out dataset
plink --file dataset --read-genome dataset --mds-plot $k --out "dataset_"$k

($k is looped in and is the number of MDS dimensions ranging from 1 to 20).

The first line (genome file creation) does take a while, but I have noticed that the actual mds generation takes about 10 minutes per run and uses about half a gigabyte of RAM, which seems suspiciously quick and non-intensive.

Anyone have any experience with this? (i.e., am I doing something wrong, or is this normal)

[chrchang523]

Actually, once your data has been converted to binary, genome file creation should take less than two minutes with your dataset with PLINK 1.9 on most systems, and --mds-plot should take less than one.

[devenvyas]

This was running on Plink 1.07, single threaded. HPC just got Plink 1.9 installed this morning, so I haven't tried it out yet.