Table 3 Computational times involved in some of the most demanding tasks of the pipeline, performed on a node with four cores and 350 GB of RAM provided by the MSU High Performance Computing Center (HPCC).
TaskDimensionMedian Time (SD) in either seconds (s) or hours (hr)
Summariesn = 410K×p = 805K0.27 hr (23.94 s)
Block of Genomic Relationship Matrixn = 20K×n = 20K1.00 hr (105.32 s)
GWASn = 223K×p = 625K0.57 hr (139.9 s)
BGLR Regression (single iteration)n = 223K×p = 0.5K0.156 s (0.039 s)
n = 223K×p = 1K0.391 s (0.061 s)
n = 223K×p = 2K0.612 s (0.042 s)
n = 223K×p = 5K1.665 s (0.095 s)
n = 223K×p = 10K3.355 s (0.126 s)
n = 223K×p = 20K6.858 s (0.174 s)
n = 223K×p = 30K10.804 s (0.240 s)
n = 223K×p = 40K14.985 s (1.200 s)
n = 223K×p = 50K20.901 s (0.536 s)
  • 223K and 625K were n = 222,661 and p = 624,528.