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Table 6 Association analysis max(T) permutation test times (sec)

From: Second-generation PLINK: rising to the challenge of larger and richer datasets

Other parameter(s) Dataset Machine PLINK 1.07 PERMORY 1.1 PLINK 1.90 Ratio
–trend (C/C) synth1 Mac-2 20 k   18.7 1.1 k
   Mac-12 16 k   2.8 5.7 k
   Linux32-2 21 k   65.0 320
   Linux64-512 17 k 285.0 2.8  
   Win32-2 35 k 1444.2 61.5  
   Win64-2 25 k 889.7 14.4  
  synth2 Mac-2 170 k   42.4 4.0 k
   Mac-12 180 k   6.4 28 k
   Linux32-2 410 k   391.0 1.0 k
   Linux64-512 200 k 580.9 13.7  
   Win32-2 1100 k 2362.5 198.0  
   Win64-2 370 k 1423.6 34.0  
–fisher (C/C) synth1 Mac-2 150 k   21.9 6.9 k
   Mac-12 150 k   3.7 41 k
   Linux32-2 170 k   57.8 2.9 k
   Linux64-512 120 k   3.4 35 k
   Win32-2 440 k   64.9 6.8 k
   Win64-2 200 k   22.0 9.1 k
  synth2 Mac-2 890 k   49.8 18 k
   Mac-12 690 k   7.6 91 k
   Linux32-2 1300 k   393.7 3.3 k
   Linux64-512 720 k   13.0 55 k
   Win32-2 3600 k   208.3 17 k
   Win64-2 1700 k   35.6 48 k
–assoc (QT) synth1 Mac-2 30 k   148.0 200
   Mac-12 22 k   22.6 970
   Linux32-2 68 k   847.2 80
   Linux64-512 29 k   29.2 990
   Win32-2 58 k   896.1 65
   Win64-2 36 k   264.2 140
–assoc lin (QT) synth1 Mac-2    606.8  
   Mac-12    34.7  
   Linux32-2    3212.6  
   Linux64-512   1259.8 46.4 27.2
   Win32-2   2115.7 3062.7 0.69
   Win64-2   972.6 336.6 2.89
  1. All runs are with 10000 permutations and –seed 1. The PLINK 1.9 implementation extends Pahl et al.’s PERMORY algorithm [29] with multithreading (note the 12- and 512-core machine results) and additional low-level optimizations.