Table 2

GFlasso processing pipeline

Step No.

Description

Stage

No. Jobs using yeast data

Av. Time/Job on yeast data

Hours:min:sec

Actual time from start to finish

Time saved via parallelization


1

Lasso stage 1

Preprocessing SNPs

23

00:00:25

00:02:59

00:06:36


2

Lasso validation error

Preprocessing SNPs

1

00:02:14

00:02:14

00:00:00


3

Lasso stage 2

Preprocessing SNPs

23

00:01:16

00:03:40

00:25:34


4

Lasso validation error

Preprocessing SNPs

1

00:00:39

00:00:39

00:00:00


5

Marker Processing

Preprocessing SNPs

1

00:00:10

00:00:10

00:00:00


6

Connected component analysis

Preprocessing traits

1

00:00:56

00:00:56

00:00:00


7

Spectral clustering

Preprocessing traits

118

00:00:56

00:06:44

01:43:03


8

Trait Processing

Preprocessing traits

1

00:06:02

00:06:02

00:00:00


9

GFlasso stage 1

GFlasso optimization

130

00:51:34

01:41:36

110:02:30


10

GFlasso validation error stage 1

GFlasso optimization

1

01:43:01

01:43:01

00:00:00


11

GFlasso stage 2

GFlasso optimization

130

05:49:08

29:27:45

726:59:05


12

GFlasso validation error stage 2

GFlasso optimization

1

00:45:26

00:45:26

00:00:00


13

GFlasso stage 3

GFlasso optimization

130

03:18:04

10:56:18

418:12:37


14

GFlasso validation error stage 3

GFlasso optimization

1

00:56:32

00:56:32

00:00:00


Curtis et al. BMC Genetics 2012 13:24   doi:10.1186/1471-2156-13-24

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