Complete rewrite from the group up of Introgression Browser
data/
|-- [6.9G] 150_VCFs_2.50.tar.gz
|-- [1022M] 360_merged_2.50.vcf.gz
`-- [594M] 360_merged_2.50.vcf.gz_ib
`-- [594M] 250000
|-- [2.6K] 360_merged_2.50.vcf.gz.npz
|-- [387M] jaccard
| |-- [8.7M] ib_000000.SL2.50ch00.npz
| |-- [ 44M] ib_000001.SL2.50ch01.npz
| |-- [ 26M] ib_000002.SL2.50ch02.npz
| |-- [ 35M] ib_000003.SL2.50ch03.npz
| |-- [ 30M] ib_000004.SL2.50ch04.npz
| |-- [ 33M] ib_000005.SL2.50ch05.npz
| |-- [ 25M] ib_000006.SL2.50ch06.npz
| |-- [ 35M] ib_000007.SL2.50ch07.npz
| |-- [ 33M] ib_000008.SL2.50ch08.npz
| |-- [ 37M] ib_000009.SL2.50ch09.npz
| |-- [ 32M] ib_000010.SL2.50ch10.npz
| |-- [ 21M] ib_000011.SL2.50ch11.npz
| `-- [ 28M] ib_000012.SL2.50ch12.npz
`-- [207M] RAW
|-- [5.6M] ib_000000.SL2.50ch00.npz
|-- [ 24M] ib_000001.SL2.50ch01.npz
|-- [ 13M] ib_000002.SL2.50ch02.npz
|-- [ 16M] ib_000003.SL2.50ch03.npz
|-- [ 19M] ib_000004.SL2.50ch04.npz
|-- [ 18M] ib_000005.SL2.50ch05.npz
|-- [ 11M] ib_000006.SL2.50ch06.npz
|-- [ 16M] ib_000007.SL2.50ch07.npz
|-- [ 16M] ib_000008.SL2.50ch08.npz
|-- [ 16M] ib_000009.SL2.50ch09.npz
|-- [ 17M] ib_000010.SL2.50ch10.npz
|-- [ 16M] ib_000011.SL2.50ch11.npz
`-- [ 20M] ib_000012.SL2.50ch12.npz
8.5G used in 4 directories, 29 files
python requirements:
numpy
scipy
flexx
system requirements:
bgzip
optional requirements:
pypy
system requirements pypy:
libatlas-base-dev libblas3 liblapack3 liblapack-dev libblas-dev gfortran
1023M 360_merged_2.50.vcf.gz
w/o alignment
5.3M 360_merged_2.50.vcf.gz.250000.000000.SL2.50ch00.npz
23M 360_merged_2.50.vcf.gz.250000.000001.SL2.50ch01.npz
12M 360_merged_2.50.vcf.gz.250000.000002.SL2.50ch02.npz
15M 360_merged_2.50.vcf.gz.250000.000003.SL2.50ch03.npz
18M 360_merged_2.50.vcf.gz.250000.000004.SL2.50ch04.npz
16M 360_merged_2.50.vcf.gz.250000.000005.SL2.50ch05.npz
11M 360_merged_2.50.vcf.gz.250000.000006.SL2.50ch06.npz
14M 360_merged_2.50.vcf.gz.250000.000007.SL2.50ch07.npz
15M 360_merged_2.50.vcf.gz.250000.000008.SL2.50ch08.npz
15M 360_merged_2.50.vcf.gz.250000.000009.SL2.50ch09.npz
16M 360_merged_2.50.vcf.gz.250000.000010.SL2.50ch10.npz
15M 360_merged_2.50.vcf.gz.250000.000011.SL2.50ch11.npz
19M 360_merged_2.50.vcf.gz.250000.000012.SL2.50ch12.npz
4.0K 360_merged_2.50.vcf.gz.250000.npz
496K 360_merged_2.50.vcf.gz.csi
2.8M 360_merged_2.50.vcf.gz.gzi
8.0K 360_merged_2.50.vcf.gz.gzj
w/ alignment
5.7M 360_merged_2.50.vcf.gz.250000.000000.SL2.50ch00.npz
25M 360_merged_2.50.vcf.gz.250000.000001.SL2.50ch01.npz
13M 360_merged_2.50.vcf.gz.250000.000002.SL2.50ch02.npz
16M 360_merged_2.50.vcf.gz.250000.000003.SL2.50ch03.npz
19M 360_merged_2.50.vcf.gz.250000.000004.SL2.50ch04.npz
18M 360_merged_2.50.vcf.gz.250000.000005.SL2.50ch05.npz
12M 360_merged_2.50.vcf.gz.250000.000006.SL2.50ch06.npz
16M 360_merged_2.50.vcf.gz.250000.000007.SL2.50ch07.npz
16M 360_merged_2.50.vcf.gz.250000.000008.SL2.50ch08.npz
17M 360_merged_2.50.vcf.gz.250000.000009.SL2.50ch09.npz
17M 360_merged_2.50.vcf.gz.250000.000010.SL2.50ch10.npz
16M 360_merged_2.50.vcf.gz.250000.000011.SL2.50ch11.npz
20M 360_merged_2.50.vcf.gz.250000.000012.SL2.50ch12.npz
4.0K 360_merged_2.50.vcf.gz.250000.npz
1 thread - no alignment
real 220m11.411s
user 436m20.040s
sys 0m41.524s
4 threads - no alignment
real 80m24.037s
user 373m12.301s
sys 0m40.070s
6 threads - no alignment
real 81m47.819s
user 498m14.096s
sys 1m27.114s
8 threads - no alignment
real 57m19.298s
user 398m 2.372s
sys 3m 0.994s
===========
6 threads - no alignment - 20 bins
real 6m12.305s
user 39m 2.290s
sys 0m 4.687s
6 threads - w/ alignment - 20 bins
real 7m18.622s
user 45m43.042s
sys 0m 5.512s
==========
6 threads - w/ alignment
real 99m40.466s
user 611m 1.784s
sys 1m46.982s