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Benchmarks
Diogo Silva edited this page Jul 28, 2017
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These time and RAM benchmarks were gathered for all major operations of the Process module using the CLI version (TriSeq).
- Version: 1.0.0rc1
- Hardware: Intel i7-7500 @ 2.70Ghz - HD620 - NVMe SSD
- Operating system: ArchLinux
| DS1 | DS2 | DS3 | DS4 | DS5 | DS6 | DS7 | DS8 | DS9 | DS10 | DS11 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Files | 614 | 3093 | 3093 | 3093 | 7378 | 1 | 1 | 1 | 1 | 2 | 52284 |
| Taxa | 50 | 48 | 141 | 376 | 29 | 40 | 40 | 40 | 376 | 40 | 40 |
| Total bases (MB) | 17.536 | 72.385 | 212.630 | 567.013 | 18.405 | 182.265 | 182.265 | 182.265 | 567.012 | 364.530 | 180.801 |
| Notes | Interleave (phylip) | Interleave (nexus) | |||||||||
| Parsing | |||||||||||
| Alignment reading | 0.7s / 5.8Mb | 2.7s / 15.3Mb | 6.7s / 15.9Mb | 18.1s / 17.6Mb | 4.0s / 35.5Mb | 0.7s / 33.5Mb | 18.1s / 27.2Mb | 69.2s / 23.6Mb | 2.6s / 14.5Mb | 1.9s / 33.3Mb | 34.4s / 209.2Mb |
| Main operations | |||||||||||
| Conversion (nexus) | 0.2s / 0.1Mb | 0.7s / 0.2Mb | 1.7s / 0.1Mb | 4.5s / 0.1Mb | 0.8s / 0.3Mb | 0.8s / 62.8Mb | 0.9s / 62.0Mb | 1.0s / 60.9Mb | 2.4s / 20.2Mb | 1.5s / 52.4Mb | 6.4s / 0.5Mb |
| Conversion (interleave) | 2.8s / 0.1Mb | 6.8s / 0.3Mb | 17.7s / 0.5Mb | 45.4s / 2.1Mb | 6.1s / 0.4Mb | 19.1s / 56.4Mb | 18.9s / 56.3Mb | 18.8s / 56.3Mb | 82.1s / 17.0Mb | 38.9s / 52.0Mb | 49.9s / 0.8Mb |
| Concatenation | 0.9 / 6.4Mb | 3.2s / 25.0Mb | 9.0s / 24.8Mb | 27.2s / 33.2Mb | 3.3s / 13.0Mb | NA / NA | NA / NA | NA / NA | NA / NA | 5.0s / 151.3Mb | 32.5s / 70.7Mb |
| Secondary operations | |||||||||||
| Collapse | 0.5s / 0.1Mb | 1.5s / 0.2Mb | 2.7s / 0.1Mb | 5.4s / 0.1Mb | 1.0s / 0.2Mb | 1.5s / 61.2Mb | 1.5s / 61.2Mb | 1.5s / 61.2Mb | 3.6s / 21.1Mb | 3.0s / 61.5Mb | 8.0s / 0.1Mb |
| Consensus (Soft mask/ single file) | 1.5s / 1.1Mb | 6.9s / 0.5Mb | 13.6s / 2.3Mb | 29.8s / 8.2Mb | 1.7s / 0.3Mb | 19.1s / 59.7Mb | 15.7s / 56.1Mb | 15.7s / 53.5Mb | 30.9s / 440.1Mb | 47.8s / 68.5Mb | 54.6s / 2.3Mb |
| Filter (Taxa contain) | 0.2s / 0.3Mb | 0.7s / 0.8Mb | 1.6s / 0.9Mb | 4.1s / 0.9Mb | 1.1s / 5.0Mb | NA / NA | NA / NA | NA / NA | NA / NA | 0.0s / 0.2Mb | 29.1s / 17.9Mb |
| filter (Minimum taxa; 80%) | 0.3s / 0.6Mb | 1.1s / 1.0Mb | 2.8s / 3.1Mb | 7.0s / 8.7Mb | 2.6s / 1.5Mb | NA / NA | NA / NA | NA / NA | NA / NA | 0.0s / 0.2Mb | 48.2s / 20.1Mb |
| Filter (Missing data; G50; M75) | 4.7s / 3.8Mb | 17.0s / 13.5Mb | 46.3s / 14.1Mb | 119.7s / 19.3Mb | 9.4s / 8.1Mb | 47.6s / 173.2Mb | 47.6s / 170.9Mb | 48.0s / 170.9Mb | 128.3s / 443Mb | 101.7s / 115.1Mb | 123.7s / 51.9Mb |
| Filter (Codons; 1 2) | 1.9s / 0.2Mb | 6.1s / 0.5Mb | 20.8s / 0.3Mb | 46.5s / 0.4Mb | 4.1s / 1.0Mb | 15.5s / 164.7Mb | 16.2s / 164.7Mb | 15.5s / 164.7Mb | 49.8s / 54.5Mb | 31.7s / 142.8Mb | 40.8s / 3.4Mb |
| Filter (Variable ; 0, 200) | 1.4s / 1.3Mb | 6.7s / 1.9Mb | 13.3s / 3.8Mb | 35.0s / 9.7Mb | 3.0s / 4.1Mb | NA / NA | NA / NA | NA / NA | NA / NA | 45.6s / 53.6Mb | 84.7s / 28.3Mb |
| Filter (Informative ; 0, 200) | 2.9s / 1.3Mb | 12.6s / 1.9Mb | 27.5s / 3.8Mb | 64.2s / 10.2Mb | 8.1s / 4.0Mb | NA / NA | NA / NA | NA / NA | NA / NA | 49.5s / 53.9Mb | 128.6s / 28.3Mb |
| Code gaps | 3.6s / 6.3Mb | 14.4s / 28.3Mb | 45.5s / 28.1Mb | 116.9s / 27.0Mb | 2.3s / 2.9Mb | 72.3s / 116.2Mb | 64.1s / 116.0Mb | 88.0s / 116.2Mb | NA / NA | 195.9s / 88.3Mb | 19.4s / 11.6Mb |
| Reverse concatenation | |||||||||||
| Reverse concatenation only | 0.3s / 6.5Mb | 1.4s / 34.8Mb | 3.9s / 36.2Mb | 9.0s / 34.1Mb | 1.6s / 76.0Mb | NA / NA | NA / NA | NA / NA | NA / NA | 3.9s / 137.7Mb | 14.7s / 993.8Mb |
| Reverse concatenation + conversion (nexus) | 0.4s / 6.5Mb | 1.7s / 34.8Mb | 4.8s / 36.4Mb | 11.6s / 38.2Mb | 1.8s / 76.0Mb | NA / NA | NA / NA | NA / NA | NA / NA | 5.6s / 139.2Mb | 17.1s / 1000.8Mb |