Table 4:
Execution times (seconds) using different number of cores: locate command. Highlighted are fastest time and number of times faster than sequential BigSeqKit
| 1 | 2 | 4 | 8 | 16 | 32 | 64 (2 nodes) | 128 (4 nodes) | 256 (8 nodes) | |
|---|---|---|---|---|---|---|---|---|---|
| D1 | |||||||||
| pyfastx | 11,523.5 [1.0×] | – | – | – | – | – | – | – | – |
| seqkit | 12,822.9 | 6,385.0 | 3,210.9 | 1,731.4 | 940.5 | 612.4 [18.8×] | – | – | – |
| BigSeqKit | 11,486.2 | 6,286.1 | 3,180.0 | 1,637.3 | 850.9 | 470.6 [24.4×] | 264.6 | 156.9 | 110.3 [104.1×] |
| D2 | |||||||||
| pyfastx | 8,841.2 [1.2×] | – | – | – | – | – | – | – | – |
| seqkit | 12,319.8 | 6,909.4 | 3,335.9 | 1,746.2 | 997.3 | 971.2 [10.5×] | – | – | – |
| BigSeqKit | 10,168.6 | 5,264.5 | 2,711.5 | 1,412.2 | 814.6 | 545.4 [18.6×] | 384.7 | 293.5 | 234.9 [43.3×] |
| D3 | |||||||||
| pyfastx | 13,075.3 [1.1×] | – | – | – | – | – | – | – | – |
| seqkit | 14,281.6 | 8,161.7 | 5,009.6 | 3,184.1 | 1,832.4 | 1,054.9 [14.1×] | – | – | – |
| BigSeqKit | 14,834.2 | 8,223.3 | 4,572.8 | 2,585.6 | 1,494.6 | 872.1 [17.0×] | 532.8 | 365.9 | 262.5 [56.5×] |
| D4 | |||||||||
| pyfastx | 30,028.3 [1.05×] | – | – | – | – | – | – | – | – |
| seqkit | 39,640.5 | 21,257.6 | 10,803.1 | 5,715.1 | 3,369.7 | 2,795.2 [11.3×] | – | – | – |
| BigSeqKit | 31,615.2 | 16,832.1 | 8,531.9 | 4,433.3 | 2,466.8 | 1,609.9 [19.6×] | 1,074.7 | 794.6 | 633.5 [49.9×] |
| D5 | |||||||||
| pyfastx | 27,876.5 [1.06×] | – | – | – | – | – | – | – | – |
| seqkit | 31,301.8 | 16,884.7 | 9,141.1 | 4,698.4 | 2,971.8 | 2,802.9 [10.5×] | – | – | – |
| BigSeqKit | 29,540.7 | 15,431.3 | 8,120.2 | 4,401.4 | 2,454.5 | 1,443.9 [20.5×] | 908.1 | 599.5 | 440.9 [67×] |
| D6 | |||||||||
| pyfastx | 270,214 [1.02×] | – | – | – | – | – | – | – | – |
| seqkit | Out of Mem. | Out of Mem. | Out of Mem. | 40,122 | 23,075 | 18,309 [15.0×] | – | – | – |
| BigSeqKit | 275,680 | 141,095 | 72,110 | 37,140 | 19,810 | 11,477 [24.0×] | 7,003 | 4,422 | 3,080 [89.5×] |