Summary
- Implement chromosome-level parallelization for the
modcall and phase commands. The overall execution time is reduced 71% ~ 88%.
- Replace
malloc with jemalloc.
- Remove and simplify unused parameters to improve memory usage.
- Adjust the weighting of low-quality variants in phasing.
- The VCF generated by
modcall can be directly imported into IGV. Additionally, modcall can output all detected coordinates by using the --all parameter.
see detail changes
| phase (-t 24) |
v1.5.2 (Time) |
v1.5.2 (Memory) |
v1.6 (Time) |
v1.6 (Memory) |
| HG002 ONT R10.4.1 10x |
153s |
7.7G |
39s |
15.1G |
| HG002 ONT R10.4.1 20x |
444s |
8.2G |
53s |
15.6G |
| HG002 ONT R10.4.1 30x |
355s |
8.5G |
68s |
24.4G |
| HG002 ONT R10.4.1 40x |
908s |
8.8G |
217s |
26.6G |
| HG002 ONT R10.4.1 50x |
1043s |
9.2G |
262s |
22.2G |
| HG002 ONT R10.4.1 60x |
640s |
9.5G |
113s |
33.4G |
| modcall (-t 24) |
v1.5.2 (Time) |
v1.5.2 (Memory) |
v1.6 (Time) |
v1.6 (Memory) |
| HG002 ONT R10.4.1 10x |
322s |
11.0G |
93s |
22.2G |
| HG002 ONT R10.4.1 20x |
635s |
14.6G |
199s |
31.6G |
| HG002 ONT R10.4.1 30x |
746s |
18.2G |
125s |
48.1G |
| HG002 ONT R10.4.1 40x |
1308s |
21.5G |
292s |
55.8G |
| HG002 ONT R10.4.1 50x |
1570s |
25.0G |
317s |
68.8G |
| HG002 ONT R10.4.1 60x |
1454s |
28.4G |
248s |
84.0G |
*If the device is running low on memory, you can control memory usage by reducing the number of threads (-t).
