Benchmark of PrecisonProDB 2.0

Benchmark

Tested with a computing node with AMD EPYC 9754 128-Core Processor and 1TB memory, data were stored on a 4TB NVME SSD (reading speed 7400 MB/sec and writing speed of 6500/sec) with GENCODE gene models v47 and a variant file in text format from gnomAD 3.1 as input.

• Depending on the available resources, a thread of 8 to 12 is recommendded.
  • If the variant file is in text format, typical running time will be 8 to 9 minutes
    • If running with the sqlite option enabled, and pre-build the sqlite file before running, the running time will reduce to 4 to 6 minutes.
  • If the variant file is in VCF format, typical running time will be 15 to 20 minutes.
    • If running with the sqlite option enabled, the running time will reduce to 8 to 12 minutes.

CPU/memory usage 8 threads

without sqlite

run without sqlite

with sqlite

build sqlite

run with sqlite

Running time and required memory with different threads