Skip to content

Latest commit

 

History

History
100 lines (86 loc) · 2.76 KB

bench_res.md

File metadata and controls

100 lines (86 loc) · 2.76 KB
Raw

Bench 1: Paired End Scanning (vs Original)

TestNum Running Time(C) Mem Usage(C) Running Time(E) Mem Usage(E) Speed ratio(E to C) Mem Usage Ratio(E to C)
#1 193.65s 8.1G 28.04s 8.13G 691% 100%
#2 193.75s 8.16G 28.02s 8.23G 691% 101%
#3 120.26s 5.02G 16.29s 5.62G 738% 112%
#4 120.34s 5.08G 18.64s 5.78G 646% 114%
#5 110.44s 6.06G 18.41s 5.72G 600% 94%
#6 79.57s 4.85G 13.11s 5.14G 607% 106%
  • C: Control, original version, E: Experimental, this version.
  • Mean speed ratio = 662%
  • Mean mem usage ratio = 105%

Bench 1: Test options

tn="mc" #1
target/release/genefuse \
    -r genefuse_rust/hg19.fa \
    -f genefuse_rust/genes/cancer.hg19.csv \
    -1 genefuse_rust/genefuse.R1.fq \
    -2 genefuse_rust/genefuse.R2.fq \
    -h pe_report_${tn}.html \
    -j pe_report_${tn}.json

tn="mc38" #2
target/release/genefuse \
    -r genefuse_rust/hg38.fa \
    -f genefuse_rust/genes/cancer.hg38.csv \
    -1 genefuse_rust/genefuse.R1.fq \
    -2 genefuse_rust/genefuse.R2.fq \
    -h pe_report_${tn}.html \
    -j pe_report_${tn}.json

tn="md" #3
target/release/genefuse \
    -r genefuse_rust/hg19.fa \
    -f genefuse_rust/genes/druggable.hg19.csv \
    -1 genefuse_rust/genefuse.R1.fq \
    -2 genefuse_rust/genefuse.R2.fq \
    -h pe_report_${tn}.html \
    -j pe_report_${tn}.json

tn="md38" #4
target/release/genefuse \
    -r genefuse_rust/hg38.fa \
    -f genefuse_rust/genes/druggable.hg38.csv \
    -1 genefuse_rust/genefuse.R1.fq \
    -2 genefuse_rust/genefuse.R2.fq \
    -h pe_report_${tn}.html \
    -j pe_report_${tn}.json

tn="mtc" #5
target/release/genefuse \
    -r genefuse_rust/hg19.fa \
    -f genefuse_rust/testdata/cancer.csv \
    -1 genefuse_rust/testdata/R1.fq \
    -2 genefuse_rust/testdata/R2.fq \
    -h pe_report_${tn}.html \
    -j pe_report_${tn}.json

tn="mtf" #6
target/release/genefuse \
    -r genefuse_rust/hg19.fa \
    -f genefuse_rust/testdata/fusions.csv \
    -1 genefuse_rust/testdata/R1.fq \
    -2 genefuse_rust/testdata/R2.fq \
    -h pe_report_${tn}.html \
    -j pe_report_${tn}.json

Bench 2: Multi csv input mode (vs GeneFuse_Plus)

TestNum Running Time(C) Mem Usage(C) Running Time(E) Mem Usage(E) Speed ratio(E to C) Mem Usage Ratio(E to C)
#1 6328.27s 9.59G 166.65s 16.65G 3797% 174%

Bench 2: Test Options

tn="hg38l"
target/release/genefuse \
    -r genefuse_rust/hg38.fa \
    -f hg38_fusion_csv_list.txt \
    -1 genefuse_rust/genefuse.R1.fq \
    -2 genefuse_rust/genefuse.R2.fq \
    -t 4 \
    -h mfmp_report_${tn}.html \
    -j mfmp_report_${tn}.json

Test machine specs

System: Windows 11 WSL2 Ubuntu 22.04.4 LTS
CPU: AMD Ryzen 7 5800x 
MEM: 32GB
NVME SSD