From subsecret
Jump to: navigation, search
No edit summary
No edit summary
Line 9: Line 9:
*Retrieve ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
*Retrieve ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
*Retrieve https://s3.amazonaws.com/public.ged.msu.edu/ecoli_ref-5m-trim.fastq.gz
*Retrieve https://s3.amazonaws.com/public.ged.msu.edu/ecoli_ref-5m-trim.fastq.gz
*Run gunzip GCF_000005845.2_ASM584v2_genomic.fna.gz
*Run bwa index GCF_000005845.2_ASM584v2_genomic.fna.gz
*Run gunzip ecoli_ref-5m-trim.fastq.gz
*Run bwa index GCF_000005845.2_ASM584v2_genomic.fna
==Running Benchmark==
==Running Benchmark==
Benchmark command
Benchmark command
*1 thread
*1 thread
**bwa aln GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null
**bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null
*4 threads  
*4 threads  
**bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null
**bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null





Revision as of 14:23, 4 August 2016

BWA Benchmark

BWA is a tool for mapping reads against a genome. This is nice for doing a non-synthetic benchmark, as meaningful work is done, and IO, Memory and CPU is all used.

BWA Setup instructions

Running Benchmark

Benchmark command

  • 1 thread
    • bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null
  • 4 threads
    • bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null


Results

Device ARCH Kernel OS GCC 1 thread walltime (sec.) 4 thread walltime (sec.)
PC (i7-6700k@4.5 GHz) x86 4.6.4-301.fc24.x86_64 Fedora 24 6.1.1 144.221 53.833
PC (i7-6700k@4.5 GHz) x64 4.6.4-301.fc24.x86_64 Fedora 24 6.1.1 77.836 27.840
ODROID U2 armhf 3.8.13.30 Ubuntu 14.04.4 LTS 4.8.4 939.300 266.262
ODROID C2 aarch64 3.14.65-73 Ubuntu 16.04 LTS 5.4.0 797.158 235.510
Raspberry Pi 3 aarch64 4.6.4-1-main Fedora 24 6.1.1 1521.175 486.585
Raspberry Pi 3 armhf 4.6.4-1-main Fedora 24 6.1.1 2172.660 649.805
Raspberry Pi 3 armhf 4.4.13-v7+ Raspbian Jessie 4.9.2 1224.290 355.897