Friday, 9 April 2010

bowtie build time statistics / benchmark

Recently Built colorspace index for hg19 (from ftp://ftp.sanger.ac.uk/pub/1000genomes/tk2/main_project_reference/)

AMD Phenom II X4 955 chip
8 GB RAM

SATA2 HDD

Wrote 822714402 bytes to primary EBWT file: hg19.rev.1.ebwt
Wrote 358098108 bytes to secondary EBWT file: hg19.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2864784823
    bwtLen: 2864784824
    sz: 716196206
    bwtSz: 716196206
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 89524526
    offsSz: 358098104
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 6394609
    numSides: 12789218
    numLines: 12789218
    ebwtTotLen: 818509952
    ebwtTotSz: 818509952
Total time for backward call to driver() for mirror index: 01:24:19

Gosh and I thought it will take hours!

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