workMACS$ tar xvf MACS-1.4.1.tar.tar
workMACS/MACS-1.4.1$ python setup.py install
/usr/lib/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution opti
on: 'console'
/usr/lib/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution opti
on: 'app'
running install
running build
running build_py
creating build
creating build/lib
creating build/lib/MACS14
copying lib/Constants.py -> build/lib/MACS14
copying lib/OptValidator.py -> build/lib/MACS14
copying lib/OutputWriter.py -> build/lib/MACS14
copying lib/PeakDetect.py -> build/lib/MACS14
copying lib/PeakModel.py -> build/lib/MACS14
copying lib/Prob.py -> build/lib/MACS14
copying lib/__init__.py -> build/lib/MACS14
creating build/lib/MACS14/IO
copying lib/IO/bedGraphIO.py -> build/lib/MACS14/IO
copying lib/IO/BinKeeper.py -> build/lib/MACS14/IO
copying lib/IO/FeatIO.py -> build/lib/MACS14/IO
copying lib/IO/Parser.py -> build/lib/MACS14/IO
copying lib/IO/WiggleIO.py -> build/lib/MACS14/IO
copying lib/IO/__init__.py -> build/lib/MACS14/IO
running build_scripts
creating build/scripts-2.6
copying and adjusting bin/macs14 -> build/scripts-2.6
copying and adjusting bin/elandmulti2bed -> build/scripts-2.6
copying and adjusting bin/elandresult2bed -> build/scripts-2.6
copying and adjusting bin/elandexport2bed -> build/scripts-2.6
copying and adjusting bin/sam2bed -> build/scripts-2.6
copying and adjusting bin/wignorm -> build/scripts-2.6
changing mode of build/scripts-2.6/macs14 from 644 to 755
changing mode of build/scripts-2.6/elandmulti2bed from 644 to 755
changing mode of build/scripts-2.6/elandresult2bed from 644 to 755
changing mode of build/scripts-2.6/elandexport2bed from 644 to 755
changing mode of build/scripts-2.6/sam2bed from 644 to 755
changing mode of build/scripts-2.6/wignorm from 644 to 755
running install_lib
creating /usr/lib/python2.6/site-packages/MACS14
copying build/lib/MACS14/Constants.py -> /usr/lib/python2.6/site-packages/MACS14
creating /usr/lib/python2.6/site-packages/MACS14/IO
copying build/lib/MACS14/IO/bedGraphIO.py -> /usr/lib/python2.6/site-packages/MACS14/IO
copying build/lib/MACS14/IO/BinKeeper.py -> /usr/lib/python2.6/site-packages/MACS14/IO
copying build/lib/MACS14/IO/FeatIO.py -> /usr/lib/python2.6/site-packages/MACS14/IO
copying build/lib/MACS14/IO/Parser.py -> /usr/lib/python2.6/site-packages/MACS14/IO
copying build/lib/MACS14/IO/WiggleIO.py -> /usr/lib/python2.6/site-packages/MACS14/IO
copying build/lib/MACS14/IO/__init__.py -> /usr/lib/python2.6/site-packages/MACS14/IO
copying build/lib/MACS14/OptValidator.py -> /usr/lib/python2.6/site-packages/MACS14
copying build/lib/MACS14/OutputWriter.py -> /usr/lib/python2.6/site-packages/MACS14
copying build/lib/MACS14/PeakDetect.py -> /usr/lib/python2.6/site-packages/MACS14
copying build/lib/MACS14/PeakModel.py -> /usr/lib/python2.6/site-packages/MACS14
copying build/lib/MACS14/Prob.py -> /usr/lib/python2.6/site-packages/MACS14
copying build/lib/MACS14/__init__.py -> /usr/lib/python2.6/site-packages/MACS14
byte-compiling /usr/lib/python2.6/site-packages/MACS14/Constants.py to Constants.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/IO/bedGraphIO.py to bedGraphIO.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/IO/BinKeeper.py to BinKeeper.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/IO/FeatIO.py to FeatIO.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/IO/Parser.py to Parser.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/IO/WiggleIO.py to WiggleIO.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/IO/__init__.py to __init__.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/OptValidator.py to OptValidator.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/OutputWriter.py to OutputWriter.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/PeakDetect.py to PeakDetect.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/PeakModel.py to PeakModel.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/Prob.py to Prob.pyc
byte-compiling /usr/lib/python2.6/site-packages/MACS14/__init__.py to __init__.pyc
running install_scripts
copying build/scripts-2.6/elandexport2bed -> /usr/bin
copying build/scripts-2.6/elandmulti2bed -> /usr/bin
copying build/scripts-2.6/elandresult2bed -> /usr/bin
copying build/scripts-2.6/macs14 -> /usr/bin
copying build/scripts-2.6/sam2bed -> /usr/bin
copying build/scripts-2.6/wignorm -> /usr/bin
changing mode of /usr/bin/elandexport2bed to 755
changing mode of /usr/bin/elandmulti2bed to 755
changing mode of /usr/bin/elandresult2bed to 755
changing mode of /usr/bin/macs14 to 755
changing mode of /usr/bin/sam2bed to 755
changing mode of /usr/bin/wignorm to 755
running install_egg_info
Writing /usr/lib/python2.6/site-packages/MACS-1.4.1-py2.6.egg-info
workMACS/MACS-1.4.1$ ./bin/macs14
Usage: macs14 <-t tfile> [-n name] [-g genomesize] [options]

Example: macs14 -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeak

macs14 -- Model-based Analysis for ChIP-Sequencing

  --version             show program's version number and exit
  -h, --help            show this help message and exit.
  -t TFILE, --treatment=TFILE
                        ChIP-seq treatment files. REQUIRED. When ELANDMULTIPET
                        is selected, you must provide two files separated by
                        comma, e.g.
  -c CFILE, --control=CFILE
                        Control files. When ELANDMULTIPET is selected, you
                        must provide two files separated by comma, e.g.
  -n NAME, --name=NAME  Experiment name, which will be used to generate output
                        file names. DEFAULT: "NA"
  -f FORMAT, --format=FORMAT
                        Format of tag file, "AUTO", "BED" or "ELAND" or
                        "ELANDMULTI" or "ELANDMULTIPET" or "ELANDEXPORT" or
                        "SAM" or "BAM" or "BOWTIE". The default AUTO option
                        will let MACS decide which format the file is. Please
                        check the definition in 00README file if you choose EL
                        E. DEFAULT: "AUTO"
  --petdist=PETDIST     Best distance between Pair-End Tags. Only available
                        when format is 'ELANDMULTIPET'. DEFAULT: 200
  -g GSIZE, --gsize=GSIZE
                        Effective genome size. It can be 1.0e+9 or 1000000000,
                        or shortcuts:'hs' for human (2.7e9), 'mm' for mouse
                        (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for
                        fruitfly (1.2e8), Default:hs
  -s TSIZE, --tsize=TSIZE
                        Tag size. This will overide the auto detected tag
  --bw=BW               Band width. This value is only used while building the
                        shifting model. DEFAULT: 300
  -p PVALUE, --pvalue=PVALUE
                        Pvalue cutoff for peak detection. DEFAULT: 1e-5
  -m MFOLD, --mfold=MFOLD
                        Select the regions within MFOLD range of high-
                        confidence enrichment ratio against background to
                        build model. The regions must be lower than upper
                        limit, and higher than the lower limit. DEFAULT:10,30
  --nolambda            If True, MACS will use fixed background lambda as
                        local lambda for every peak region. Normally, MACS
                        calculates a dynamic local lambda to reflect the local
                        bias due to potential chromatin structure.
  --slocal=SMALLLOCAL   The small nearby region in basepairs to calculate
                        dynamic lambda. This is used to capture the bias near
                        the peak summit region. Invalid if there is no control
                        data. DEFAULT: 1000
  --llocal=LARGELOCAL   The large nearby region in basepairs to calculate
                        dynamic lambda. This is used to capture the surround
                        bias. DEFAULT: 10000.
  --off-auto            Whether turn off the auto pair model process. If not
                        set, when MACS failed to build paired model, it will
                        use the nomodel settings, the '--shiftsize' parameter
                        to shift and extend each tags. DEFAULT: False
  --nomodel             Whether or not to build the shifting model. If True,
                        MACS will not build model. by default it means
                        shifting size = 100, try to set shiftsize to change
                        it. DEFAULT: False
                        The arbitrary shift size in bp. When nomodel is true,
                        MACS will use this value as 1/2 of fragment size.
                        DEFAULT: 100
                        It controls the MACS behavior towards duplicate tags
                        at the exact same location -- the same coordination
                        and the same strand. The default 'auto' option makes
                        MACS calculate the maximum tags at the exact same
                        location based on binomal distribution using 1e-5 as
                        pvalue cutoff; and the 'all' option keeps every tags.
                        If an integer is given, at most this number of tags
                        will be kept at the same location. Default: auto
  --to-small            When set, scale the larger dataset down to the smaller
                        dataset, by default, the smaller dataset will be
                        scaled towards the larger dataset. DEFAULT: False
  -w, --wig             Whether or not to save extended fragment pileup at
                        every WIGEXTEND bps into a wiggle file. When --single-
                        profile is on, only one file for the whole genome is
                        saved. WARNING: this process is time/space consuming!!
  -B, --bdg             Whether or not to save extended fragment pileup at
                        every bp into a bedGraph file. When it's on, -w,
                        --space and --call-subpeaks will be ignored. When
                        --single-profile is on, only one file for the whole
                        genome is saved. WARNING: this process is time/space
  -S, --single-profile  When set, a single wiggle file will be saved for
                        treatment and input. Default: False
  --space=SPACE         The resoluation for saving wiggle files, by default,
                        MACS will save the raw tag count every 10 bps. Usable
                        only with '--wig' option.
  --call-subpeaks       If set, MACS will invoke Mali Salmon's PeakSplitter
                        soft through system call. If PeakSplitter can't be
                        found, an instruction will be shown for downloading
                        and installing the PeakSplitter package. -w option
                        needs to be on and -B should be off to let it work.
                        DEFAULT: False
  --verbose=VERBOSE     Set verbose level. 0: only show critical message, 1:
                        show additional warning message, 2: show process
                        information, 3: show debug messages. DEFAULT:2
  --diag                Whether or not to produce a diagnosis report. It's up
                        to 9X time consuming. Please check 00README file for
                        detail. DEFAULT: False
  --fe-min=FEMIN        For diagnostics, min fold enrichment to consider.
                        DEFAULT: 0
  --fe-max=FEMAX        For diagnostics, max fold enrichment to consider.
                        DEFAULT: maximum fold enrichment
  --fe-step=FESTEP      For diagnostics, fold enrichment step.  DEFAULT: 20

Last edited by hzhang , based on work by nobfujii .
Page last modified on 火曜日 23 of October, 2012 16:09:02 JST.