➜ redundans git:(master) ✗ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose
[sudo] password for urbe:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic
linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic
linux-signed-image-4.4.0-116-generic runc ubuntu-fan
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
blt fonts-lyx fonts-mathjax ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2 libhdf5-10 libjs-highlight
libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4 python-chardet python-cvxopt
python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging python-jdcal python-jinja2 python-joblib
python-lxml python-markupsafe python-matplotlib-data python-mpmath python-numexpr python-openpyxl python-pandas-lib python-patsy python-pexpect
python-pil python-ptyprocess python-py python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-simplegeneric
python-simplejson python-statsmodels python-statsmodels-lib python-sympy-doc python-tables python-tables-data python-tables-lib python-tk
python-tornado python-tz python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera
Suggested packages:
blt-demo ipython-doc ipython-qtconsole python-pygments nodejs pandoc libiodbc2-dev libmysqlclient-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html libjs-jquery-ui-docs fonts-mathjax-extras libjs-mathjax-doc python-gtk2-doc python-genshi python-jinja2-doc python-lxml-dbg
python-lxml-doc ffmpeg inkscape python-cairocffi python-configobj python-excelerator python-matplotlib-doc python-qt4 python-sip python-traits
python-wxgtk3.0 ttf-staypuft python-gmpy2 python-mpmath-doc python-coverage python-nose-doc python-numpy-dbg python-numpy-doc python-pandas-doc
python-patsy-doc python-pexpect-doc python-pil-doc python-pil-dbg subversion python-pytest-xdist libcurl4-gnutls-dev python-pycurl-dbg
python-pycurl-doc python-pymysql-doc python-mock python-scipy-doc python-statsmodels-doc python-tables-doc python-netcdf vitables tix
python-tk-dbg
The following NEW packages will be installed:
blt fonts-lyx fonts-mathjax ipython ipython-notebook ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2
libhdf5-10 libjs-highlight libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4
python-chardet python-cvxopt python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging
python-jdcal python-jinja2 python-joblib python-lxml python-markupsafe python-matplotlib python-matplotlib-data python-mpmath python-nose
python-numexpr python-numpy python-openpyxl python-pandas python-pandas-lib python-patsy python-pexpect python-pil python-ptyprocess python-py
python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-scipy python-simplegeneric python-simplejson python-statsmodels
python-statsmodels-lib python-sympy python-sympy-doc python-tables python-tables-data python-tables-lib python-tk python-tornado python-tz
python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera
0 upgraded, 73 newly installed, 0 to remove and 35 not upgraded.
Need to get 49,5 MB of archives.
After this operation, 271 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pymysql all 0.7.2-1ubuntu1 [56,4 kB]
Get:2 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-3 [574 kB]
Get:3 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 blt amd64 2.5.3+dfsg-3 [4.852 B]
Get:4 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 fonts-lyx all 2.1.4-2 [161 kB]
Get:5 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 fonts-mathjax all 2.6.1-1 [960 kB]
Get:6 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-decorator all 4.0.6-1 [9.326 B]
Get:7 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-ptyprocess all 0.5-1 [12,9 kB]
Get:8 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pexpect all 4.0.1-1 [40,5 kB]
Get:9 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-simplegeneric all 0.8.1-1 [11,5 kB]
Get:10 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython all 2.4.1-1 [610 kB]
Get:11 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-highlight.js all 8.2+ds-4build1 [151 kB]
Get:12 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-highlight all 8.2+ds-4build1 [7.032 B]
Get:13 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-jquery-ui all 1.10.1+dfsg-1 [458 kB]
Get:14 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-marked all 0.3.2+dfsg-1 [12,7 kB]
Get:15 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-mathjax all 2.6.1-1 [5.601 kB]
Get:16 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libjs-underscore all 1.7.0~dfsg-1ubuntu1 [46,7 kB]
Get:17 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython-notebook-common all 2.4.1-1 [712 kB]
Get:18 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-markupsafe amd64 0.23-2build2 [15,5 kB]
Get:19 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-jinja2 all 2.8-1 [109 kB]
Get:20 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-pycurl amd64 7.43.0-1ubuntu1 [43,3 kB]
Get:21 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tornado amd64 4.2.1-1ubuntu3 [273 kB]
Get:22 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-zmq amd64 15.2.0-0ubuntu4 [200 kB]
Get:23 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython-notebook all 2.4.1-1 [48,4 kB]
Get:24 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 isympy all 0.7.6.1-1 [82,5 kB]
Get:25 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libaec0 amd64 0.3.2-1 [18,0 kB]
Get:26 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libamd2.4.1 amd64 1:4.4.6-1 [21,3 kB]
Get:27 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libglpk36 amd64 4.57-1build3 [386 kB]
Get:28 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libgsl2 amd64 2.1+dfsg-2 [840 kB]
Get:29 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libsz2 amd64 0.3.2-1 [5.048 B]
Get:30 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-10 amd64 1.8.16+docs-4ubuntu1 [995 kB]
Get:31 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-antlr all 2.7.7+dfsg-6ubuntu1 [19,0 kB]
Get:32 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-bs4 all 4.4.1-1 [64,2 kB]
Get:33 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-chardet all 2.3.0-2 [96,3 kB]
Get:34 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libdsdp-5.8gf amd64 5.8-9.1ubuntu2 [192 kB]
Get:35 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-cvxopt amd64 1.1.4-1.4 [1.344 kB]
Get:36 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-cycler all 0.9.0-1 [5.426 B]
Get:37 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-dateutil all 2.4.2-1 [42,5 kB]
Get:38 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-glade2 amd64 2.24.0-4ubuntu1 [9.078 B]
Get:39 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-gmpy amd64 1.17-1 [91,1 kB]
Get:40 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-html5lib all 0.999-4 [83,1 kB]
Get:41 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pil amd64 3.1.2-0ubuntu1.1 [312 kB]
Get:42 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 python-imaging all 3.1.2-0ubuntu1.1 [4.596 B]
Get:43 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-jdcal all 1.0-1build1 [7.702 B]
Get:44 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-joblib all 0.9.4-1 [74,6 kB]
Get:45 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-lxml amd64 3.5.0-1build1 [819 kB]
Get:46 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ttf-bitstream-vera all 1.10-8 [352 kB]
Get:47 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-matplotlib-data all 1.5.1-1ubuntu1 [2.414 kB]
Get:48 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pyparsing all 2.0.3+dfsg1-1ubuntu0.1 [35,4 kB]
Get:49 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-tz all 2014.10~dfsg1-0ubuntu2 [31,5 kB]
Get:50 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-numpy amd64 1:1.11.0-1ubuntu1 [1.763 kB]
Get:51 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-matplotlib amd64 1.5.1-1ubuntu1 [3.888 kB]
Get:52 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-mpmath all 0.19-3 [387 kB]
Get:53 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-nose all 1.3.7-1 [116 kB]
Get:54 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-numexpr amd64 2.4.3-1ubuntu1 [129 kB]
Get:55 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-openpyxl all 2.3.0-1 [193 kB]
Get:56 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pandas-lib amd64 0.17.1-3ubuntu2 [1.538 kB]
Get:57 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pandas all 0.17.1-3ubuntu2 [2.386 kB]
Get:58 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-patsy all 0.4.1-2 [169 kB]
Get:59 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-py all 1.4.31-1 [62,5 kB]
Get:60 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pyglet all 1.1.4.dfsg-3 [726 kB]
Get:61 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pytest all 2.8.7-4 [119 kB]
Get:62 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-simplejson amd64 3.8.1-1ubuntu2 [60,4 kB]
Get:63 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-sympy all 0.7.6.1-1 [2.252 kB]
Get:64 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-sympy-doc all 0.7.6.1-1 [4.774 kB]
Get:65 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables-lib amd64 3.2.2-2 [353 kB]
Get:66 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables-data all 3.2.2-2 [45,3 kB]
Get:67 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables all 3.2.2-2 [335 kB]
Get:68 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-tk amd64 2.7.12-1~16.04 [26,3 kB]
Get:69 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-xlrd all 0.9.4-1 [107 kB]
Get:70 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-xlwt all 0.7.5+debian1-1 [83,5 kB]
Get:71 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-scipy amd64 0.17.0-1 [8.733 kB]
Get:72 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-statsmodels-lib amd64 0.6.1-4 [173 kB]
Get:73 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-statsmodels all 0.6.1-4 [2.581 kB]
Fetched 49,5 MB in 0s (52,8 MB/s)
Extracting templates from packages: 100%
Selecting previously unselected package python-pymysql.
(Reading database ... 435155 files and directories currently installed.)
Preparing to unpack .../python-pymysql_0.7.2-1ubuntu1_all.deb ...
Unpacking python-pymysql (0.7.2-1ubuntu1) ...
Selecting previously unselected package tk8.6-blt2.5.
Preparing to unpack .../tk8.6-blt2.5_2.5.3+dfsg-3_amd64.deb ...
Unpacking tk8.6-blt2.5 (2.5.3+dfsg-3) ...
Selecting previously unselected package blt.
Preparing to unpack .../blt_2.5.3+dfsg-3_amd64.deb ...
Unpacking blt (2.5.3+dfsg-3) ...
Selecting previously unselected package fonts-lyx.
Preparing to unpack .../fonts-lyx_2.1.4-2_all.deb ...
Unpacking fonts-lyx (2.1.4-2) ...
Selecting previously unselected package fonts-mathjax.
Preparing to unpack .../fonts-mathjax_2.6.1-1_all.deb ...
Unpacking fonts-mathjax (2.6.1-1) ...
Selecting previously unselected package python-decorator.
Preparing to unpack .../python-decorator_4.0.6-1_all.deb ...
Unpacking python-decorator (4.0.6-1) ...
Selecting previously unselected package python-ptyprocess.
Preparing to unpack .../python-ptyprocess_0.5-1_all.deb ...
Unpacking python-ptyprocess (0.5-1) ...
Selecting previously unselected package python-pexpect.
Preparing to unpack .../python-pexpect_4.0.1-1_all.deb ...
Unpacking python-pexpect (4.0.1-1) ...
Selecting previously unselected package python-simplegeneric.
Preparing to unpack .../python-simplegeneric_0.8.1-1_all.deb ...
Unpacking python-simplegeneric (0.8.1-1) ...
Selecting previously unselected package ipython.
Preparing to unpack .../ipython_2.4.1-1_all.deb ...
Unpacking ipython (2.4.1-1) ...
Selecting previously unselected package libjs-highlight.js.
Preparing to unpack .../libjs-highlight.js_8.2+ds-4build1_all.deb ...
Unpacking libjs-highlight.js (8.2+ds-4build1) ...
Selecting previously unselected package libjs-highlight.
Preparing to unpack .../libjs-highlight_8.2+ds-4build1_all.deb ...
Unpacking libjs-highlight (8.2+ds-4build1) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../libjs-jquery-ui_1.10.1+dfsg-1_all.deb ...
Unpacking libjs-jquery-ui (1.10.1+dfsg-1) ...
Selecting previously unselected package libjs-marked.
Preparing to unpack .../libjs-marked_0.3.2+dfsg-1_all.deb ...
Unpacking libjs-marked (0.3.2+dfsg-1) ...
Selecting previously unselected package libjs-mathjax.
Preparing to unpack .../libjs-mathjax_2.6.1-1_all.deb ...
Unpacking libjs-mathjax (2.6.1-1) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../libjs-underscore_1.7.0~dfsg-1ubuntu1_all.deb ...
Unpacking libjs-underscore (1.7.0~dfsg-1ubuntu1) ...
Selecting previously unselected package ipython-notebook-common.
Preparing to unpack .../ipython-notebook-common_2.4.1-1_all.deb ...
Unpacking ipython-notebook-common (2.4.1-1) ...
Selecting previously unselected package python-markupsafe.
Preparing to unpack .../python-markupsafe_0.23-2build2_amd64.deb ...
Unpacking python-markupsafe (0.23-2build2) ...
Selecting previously unselected package python-jinja2.
Preparing to unpack .../python-jinja2_2.8-1_all.deb ...
Unpacking python-jinja2 (2.8-1) ...
Selecting previously unselected package python-pycurl.
Preparing to unpack .../python-pycurl_7.43.0-1ubuntu1_amd64.deb ...
Unpacking python-pycurl (7.43.0-1ubuntu1) ...
Selecting previously unselected package python-tornado.
Preparing to unpack .../python-tornado_4.2.1-1ubuntu3_amd64.deb ...
Unpacking python-tornado (4.2.1-1ubuntu3) ...
Selecting previously unselected package python-zmq.
Preparing to unpack .../python-zmq_15.2.0-0ubuntu4_amd64.deb ...
Unpacking python-zmq (15.2.0-0ubuntu4) ...
Selecting previously unselected package ipython-notebook.
Preparing to unpack .../ipython-notebook_2.4.1-1_all.deb ...
Unpacking ipython-notebook (2.4.1-1) ...
Selecting previously unselected package isympy.
Preparing to unpack .../isympy_0.7.6.1-1_all.deb ...
Unpacking isympy (0.7.6.1-1) ...
Selecting previously unselected package libaec0:amd64.
Preparing to unpack .../libaec0_0.3.2-1_amd64.deb ...
Unpacking libaec0:amd64 (0.3.2-1) ...
Selecting previously unselected package libamd2.4.1:amd64.
Preparing to unpack .../libamd2.4.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libamd2.4.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libglpk36:amd64.
Preparing to unpack .../libglpk36_4.57-1build3_amd64.deb ...
Unpacking libglpk36:amd64 (4.57-1build3) ...
Selecting previously unselected package libgsl2:amd64.
Preparing to unpack .../libgsl2_2.1+dfsg-2_amd64.deb ...
Unpacking libgsl2:amd64 (2.1+dfsg-2) ...
Selecting previously unselected package libsz2:amd64.
Preparing to unpack .../libsz2_0.3.2-1_amd64.deb ...
Unpacking libsz2:amd64 (0.3.2-1) ...
Selecting previously unselected package libhdf5-10:amd64.
Preparing to unpack .../libhdf5-10_1.8.16+docs-4ubuntu1_amd64.deb ...
Unpacking libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
Selecting previously unselected package python-antlr.
Preparing to unpack .../python-antlr_2.7.7+dfsg-6ubuntu1_all.deb ...
Unpacking python-antlr (2.7.7+dfsg-6ubuntu1) ...
Selecting previously unselected package python-bs4.
Preparing to unpack .../python-bs4_4.4.1-1_all.deb ...
Unpacking python-bs4 (4.4.1-1) ...
Selecting previously unselected package python-chardet.
Preparing to unpack .../python-chardet_2.3.0-2_all.deb ...
Unpacking python-chardet (2.3.0-2) ...
Selecting previously unselected package libdsdp-5.8gf.
Preparing to unpack .../libdsdp-5.8gf_5.8-9.1ubuntu2_amd64.deb ...
Unpacking libdsdp-5.8gf (5.8-9.1ubuntu2) ...
Selecting previously unselected package python-cvxopt.
Preparing to unpack .../python-cvxopt_1.1.4-1.4_amd64.deb ...
Unpacking python-cvxopt (1.1.4-1.4) ...
Selecting previously unselected package python-cycler.
Preparing to unpack .../python-cycler_0.9.0-1_all.deb ...
Unpacking python-cycler (0.9.0-1) ...
Selecting previously unselected package python-dateutil.
Preparing to unpack .../python-dateutil_2.4.2-1_all.deb ...
Unpacking python-dateutil (2.4.2-1) ...
Selecting previously unselected package python-glade2.
Preparing to unpack .../python-glade2_2.24.0-4ubuntu1_amd64.deb ...
Unpacking python-glade2 (2.24.0-4ubuntu1) ...
Selecting previously unselected package python-gmpy.
Preparing to unpack .../python-gmpy_1.17-1_amd64.deb ...
Unpacking python-gmpy (1.17-1) ...
Selecting previously unselected package python-html5lib.
Preparing to unpack .../python-html5lib_0.999-4_all.deb ...
Unpacking python-html5lib (0.999-4) ...
Selecting previously unselected package python-pil:amd64.
Preparing to unpack .../python-pil_3.1.2-0ubuntu1.1_amd64.deb ...
Unpacking python-pil:amd64 (3.1.2-0ubuntu1.1) ...
Selecting previously unselected package python-imaging.
Preparing to unpack .../python-imaging_3.1.2-0ubuntu1.1_all.deb ...
Unpacking python-imaging (3.1.2-0ubuntu1.1) ...
Selecting previously unselected package python-jdcal.
Preparing to unpack .../python-jdcal_1.0-1build1_all.deb ...
Unpacking python-jdcal (1.0-1build1) ...
Selecting previously unselected package python-joblib.
Preparing to unpack .../python-joblib_0.9.4-1_all.deb ...
Unpacking python-joblib (0.9.4-1) ...
Selecting previously unselected package python-lxml.
Preparing to unpack .../python-lxml_3.5.0-1build1_amd64.deb ...
Unpacking python-lxml (3.5.0-1build1) ...
Selecting previously unselected package ttf-bitstream-vera.
Preparing to unpack .../ttf-bitstream-vera_1.10-8_all.deb ...
Unpacking ttf-bitstream-vera (1.10-8) ...
Selecting previously unselected package python-matplotlib-data.
Preparing to unpack .../python-matplotlib-data_1.5.1-1ubuntu1_all.deb ...
Unpacking python-matplotlib-data (1.5.1-1ubuntu1) ...
Selecting previously unselected package python-pyparsing.
Preparing to unpack .../python-pyparsing_2.0.3+dfsg1-1ubuntu0.1_all.deb ...
Unpacking python-pyparsing (2.0.3+dfsg1-1ubuntu0.1) ...
Selecting previously unselected package python-tz.
Preparing to unpack .../python-tz_2014.10~dfsg1-0ubuntu2_all.deb ...
Unpacking python-tz (2014.10~dfsg1-0ubuntu2) ...
Selecting previously unselected package python-numpy.
Preparing to unpack .../python-numpy_1%3a1.11.0-1ubuntu1_amd64.deb ...
Unpacking python-numpy (1:1.11.0-1ubuntu1) ...
Selecting previously unselected package python-matplotlib.
Preparing to unpack .../python-matplotlib_1.5.1-1ubuntu1_amd64.deb ...
Unpacking python-matplotlib (1.5.1-1ubuntu1) ...
Selecting previously unselected package python-mpmath.
Preparing to unpack .../python-mpmath_0.19-3_all.deb ...
Unpacking python-mpmath (0.19-3) ...
Selecting previously unselected package python-nose.
Preparing to unpack .../python-nose_1.3.7-1_all.deb ...
Unpacking python-nose (1.3.7-1) ...
Selecting previously unselected package python-numexpr.
Preparing to unpack .../python-numexpr_2.4.3-1ubuntu1_amd64.deb ...
Unpacking python-numexpr (2.4.3-1ubuntu1) ...
Selecting previously unselected package python-openpyxl.
Preparing to unpack .../python-openpyxl_2.3.0-1_all.deb ...
Unpacking python-openpyxl (2.3.0-1) ...
Selecting previously unselected package python-pandas-lib.
Preparing to unpack .../python-pandas-lib_0.17.1-3ubuntu2_amd64.deb ...
Unpacking python-pandas-lib (0.17.1-3ubuntu2) ...
Selecting previously unselected package python-pandas.
Preparing to unpack .../python-pandas_0.17.1-3ubuntu2_all.deb ...
Unpacking python-pandas (0.17.1-3ubuntu2) ...
Selecting previously unselected package python-patsy.
Preparing to unpack .../python-patsy_0.4.1-2_all.deb ...
Unpacking python-patsy (0.4.1-2) ...
Selecting previously unselected package python-py.
Preparing to unpack .../python-py_1.4.31-1_all.deb ...
Unpacking python-py (1.4.31-1) ...
Selecting previously unselected package python-pyglet.
Preparing to unpack .../python-pyglet_1.1.4.dfsg-3_all.deb ...
Unpacking python-pyglet (1.1.4.dfsg-3) ...
Selecting previously unselected package python-pytest.
Preparing to unpack .../python-pytest_2.8.7-4_all.deb ...
Unpacking python-pytest (2.8.7-4) ...
Selecting previously unselected package python-simplejson.
Preparing to unpack .../python-simplejson_3.8.1-1ubuntu2_amd64.deb ...
Unpacking python-simplejson (3.8.1-1ubuntu2) ...
Selecting previously unselected package python-sympy.
Preparing to unpack .../python-sympy_0.7.6.1-1_all.deb ...
Unpacking python-sympy (0.7.6.1-1) ...
Selecting previously unselected package python-sympy-doc.
Preparing to unpack .../python-sympy-doc_0.7.6.1-1_all.deb ...
Unpacking python-sympy-doc (0.7.6.1-1) ...
Selecting previously unselected package python-tables-lib.
Preparing to unpack .../python-tables-lib_3.2.2-2_amd64.deb ...
Unpacking python-tables-lib (3.2.2-2) ...
Selecting previously unselected package python-tables-data.
Preparing to unpack .../python-tables-data_3.2.2-2_all.deb ...
Unpacking python-tables-data (3.2.2-2) ...
Selecting previously unselected package python-tables.
Preparing to unpack .../python-tables_3.2.2-2_all.deb ...
Unpacking python-tables (3.2.2-2) ...
Selecting previously unselected package python-tk.
Preparing to unpack .../python-tk_2.7.12-1~16.04_amd64.deb ...
Unpacking python-tk (2.7.12-1~16.04) ...
Selecting previously unselected package python-xlrd.
Preparing to unpack .../python-xlrd_0.9.4-1_all.deb ...
Unpacking python-xlrd (0.9.4-1) ...
Selecting previously unselected package python-xlwt.
Preparing to unpack .../python-xlwt_0.7.5+debian1-1_all.deb ...
Unpacking python-xlwt (0.7.5+debian1-1) ...
Selecting previously unselected package python-scipy.
Preparing to unpack .../python-scipy_0.17.0-1_amd64.deb ...
Unpacking python-scipy (0.17.0-1) ...
Selecting previously unselected package python-statsmodels-lib.
Preparing to unpack .../python-statsmodels-lib_0.6.1-4_amd64.deb ...
Unpacking python-statsmodels-lib (0.6.1-4) ...
Selecting previously unselected package python-statsmodels.
Preparing to unpack .../python-statsmodels_0.6.1-4_all.deb ...
Unpacking python-statsmodels (0.6.1-4) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
Processing triggers for fontconfig (2.11.94-0ubuntu1.1) ...
Processing triggers for man-db (2.7.5-1) ...
Processing triggers for hicolor-icon-theme (0.15-0ubuntu1) ...
Processing triggers for gnome-menus (3.13.3-6ubuntu3.1) ...
Processing triggers for desktop-file-utils (0.22-1ubuntu5.1) ...
Processing triggers for mime-support (3.59ubuntu1) ...
Processing triggers for doc-base (0.10.7) ...
Processing 5 added doc-base files...
Setting up python-pymysql (0.7.2-1ubuntu1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-3) ...
Setting up blt (2.5.3+dfsg-3) ...
Setting up fonts-lyx (2.1.4-2) ...
Setting up fonts-mathjax (2.6.1-1) ...
Setting up python-decorator (4.0.6-1) ...
Setting up python-ptyprocess (0.5-1) ...
Setting up python-pexpect (4.0.1-1) ...
Setting up python-simplegeneric (0.8.1-1) ...
Setting up ipython (2.4.1-1) ...
Setting up libjs-highlight.js (8.2+ds-4build1) ...
Setting up libjs-highlight (8.2+ds-4build1) ...
Setting up libjs-jquery-ui (1.10.1+dfsg-1) ...
Setting up libjs-marked (0.3.2+dfsg-1) ...
Setting up libjs-mathjax (2.6.1-1) ...
Setting up libjs-underscore (1.7.0~dfsg-1ubuntu1) ...
Setting up ipython-notebook-common (2.4.1-1) ...
Setting up python-markupsafe (0.23-2build2) ...
Setting up python-jinja2 (2.8-1) ...
Setting up python-pycurl (7.43.0-1ubuntu1) ...
Setting up python-tornado (4.2.1-1ubuntu3) ...
Setting up python-zmq (15.2.0-0ubuntu4) ...
Setting up ipython-notebook (2.4.1-1) ...
Setting up isympy (0.7.6.1-1) ...
Setting up libaec0:amd64 (0.3.2-1) ...
Setting up libamd2.4.1:amd64 (1:4.4.6-1) ...
Setting up libglpk36:amd64 (4.57-1build3) ...
Setting up libgsl2:amd64 (2.1+dfsg-2) ...
Setting up libsz2:amd64 (0.3.2-1) ...
Setting up libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
Setting up python-antlr (2.7.7+dfsg-6ubuntu1) ...
Setting up python-bs4 (4.4.1-1) ...
Setting up python-chardet (2.3.0-2) ...
Setting up libdsdp-5.8gf (5.8-9.1ubuntu2) ...
Setting up python-cvxopt (1.1.4-1.4) ...
Setting up python-cycler (0.9.0-1) ...
Setting up python-dateutil (2.4.2-1) ...
Setting up python-glade2 (2.24.0-4ubuntu1) ...
Setting up python-gmpy (1.17-1) ...
Setting up python-html5lib (0.999-4) ...
Setting up python-pil:amd64 (3.1.2-0ubuntu1.1) ...
Setting up python-imaging (3.1.2-0ubuntu1.1) ...
Setting up python-jdcal (1.0-1build1) ...
Setting up python-joblib (0.9.4-1) ...
Setting up python-lxml (3.5.0-1build1) ...
Setting up ttf-bitstream-vera (1.10-8) ...
Setting up python-matplotlib-data (1.5.1-1ubuntu1) ...
Setting up python-pyparsing (2.0.3+dfsg1-1ubuntu0.1) ...
Setting up python-tz (2014.10~dfsg1-0ubuntu2) ...
Setting up python-numpy (1:1.11.0-1ubuntu1) ...
Setting up python-matplotlib (1.5.1-1ubuntu1) ...
Setting up python-mpmath (0.19-3) ...
Setting up python-nose (1.3.7-1) ...
Setting up python-numexpr (2.4.3-1ubuntu1) ...
Setting up python-openpyxl (2.3.0-1) ...
Setting up python-pandas-lib (0.17.1-3ubuntu2) ...
Setting up python-pandas (0.17.1-3ubuntu2) ...
Setting up python-patsy (0.4.1-2) ...
Setting up python-py (1.4.31-1) ...
Setting up python-pyglet (1.1.4.dfsg-3) ...
Setting up python-pytest (2.8.7-4) ...
Setting up python-simplejson (3.8.1-1ubuntu2) ...
Setting up python-sympy (0.7.6.1-1) ...
Setting up python-sympy-doc (0.7.6.1-1) ...
Setting up python-tables-lib (3.2.2-2) ...
Setting up python-tables-data (3.2.2-2) ...
Setting up python-tables (3.2.2-2) ...
Setting up python-tk (2.7.12-1~16.04) ...
Setting up python-xlrd (0.9.4-1) ...
Setting up python-xlwt (0.7.5+debian1-1) ...
Setting up python-scipy (0.17.0-1) ...
Setting up python-statsmodels-lib (0.6.1-4) ...
Setting up python-statsmodels (0.6.1-4) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
➜ redundans git:(master) ✗ python2 redundans.py -v -i test/*_?.fq.gz -f test/contigs.fa -o test/run1
Options: Namespace(fasta='test/contigs.fa', fastq=['test/5000_1.fq.gz', 'test/5000_2.fq.gz', 'test/600_1.fq.gz', 'test/600_2.fq.gz'], identity=0.51, iters=2, joins=5, limit=0.2, linkratio=0.7, log=', mode 'w' at 0x7f85d1de31e0>, longreads=[], mapq=10, mem=16, minLength=200, nocleaning=True, nogapclosing=True, norearrangements=False, noreduction=True, noscaffolding=True, outdir='test/run1', overlap=0.8, reference='', resume=False, threads=4, tmp='/tmp', usebwa=False, verbose=True)
##################################################
[Mon May 7 11:29:18 2018] Reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80
##################################################
[Mon May 7 11:29:29 2018] Estimating parameters of libraries...
Aligning 19504 mates per library...
Insert size statistics Mates orientation stats
FastQ files read length median mean stdev FF FR RF RR
test/5000_1.fq.gz test/5000_2.fq.gz 50 4998 4990.20 721.47 0 4674 0 0
test/600_1.fq.gz test/600_2.fq.gz 100 599 598.63 47.68 0 10000 0 0
##################################################
[Mon May 7 11:29:29 2018] Scaffolding...
iteration 1.1: test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
19505 pairs. 17302 passed filtering [88.71%]. 1627 in different contigs [8.34%].
1526 pairs. 558 in different contigs [36.57%].
iteration 1.2: test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 17607 passed filtering [90.27%]. 182 in different contigs [0.93%].
1077 pairs. 124 in different contigs [11.51%].
iteration 2.1: test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 15112 passed filtering [77.48%]. 1295 in different contigs [6.64%].
3417 pairs. 396 in different contigs [11.59%].
iteration 2.2: test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
19505 pairs. 15152 passed filtering [77.68%]. 0 in different contigs [0.00%].
3398 pairs. 0 in different contigs [0.00%].
##################################################
[Mon May 7 11:29:34 2018] Gap closing...
iteration 1.1: test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
##################################################
[Mon May 7 11:29:35 2018] Final reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
[WARNING] Nothing reduced!
test/run1/scaffolds.filled.fa 99390 1 0 0.00 0 0.00 0.000 0 99390 100.00 1 100.00
##################################################
[Mon May 7 11:29:35 2018] Reporting statistics...
#fname contigs bases GC [%] contigs >1kb bases in contigs >1kb N50 N90 Ns longest
test/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_sspace.2.2.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_gapcloser.1.1.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.filled.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.reduced.fa 1 99390 39.689 1 99390 99390 99390 2 99390
##################################################
[Mon May 7 11:29:35 2018] Cleaning-up...
#Time elapsed: 0:00:17.376924
