BOL

➜ 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]
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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]
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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]
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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]
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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]
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➜ 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