tutorial_2-Preparation_of_the_reference_genome


Preparation of the reference genome

Usually NGS reads are mapped against a reference genome containing only the assembled chromosomes, and not the remaining contigs. And this methodology is perfectly valid. However in order to decrease the probability of having mapping errors, adding all unassembled contigs may help:

For variant discovery, RNA-seq and ChIP-seq, it is recommended to use the entire primary assembly, including assembled chromosomes AND unlocalized/unplaced contigs, for the purpose of read mapping. Not including unlocalized and unplaced contigs potentially leads to more mapping errors.

from: http://lh3lh3.users.sourceforge.net/humanref.shtml

We are thus going to download full chromosomes and unassembled contigs. From these sequences we are then going to create two reference genomes:

  • one "classic" reference genome with only assembled chromosomes, used to compute statistics on the genome (GC content, number of restriction sites or mappability)
  • one that would contain all chromosomes and unassembled contigs, used exclusively for mapping.

Mus musculus's reference genome sequence

We search for the most recent reference genome corresponding to Mouse (https://www.ncbi.nlm.nih.gov/genome?term=mus%20musculus).

From there we obtain these identifiers:


In [2]:
species  = 'Mus_musculus'
taxid    = '10090'
assembly = 'GRCm38.p6'
genbank  = 'GCF_000001635.26'

The variables defined above can be modified for any other species, resulting in new results for the following commands.

Download from the NCBI

List of chromosomes/contigs


In [4]:
sumurl = ('ftp://ftp.ncbi.nlm.nih.gov/genomes/all/{0}/{1}/{2}/{3}/{4}_{5}/'
          '{4}_{5}_assembly_report.txt').format(genbank[:3], genbank[4:7], genbank[7:10], 
                                                genbank[10:13], genbank, assembly)

crmurl = ('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
          '?db=nuccore&id=%s&rettype=fasta&retmode=text')

In [4]:
print sumurl


ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_assembly_report.txt

In [5]:
! wget -q $sumurl -O chromosome_list.txt

In [6]:
! head chromosome_list.txt











Sequences of each chromosome/contig


In [1]:
import os

In [4]:
dirname = 'genome'
! mkdir -p {dirname}

For each contig/chromosome download the corresponding FASTA file from NCBI


In [16]:
contig = []
for line in open('chromosome_list.txt'):
    if line.startswith('#'):
        continue
    seq_name, seq_role, assigned_molecule, _, genbank, _, refseq, _ = line.split(None, 7)
    if seq_role == 'assembled-molecule':
        name = 'chr%s.fasta' % assigned_molecule
    else:
        name = 'chr%s_%s.fasta' % (assigned_molecule, seq_name.replace('/', '-'))
    contig.append(name)

    outfile = os.path.join(dirname, name)
    if os.path.exists(outfile) and os.path.getsize(outfile) > 10:
        continue
    error_code = os.system('wget "%s" --no-check-certificate -O %s' % (crmurl % (genbank), outfile))
    if error_code:
        error_code = os.system('wget "%s" --no-check-certificate -O %s' % (crmurl % (refseq), outfile))
    if error_code:
        print genbank


CM001008.2

Concatenate all contigs/chromosomes into single files


In [17]:
def write_to_fasta(line):
    contig_file.write(line)

def write_to_fastas(line):
    contig_file.write(line)
    simple_file.write(line)

In [18]:
os.system('mkdir -p {}/{}-{}'.format(dirname, species, assembly))


Out[18]:
0

In [29]:
contig_file = open('{0}/{1}-{2}/{1}-{2}_contigs.fa'.format(dirname, species, assembly),'w')
simple_file = open('{0}/{1}-{2}/{1}-{2}.fa'.format(dirname, species, assembly),'w')

for molecule in contig:
    fh = open('{0}/{1}'.format(dirname, molecule))
    oline = '>%s\n' % (molecule.replace('.fasta', ''))
    _ = fh.next()
    # if molecule is an assembled chromosome we write to both files, otherwise only to the *_contigs one
    write = write_to_fasta if '_' in molecule else write_to_fastas
    for line in fh:
        write(oline)
        oline = line
    # last line usually empty...
    if line.strip():
        write(line)
contig_file.close()
simple_file.close()

Remove all the other files (with single chromosome/contig)


In [12]:
! rm -f {dirname}/*.fasta

Creation of an index file for GEM mapper


In [8]:
! gem-indexer -T 8 -i {dirname}/{species}-{assembly}/{species}-{assembly}_contigs.fa -o {dirname}/{species}-{assembly}/{species}-{assembly}_contigs


Welcome to GEM-indexer build 1.423 (beta) - (2013/04/01 01:02:13 GMT)
 (c) 2008-2013 Paolo Ribeca <paolo.ribeca@gmail.com>
 (c) 2010-2013 Santiago Marco Sola <santiagomsola@gmail.com>
 (c) 2010-2013 Leonor Frias Moya <leonor.frias@gmail.com>
For the terms of use, run the program with the option --show-license.
************************************************************************
* WARNING: this is a beta version, provided for testing purposes only; *
*          check for updates at <http://gemlibrary.sourceforge.net>.   *
************************************************************************
Creating sequence and location files... done.
Computing DNA BWT (likely to take long)... done.
Generating index (likely to take long)... done.
Cleaning up... done.

The path to the index file will be: {dirname}/{species}-{assembly}/{species}_contigs.gem

Compute mappability values needed for bias specific normalizations

In this case we can use the FASTA of the genome whithout contigs and follow these step:


In [16]:
! gem-indexer -i {dirname}/{species}-{assembly}/{species}-{assembly}.fa \
   -o {dirname}/{species}-{assembly}/{species}-{assembly} -T 8

! gem-mappability -I {dirname}/{species}-{assembly}/{species}-{assembly}.gem -l 50 \
   -o {dirname}/{species}-{assembly}/{species}-{assembly}.50mer -T 8

! gem-2-wig -I {dirname}/{species}-{assembly}/{species}-{assembly}.gem \
   -i {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.mappability \
   -o {dirname}/{species}-{assembly}/{species}-{assembly}.50mer

! wigToBigWig {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.wig \
   {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.sizes \
   {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.bw

! bigWigToBedGraph {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.bw  \
   {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.bedGraph


Welcome to GEM-indexer build 1.423 (beta) - (2013/04/01 01:02:13 GMT)
 (c) 2008-2013 Paolo Ribeca <paolo.ribeca@gmail.com>
 (c) 2010-2013 Santiago Marco Sola <santiagomsola@gmail.com>
 (c) 2010-2013 Leonor Frias Moya <leonor.frias@gmail.com>
For the terms of use, run the program with the option --show-license.
************************************************************************
* WARNING: this is a beta version, provided for testing purposes only; *
*          check for updates at <http://gemlibrary.sourceforge.net>.   *
************************************************************************
Creating sequence and location files... done.
Computing DNA BWT (likely to take long)... done.
Generating index (likely to take long)... done.
Cleaning up... done.
Welcome to GEM-mappability build 1.315 (beta) - (2013/03/29 02:59:40 GMT)
 (c) 2008-2013 Paolo Ribeca <paolo.ribeca@gmail.com>
 (c) 2010-2013 Santiago Marco Sola <santiagomsola@gmail.com>
 (c) 2010-2013 Leonor Frias Moya <leonor.frias@gmail.com>
For the terms of use, run the program with the option --show-license.
************************************************************************
* WARNING: this is a beta version, provided for testing purposes only; *
*          check for updates at <http://gemlibrary.sourceforge.net>.   *
************************************************************************
Sat Jan 12 13:01:12 2019 -- Loading index (likely to take long)... done.
Sat Jan 12 13:01:23 2019 -- Starting (2647560565 positions to go)...
Sat Jan 12 18:36:34 2019 -- Pos=70.6% Done=1958248739(74%) Uniq=79.9%9%%%%%Pos=1.01% Done=218406036(8.25%) Uniq=9.74%Pos=1.81% Done=248796621(9.4%) Uniq=15.7%Pos=2.25% Done=263468826(9.95%) Uniq=18.6%Pos=2.26% Done=263625126(9.96%) Uniq=18.7%Pos=2.47% Done=270271292(10.2%) Uniq=20%Pos=2.67% Done=276275609(10.4%) Uniq=21.3% 12 13:27:10 2019 -- Pos=3.18% Done=291757822(11%) Uniq=24.1%Pos=4.35% Done=327462213(12.4%) Uniq=29.1% 12 14:08:03 2019 -- Pos=10.6% Done=496486782(18.8%) Uniq=48.2% 12 14:19:01 2019 -- Pos=12.9% Done=556078649(21%) Uniq=52.6%Pos=13% Done=557520928(21.1%) Uniq=52.7%Pos=13.3% Done=566507363(21.4%) Uniq=53.4%Pos=14.1% Done=586327353(22.1%) Uniq=54.3% 12 14:35:44 2019 -- Pos=16.2% Done=639147470(24.1%) Uniq=56.9%Pos=16.9% Done=655461253(24.8%) Uniq=57.7% 12 14:40:36 2019 -- Pos=17.2% Done=662932614(25%) Uniq=58.1% 12 14:40:37 2019 -- Pos=17.2% Done=662994581(25%) Uniq=58.1%Pos=17.2% Done=663086915(25%) Uniq=58.1%Pos=17.3% Done=665932815(25.2%) Uniq=58.2%Pos=17.6% 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Uniq=73.3%Pos=43.7% Done=1311200618(49.5%) Uniq=73.6%Pos=44.1% Done=1320126372(49.9%) Uniq=73.7%Pos=44.3% Done=1323089841(50%) Uniq=73.8%Pos=44.5% Done=1329283262(50.2%) Uniq=73.8%Pos=44.6% Done=1331556300(50.3%) Uniq=73.9%Pos=44.7% Done=1333548798(50.4%) Uniq=73.9%Pos=44.8% Done=1335604448(50.4%) Uniq=73.9%Pos=45.2% Done=1345158159(50.8%) Uniq=74.1%Pos=45.7% Done=1358894699(51.3%) Uniq=74.3%Pos=45.9% Done=1361634196(51.4%) Uniq=74.3% 12 16:52:54 2019 -- Pos=46% Done=1365095583(51.6%) Uniq=74.4%Pos=47.1% Done=1392288414(52.6%) Uniq=74.8%Pos=47.2% Done=1394490530(52.7%) Uniq=74.8%Pos=47.5% Done=1401998386(53%) Uniq=74.9%Pos=47.6% Done=1403219797(53%) Uniq=74.9% 12 17:02:09 2019 -- Pos=48% Done=1414538194(53.4%) Uniq=75.1%Pos=48.7% Done=1431137135(54.1%) Uniq=75.3%Pos=48.8% Done=1432121017(54.1%) Uniq=75.3%Pos=49% Done=1439392015(54.4%) Uniq=75.4%Pos=49.7% Done=1454815543(54.9%) Uniq=75.7%Pos=50% Done=1462423784(55.2%) Uniq=75.8%Pos=50.3% Done=1470546701(55.5%) Uniq=75.8% 12 17:11:54 2019 -- Pos=50.5% Done=1474303143(55.7%) Uniq=75.9%Pos=51% Done=1486804920(56.2%) Uniq=76.1%Pos=51.1% Done=1489886633(56.3%) Uniq=76.1%Pos=51.5% Done=1500250073(56.7%) Uniq=76.2% 12 17:16:26 2019 -- Pos=51.6% Done=1501766350(56.7%) Uniq=76.2%Pos=52.3% Done=1517869884(57.3%) Uniq=76.4%Pos=52.8% Done=1529262720(57.8%) Uniq=76.6%Pos=53.6% Done=1548337180(58.5%) Uniq=76.8%Pos=53.9% Done=1555652827(58.8%) Uniq=76.9%Pos=54.1% Done=1561752113(59%) Uniq=76.9% 12 17:28:19 2019 -- Pos=54.2% Done=1564899726(59.1%) Uniq=77%Pos=54.3% Done=1565343755(59.1%) Uniq=77%Pos=54.6% Done=1573216971(59.4%) Uniq=77% 12 17:29:53 2019 -- Pos=54.6% Done=1574089218(59.5%) Uniq=77.1% 12 17:31:18 2019 -- Pos=55% Done=1583099060(59.8%) Uniq=77.2%Pos=55.4% Done=1593216486(60.2%) Uniq=77.3%Pos=55.9% Done=1606337152(60.7%) Uniq=77.4%Pos=56.1% Done=1609808539(60.8%) Uniq=77.5% 12 17:35:55 2019 -- Pos=56.1% Done=1609862112(60.8%) Uniq=77.5% 12 17:42:27 2019 -- Pos=57.5% Done=1642858287(62.1%) Uniq=77.8%Pos=57.5% Done=1643121726(62.1%) Uniq=77.8%Pos=57.5% Done=1644007927(62.1%) Uniq=77.8%Pos=58% Done=1656404952(62.6%) Uniq=77.9% 12 17:45:23 2019 -- Pos=58.2% Done=1660423084(62.7%) Uniq=78%Pos=58.4% Done=1666069286(62.9%) Uniq=78%Pos=58.8% Done=1675581823(63.3%) Uniq=78.2% 12 17:49:23 2019 -- Pos=59.2% Done=1685412790(63.7%) Uniq=78.3%Pos=59.5% Done=1693653319(64%) Uniq=78.3%Pos=60.2% Done=1709214429(64.6%) Uniq=78.5%Pos=60.7% Done=1722756903(65.1%) Uniq=78.7%Pos=61.1% Done=1732331764(65.4%) Uniq=78.7%Pos=61.3% Done=1736515659(65.6%) Uniq=78.8%Pos=62.2% Done=1759278288(66.4%) Uniq=78.8% 12 18:06:17 2019 -- Pos=63.2% Done=1782560137(67.3%) Uniq=79%Pos=63.3% Done=1785027294(67.4%) Uniq=79%Pos=63.8% Done=1795924461(67.8%) Uniq=79.1%Pos=63.9% Done=1799047188(68%) Uniq=79.1%Pos=63.9% Done=1799216528(68%) Uniq=79.1%Pos=65.1% Done=1827177837(69%) Uniq=79.3% 12 18:15:27 2019 -- Pos=65.4% Done=1835549918(69.3%) Uniq=79.4%Pos=65.9% Done=1846126749(69.7%) Uniq=79.4%Pos=66.4% Done=1859131312(70.2%) Uniq=79.5%Pos=66.4% Done=1859670264(70.2%) Uniq=79.5%Pos=66.6% Done=1864236016(70.4%) Uniq=79.5% 12 18:20:29 2019 -- Pos=66.6% Done=1864538064(70.4%) Uniq=79.5%Pos=66.9% Done=1870206871(70.6%) Uniq=79.6% 12 18:21:32 2019 -- Pos=66.9% Done=1871698423(70.7%) Uniq=79.6%Pos=67.1% Done=1875120143(70.8%) Uniq=79.6%Pos=67.2% Done=1877997202(70.9%) Uniq=79.6%Pos=67.2% Done=1878269502(70.9%) Uniq=79.7%Pos=67.6% Done=1887010143(71.3%) Uniq=79.6%Pos=67.7% Done=1889944239(71.4%) Uniq=79.6%Pos=67.9% Done=1894198380(71.5%) Uniq=79.7% 12 18:26:30 2019 -- Pos=68.1% Done=1899871149(71.8%) Uniq=79.7%Pos=68.4% Done=1905362368(72%) Uniq=79.7%Pos=69% Done=1920184966(72.5%) Uniq=79.9%Pos=69.2% Done=1925805126(72.7%) Uniq=79.9%Pos=69.2% Done=1925834743(72.7%) Uniq=79.9%Pos=69.2% Done=1926179506(72.8%) Uniq=79.9%Pos=69.3% Done=1928790007(72.9%) Uniq=79.9%Pos=69.4% Done=1931196834(72.9%) Uniq=80%Pos=69.5% Done=1933456741(73%) Uniq=80%Pos=69.5% Done=1933876410(73%) Uniq=80%Pos=69.8% Done=1940867480(73.3%) Uniq=79.8%Pos=70% Done=1943951816(73.4%) Uniq=79.8%Pos=70.2% Done=1949902159(73.6%) Uniq=79.9%Pos=70.2% Done=1950034273(73.7%) Uniq=79.9%Pos=70.3% Done=1951546353(73.7%) Uniq=79.9% 12 18:35:44 2019 -- Pos=70.3% Done=1952490966(73.7%) Uniq=79.9%Pos=70.6% Done=1958207268(74%) Uniq=79.9%Sat Jan 12 20:33:43 2019 -- Pos=99.4% Done=2646872857(100%) Uniq=80.3%%s=70.6% Done=1959719004(74%) Uniq=80%Pos=70.7% Done=1961694822(74.1%) Uniq=80%Pos=70.9% Done=1967604934(74.3%) Uniq=80%Pos=71.2% Done=1974525088(74.6%) Uniq=79.9%Pos=71.3% Done=1974972286(74.6%) Uniq=79.9% 12 18:39:35 2019 -- Pos=71.3% Done=1976759614(74.7%) Uniq=80%Pos=71.4% Done=1977595226(74.7%) Uniq=80%Pos=71.4% Done=1978715396(74.7%) Uniq=79.9%Pos=71.5% Done=1979887820(74.8%) Uniq=79.9%Pos=71.6% Done=1982403833(74.9%) Uniq=80%Pos=71.7% Done=1985897278(75%) Uniq=80%Pos=72.2% Done=1996685945(75.4%) Uniq=80.1%Pos=72.2% Done=1996942152(75.4%) Uniq=80.1%Pos=72.2% Done=1998072312(75.5%) Uniq=80.1%Pos=72.4% Done=2001445562(75.6%) Uniq=80.1%Pos=72.4% Done=2002188372(75.6%) Uniq=80.1%Pos=72.5% Done=2005506492(75.7%) Uniq=80.1%Pos=72.5% Done=2006019757(75.8%) Uniq=80.1%Pos=72.8% Done=2012280596(76%) Uniq=80.2%Pos=72.9% Done=2013673384(76.1%) Uniq=80.2%Pos=73.1% Done=2019490614(76.3%) Uniq=80.2%Pos=73.3% Done=2023910709(76.4%) Uniq=80.3%Pos=73.6% Done=2030700632(76.7%) Uniq=80.3%Pos=73.8% Done=2034361559(76.8%) Uniq=80.3%Pos=74.1% Done=2042470991(77.1%) Uniq=80.4%Pos=74.5% Done=2051204004(77.5%) Uniq=80.5%Pos=74.9% Done=2060026135(77.8%) Uniq=80.5%Pos=74.9% Done=2060237589(77.8%) Uniq=80.5%Pos=75% Done=2062038184(77.9%) Uniq=80.6%Pos=75% Done=2062602058(77.9%) Uniq=80.6%Pos=75.1% Done=2065986247(78%) Uniq=80.6%Pos=75.2% Done=2067330704(78.1%) Uniq=80.6%Pos=75.2% Done=2068228038(78.1%) Uniq=80.6%Pos=75.3% Done=2070295893(78.2%) Uniq=80.6%Pos=75.7% Done=2080333393(78.6%) Uniq=80.7%Pos=76.1% Done=2088639870(78.9%) Uniq=80.7% 12 19:00:23 2019 -- Pos=76.2% Done=2090500386(79%) Uniq=80.8%Pos=76.3% Done=2093775541(79.1%) Uniq=80.8%Pos=76.3% Done=2094319021(79.1%) Uniq=80.8%Pos=76.3% Done=2094588474(79.1%) Uniq=80.8%Pos=76.6% Done=2100115538(79.3%) Uniq=80.8%Pos=76.6% Done=2100885189(79.4%) Uniq=80.8%Pos=76.6% Done=2101971885(79.4%) Uniq=80.8%Pos=76.6% Done=2102015589(79.4%) Uniq=80.8% Jan 12 19:02:40 2019 -- Pos=76.7% Done=2104395732(79.5%) Uniq=80.9%Pos=76.9% Done=2108324137(79.6%) Uniq=80.9%Pos=77.1% Done=2112676445(79.8%) Uniq=80.9%Pos=77.4% Done=2120614755(80.1%) Uniq=81%Pos=77.5% Done=2122921824(80.2%) Uniq=81%Pos=77.7% Done=2127825701(80.4%) Uniq=81%Pos=77.7% Done=2128154697(80.4%) Uniq=81% 12 19:06:26 2019 -- Pos=77.7% Done=2129166946(80.4%) Uniq=81%Pos=78% Done=2135759524(80.7%) Uniq=81.1%Pos=78.2% Done=2140909782(80.9%) Uniq=81.1%Pos=78.2% Done=2140995816(80.9%) Uniq=81.1%Pos=78.2% Done=2141235549(80.9%) Uniq=81.1%Pos=78.2% Done=2141274201(80.9%) Uniq=81.1%Pos=78.5% Done=2146413313(81.1%) Uniq=81.1%Pos=78.5% Done=2147993533(81.1%) Uniq=81.2%Pos=78.6% Done=2149948452(81.2%) Uniq=81.2%Pos=78.9% Done=2156347825(81.4%) Uniq=81.2%Pos=78.9% Done=2157928846(81.5%) Uniq=81.2%Pos=79% Done=2159776896(81.6%) Uniq=81.2%Pos=79.1% Done=2161427090(81.6%) Uniq=81.2%Pos=79.4% Done=2168554089(81.9%) Uniq=81.3%Pos=79.4% Done=2170233929(82%) Uniq=81.3%Pos=79.5% Done=2171948457(82%) Uniq=81.3%Pos=79.7% Done=2176656525(82.2%) Uniq=81.3%Pos=79.8% Done=2177852038(82.3%) Uniq=81.4%Pos=80% Done=2183259873(82.5%) Uniq=81.4%Pos=80.1% Done=2184869735(82.5%) Uniq=81.4% 12 19:17:03 2019 -- Pos=80.3% Done=2189979212(82.7%) Uniq=81.4%Pos=80.3% Done=2190734677(82.7%) Uniq=81.4%Pos=81.4% Done=2215182864(83.7%) Uniq=81.6%Pos=81.5% Done=2219001585(83.8%) Uniq=81.6%Pos=81.5% Done=2219132688(83.8%) Uniq=81.6% 12 19:22:32 2019 -- Pos=81.7% Done=2223004456(84%) Uniq=81.6%Pos=81.7% Done=2224615857(84%) Uniq=81.6%Pos=82.2% Done=2236418353(84.5%) Uniq=81.6%Pos=82.4% Done=2239910226(84.6%) Uniq=81.6%Pos=82.6% Done=2244093004(84.8%) Uniq=81.7%Pos=82.7% Done=2246565721(84.9%) Uniq=81.7%Pos=82.7% Done=2246783960(84.9%) Uniq=81.7%Pos=83% Done=2253960803(85.1%) Uniq=81.7%Pos=83.2% Done=2258180897(85.3%) Uniq=81.7%Pos=83.2% Done=2259167462(85.3%) Uniq=81.7%Pos=83.5% Done=2265464290(85.6%) Uniq=81.8% 12 19:32:42 2019 -- Pos=84% Done=2277688893(86%) Uniq=81.8%Pos=84.3% Done=2285025312(86.3%) Uniq=81.9%Pos=84.3% Done=2286580226(86.4%) Uniq=81.9%Pos=84.7% Done=2296367990(86.7%) Uniq=82%Pos=85.5% Done=2314686138(87.4%) Uniq=82.1%Pos=85.6% Done=2315220128(87.4%) Uniq=82.1%Pos=85.9% Done=2322172070(87.7%) Uniq=82.1%Pos=86% Done=2326739936(87.9%) Uniq=82.1%Pos=86.1% Done=2328548748(88%) Uniq=82.1%Pos=86.1% Done=2328848056(88%) Uniq=82.1% 12 19:42:17 2019 -- Pos=86.2% Done=2331080816(88%) Uniq=82.2%Pos=86.2% Done=2331155724(88%) Uniq=82.2%Pos=86.3% Done=2331875815(88.1%) Uniq=82.2%Pos=86.6% Done=2340021840(88.4%) Uniq=82.2%Pos=86.8% Done=2344599437(88.6%) Uniq=82.2%Pos=87% Done=2349705548(88.7%) Uniq=82.3%Pos=87.1% Done=2351361250(88.8%) Uniq=82.3%Pos=87.1% Done=2352999360(88.9%) Uniq=82.3%Pos=87.4% Done=2358589856(89.1%) Uniq=82.3% 12 19:47:12 2019 -- Pos=87.5% Done=2361715228(89.2%) Uniq=82.3%Pos=87.6% Done=2365070308(89.3%) Uniq=82.4%Pos=87.7% Done=2365970342(89.4%) Uniq=82.4%Pos=87.7% Done=2367336396(89.4%) Uniq=82.4%Pos=88.2% Done=2379097284(89.9%) Uniq=82.4%Pos=88.2% Done=2379806891(89.9%) Uniq=82.5%Pos=88.2% Done=2379976690(89.9%) Uniq=82.5%Pos=88.7% Done=2390852190(90.3%) Uniq=82.5%Pos=88.9% Done=2394167627(90.4%) Uniq=82.5% 12 19:53:33 2019 -- Pos=89% Done=2398270384(90.6%) Uniq=82.5%Pos=89.1% Done=2400699017(90.7%) Uniq=82.5%Pos=89.4% Done=2408024945(91%) Uniq=82.6%Pos=89.6% Done=2411522999(91.1%) Uniq=82.6%Pos=89.7% Done=2413782730(91.2%) Uniq=82.6%Pos=89.8% Done=2416868515(91.3%) Uniq=82.6%Pos=89.9% Done=2420426517(91.4%) Uniq=82.6%Pos=90.2% Done=2427484877(91.7%) Uniq=82.7% 12 19:58:43 2019 -- Pos=90.4% Done=2431535917(91.8%) Uniq=82.7%Pos=90.4% Done=2432847831(91.9%) Uniq=82.7%Pos=90.5% Done=2433376027(91.9%) Uniq=82.7%Pos=90.5% Done=2437160669(92.1%) Uniq=82.6%2921724(92.3%) Uniq=82.6%Pos=90.8% Done=2443185320(92.3%) Uniq=82.6%5176578(92.4%) Uniq=82.6%019 -- Pos=91.2% Done=2452059153(92.6%) Uniq=82.7%Pos=91.3% Done=2456039212(92.8%) Uniq=82.6%Pos=91.4% Done=2458041197(92.8%) Uniq=82.5%Pos=91.6% Done=2458325610(92.9%) Uniq=82.5%Pos=91.6% Done=2458328085(92.9%) Uniq=82.5%Pos=92.1% Done=2468962214(93.3%) Uniq=82.5%Pos=92.1% Done=2469568743(93.3%) Uniq=82.5%Pos=92.2% Done=2470853460(93.3%) Uniq=82.5%Pos=92.3% Done=2473444675(93.4%) Uniq=82.5%Pos=92.4% Done=2474880377(93.5%) Uniq=82.5%Pos=92.4% Done=2476253377(93.5%) Uniq=82.5%Pos=92.7% Done=2482797163(93.8%) Uniq=82.5%Pos=92.8% Done=2483134553(93.8%) Uniq=82.5%Pos=93% Done=2487559441(94%) Uniq=82.5%Pos=93% Done=2489047714(94%) Uniq=82.5%Pos=93.1% Done=2491893446(94.1%) Uniq=82.5%Pos=93.2% Done=2492153179(94.1%) Uniq=82.5%Pos=93.2% Done=2493474237(94.2%) Uniq=82.5%Pos=93.2% Done=2493606504(94.2%) Uniq=82.5%Pos=93.8% Done=2506942288(94.7%) Uniq=82.6%Pos=94.1% Done=2512391348(94.9%) Uniq=82.6%Pos=94.1% Done=2513855037(94.9%) Uniq=82.6%Pos=94.2% Done=2514531745(95%) Uniq=82.6% 12 20:17:05 2019 -- Pos=94.3% Done=2516619704(95.1%) Uniq=82.6%Pos=94.3% Done=2518074083(95.1%) Uniq=82.6% 12 20:19:35 2019 -- Pos=94.7% Done=2526617096(95.4%) Uniq=82.7%Pos=95% Done=2538065044(95.9%) Uniq=82.4%Pos=95.5% Done=2547888273(96.2%) Uniq=82.5% 12 20:23:29 2019 -- Pos=95.5% Done=2549142174(96.3%) Uniq=82.5% 12 20:24:02 2019 -- Pos=95.7% Done=2552419951(96.4%) Uniq=82.5%Pos=95.9% Done=2557566599(96.6%) Uniq=82.4%Pos=96% Done=2559143710(96.7%) Uniq=82.5%Pos=96% Done=2560238850(96.7%) Uniq=82.5%Pos=96.5% Done=2569905239(97.1%) Uniq=82.5%Pos=96.5% Done=2570016956(97.1%) Uniq=82.5%Pos=96.7% Done=2575103817(97.3%) Uniq=82.5%Pos=96.7% Done=2576365002(97.3%) Uniq=82.5%Pos=97.1% Done=2635495455(99.5%) Uniq=80.7%Pos=97.6% Done=2643228087(99.8%) Uniq=80.4%Pos=97.7% Done=2643473209(99.8%) Uniq=80.4%Pos=97.7% Done=2643516232(99.8%) Uniq=80.4%Pos=97.7% Done=2644031365(99.9%) Uniq=80.4%Pos=98.1% Done=2644723756(99.9%) Uniq=80.4%Pos=98.1% Done=2644748932(99.9%) Uniq=80.4%Pos=98.1% Done=2644887138(99.9%) Uniq=80.4%Pos=98.2% Done=2645106477(99.9%) Uniq=80.4% 12 20:33:00 2019 -- Pos=98.2% Done=2645124609(99.9%) Uniq=80.4%Pos=98.6% Done=2646123294(99.9%) Uniq=80.4%Pos=98.7% Done=2646306152(100%) Uniq=80.4%Pos=98.8% Done=2646584817(100%) Uniq=80.3%Pos=98.8% Done=2646593159(100%) Uniq=80.3%Pos=98.8% Done=2646604488(100%) Uniq=80.3%Pos=98.9% Done=2646615780(100%) Uniq=80.3%Pos=99.4% Done=2646872360(100%) Uniq=80.3%Sat Jan 12 20:34:17 2019 -- ...done. Done=2647550675(100%) Uniq=80.3%%Pos=99.5% Done=2646951969(100%) Uniq=80.3%[KSat Jan 12 20:33:50 2019 -- Pos=99.6% Done=2647010860(100%) Uniq=80.3%Pos=99.8% Done=2647192463(100%) Uniq=80.3%Pos=99.8% Done=2647216681(100%) Uniq=80.3% 12 20:34:06 2019 -- Pos=99.9% Done=2647298651(100%) Uniq=80.3%
Sat Jan 12 20:34:17 2019 -- Writing frequencies to disk...
Sat Jan 12 20:34:27 2019 -- ...done.
Welcome to GEM-2-wig build 1.423 (beta) - (2013/04/01 01:02:13 GMT)
 (c) 2008-2013 Paolo Ribeca <paolo.ribeca@gmail.com>
 (c) 2010-2013 Santiago Marco Sola <santiagomsola@gmail.com>
 (c) 2010-2013 Leonor Frias Moya <leonor.frias@gmail.com>
For the terms of use, run the program with the option --show-license.
************************************************************************
* WARNING: this is a beta version, provided for testing purposes only; *
*          check for updates at <http://gemlibrary.sourceforge.net>.   *
************************************************************************
Sat Jan 12 20:34:28 2019 -- Loading index (likely to take long)... done.
Sat Jan 12 20:34:41 2019 -- Inverting locations... done.
genome/Mus_musculus-GRCm38.p6/Mus_musculus-GRCm38.p6.50mer.bw is not a bpt b-plus tree index file

Cleanup


In [ ]:
! rm -f {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.mappability
! rm -f {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.wig
! rm -f {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.bw
! rm -f {dirname}/{species}-{assembly}/{species}-{assembly}.50mer.sizes
! rm -f {dirname}/{species}-{assembly}/*.log