In [1]:
%load_ext autoreload
%autoreload 2
In [3]:
%pylab inline
%config InlineBackend.figure_format = 'retina'
import py
import pandas as pd
import seaborn as sns
from collections import OrderedDict
import glob
import os
import re
from IPython.display import FileLink
import pyprind
from khmer import Countgraph
#from khmer._oxli.partitioning import StreamingPartitioner
#from khmer._oxli.app import PartitioningApp
from khmer import LinearAssembler
import json
Populating the interactive namespace from numpy and matplotlib
In [4]:
sns.set_style('ticks')
In [134]:
def get_readnum(path):
reg = re.compile(r'.*-(?P<num>[0-9]*)\.stats\.csv$')
return int(reg.search(path).groupdict()['num'])
def parse_stats_files(stats_dir, read_num_func=get_readnum):
stats_files = [os.path.abspath(p) for p in glob.glob(os.path.join(stats_dir,'*.csv'))]
stats_files.sort(key=read_num_func)
bar = pyprind.ProgBar(len(stats_files), monitor=True)
data = OrderedDict()
for filename in stats_files:
df = pd.read_csv(filename, header=None, names=['comp_id', 'n_tags', 'mean_cov'])
data[read_num_func(filename)] = df
bar.update()
return data
In [6]:
full_data = parse_stats_files('../../khmer/test-stats/')
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[##############################] | ETA: 00:00:00
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sns.distplot(np.log(full_data[list(full_data.keys())[-1]].n_tags), kde=False, label='log(n_tags)')
title('Tag Distribution, Full Run')
Out[10]:
<matplotlib.text.Text at 0x7fe81d24eb00>
Component number quickly levels out, and eventually, reduces slightly. Total number of tags keeps increasing; this actually seems odd to me, as I'd expect tag number to level off sometime after component saturation. I also expected steady increase in component number followed by a sharp peak and decline, but instead, we got this nice smooth sort of asymptotic approach to the max number of components.
In [13]:
plot(list(full_data.keys()), [len(d) for d in full_data.values()], label='Num Components')
plot(list(full_data.keys()), [d.n_tags.sum() for d in full_data.values()], label='Num Tags')
xlabel('Read Number')
legend(loc='upper left')
title('Tags and Components vs Reads Observed, Full Data')
savefig('components_v_reads_full.png', dpi=600)
In [14]:
FileLink('components_v_reads_full.png')
Out[14]:
A quick examination of the component sizes provides some insight into this behavior -- the so called "lump" is here in full force. That expected sharp growth and decline is likely being blocked by the lump gathering up far more potential components than it should.
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full_data[list(full_data.keys())[-1]].sort_values('n_tags', ascending=False).head()
Out[15]:
comp_id
n_tags
mean_cov
1
1
503519
33.569229
211
420
3969
28.012598
444
859
2428
19.813839
146
302
1887
57.498146
206
411
1817
50.170612
The size of the largest component increases steadily throughout the process.
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plot(list(full_data.keys()), [df.n_tags.max() for df in full_data.values()])
plot(list(full_data.keys()), [df.n_tags.median() for df in full_data.values()])
Out[16]:
[<matplotlib.lines.Line2D at 0x7fe81c31d550>]
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normed_data = parse_stats_files('../../khmer/test-stats-norm')
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plot(list(normed_data.keys()), [len(d) for d in normed_data.values()], label='Num Components')
plot(list(normed_data.keys()), [d.n_tags.sum() for d in normed_data.values()], label='Num Tags')
xlabel('Read Number')
legend(loc='upper left')
title('Tags and Components vs Reads Observed, Normed Data')
savefig('components_v_reads_norm.png', dpi=600)
In [36]:
plot(list(normed_data.keys()), [df.n_tags.max() for df in normed_data.values()])
plot(list(normed_data.keys()), [df.n_tags.median() for df in normed_data.values()])
Out[36]:
[<matplotlib.lines.Line2D at 0x7fe819a07940>]
In [17]:
from khmer._oxli.partitioning import Component
from khmer import reverse_hash as revhash
Perhaps we can figure out something about this component by inspecting it more closely. I'll repartition the data, but this time, I'll use the faster lower-level consume functionality, and keep the partitioner around.
In [ ]:
cg = Countgraph(25, 2e9, 4)
sp = StreamingPartitioner(cg)
sp.consume_fasta('/store/biodb/MMETSP/data/Asterionellopsis_glacialis/SRR1300451/SRR1300451_1.fastq')
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comps = [(comp.component_id, comp) for comp in sp.components()]
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lump = comps[0][1]
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lump_counts = {tag: cg.get(revhash(tag, 25)) for tag in lump}
The $k$-mer spectrum is clearly bimodal, though the limitations of our counting structure truncate the high abundance spectrum. Regardless, there is a group of extremely high abundance $k$-mers that we can assume binds the lump together.
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sns.distplot(list(lump_counts.values()), kde=False, axlabel='Tag $k$-mer count', )
title('$k$-mer spectrum of tags in "lump" component')
Out[60]:
<matplotlib.text.Text at 0x7fc0b46b5c18>
In [40]:
sticky_nodes = {revhash(tag, 25): count for tag, count in lump_counts.items() if count == 255}
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with open('lump-nodes.json', 'w') as fp:
json.dump(lump_counts, fp, indent=4)
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asm = LinearAssembler(cg)
In [66]:
asm.assemble(sorted(list(sticky_nodes.keys()))[2])
Out[66]:
'AAAAAAAGACAAACTTTTAACCGAG'
In [135]:
paired_data = parse_stats_files('/work/streaming-assembly/data/Asterionellopsis_glacialis_CCMP1581_SRR1300451_MMETSP1394/SRR1300451-comp-stats/')
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single_data = parse_stats_files('/work/streaming-assembly/data/Asterionellopsis_glacialis_CCMP1581_SRR1300451_MMETSP1394/SRR1300451-single-comp-stats/')
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In [139]:
from ficus import FigureManager
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with FigureManager(show=True, nrows=2, sharex=True, figsize=(8,4)) as (fig, ax):
ax[0].plot(list(paired_data.keys()), [len(d) for d in paired_data.values()], label='Paired')
ax[0].plot(list(single_data.keys()), [len(d) for d in single_data.values()], label='Single')
ax[0].set_ylabel('Num Components')
ax[1].plot(list(paired_data.keys()), [df.n_tags.max() for df in paired_data.values()], label='Paired')
ax[1].plot(list(single_data.keys()), [df.n_tags.max() for df in single_data.values()], label='Single')
ax[1].set_xlabel('Read Number')
ax[1].set_ylabel('Tags in Lump')
for _ in ax:
_.xaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(lambda x, p: format(int(x), ',')))
_.yaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(lambda x, p: format(int(x), ',')))
start, end = _.get_ylim()
_.yaxis.set_ticks(np.arange(start, end+1, end/4))
# Modify x-axis ticks
start, end = ax[1].get_xlim()
ax[1].xaxis.set_ticks(np.arange(start, end+1, end/3))
ax[0].legend(loc='center right')
#ax[1].legend(loc='center right')
#ax[0].set_title('Component growth during assemly graph construction, SRR1300451')
fig.savefig('/work/recomb-poster/output/img/lump_domination.png', dpi=300)
In [157]:
for _ in ax:
print(_)
Axes(0.125,0.547727;0.775x0.352273)
Axes(0.125,0.125;0.775x0.352273)
In [70]:
plot(list(paired_data.keys()), [df.n_tags.max() for df in paired_data.values()], label='Paired-end')
plot(list(single_data.keys()), [df.n_tags.max() for df in single_data.values()], label='Single-end')
xlabel('Read Number')
ylabel('Num of Tags')
legend(loc='upper left')
title('Tags in Largest Component, SRR1300451')
savefig('largest_component_size_paired_and_single.png', dpi=600)
In [19]:
cg = Countgraph(25, 2e9, 4)
cg.consume_fasta('/store/biodb/MMETSP/data/Asterionellopsis_glacialis/SRR1300451/SRR1300451_1.fastq')
cg.consume_fasta('/store/biodb/MMETSP/data/Asterionellopsis_glacialis/SRR1300451/SRR1300451_2.fastq')
Out[19]:
(13221196, 343278910)
In [7]:
partapp = PartitioningApp(['--ksize', '25', '-x', '2e9', '--stats-dir', 'SRR1300451-comp-stats-2',
'--stats-interval', '50000', '--pairing-mode', 'split',
'/store/biodb/MMETSP/data/Asterionellopsis_glacialis/SRR1300451/SRR1300451_1.fastq',
'/store/biodb/MMETSP/data/Asterionellopsis_glacialis/SRR1300451/SRR1300451_2.fastq'])
In [ ]:
%time P_paired = partapp.run()
== Starting (/store/biodb/MMETSP/data/Asterionellopsis_glacialis/SRR1300451/SRR1300451_1.fastq./store/biodb/MMETSP/data/Asterionellopsis_glacialis/SRR1300451/SRR1300451_2.fastq) ==
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# 50000: 533230 tags, 41146 components.
writing results to file -> SRR1300451-comp-stats-2/50000.SRR1300451_2.fastq.stats.csv
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# 100000: 533230 tags, 41146 components.
writing results to file -> SRR1300451-comp-stats-2/100000.SRR1300451_2.fastq.stats.csv
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# 150000: 533230 tags, 41146 components.
writing results to file -> SRR1300451-comp-stats-2/150000.SRR1300451_2.fastq.stats.csv
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# 200000: 533230 tags, 41146 components.
writing results to file -> SRR1300451-comp-stats-2/200000.SRR1300451_2.fastq.stats.csv
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# 250000: 566824 tags, 42588 components.
writing results to file -> SRR1300451-comp-stats-2/250000.SRR1300451_2.fastq.stats.csv
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# 300000: 662513 tags, 46249 components.
writing results to file -> SRR1300451-comp-stats-2/300000.SRR1300451_2.fastq.stats.csv
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# 350000: 755593 tags, 49399 components.
writing results to file -> SRR1300451-comp-stats-2/350000.SRR1300451_2.fastq.stats.csv
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# 400000: 845481 tags, 51962 components.
writing results to file -> SRR1300451-comp-stats-2/400000.SRR1300451_2.fastq.stats.csv
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# 450000: 932854 tags, 54222 components.
writing results to file -> SRR1300451-comp-stats-2/450000.SRR1300451_2.fastq.stats.csv
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# 500000: 1018629 tags, 56262 components.
writing results to file -> SRR1300451-comp-stats-2/500000.SRR1300451_2.fastq.stats.csv
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# 550000: 1101919 tags, 57957 components.
writing results to file -> SRR1300451-comp-stats-2/550000.SRR1300451_2.fastq.stats.csv
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# 600000: 1183780 tags, 59370 components.
writing results to file -> SRR1300451-comp-stats-2/600000.SRR1300451_2.fastq.stats.csv
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# 650000: 1263490 tags, 60545 components.
writing results to file -> SRR1300451-comp-stats-2/650000.SRR1300451_2.fastq.stats.csv
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# 700000: 1341640 tags, 61441 components.
writing results to file -> SRR1300451-comp-stats-2/700000.SRR1300451_2.fastq.stats.csv
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# 750000: 1418000 tags, 62334 components.
writing results to file -> SRR1300451-comp-stats-2/750000.SRR1300451_2.fastq.stats.csv
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# 800000: 1493200 tags, 63147 components.
writing results to file -> SRR1300451-comp-stats-2/800000.SRR1300451_2.fastq.stats.csv
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# 850000: 1566855 tags, 63710 components.
writing results to file -> SRR1300451-comp-stats-2/850000.SRR1300451_2.fastq.stats.csv
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# 900000: 1639539 tags, 64128 components.
writing results to file -> SRR1300451-comp-stats-2/900000.SRR1300451_2.fastq.stats.csv
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# 950000: 1711327 tags, 64499 components.
writing results to file -> SRR1300451-comp-stats-2/950000.SRR1300451_2.fastq.stats.csv
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# 1000000: 1781488 tags, 64735 components.
writing results to file -> SRR1300451-comp-stats-2/1000000.SRR1300451_2.fastq.stats.csv
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# 1050000: 1849821 tags, 64992 components.
writing results to file -> SRR1300451-comp-stats-2/1050000.SRR1300451_2.fastq.stats.csv
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# 1100000: 1918122 tags, 65212 components.
writing results to file -> SRR1300451-comp-stats-2/1100000.SRR1300451_2.fastq.stats.csv
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# 1150000: 1985850 tags, 65330 components.
writing results to file -> SRR1300451-comp-stats-2/1150000.SRR1300451_2.fastq.stats.csv
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# 1200000: 2052486 tags, 65431 components.
writing results to file -> SRR1300451-comp-stats-2/1200000.SRR1300451_2.fastq.stats.csv
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# 1250000: 2117672 tags, 65364 components.
writing results to file -> SRR1300451-comp-stats-2/1250000.SRR1300451_2.fastq.stats.csv
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# 1300000: 2182537 tags, 65341 components.
writing results to file -> SRR1300451-comp-stats-2/1300000.SRR1300451_2.fastq.stats.csv
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# 1350000: 2246687 tags, 65229 components.
writing results to file -> SRR1300451-comp-stats-2/1350000.SRR1300451_2.fastq.stats.csv
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# 1400000: 2309496 tags, 65157 components.
writing results to file -> SRR1300451-comp-stats-2/1400000.SRR1300451_2.fastq.stats.csv
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# 1450000: 2372070 tags, 65031 components.
writing results to file -> SRR1300451-comp-stats-2/1450000.SRR1300451_2.fastq.stats.csv
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# 1500000: 2434218 tags, 64944 components.
writing results to file -> SRR1300451-comp-stats-2/1500000.SRR1300451_2.fastq.stats.csv
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# 1550000: 2495403 tags, 64811 components.
writing results to file -> SRR1300451-comp-stats-2/1550000.SRR1300451_2.fastq.stats.csv
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# 1600000: 2555743 tags, 64612 components.
writing results to file -> SRR1300451-comp-stats-2/1600000.SRR1300451_2.fastq.stats.csv
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# 1650000: 2615843 tags, 64382 components.
writing results to file -> SRR1300451-comp-stats-2/1650000.SRR1300451_2.fastq.stats.csv
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# 1700000: 2675020 tags, 64288 components.
writing results to file -> SRR1300451-comp-stats-2/1700000.SRR1300451_2.fastq.stats.csv
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# 1750000: 2734075 tags, 64083 components.
writing results to file -> SRR1300451-comp-stats-2/1750000.SRR1300451_2.fastq.stats.csv
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# 1800000: 2792389 tags, 63823 components.
writing results to file -> SRR1300451-comp-stats-2/1800000.SRR1300451_2.fastq.stats.csv
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# 1850000: 2849494 tags, 63653 components.
writing results to file -> SRR1300451-comp-stats-2/1850000.SRR1300451_2.fastq.stats.csv
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# 1900000: 2907019 tags, 63460 components.
writing results to file -> SRR1300451-comp-stats-2/1900000.SRR1300451_2.fastq.stats.csv
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# 1950000: 2963797 tags, 63211 components.
writing results to file -> SRR1300451-comp-stats-2/1950000.SRR1300451_2.fastq.stats.csv
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# 2000000: 3020225 tags, 63040 components.
writing results to file -> SRR1300451-comp-stats-2/2000000.SRR1300451_2.fastq.stats.csv
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# 2050000: 3075888 tags, 62816 components.
writing results to file -> SRR1300451-comp-stats-2/2050000.SRR1300451_2.fastq.stats.csv
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# 2100000: 3130709 tags, 62471 components.
writing results to file -> SRR1300451-comp-stats-2/2100000.SRR1300451_2.fastq.stats.csv
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# 2150000: 3185579 tags, 62238 components.
writing results to file -> SRR1300451-comp-stats-2/2150000.SRR1300451_2.fastq.stats.csv
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# 2200000: 3239218 tags, 61941 components.
writing results to file -> SRR1300451-comp-stats-2/2200000.SRR1300451_2.fastq.stats.csv
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# 2250000: 3293585 tags, 61645 components.
writing results to file -> SRR1300451-comp-stats-2/2250000.SRR1300451_2.fastq.stats.csv
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# 2300000: 3346960 tags, 61304 components.
writing results to file -> SRR1300451-comp-stats-2/2300000.SRR1300451_2.fastq.stats.csv
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# 2350000: 3399913 tags, 60990 components.
writing results to file -> SRR1300451-comp-stats-2/2350000.SRR1300451_2.fastq.stats.csv
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# 2400000: 3451712 tags, 60605 components.
writing results to file -> SRR1300451-comp-stats-2/2400000.SRR1300451_2.fastq.stats.csv
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# 2450000: 3503748 tags, 60285 components.
writing results to file -> SRR1300451-comp-stats-2/2450000.SRR1300451_2.fastq.stats.csv
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# 2500000: 3555124 tags, 59980 components.
writing results to file -> SRR1300451-comp-stats-2/2500000.SRR1300451_2.fastq.stats.csv
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# 2550000: 3606675 tags, 59656 components.
writing results to file -> SRR1300451-comp-stats-2/2550000.SRR1300451_2.fastq.stats.csv
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# 2600000: 3658111 tags, 59324 components.
writing results to file -> SRR1300451-comp-stats-2/2600000.SRR1300451_2.fastq.stats.csv
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# 2650000: 3709108 tags, 58981 components.
writing results to file -> SRR1300451-comp-stats-2/2650000.SRR1300451_2.fastq.stats.csv
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# 2700000: 3759529 tags, 58641 components.
writing results to file -> SRR1300451-comp-stats-2/2700000.SRR1300451_2.fastq.stats.csv
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# 2750000: 3809697 tags, 58274 components.
writing results to file -> SRR1300451-comp-stats-2/2750000.SRR1300451_2.fastq.stats.csv
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# 2800000: 3858954 tags, 57890 components.
writing results to file -> SRR1300451-comp-stats-2/2800000.SRR1300451_2.fastq.stats.csv
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# 2850000: 3908778 tags, 57598 components.
writing results to file -> SRR1300451-comp-stats-2/2850000.SRR1300451_2.fastq.stats.csv
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# 2900000: 3957624 tags, 57248 components.
writing results to file -> SRR1300451-comp-stats-2/2900000.SRR1300451_2.fastq.stats.csv
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# 2950000: 4006321 tags, 56952 components.
writing results to file -> SRR1300451-comp-stats-2/2950000.SRR1300451_2.fastq.stats.csv
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# 3000000: 4053938 tags, 56585 components.
writing results to file -> SRR1300451-comp-stats-2/3000000.SRR1300451_2.fastq.stats.csv
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# 3050000: 4101809 tags, 56317 components.
writing results to file -> SRR1300451-comp-stats-2/3050000.SRR1300451_2.fastq.stats.csv
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# 3100000: 4149260 tags, 56047 components.
writing results to file -> SRR1300451-comp-stats-2/3100000.SRR1300451_2.fastq.stats.csv
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# 3150000: 4197022 tags, 55758 components.
writing results to file -> SRR1300451-comp-stats-2/3150000.SRR1300451_2.fastq.stats.csv
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# 3200000: 4243965 tags, 55454 components.
writing results to file -> SRR1300451-comp-stats-2/3200000.SRR1300451_2.fastq.stats.csv
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# 3250000: 4291492 tags, 55181 components.
writing results to file -> SRR1300451-comp-stats-2/3250000.SRR1300451_2.fastq.stats.csv
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# 3300000: 4338338 tags, 54893 components.
writing results to file -> SRR1300451-comp-stats-2/3300000.SRR1300451_2.fastq.stats.csv
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# 3350000: 4385451 tags, 54604 components.
writing results to file -> SRR1300451-comp-stats-2/3350000.SRR1300451_2.fastq.stats.csv
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# 3400000: 4431998 tags, 54365 components.
writing results to file -> SRR1300451-comp-stats-2/3400000.SRR1300451_2.fastq.stats.csv
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# 3450000: 4478151 tags, 54037 components.
writing results to file -> SRR1300451-comp-stats-2/3450000.SRR1300451_2.fastq.stats.csv
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# 3500000: 4523816 tags, 53709 components.
writing results to file -> SRR1300451-comp-stats-2/3500000.SRR1300451_2.fastq.stats.csv
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# 3550000: 4569115 tags, 53441 components.
writing results to file -> SRR1300451-comp-stats-2/3550000.SRR1300451_2.fastq.stats.csv
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# 3600000: 4613753 tags, 53152 components.
writing results to file -> SRR1300451-comp-stats-2/3600000.SRR1300451_2.fastq.stats.csv
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# 3650000: 4658098 tags, 52853 components.
writing results to file -> SRR1300451-comp-stats-2/3650000.SRR1300451_2.fastq.stats.csv
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# 3700000: 4702707 tags, 52618 components.
writing results to file -> SRR1300451-comp-stats-2/3700000.SRR1300451_2.fastq.stats.csv
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# 3750000: 4746498 tags, 52386 components.
writing results to file -> SRR1300451-comp-stats-2/3750000.SRR1300451_2.fastq.stats.csv
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# 3800000: 4790769 tags, 52193 components.
writing results to file -> SRR1300451-comp-stats-2/3800000.SRR1300451_2.fastq.stats.csv
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# 3850000: 4834225 tags, 51909 components.
writing results to file -> SRR1300451-comp-stats-2/3850000.SRR1300451_2.fastq.stats.csv
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# 3900000: 4877709 tags, 51640 components.
writing results to file -> SRR1300451-comp-stats-2/3900000.SRR1300451_2.fastq.stats.csv
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# 3950000: 4920652 tags, 51334 components.
writing results to file -> SRR1300451-comp-stats-2/3950000.SRR1300451_2.fastq.stats.csv
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# 4000000: 4963472 tags, 51098 components.
writing results to file -> SRR1300451-comp-stats-2/4000000.SRR1300451_2.fastq.stats.csv
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# 4050000: 5006357 tags, 50800 components.
writing results to file -> SRR1300451-comp-stats-2/4050000.SRR1300451_2.fastq.stats.csv
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# 4100000: 5049465 tags, 50617 components.
writing results to file -> SRR1300451-comp-stats-2/4100000.SRR1300451_2.fastq.stats.csv
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# 4150000: 5091935 tags, 50362 components.
writing results to file -> SRR1300451-comp-stats-2/4150000.SRR1300451_2.fastq.stats.csv
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# 4200000: 5134225 tags, 50075 components.
writing results to file -> SRR1300451-comp-stats-2/4200000.SRR1300451_2.fastq.stats.csv
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# 4250000: 5176233 tags, 49795 components.
writing results to file -> SRR1300451-comp-stats-2/4250000.SRR1300451_2.fastq.stats.csv
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# 4300000: 5218566 tags, 49561 components.
writing results to file -> SRR1300451-comp-stats-2/4300000.SRR1300451_2.fastq.stats.csv
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# 4350000: 5259862 tags, 49360 components.
writing results to file -> SRR1300451-comp-stats-2/4350000.SRR1300451_2.fastq.stats.csv
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# 4400000: 5300671 tags, 49086 components.
writing results to file -> SRR1300451-comp-stats-2/4400000.SRR1300451_2.fastq.stats.csv
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# 4450000: 5341596 tags, 48883 components.
writing results to file -> SRR1300451-comp-stats-2/4450000.SRR1300451_2.fastq.stats.csv
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# 4500000: 5382150 tags, 48615 components.
writing results to file -> SRR1300451-comp-stats-2/4500000.SRR1300451_2.fastq.stats.csv
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# 4550000: 5422934 tags, 48392 components.
writing results to file -> SRR1300451-comp-stats-2/4550000.SRR1300451_2.fastq.stats.csv
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# 4600000: 5463499 tags, 48115 components.
writing results to file -> SRR1300451-comp-stats-2/4600000.SRR1300451_2.fastq.stats.csv
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# 4650000: 5503385 tags, 47849 components.
writing results to file -> SRR1300451-comp-stats-2/4650000.SRR1300451_2.fastq.stats.csv
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# 4700000: 5543495 tags, 47616 components.
writing results to file -> SRR1300451-comp-stats-2/4700000.SRR1300451_2.fastq.stats.csv
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# 4750000: 5583434 tags, 47407 components.
writing results to file -> SRR1300451-comp-stats-2/4750000.SRR1300451_2.fastq.stats.csv
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# 4800000: 5623129 tags, 47214 components.
writing results to file -> SRR1300451-comp-stats-2/4800000.SRR1300451_2.fastq.stats.csv
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# 4850000: 5662804 tags, 46959 components.
writing results to file -> SRR1300451-comp-stats-2/4850000.SRR1300451_2.fastq.stats.csv
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# 4900000: 5701908 tags, 46755 components.
writing results to file -> SRR1300451-comp-stats-2/4900000.SRR1300451_2.fastq.stats.csv
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# 4950000: 5740758 tags, 46551 components.
writing results to file -> SRR1300451-comp-stats-2/4950000.SRR1300451_2.fastq.stats.csv
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# 5000000: 5779448 tags, 46346 components.
writing results to file -> SRR1300451-comp-stats-2/5000000.SRR1300451_2.fastq.stats.csv
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# 5050000: 5818398 tags, 46116 components.
writing results to file -> SRR1300451-comp-stats-2/5050000.SRR1300451_2.fastq.stats.csv
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# 5100000: 5856852 tags, 45905 components.
writing results to file -> SRR1300451-comp-stats-2/5100000.SRR1300451_2.fastq.stats.csv
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# 5150000: 5895057 tags, 45723 components.
writing results to file -> SRR1300451-comp-stats-2/5150000.SRR1300451_2.fastq.stats.csv
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# 5200000: 5933198 tags, 45498 components.
writing results to file -> SRR1300451-comp-stats-2/5200000.SRR1300451_2.fastq.stats.csv
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# 5250000: 5971095 tags, 45278 components.
writing results to file -> SRR1300451-comp-stats-2/5250000.SRR1300451_2.fastq.stats.csv
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# 5300000: 6009216 tags, 45101 components.
writing results to file -> SRR1300451-comp-stats-2/5300000.SRR1300451_2.fastq.stats.csv
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# 5350000: 6047054 tags, 44864 components.
writing results to file -> SRR1300451-comp-stats-2/5350000.SRR1300451_2.fastq.stats.csv
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# 5400000: 6084742 tags, 44673 components.
writing results to file -> SRR1300451-comp-stats-2/5400000.SRR1300451_2.fastq.stats.csv
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# 5450000: 6121805 tags, 44483 components.
writing results to file -> SRR1300451-comp-stats-2/5450000.SRR1300451_2.fastq.stats.csv
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# 5500000: 6158703 tags, 44336 components.
writing results to file -> SRR1300451-comp-stats-2/5500000.SRR1300451_2.fastq.stats.csv
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# 5550000: 6195943 tags, 44161 components.
writing results to file -> SRR1300451-comp-stats-2/5550000.SRR1300451_2.fastq.stats.csv
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# 5600000: 6233383 tags, 43940 components.
writing results to file -> SRR1300451-comp-stats-2/5600000.SRR1300451_2.fastq.stats.csv
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# 5650000: 6270244 tags, 43707 components.
writing results to file -> SRR1300451-comp-stats-2/5650000.SRR1300451_2.fastq.stats.csv
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# 5700000: 6307058 tags, 43544 components.
writing results to file -> SRR1300451-comp-stats-2/5700000.SRR1300451_2.fastq.stats.csv
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# 5750000: 6343273 tags, 43337 components.
writing results to file -> SRR1300451-comp-stats-2/5750000.SRR1300451_2.fastq.stats.csv
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# 5800000: 6379863 tags, 43136 components.
writing results to file -> SRR1300451-comp-stats-2/5800000.SRR1300451_2.fastq.stats.csv
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# 5850000: 6416234 tags, 42970 components.
writing results to file -> SRR1300451-comp-stats-2/5850000.SRR1300451_2.fastq.stats.csv
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# 5900000: 6452217 tags, 42812 components.
writing results to file -> SRR1300451-comp-stats-2/5900000.SRR1300451_2.fastq.stats.csv
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# 5950000: 6487991 tags, 42628 components.
writing results to file -> SRR1300451-comp-stats-2/5950000.SRR1300451_2.fastq.stats.csv
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# 6000000: 6523608 tags, 42439 components.
writing results to file -> SRR1300451-comp-stats-2/6000000.SRR1300451_2.fastq.stats.csv
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# 6050000: 6558965 tags, 42252 components.
writing results to file -> SRR1300451-comp-stats-2/6050000.SRR1300451_2.fastq.stats.csv
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# 6100000: 6594298 tags, 42101 components.
writing results to file -> SRR1300451-comp-stats-2/6100000.SRR1300451_2.fastq.stats.csv
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# 6150000: 6629502 tags, 41912 components.
writing results to file -> SRR1300451-comp-stats-2/6150000.SRR1300451_2.fastq.stats.csv
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# 6200000: 6664506 tags, 41759 components.
writing results to file -> SRR1300451-comp-stats-2/6200000.SRR1300451_2.fastq.stats.csv
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# 6250000: 6699859 tags, 41610 components.
writing results to file -> SRR1300451-comp-stats-2/6250000.SRR1300451_2.fastq.stats.csv
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# 6300000: 6734855 tags, 41437 components.
writing results to file -> SRR1300451-comp-stats-2/6300000.SRR1300451_2.fastq.stats.csv
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# 6350000: 6769911 tags, 41276 components.
writing results to file -> SRR1300451-comp-stats-2/6350000.SRR1300451_2.fastq.stats.csv
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# 6400000: 6804911 tags, 41124 components.
writing results to file -> SRR1300451-comp-stats-2/6400000.SRR1300451_2.fastq.stats.csv
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# 6450000: 6839864 tags, 40973 components.
writing results to file -> SRR1300451-comp-stats-2/6450000.SRR1300451_2.fastq.stats.csv
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# 6500000: 6874346 tags, 40819 components.
writing results to file -> SRR1300451-comp-stats-2/6500000.SRR1300451_2.fastq.stats.csv
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# 6550000: 6908249 tags, 40676 components.
writing results to file -> SRR1300451-comp-stats-2/6550000.SRR1300451_2.fastq.stats.csv
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# 6600000: 6942579 tags, 40499 components.
writing results to file -> SRR1300451-comp-stats-2/6600000.SRR1300451_2.fastq.stats.csv
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# 6650000: 6976945 tags, 40346 components.
writing results to file -> SRR1300451-comp-stats-2/6650000.SRR1300451_2.fastq.stats.csv
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# 6700000: 7011014 tags, 40165 components.
writing results to file -> SRR1300451-comp-stats-2/6700000.SRR1300451_2.fastq.stats.csv
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# 6750000: 7044589 tags, 40019 components.
writing results to file -> SRR1300451-comp-stats-2/6750000.SRR1300451_2.fastq.stats.csv
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# 6800000: 7078731 tags, 39860 components.
writing results to file -> SRR1300451-comp-stats-2/6800000.SRR1300451_2.fastq.stats.csv
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# 6850000: 7112538 tags, 39728 components.
writing results to file -> SRR1300451-comp-stats-2/6850000.SRR1300451_2.fastq.stats.csv
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# 6900000: 7145591 tags, 39571 components.
writing results to file -> SRR1300451-comp-stats-2/6900000.SRR1300451_2.fastq.stats.csv
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# 6950000: 7178913 tags, 39440 components.
writing results to file -> SRR1300451-comp-stats-2/6950000.SRR1300451_2.fastq.stats.csv
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# 7000000: 7212517 tags, 39312 components.
writing results to file -> SRR1300451-comp-stats-2/7000000.SRR1300451_2.fastq.stats.csv
7001000...
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# 7050000: 7245863 tags, 39158 components.
writing results to file -> SRR1300451-comp-stats-2/7050000.SRR1300451_2.fastq.stats.csv
7051000...
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# 7100000: 7278519 tags, 39053 components.
writing results to file -> SRR1300451-comp-stats-2/7100000.SRR1300451_2.fastq.stats.csv
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# 7150000: 7311441 tags, 38943 components.
writing results to file -> SRR1300451-comp-stats-2/7150000.SRR1300451_2.fastq.stats.csv
7151000...
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# 7200000: 7344463 tags, 38785 components.
writing results to file -> SRR1300451-comp-stats-2/7200000.SRR1300451_2.fastq.stats.csv
7201000...
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# 7250000: 7377693 tags, 38658 components.
writing results to file -> SRR1300451-comp-stats-2/7250000.SRR1300451_2.fastq.stats.csv
7251000...
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# 7300000: 7410216 tags, 38545 components.
writing results to file -> SRR1300451-comp-stats-2/7300000.SRR1300451_2.fastq.stats.csv
7301000...
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# 7350000: 7442887 tags, 38449 components.
writing results to file -> SRR1300451-comp-stats-2/7350000.SRR1300451_2.fastq.stats.csv
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# 7400000: 7474910 tags, 38340 components.
writing results to file -> SRR1300451-comp-stats-2/7400000.SRR1300451_2.fastq.stats.csv
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# 7450000: 7507621 tags, 38202 components.
writing results to file -> SRR1300451-comp-stats-2/7450000.SRR1300451_2.fastq.stats.csv
7451000...
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# 7500000: 7539226 tags, 38070 components.
writing results to file -> SRR1300451-comp-stats-2/7500000.SRR1300451_2.fastq.stats.csv
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# 7550000: 7571677 tags, 37939 components.
writing results to file -> SRR1300451-comp-stats-2/7550000.SRR1300451_2.fastq.stats.csv
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# 7600000: 7603606 tags, 37848 components.
writing results to file -> SRR1300451-comp-stats-2/7600000.SRR1300451_2.fastq.stats.csv
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# 7650000: 7635253 tags, 37715 components.
writing results to file -> SRR1300451-comp-stats-2/7650000.SRR1300451_2.fastq.stats.csv
7651000...
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# 7700000: 7666968 tags, 37612 components.
writing results to file -> SRR1300451-comp-stats-2/7700000.SRR1300451_2.fastq.stats.csv
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# 7750000: 7699071 tags, 37495 components.
writing results to file -> SRR1300451-comp-stats-2/7750000.SRR1300451_2.fastq.stats.csv
7751000...
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# 7800000: 7730762 tags, 37344 components.
writing results to file -> SRR1300451-comp-stats-2/7800000.SRR1300451_2.fastq.stats.csv
7801000...
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# 7850000: 7762241 tags, 37257 components.
writing results to file -> SRR1300451-comp-stats-2/7850000.SRR1300451_2.fastq.stats.csv
7851000...
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# 7900000: 7793233 tags, 37131 components.
writing results to file -> SRR1300451-comp-stats-2/7900000.SRR1300451_2.fastq.stats.csv
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# 7950000: 7824580 tags, 37007 components.
writing results to file -> SRR1300451-comp-stats-2/7950000.SRR1300451_2.fastq.stats.csv
7951000...
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# 8000000: 7855974 tags, 36900 components.
writing results to file -> SRR1300451-comp-stats-2/8000000.SRR1300451_2.fastq.stats.csv
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# 8050000: 7887091 tags, 36768 components.
writing results to file -> SRR1300451-comp-stats-2/8050000.SRR1300451_2.fastq.stats.csv
8051000...
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8100000...
# 8100000: 7917739 tags, 36666 components.
writing results to file -> SRR1300451-comp-stats-2/8100000.SRR1300451_2.fastq.stats.csv
8101000...
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8150000...
# 8150000: 7948394 tags, 36594 components.
writing results to file -> SRR1300451-comp-stats-2/8150000.SRR1300451_2.fastq.stats.csv
8151000...
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8153000...
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# 8200000: 7979620 tags, 36493 components.
writing results to file -> SRR1300451-comp-stats-2/8200000.SRR1300451_2.fastq.stats.csv
8201000...
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# 8250000: 8010273 tags, 36395 components.
writing results to file -> SRR1300451-comp-stats-2/8250000.SRR1300451_2.fastq.stats.csv
8251000...
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8300000...
# 8300000: 8040593 tags, 36293 components.
writing results to file -> SRR1300451-comp-stats-2/8300000.SRR1300451_2.fastq.stats.csv
8301000...
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# 8350000: 8071306 tags, 36189 components.
writing results to file -> SRR1300451-comp-stats-2/8350000.SRR1300451_2.fastq.stats.csv
8351000...
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8400000...
# 8400000: 8101524 tags, 36099 components.
writing results to file -> SRR1300451-comp-stats-2/8400000.SRR1300451_2.fastq.stats.csv
8401000...
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# 8450000: 8132064 tags, 36010 components.
writing results to file -> SRR1300451-comp-stats-2/8450000.SRR1300451_2.fastq.stats.csv
8451000...
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8500000...
# 8500000: 8162268 tags, 35914 components.
writing results to file -> SRR1300451-comp-stats-2/8500000.SRR1300451_2.fastq.stats.csv
8501000...
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# 8550000: 8192228 tags, 35807 components.
writing results to file -> SRR1300451-comp-stats-2/8550000.SRR1300451_2.fastq.stats.csv
8551000...
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# 8600000: 8222399 tags, 35729 components.
writing results to file -> SRR1300451-comp-stats-2/8600000.SRR1300451_2.fastq.stats.csv
8601000...
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# 8650000: 8252347 tags, 35629 components.
writing results to file -> SRR1300451-comp-stats-2/8650000.SRR1300451_2.fastq.stats.csv
8651000...
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8700000...
# 8700000: 8282572 tags, 35512 components.
writing results to file -> SRR1300451-comp-stats-2/8700000.SRR1300451_2.fastq.stats.csv
8701000...
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8750000...
# 8750000: 8312421 tags, 35433 components.
writing results to file -> SRR1300451-comp-stats-2/8750000.SRR1300451_2.fastq.stats.csv
8751000...
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# 8800000: 8342367 tags, 35337 components.
writing results to file -> SRR1300451-comp-stats-2/8800000.SRR1300451_2.fastq.stats.csv
8801000...
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# 8850000: 8371753 tags, 35252 components.
writing results to file -> SRR1300451-comp-stats-2/8850000.SRR1300451_2.fastq.stats.csv
8851000...
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# 8900000: 8400782 tags, 35166 components.
writing results to file -> SRR1300451-comp-stats-2/8900000.SRR1300451_2.fastq.stats.csv
8901000...
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# 8950000: 8429825 tags, 35068 components.
writing results to file -> SRR1300451-comp-stats-2/8950000.SRR1300451_2.fastq.stats.csv
8951000...
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9000000...
# 9000000: 8459514 tags, 34966 components.
writing results to file -> SRR1300451-comp-stats-2/9000000.SRR1300451_2.fastq.stats.csv
9001000...
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# 9050000: 8488863 tags, 34860 components.
writing results to file -> SRR1300451-comp-stats-2/9050000.SRR1300451_2.fastq.stats.csv
9051000...
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9100000...
# 9100000: 8517327 tags, 34782 components.
writing results to file -> SRR1300451-comp-stats-2/9100000.SRR1300451_2.fastq.stats.csv
9101000...
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9150000...
# 9150000: 8546340 tags, 34687 components.
writing results to file -> SRR1300451-comp-stats-2/9150000.SRR1300451_2.fastq.stats.csv
9151000...
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# 9200000: 8575237 tags, 34595 components.
writing results to file -> SRR1300451-comp-stats-2/9200000.SRR1300451_2.fastq.stats.csv
9201000...
9202000...
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9250000...
# 9250000: 8603924 tags, 34464 components.
writing results to file -> SRR1300451-comp-stats-2/9250000.SRR1300451_2.fastq.stats.csv
9251000...
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9300000...
# 9300000: 8632197 tags, 34378 components.
writing results to file -> SRR1300451-comp-stats-2/9300000.SRR1300451_2.fastq.stats.csv
9301000...
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9350000...
# 9350000: 8660405 tags, 34285 components.
writing results to file -> SRR1300451-comp-stats-2/9350000.SRR1300451_2.fastq.stats.csv
9351000...
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9400000...
# 9400000: 8689214 tags, 34200 components.
writing results to file -> SRR1300451-comp-stats-2/9400000.SRR1300451_2.fastq.stats.csv
9401000...
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# 9450000: 8717462 tags, 34117 components.
writing results to file -> SRR1300451-comp-stats-2/9450000.SRR1300451_2.fastq.stats.csv
9451000...
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9500000...
# 9500000: 8745562 tags, 34002 components.
writing results to file -> SRR1300451-comp-stats-2/9500000.SRR1300451_2.fastq.stats.csv
9501000...
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# 9550000: 8773679 tags, 33931 components.
writing results to file -> SRR1300451-comp-stats-2/9550000.SRR1300451_2.fastq.stats.csv
9551000...
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9600000...
# 9600000: 8801756 tags, 33876 components.
writing results to file -> SRR1300451-comp-stats-2/9600000.SRR1300451_2.fastq.stats.csv
9601000...
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# 9650000: 8829917 tags, 33810 components.
writing results to file -> SRR1300451-comp-stats-2/9650000.SRR1300451_2.fastq.stats.csv
9651000...
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# 9700000: 8857854 tags, 33704 components.
writing results to file -> SRR1300451-comp-stats-2/9700000.SRR1300451_2.fastq.stats.csv
9701000...
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9750000...
# 9750000: 8885609 tags, 33601 components.
writing results to file -> SRR1300451-comp-stats-2/9750000.SRR1300451_2.fastq.stats.csv
9751000...
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9800000...
# 9800000: 8913592 tags, 33540 components.
writing results to file -> SRR1300451-comp-stats-2/9800000.SRR1300451_2.fastq.stats.csv
9801000...
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9850000...
# 9850000: 8941300 tags, 33448 components.
writing results to file -> SRR1300451-comp-stats-2/9850000.SRR1300451_2.fastq.stats.csv
9851000...
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9900000...
# 9900000: 8969263 tags, 33423 components.
writing results to file -> SRR1300451-comp-stats-2/9900000.SRR1300451_2.fastq.stats.csv
9901000...
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# 9950000: 8996726 tags, 33361 components.
writing results to file -> SRR1300451-comp-stats-2/9950000.SRR1300451_2.fastq.stats.csv
9951000...
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9999000...
10000000...
# 10000000: 9024301 tags, 33280 components.
writing results to file -> SRR1300451-comp-stats-2/10000000.SRR1300451_2.fastq.stats.csv
10001000...
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# 10050000: 9051727 tags, 33192 components.
writing results to file -> SRR1300451-comp-stats-2/10050000.SRR1300451_2.fastq.stats.csv
10051000...
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10100000...
# 10100000: 9079446 tags, 33108 components.
writing results to file -> SRR1300451-comp-stats-2/10100000.SRR1300451_2.fastq.stats.csv
10101000...
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# 10150000: 9107047 tags, 33024 components.
writing results to file -> SRR1300451-comp-stats-2/10150000.SRR1300451_2.fastq.stats.csv
10151000...
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# 10200000: 9134763 tags, 32970 components.
writing results to file -> SRR1300451-comp-stats-2/10200000.SRR1300451_2.fastq.stats.csv
10201000...
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# 10250000: 9161921 tags, 32916 components.
writing results to file -> SRR1300451-comp-stats-2/10250000.SRR1300451_2.fastq.stats.csv
10251000...
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# 10300000: 9189080 tags, 32845 components.
writing results to file -> SRR1300451-comp-stats-2/10300000.SRR1300451_2.fastq.stats.csv
10301000...
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# 10350000: 9215639 tags, 32795 components.
writing results to file -> SRR1300451-comp-stats-2/10350000.SRR1300451_2.fastq.stats.csv
10351000...
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# 10400000: 9242767 tags, 32753 components.
writing results to file -> SRR1300451-comp-stats-2/10400000.SRR1300451_2.fastq.stats.csv
10401000...
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# 10450000: 9269832 tags, 32677 components.
writing results to file -> SRR1300451-comp-stats-2/10450000.SRR1300451_2.fastq.stats.csv
10451000...
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# 10500000: 9296721 tags, 32620 components.
writing results to file -> SRR1300451-comp-stats-2/10500000.SRR1300451_2.fastq.stats.csv
10501000...
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# 10550000: 9323570 tags, 32533 components.
writing results to file -> SRR1300451-comp-stats-2/10550000.SRR1300451_2.fastq.stats.csv
10551000...
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10600000...
# 10600000: 9350564 tags, 32483 components.
writing results to file -> SRR1300451-comp-stats-2/10600000.SRR1300451_2.fastq.stats.csv
10601000...
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# 10650000: 9377310 tags, 32435 components.
writing results to file -> SRR1300451-comp-stats-2/10650000.SRR1300451_2.fastq.stats.csv
10651000...
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# 10700000: 9404263 tags, 32351 components.
writing results to file -> SRR1300451-comp-stats-2/10700000.SRR1300451_2.fastq.stats.csv
10701000...
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# 10750000: 9430994 tags, 32305 components.
writing results to file -> SRR1300451-comp-stats-2/10750000.SRR1300451_2.fastq.stats.csv
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# 10800000: 9457744 tags, 32272 components.
writing results to file -> SRR1300451-comp-stats-2/10800000.SRR1300451_2.fastq.stats.csv
10801000...
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# 10850000: 9484348 tags, 32234 components.
writing results to file -> SRR1300451-comp-stats-2/10850000.SRR1300451_2.fastq.stats.csv
10851000...
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# 10900000: 9511219 tags, 32179 components.
writing results to file -> SRR1300451-comp-stats-2/10900000.SRR1300451_2.fastq.stats.csv
10901000...
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# 10950000: 9537641 tags, 32081 components.
writing results to file -> SRR1300451-comp-stats-2/10950000.SRR1300451_2.fastq.stats.csv
10951000...
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# 11000000: 9564188 tags, 32055 components.
writing results to file -> SRR1300451-comp-stats-2/11000000.SRR1300451_2.fastq.stats.csv
11001000...
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# 11050000: 9590340 tags, 31972 components.
writing results to file -> SRR1300451-comp-stats-2/11050000.SRR1300451_2.fastq.stats.csv
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# 11100000: 9616196 tags, 31898 components.
writing results to file -> SRR1300451-comp-stats-2/11100000.SRR1300451_2.fastq.stats.csv
11101000...
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# 11150000: 9642176 tags, 31845 components.
writing results to file -> SRR1300451-comp-stats-2/11150000.SRR1300451_2.fastq.stats.csv
11151000...
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# 11200000: 9667914 tags, 31784 components.
writing results to file -> SRR1300451-comp-stats-2/11200000.SRR1300451_2.fastq.stats.csv
11201000...
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# 11250000: 9693934 tags, 31746 components.
writing results to file -> SRR1300451-comp-stats-2/11250000.SRR1300451_2.fastq.stats.csv
11251000...
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# 11300000: 9719791 tags, 31693 components.
writing results to file -> SRR1300451-comp-stats-2/11300000.SRR1300451_2.fastq.stats.csv
11301000...
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# 11350000: 9745543 tags, 31631 components.
writing results to file -> SRR1300451-comp-stats-2/11350000.SRR1300451_2.fastq.stats.csv
11351000...
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# 11400000: 9771068 tags, 31561 components.
writing results to file -> SRR1300451-comp-stats-2/11400000.SRR1300451_2.fastq.stats.csv
11401000...
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# 11450000: 9796499 tags, 31501 components.
writing results to file -> SRR1300451-comp-stats-2/11450000.SRR1300451_2.fastq.stats.csv
11451000...
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# 11500000: 9822091 tags, 31443 components.
writing results to file -> SRR1300451-comp-stats-2/11500000.SRR1300451_2.fastq.stats.csv
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# 11550000: 9847402 tags, 31388 components.
writing results to file -> SRR1300451-comp-stats-2/11550000.SRR1300451_2.fastq.stats.csv
11551000...
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# 11600000: 9872796 tags, 31329 components.
writing results to file -> SRR1300451-comp-stats-2/11600000.SRR1300451_2.fastq.stats.csv
11601000...
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# 11650000: 9898017 tags, 31272 components.
writing results to file -> SRR1300451-comp-stats-2/11650000.SRR1300451_2.fastq.stats.csv
11651000...
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# 11700000: 9923870 tags, 31240 components.
writing results to file -> SRR1300451-comp-stats-2/11700000.SRR1300451_2.fastq.stats.csv
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# 11750000: 9949403 tags, 31199 components.
writing results to file -> SRR1300451-comp-stats-2/11750000.SRR1300451_2.fastq.stats.csv
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11800000...
# 11800000: 9974389 tags, 31165 components.
writing results to file -> SRR1300451-comp-stats-2/11800000.SRR1300451_2.fastq.stats.csv
11801000...
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# 11850000: 9999758 tags, 31111 components.
writing results to file -> SRR1300451-comp-stats-2/11850000.SRR1300451_2.fastq.stats.csv
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11900000...
# 11900000: 10025160 tags, 31055 components.
writing results to file -> SRR1300451-comp-stats-2/11900000.SRR1300451_2.fastq.stats.csv
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# 11950000: 10050412 tags, 31027 components.
writing results to file -> SRR1300451-comp-stats-2/11950000.SRR1300451_2.fastq.stats.csv
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12000000...
# 12000000: 10075675 tags, 30975 components.
writing results to file -> SRR1300451-comp-stats-2/12000000.SRR1300451_2.fastq.stats.csv
12001000...
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# 12050000: 10101318 tags, 30915 components.
writing results to file -> SRR1300451-comp-stats-2/12050000.SRR1300451_2.fastq.stats.csv
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# 12100000: 10126350 tags, 30876 components.
writing results to file -> SRR1300451-comp-stats-2/12100000.SRR1300451_2.fastq.stats.csv
12101000...
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# 12150000: 10151075 tags, 30818 components.
writing results to file -> SRR1300451-comp-stats-2/12150000.SRR1300451_2.fastq.stats.csv
12151000...
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# 12200000: 10175790 tags, 30734 components.
writing results to file -> SRR1300451-comp-stats-2/12200000.SRR1300451_2.fastq.stats.csv
12201000...
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# 12250000: 10200700 tags, 30712 components.
writing results to file -> SRR1300451-comp-stats-2/12250000.SRR1300451_2.fastq.stats.csv
12251000...
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# 12300000: 10225479 tags, 30672 components.
writing results to file -> SRR1300451-comp-stats-2/12300000.SRR1300451_2.fastq.stats.csv
12301000...
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# 12350000: 10250099 tags, 30632 components.
writing results to file -> SRR1300451-comp-stats-2/12350000.SRR1300451_2.fastq.stats.csv
12351000...
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# 12400000: 10274874 tags, 30592 components.
writing results to file -> SRR1300451-comp-stats-2/12400000.SRR1300451_2.fastq.stats.csv
12401000...
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# 12450000: 10299526 tags, 30542 components.
writing results to file -> SRR1300451-comp-stats-2/12450000.SRR1300451_2.fastq.stats.csv
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# 12500000: 10324168 tags, 30482 components.
writing results to file -> SRR1300451-comp-stats-2/12500000.SRR1300451_2.fastq.stats.csv
12501000...
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# 12550000: 10348997 tags, 30433 components.
writing results to file -> SRR1300451-comp-stats-2/12550000.SRR1300451_2.fastq.stats.csv
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# 12600000: 10373594 tags, 30397 components.
writing results to file -> SRR1300451-comp-stats-2/12600000.SRR1300451_2.fastq.stats.csv
12601000...
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# 12650000: 10397762 tags, 30334 components.
writing results to file -> SRR1300451-comp-stats-2/12650000.SRR1300451_2.fastq.stats.csv
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# 12700000: 10422122 tags, 30285 components.
writing results to file -> SRR1300451-comp-stats-2/12700000.SRR1300451_2.fastq.stats.csv
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# 12750000: 10446106 tags, 30240 components.
writing results to file -> SRR1300451-comp-stats-2/12750000.SRR1300451_2.fastq.stats.csv
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# 12800000: 10470234 tags, 30205 components.
writing results to file -> SRR1300451-comp-stats-2/12800000.SRR1300451_2.fastq.stats.csv
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# 12850000: 10494492 tags, 30170 components.
writing results to file -> SRR1300451-comp-stats-2/12850000.SRR1300451_2.fastq.stats.csv
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# 12900000: 10518441 tags, 30140 components.
writing results to file -> SRR1300451-comp-stats-2/12900000.SRR1300451_2.fastq.stats.csv
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# 12950000: 10542071 tags, 30094 components.
writing results to file -> SRR1300451-comp-stats-2/12950000.SRR1300451_2.fastq.stats.csv
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# 13000000: 10566211 tags, 30067 components.
writing results to file -> SRR1300451-comp-stats-2/13000000.SRR1300451_2.fastq.stats.csv
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# 13050000: 10590554 tags, 30022 components.
writing results to file -> SRR1300451-comp-stats-2/13050000.SRR1300451_2.fastq.stats.csv
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# 13100000: 10615314 tags, 29985 components.
writing results to file -> SRR1300451-comp-stats-2/13100000.SRR1300451_2.fastq.stats.csv
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# 13150000: 10639913 tags, 29937 components.
writing results to file -> SRR1300451-comp-stats-2/13150000.SRR1300451_2.fastq.stats.csv
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# 13200000: 10678071 tags, 29946 components.
writing results to file -> SRR1300451-comp-stats-2/13200000.SRR1300451_2.fastq.stats.csv
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# 13250000: 10703582 tags, 29913 components.
writing results to file -> SRR1300451-comp-stats-2/13250000.SRR1300451_2.fastq.stats.csv
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# 13300000: 10727992 tags, 29861 components.
writing results to file -> SRR1300451-comp-stats-2/13300000.SRR1300451_2.fastq.stats.csv
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# 13350000: 10751543 tags, 29819 components.
writing results to file -> SRR1300451-comp-stats-2/13350000.SRR1300451_2.fastq.stats.csv
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# 13400000: 10775236 tags, 29779 components.
writing results to file -> SRR1300451-comp-stats-2/13400000.SRR1300451_2.fastq.stats.csv
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# 13450000: 10809177 tags, 29767 components.
writing results to file -> SRR1300451-comp-stats-2/13450000.SRR1300451_2.fastq.stats.csv
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# 13500000: 10839830 tags, 29735 components.
writing results to file -> SRR1300451-comp-stats-2/13500000.SRR1300451_2.fastq.stats.csv
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# 13550000: 10867137 tags, 29727 components.
writing results to file -> SRR1300451-comp-stats-2/13550000.SRR1300451_2.fastq.stats.csv
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# 13600000: 10890355 tags, 29683 components.
writing results to file -> SRR1300451-comp-stats-2/13600000.SRR1300451_2.fastq.stats.csv
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# 13650000: 10913669 tags, 29645 components.
writing results to file -> SRR1300451-comp-stats-2/13650000.SRR1300451_2.fastq.stats.csv
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# 13700000: 10938932 tags, 29613 components.
writing results to file -> SRR1300451-comp-stats-2/13700000.SRR1300451_2.fastq.stats.csv
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# 13750000: 10963685 tags, 29557 components.
writing results to file -> SRR1300451-comp-stats-2/13750000.SRR1300451_2.fastq.stats.csv
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# 13800000: 10988162 tags, 29525 components.
writing results to file -> SRR1300451-comp-stats-2/13800000.SRR1300451_2.fastq.stats.csv
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# 13850000: 11011097 tags, 29494 components.
writing results to file -> SRR1300451-comp-stats-2/13850000.SRR1300451_2.fastq.stats.csv
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# 13900000: 11034076 tags, 29455 components.
writing results to file -> SRR1300451-comp-stats-2/13900000.SRR1300451_2.fastq.stats.csv
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# 13950000: 11059499 tags, 29404 components.
writing results to file -> SRR1300451-comp-stats-2/13950000.SRR1300451_2.fastq.stats.csv
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# 14000000: 11084965 tags, 29355 components.
writing results to file -> SRR1300451-comp-stats-2/14000000.SRR1300451_2.fastq.stats.csv
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# 14050000: 11109976 tags, 29333 components.
writing results to file -> SRR1300451-comp-stats-2/14050000.SRR1300451_2.fastq.stats.csv
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# 14100000: 11134008 tags, 29286 components.
writing results to file -> SRR1300451-comp-stats-2/14100000.SRR1300451_2.fastq.stats.csv
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# 14150000: 11160742 tags, 29262 components.
writing results to file -> SRR1300451-comp-stats-2/14150000.SRR1300451_2.fastq.stats.csv
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# 14200000: 11187687 tags, 29234 components.
writing results to file -> SRR1300451-comp-stats-2/14200000.SRR1300451_2.fastq.stats.csv
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# 14250000: 11210486 tags, 29217 components.
writing results to file -> SRR1300451-comp-stats-2/14250000.SRR1300451_2.fastq.stats.csv
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# 14300000: 11234750 tags, 29187 components.
writing results to file -> SRR1300451-comp-stats-2/14300000.SRR1300451_2.fastq.stats.csv
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# 14350000: 11257478 tags, 29148 components.
writing results to file -> SRR1300451-comp-stats-2/14350000.SRR1300451_2.fastq.stats.csv
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# 14400000: 11280443 tags, 29128 components.
writing results to file -> SRR1300451-comp-stats-2/14400000.SRR1300451_2.fastq.stats.csv
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# 14450000: 11303308 tags, 29080 components.
writing results to file -> SRR1300451-comp-stats-2/14450000.SRR1300451_2.fastq.stats.csv
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# 14500000: 11328286 tags, 29049 components.
writing results to file -> SRR1300451-comp-stats-2/14500000.SRR1300451_2.fastq.stats.csv
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# 14550000: 11350766 tags, 29022 components.
writing results to file -> SRR1300451-comp-stats-2/14550000.SRR1300451_2.fastq.stats.csv
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# 14600000: 11375835 tags, 28982 components.
writing results to file -> SRR1300451-comp-stats-2/14600000.SRR1300451_2.fastq.stats.csv
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# 14650000: 11401361 tags, 28972 components.
writing results to file -> SRR1300451-comp-stats-2/14650000.SRR1300451_2.fastq.stats.csv
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# 14700000: 11427552 tags, 28929 components.
writing results to file -> SRR1300451-comp-stats-2/14700000.SRR1300451_2.fastq.stats.csv
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# 14750000: 11449732 tags, 28897 components.
writing results to file -> SRR1300451-comp-stats-2/14750000.SRR1300451_2.fastq.stats.csv
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# 14800000: 11475570 tags, 28890 components.
writing results to file -> SRR1300451-comp-stats-2/14800000.SRR1300451_2.fastq.stats.csv
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# 14850000: 11497582 tags, 28837 components.
writing results to file -> SRR1300451-comp-stats-2/14850000.SRR1300451_2.fastq.stats.csv
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# 14900000: 11519504 tags, 28816 components.
writing results to file -> SRR1300451-comp-stats-2/14900000.SRR1300451_2.fastq.stats.csv
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# 14950000: 11541932 tags, 28787 components.
writing results to file -> SRR1300451-comp-stats-2/14950000.SRR1300451_2.fastq.stats.csv
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# 15000000: 11564365 tags, 28756 components.
writing results to file -> SRR1300451-comp-stats-2/15000000.SRR1300451_2.fastq.stats.csv
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# 15050000: 11586613 tags, 28721 components.
writing results to file -> SRR1300451-comp-stats-2/15050000.SRR1300451_2.fastq.stats.csv
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# 15100000: 11615303 tags, 28702 components.
writing results to file -> SRR1300451-comp-stats-2/15100000.SRR1300451_2.fastq.stats.csv
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# 15150000: 11640306 tags, 28670 components.
writing results to file -> SRR1300451-comp-stats-2/15150000.SRR1300451_2.fastq.stats.csv
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# 15200000: 11662313 tags, 28637 components.
writing results to file -> SRR1300451-comp-stats-2/15200000.SRR1300451_2.fastq.stats.csv
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# 15250000: 11687518 tags, 28599 components.
writing results to file -> SRR1300451-comp-stats-2/15250000.SRR1300451_2.fastq.stats.csv
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# 15300000: 11710783 tags, 28565 components.
writing results to file -> SRR1300451-comp-stats-2/15300000.SRR1300451_2.fastq.stats.csv
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# 15350000: 11732341 tags, 28553 components.
writing results to file -> SRR1300451-comp-stats-2/15350000.SRR1300451_2.fastq.stats.csv
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# 15400000: 11761804 tags, 28531 components.
writing results to file -> SRR1300451-comp-stats-2/15400000.SRR1300451_2.fastq.stats.csv
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# 15450000: 11794152 tags, 28501 components.
writing results to file -> SRR1300451-comp-stats-2/15450000.SRR1300451_2.fastq.stats.csv
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# 15500000: 11820622 tags, 28484 components.
writing results to file -> SRR1300451-comp-stats-2/15500000.SRR1300451_2.fastq.stats.csv
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# 15550000: 11852232 tags, 28494 components.
writing results to file -> SRR1300451-comp-stats-2/15550000.SRR1300451_2.fastq.stats.csv
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# 15600000: 11879135 tags, 28470 components.
writing results to file -> SRR1300451-comp-stats-2/15600000.SRR1300451_2.fastq.stats.csv
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# 15650000: 11906905 tags, 28437 components.
writing results to file -> SRR1300451-comp-stats-2/15650000.SRR1300451_2.fastq.stats.csv
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# 15700000: 11946112 tags, 28429 components.
writing results to file -> SRR1300451-comp-stats-2/15700000.SRR1300451_2.fastq.stats.csv
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# 15750000: 11977454 tags, 28426 components.
writing results to file -> SRR1300451-comp-stats-2/15750000.SRR1300451_2.fastq.stats.csv
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# 15800000: 12010967 tags, 28396 components.
writing results to file -> SRR1300451-comp-stats-2/15800000.SRR1300451_2.fastq.stats.csv
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# 15850000: 12035153 tags, 28392 components.
writing results to file -> SRR1300451-comp-stats-2/15850000.SRR1300451_2.fastq.stats.csv
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# 15900000: 12059738 tags, 28380 components.
writing results to file -> SRR1300451-comp-stats-2/15900000.SRR1300451_2.fastq.stats.csv
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# 15950000: 12091728 tags, 28385 components.
writing results to file -> SRR1300451-comp-stats-2/15950000.SRR1300451_2.fastq.stats.csv
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# 16000000: 12124970 tags, 28367 components.
writing results to file -> SRR1300451-comp-stats-2/16000000.SRR1300451_2.fastq.stats.csv
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# 16050000: 12154674 tags, 28336 components.
writing results to file -> SRR1300451-comp-stats-2/16050000.SRR1300451_2.fastq.stats.csv
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# 16100000: 12184616 tags, 28302 components.
writing results to file -> SRR1300451-comp-stats-2/16100000.SRR1300451_2.fastq.stats.csv
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# 16150000: 12213926 tags, 28292 components.
writing results to file -> SRR1300451-comp-stats-2/16150000.SRR1300451_2.fastq.stats.csv
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# 16200000: 12262175 tags, 28318 components.
writing results to file -> SRR1300451-comp-stats-2/16200000.SRR1300451_2.fastq.stats.csv
16201000...
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# 16250000: 12298327 tags, 28337 components.
writing results to file -> SRR1300451-comp-stats-2/16250000.SRR1300451_2.fastq.stats.csv
16251000...
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# 16300000: 12345022 tags, 28362 components.
writing results to file -> SRR1300451-comp-stats-2/16300000.SRR1300451_2.fastq.stats.csv
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# 16350000: 12380308 tags, 28370 components.
writing results to file -> SRR1300451-comp-stats-2/16350000.SRR1300451_2.fastq.stats.csv
16351000...
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# 16400000: 12416922 tags, 28358 components.
writing results to file -> SRR1300451-comp-stats-2/16400000.SRR1300451_2.fastq.stats.csv
16401000...
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# 16450000: 12445448 tags, 28340 components.
writing results to file -> SRR1300451-comp-stats-2/16450000.SRR1300451_2.fastq.stats.csv
16451000...
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# 16500000: 12477055 tags, 28322 components.
writing results to file -> SRR1300451-comp-stats-2/16500000.SRR1300451_2.fastq.stats.csv
16501000...
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# 16550000: 12511592 tags, 28297 components.
writing results to file -> SRR1300451-comp-stats-2/16550000.SRR1300451_2.fastq.stats.csv
16551000...
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# 16600000: 12542016 tags, 28297 components.
writing results to file -> SRR1300451-comp-stats-2/16600000.SRR1300451_2.fastq.stats.csv
16601000...
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# 16650000: 12567965 tags, 28257 components.
writing results to file -> SRR1300451-comp-stats-2/16650000.SRR1300451_2.fastq.stats.csv
16651000...
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# 16700000: 12600167 tags, 28258 components.
writing results to file -> SRR1300451-comp-stats-2/16700000.SRR1300451_2.fastq.stats.csv
16701000...
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# 16750000: 12636252 tags, 28251 components.
writing results to file -> SRR1300451-comp-stats-2/16750000.SRR1300451_2.fastq.stats.csv
16751000...
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# 16800000: 12664709 tags, 28232 components.
writing results to file -> SRR1300451-comp-stats-2/16800000.SRR1300451_2.fastq.stats.csv
16801000...
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# 16850000: 12703708 tags, 28238 components.
writing results to file -> SRR1300451-comp-stats-2/16850000.SRR1300451_2.fastq.stats.csv
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# 16900000: 12739459 tags, 28222 components.
writing results to file -> SRR1300451-comp-stats-2/16900000.SRR1300451_2.fastq.stats.csv
16901000...
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# 16950000: 12778690 tags, 28230 components.
writing results to file -> SRR1300451-comp-stats-2/16950000.SRR1300451_2.fastq.stats.csv
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# 17000000: 12807412 tags, 28222 components.
writing results to file -> SRR1300451-comp-stats-2/17000000.SRR1300451_2.fastq.stats.csv
17001000...
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# 17050000: 12836348 tags, 28201 components.
writing results to file -> SRR1300451-comp-stats-2/17050000.SRR1300451_2.fastq.stats.csv
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# 17100000: 12869867 tags, 28230 components.
writing results to file -> SRR1300451-comp-stats-2/17100000.SRR1300451_2.fastq.stats.csv
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# 17150000: 12894511 tags, 28199 components.
writing results to file -> SRR1300451-comp-stats-2/17150000.SRR1300451_2.fastq.stats.csv
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# 17200000: 12919767 tags, 28191 components.
writing results to file -> SRR1300451-comp-stats-2/17200000.SRR1300451_2.fastq.stats.csv
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# 17250000: 12951383 tags, 28172 components.
writing results to file -> SRR1300451-comp-stats-2/17250000.SRR1300451_2.fastq.stats.csv
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# 17300000: 12973821 tags, 28130 components.
writing results to file -> SRR1300451-comp-stats-2/17300000.SRR1300451_2.fastq.stats.csv
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# 17350000: 12994411 tags, 28129 components.
writing results to file -> SRR1300451-comp-stats-2/17350000.SRR1300451_2.fastq.stats.csv
17351000...
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# 17400000: 13014798 tags, 28105 components.
writing results to file -> SRR1300451-comp-stats-2/17400000.SRR1300451_2.fastq.stats.csv
17401000...
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# 17450000: 13035760 tags, 28078 components.
writing results to file -> SRR1300451-comp-stats-2/17450000.SRR1300451_2.fastq.stats.csv
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# 17500000: 13056887 tags, 28056 components.
writing results to file -> SRR1300451-comp-stats-2/17500000.SRR1300451_2.fastq.stats.csv
17501000...
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# 17550000: 13077345 tags, 28040 components.
writing results to file -> SRR1300451-comp-stats-2/17550000.SRR1300451_2.fastq.stats.csv
17551000...
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# 17600000: 13097651 tags, 28012 components.
writing results to file -> SRR1300451-comp-stats-2/17600000.SRR1300451_2.fastq.stats.csv
17601000...
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# 17650000: 13117417 tags, 27965 components.
writing results to file -> SRR1300451-comp-stats-2/17650000.SRR1300451_2.fastq.stats.csv
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# 17700000: 13137702 tags, 27945 components.
writing results to file -> SRR1300451-comp-stats-2/17700000.SRR1300451_2.fastq.stats.csv
17701000...
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# 17750000: 13157811 tags, 27932 components.
writing results to file -> SRR1300451-comp-stats-2/17750000.SRR1300451_2.fastq.stats.csv
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# 17800000: 13178725 tags, 27917 components.
writing results to file -> SRR1300451-comp-stats-2/17800000.SRR1300451_2.fastq.stats.csv
17801000...
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# 17850000: 13198752 tags, 27902 components.
writing results to file -> SRR1300451-comp-stats-2/17850000.SRR1300451_2.fastq.stats.csv
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# 17900000: 13218827 tags, 27868 components.
writing results to file -> SRR1300451-comp-stats-2/17900000.SRR1300451_2.fastq.stats.csv
17901000...
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# 17950000: 13238383 tags, 27843 components.
writing results to file -> SRR1300451-comp-stats-2/17950000.SRR1300451_2.fastq.stats.csv
17951000...
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# 18000000: 13258393 tags, 27844 components.
writing results to file -> SRR1300451-comp-stats-2/18000000.SRR1300451_2.fastq.stats.csv
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# 18050000: 13278155 tags, 27845 components.
writing results to file -> SRR1300451-comp-stats-2/18050000.SRR1300451_2.fastq.stats.csv
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# 18100000: 13297855 tags, 27833 components.
writing results to file -> SRR1300451-comp-stats-2/18100000.SRR1300451_2.fastq.stats.csv
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# 18150000: 13317435 tags, 27807 components.
writing results to file -> SRR1300451-comp-stats-2/18150000.SRR1300451_2.fastq.stats.csv
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# 18200000: 13339279 tags, 27798 components.
writing results to file -> SRR1300451-comp-stats-2/18200000.SRR1300451_2.fastq.stats.csv
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# 18250000: 13359135 tags, 27783 components.
writing results to file -> SRR1300451-comp-stats-2/18250000.SRR1300451_2.fastq.stats.csv
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# 18300000: 13378906 tags, 27763 components.
writing results to file -> SRR1300451-comp-stats-2/18300000.SRR1300451_2.fastq.stats.csv
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# 18350000: 13398525 tags, 27737 components.
writing results to file -> SRR1300451-comp-stats-2/18350000.SRR1300451_2.fastq.stats.csv
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# 18400000: 13418269 tags, 27716 components.
writing results to file -> SRR1300451-comp-stats-2/18400000.SRR1300451_2.fastq.stats.csv
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# 18450000: 13437766 tags, 27697 components.
writing results to file -> SRR1300451-comp-stats-2/18450000.SRR1300451_2.fastq.stats.csv
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# 18500000: 13457459 tags, 27667 components.
writing results to file -> SRR1300451-comp-stats-2/18500000.SRR1300451_2.fastq.stats.csv
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# 18550000: 13478117 tags, 27634 components.
writing results to file -> SRR1300451-comp-stats-2/18550000.SRR1300451_2.fastq.stats.csv
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# 18600000: 13497659 tags, 27632 components.
writing results to file -> SRR1300451-comp-stats-2/18600000.SRR1300451_2.fastq.stats.csv
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# 18650000: 13517131 tags, 27603 components.
writing results to file -> SRR1300451-comp-stats-2/18650000.SRR1300451_2.fastq.stats.csv
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# 18700000: 13536146 tags, 27603 components.
writing results to file -> SRR1300451-comp-stats-2/18700000.SRR1300451_2.fastq.stats.csv
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# 18750000: 13555737 tags, 27583 components.
writing results to file -> SRR1300451-comp-stats-2/18750000.SRR1300451_2.fastq.stats.csv
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# 18800000: 13575323 tags, 27555 components.
writing results to file -> SRR1300451-comp-stats-2/18800000.SRR1300451_2.fastq.stats.csv
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# 18850000: 13594784 tags, 27542 components.
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In [11]:
comps = [(comp.component_id, comp) for comp in P_paired.components()]
In [12]:
lump = comps[0][1]
In [15]:
len(lump)
Out[15]:
15681997
In [248]:
condp_df = pd.read_csv('../SRR1300451-K31-sliced-c5c10/partitioner-details.csv',
skipinitialspace=True, na_values='None')
In [249]:
condp_df.head()
Out[249]:
read_n
fitness
n_tags
n_merged
comp_size
comp_cov
root_id
0
2
0.0
2
NaN
NaN
NaN
NaN
1
4
0.0
2
NaN
NaN
NaN
NaN
2
6
0.0
2
NaN
NaN
NaN
NaN
3
8
0.0
2
NaN
NaN
NaN
NaN
4
10
0.0
2
NaN
NaN
NaN
NaN
In [250]:
condp_sub = condp_df.sample(n=100000, axis=0).sort_values('read_n')
In [251]:
#scatter(condp_sub['read_n'], condp_sub['comp_size'], s=2)
scatter(condp_sub['read_n'], condp_sub['n_merged'], s=2)
Out[251]:
<matplotlib.collections.PathCollection at 0x7f9e23052710>
In [252]:
sns.violinplot(x="n_merged", y="comp_size", data=condp_sub, jitter=True)
Out[252]:
<matplotlib.axes._subplots.AxesSubplot at 0x7f9e230f4470>
In [55]:
condp_sub.set_index('read_n').n_merged.replace(to_replace=NaN, value=0).cumsum(skipna=True).plot()
Out[55]:
<matplotlib.axes._subplots.AxesSubplot at 0x7f9e24590860>
In [76]:
condp_comps = pd.read_csv('../SRR1300451-K31-detailed/global.csv',
names=['read_n', 'n_components', 'n_tags', 'new_kmers'])
In [80]:
condp_sliced_comps = pd.read_csv('../SRR1300451-K31-sliced-c5c10/global.csv',
names=['read_n', 'n_components', 'n_tags', 'new_kmers'])
In [83]:
plot(condp_comps.read_n, condp_comps.n_components, label='Min Cov: 10')
plot(condp_sliced_comps.read_n, condp_sliced_comps.n_components, label='Cov Slice: [5,10)')
legend()
Out[83]:
<matplotlib.legend.Legend at 0x7f9e2c0e9278>
In [84]:
condp_sliced = pd.read_csv('../SRR1300451-K31-sliced-c5c10/partitioner-details.csv',
skipinitialspace=True, na_values='None')
In [94]:
def parse_partition_data_dir(stats_dir, include_global=False, verbose=True):
stats_files = [os.path.abspath(p) for p in glob.glob(os.path.join(stats_dir,'*.csv')) if not \
(p.endswith('global.csv') or p.endswith('partitioner-details.csv'))]
read_num_func = lambda fn: int(os.path.basename(fn).split('.')[0])
stats_files.sort(key=read_num_func)
if verbose:
print('Parsing {0} partition files from {1}'.format(len(stats_files), stats_dir))
bar = pyprind.ProgBar(len(stats_files), monitor=False)
data = OrderedDict()
for filename in stats_files:
df = pd.read_csv(filename, header=None, names=['comp_id', 'n_tags', 'mean_cov'])
data[read_num_func(filename)] = df
if verbose:
bar.update()
return data
In [95]:
condp_all = parse_partition_data_dir('../SRR1300451-K31-sliced-c5c10/')
0% 100%
[# ] | ETA: 00:00:02
Parsing 2645 partition files from ../SRR1300451-K31-sliced-c5c10/
[##############################] | ETA: 00:00:00
Total time elapsed: 00:00:15
In [98]:
plot(list(condp_all.keys()), [df.n_tags.max() for df in condp_all.values()])
plot(condp_sliced_comps.read_n, condp_sliced_comps.n_components)
xlabel('Read Number')
ylabel('Num of Tags')
legend(loc='upper left')
#title('Tags in Largest Component, SRR1300451')
#savefig('largest_component_size_paired_and_single.png', dpi=600)
Out[98]:
<matplotlib.legend.Legend at 0x7f9e330a3f28>
In [122]:
dcov_dt = pd.concat([df.quantile(q=np.arange(.1,1,.1))[['mean_cov']].rename(columns={'mean_cov': N}).T \
for N, df in condp_all.items() if not df.empty])
In [128]:
dcov_dt.plot(logy=True)
Out[128]:
<matplotlib.axes._subplots.AxesSubplot at 0x7f9e2c763cc0>
In [193]:
quantiles = pd.concat([df.quantile(q=[.1, .25, .5, .75, .9])[['mean_cov', 'n_tags']].T \
for N, df in condp_all.items() if not df.empty])
quantiles.reset_index(inplace=True)
quantiles.rename(columns={'index': 'measure'}, inplace=True)
quantiles['read_n'] = np.repeat([N for N, df in condp_all.items() if not df.empty], 2)
In [197]:
quantiles.set_index('read_n', inplace=True)
In [245]:
with FigureManager(show=True, ncols=2, figsize=(10,4)) as (fig, ax):
#cmap = sns.color_palette("cubehelix", 8, )
#sns.set_palette("GnBu_d", )
sns.set_palette("husl")
quantiles.query('measure == "mean_cov"').plot(ax=ax[0])
ax[0].set_ylabel('Mean Component Cov.')
quantiles.query('measure == "n_tags"').plot(ax=ax[1]) #, colormap=cmap)
ax[1].set_ylabel('Component Size')
for _ in ax:
_.xaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(lambda x, p: format(round(int(x), -5), ',')))
start, end = _.get_xlim()
_.xaxis.set_ticks(list(np.arange(start, end+1, end/2)) + [end])
start, end = _.get_ylim()
#_.yaxis.set_ticks(list(np.arange(start, end, end/3)) + [end])
#_.yaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(lambda x, p: format(int(x), ',')))
#ax[0].set_title('Component growth during assemly graph construction, SRR1300451')
fig.savefig('/work/recomb-poster/output/img/component_quantiles.png', dpi=300)
In [209]:
format(round(int(54334455), -5), ',')
Out[209]:
'54,300,000'
In [ ]:
df.plot()
Content source: camillescott/boink
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