Last login: Thu Jul  7 20:20:17 on ttys000
Vascos-MacBook:~ luckylion$ bash /Users/luckylion/Documents/UNI_und_VORLESUNGEN/11\ phd\ projects/1\ Meta\ SCHMALNAU/2\ HiSeq\ biomass\ 160707/3\ cutadapt/cmd_cut.txt 
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF10_BR14_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.85 s (17 us/read; 3.62 M reads/minute).

=== Summary ===

Total reads processed:               1,741,632
Reads with adapters:                 1,741,112 (100.0%)
Reads written (passing filters):     1,741,112 (100.0%)

Total basepairs processed:   446,664,663 bp
Total written (filtered):    411,742,537 bp (92.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1741112 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2265	0.0	1	0 0 2265
19	34106	0.0	1	0 33671 435
20	1699936	0.0	2	1674672 24981 283
21	2366	0.0	2	0 2215 151
22	2439	0.0	2	0 0 2439

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF10_BR14_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.51 s (16 us/read; 3.66 M reads/minute).

=== Summary ===

Total reads processed:               1,741,112
Reads with adapters:                 1,739,496 (99.9%)
Reads written (passing filters):     1,739,496 (99.9%)

Total basepairs processed:   411,742,537 bp
Total written (filtered):    376,580,583 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 1739496 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 90.7%
  C: 0.2%
  G: 0.4%
  T: 8.7%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	760	0.0	1	0 0 760
19	8129	0.0	1	0 8022 107
20	1729660	0.0	2	1704042 25160 458
21	947	0.0	2	0 935 12

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF10_BR24_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 30.31 s (19 us/read; 3.16 M reads/minute).

=== Summary ===

Total reads processed:               1,595,596
Reads with adapters:                 1,595,009 (100.0%)
Reads written (passing filters):     1,595,009 (100.0%)

Total basepairs processed:   567,394,349 bp
Total written (filtered):    535,317,123 bp (94.3%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1595009 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2225	0.0	1	0 0 2225
19	32748	0.0	1	0 32213 535
20	1555246	0.0	2	1528476 26516 254
21	2140	0.0	2	0 1941 199
22	2650	0.0	2	0 0 2650

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF10_BR24_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 30.61 s (19 us/read; 3.13 M reads/minute).

=== Summary ===

Total reads processed:               1,595,009
Reads with adapters:                 1,591,640 (99.8%)
Reads written (passing filters):     1,591,640 (99.8%)

Total basepairs processed:   535,317,123 bp
Total written (filtered):    502,386,676 bp (93.8%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1591640 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 1.0%
  C: 42.3%
  G: 0.0%
  T: 56.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	2015	0.0	1	0 0 2015
19	21233	0.0	1	0 20608 625
20	1567143	0.0	2	1516967 48848 1328
21	1244	0.0	2	0 1176 68
22	5	0.0	2	0 0 5

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF11_BR13_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 31.90 s (17 us/read; 3.46 M reads/minute).

=== Summary ===

Total reads processed:               1,841,509
Reads with adapters:                 1,840,607 (100.0%)
Reads written (passing filters):     1,840,607 (100.0%)

Total basepairs processed:   472,704,200 bp
Total written (filtered):    435,708,952 bp (92.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1840607 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4229	0.0	1	0 0 4229
19	47331	0.0	1	0 46540 791
20	1783584	0.0	2	1744706 38344 534
21	2755	0.0	2	0 2564 191
22	2708	0.0	2	0 0 2708

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF11_BR13_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 30.19 s (16 us/read; 3.66 M reads/minute).

=== Summary ===

Total reads processed:               1,840,607
Reads with adapters:                 1,838,915 (99.9%)
Reads written (passing filters):     1,838,915 (99.9%)

Total basepairs processed:   435,708,952 bp
Total written (filtered):    398,537,420 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 1838915 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 74.0%
  C: 0.1%
  G: 0.2%
  T: 25.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	764	0.0	1	0 0 764
19	7162	0.0	1	0 7023 139
20	1830063	0.0	2	1801634 27856 573
21	925	0.0	2	0 913 12
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF11_BR23_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 22.97 s (19 us/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:               1,230,260
Reads with adapters:                 1,229,570 (99.9%)
Reads written (passing filters):     1,229,570 (99.9%)

Total basepairs processed:   437,746,509 bp
Total written (filtered):    412,942,313 bp (94.3%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1229570 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2962	0.0	1	0 0 2962
19	32322	0.0	1	0 31676 646
20	1189590	0.0	2	1160442 28797 351
21	1885	0.0	2	0 1716 169
22	2811	0.0	2	0 0 2811

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF11_BR23_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 23.62 s (19 us/read; 3.12 M reads/minute).

=== Summary ===

Total reads processed:               1,229,570
Reads with adapters:                 1,227,086 (99.8%)
Reads written (passing filters):     1,227,086 (99.8%)

Total basepairs processed:   412,942,313 bp
Total written (filtered):    387,583,788 bp (93.9%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1227086 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 80.5%
  G: 0.0%
  T: 19.4%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "C" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "C" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1539	0.0	1	0 0 1539
19	11060	0.0	1	0 10766 294
20	1213356	0.0	2	1180554 31930 872
21	1130	0.0	2	0 1093 37
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF12_BR12_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 31.50 s (17 us/read; 3.56 M reads/minute).

=== Summary ===

Total reads processed:               1,869,411
Reads with adapters:                 1,868,403 (99.9%)
Reads written (passing filters):     1,868,403 (99.9%)

Total basepairs processed:   478,809,517 bp
Total written (filtered):    441,232,187 bp (92.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1868403 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	3789	0.0	1	0 0 3789
19	49415	0.0	1	0 48514 901
20	1806606	0.0	2	1762248 43611 747
21	7682	0.0	2	0 7466 216
22	911	0.0	2	0 0 911

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF12_BR12_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 32.02 s (17 us/read; 3.50 M reads/minute).

=== Summary ===

Total reads processed:               1,868,403
Reads with adapters:                 1,866,695 (99.9%)
Reads written (passing filters):     1,866,695 (99.9%)

Total basepairs processed:   441,232,187 bp
Total written (filtered):    403,503,505 bp (91.4%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 1866695 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 82.9%
  C: 0.1%
  G: 0.3%
  T: 16.7%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	801	0.0	1	0 0 801
19	6716	0.0	1	0 6567 149
20	1858218	0.0	2	1822462 35000 756
21	959	0.0	2	0 949 10
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF12_BR22_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.27 s (20 us/read; 2.99 M reads/minute).

=== Summary ===

Total reads processed:               1,410,719
Reads with adapters:                 1,409,776 (99.9%)
Reads written (passing filters):     1,409,776 (99.9%)

Total basepairs processed:   501,722,544 bp
Total written (filtered):    473,226,542 bp (94.3%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1409776 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2956	0.0	1	0 0 2956
19	37421	0.0	1	0 36549 872
20	1362405	0.0	2	1324708 37070 627
21	3905	0.0	2	0 3668 237
22	3089	0.0	2	0 0 3089

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF12_BR22_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 27.87 s (20 us/read; 3.04 M reads/minute).

=== Summary ===

Total reads processed:               1,409,776
Reads with adapters:                 1,407,245 (99.8%)
Reads written (passing filters):     1,407,245 (99.8%)

Total basepairs processed:   473,226,542 bp
Total written (filtered):    444,252,690 bp (93.9%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1407245 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 86.3%
  G: 0.0%
  T: 13.6%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "C" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "C" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1610	0.0	1	0 0 1610
19	12411	0.0	1	0 12102 309
20	1392238	0.0	2	1360008 31327 903
21	985	0.0	2	0 959 26
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF13_BR11_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.85 s (18 us/read; 3.30 M reads/minute).

=== Summary ===

Total reads processed:               2,245,064
Reads with adapters:                 2,241,772 (99.9%)
Reads written (passing filters):     2,241,772 (99.9%)

Total basepairs processed:   575,497,930 bp
Total written (filtered):    529,896,823 bp (92.1%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 2241772 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	19554	0.0	1	0 0 19554
19	170916	0.0	1	0 167201 3715
20	1952416	0.0	2	1908140 40102 4174
21	59149	0.0	2	0 57982 1167
22	39737	0.0	2	0 0 39737

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF13_BR11_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 38.80 s (17 us/read; 3.47 M reads/minute).

=== Summary ===

Total reads processed:               2,241,772
Reads with adapters:                 2,239,822 (99.9%)
Reads written (passing filters):     2,239,822 (99.9%)

Total basepairs processed:   529,896,823 bp
Total written (filtered):    484,661,016 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2239822 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 78.3%
  C: 0.1%
  G: 0.3%
  T: 21.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	864	0.0	1	0 0 864
19	20395	0.0	1	0 20131 264
20	2217557	0.0	2	2177429 39147 981
21	1006	0.0	2	0 987 19

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF13_BR21_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 29.22 s (20 us/read; 3.07 M reads/minute).

=== Summary ===

Total reads processed:               1,493,965
Reads with adapters:                 1,491,540 (99.8%)
Reads written (passing filters):     1,491,540 (99.8%)

Total basepairs processed:   531,143,446 bp
Total written (filtered):    500,504,673 bp (94.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1491540 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	13846	0.0	1	0 0 13846
19	117159	0.0	1	0 113950 3209
20	1293687	0.0	2	1260216 30794 2677
21	35966	0.0	2	0 35054 912
22	30882	0.0	2	0 0 30882

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF13_BR21_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 30.83 s (21 us/read; 2.90 M reads/minute).

=== Summary ===

Total reads processed:               1,491,540
Reads with adapters:                 1,488,850 (99.8%)
Reads written (passing filters):     1,488,850 (99.8%)

Total basepairs processed:   500,504,673 bp
Total written (filtered):    469,852,006 bp (93.9%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1488850 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 70.8%
  G: 0.0%
  T: 29.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1708	0.0	1	0 0 1708
19	12440	0.0	1	0 12144 296
20	1473445	0.0	2	1442004 30471 970
21	1257	0.0	2	0 1236 21

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF14_BR10_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.58 s (18 us/read; 3.42 M reads/minute).

=== Summary ===

Total reads processed:               1,972,806
Reads with adapters:                 1,972,333 (100.0%)
Reads written (passing filters):     1,972,333 (100.0%)

Total basepairs processed:   506,141,567 bp
Total written (filtered):    466,572,433 bp (92.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1972333 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	962	0.0	1	0 0 962
19	9918	0.0	1	0 9732 186
20	1957712	0.0	2	1920757 36592 363
21	1807	0.0	2	0 1724 83
22	1934	0.0	2	0 0 1934

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF14_BR10_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.17 s (17 us/read; 3.46 M reads/minute).

=== Summary ===

Total reads processed:               1,972,333
Reads with adapters:                 1,970,831 (99.9%)
Reads written (passing filters):     1,970,831 (99.9%)

Total basepairs processed:   466,572,433 bp
Total written (filtered):    426,817,075 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 1970831 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 92.9%
  C: 0.1%
  G: 0.3%
  T: 6.8%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	669	0.0	1	0 0 669
19	15677	0.0	1	0 15485 192
20	1953941	0.0	2	1928253 25112 576
21	543	0.0	2	0 537 6
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF14_BR20_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 27.63 s (19 us/read; 3.09 M reads/minute).

=== Summary ===

Total reads processed:               1,423,849
Reads with adapters:                 1,423,513 (100.0%)
Reads written (passing filters):     1,423,513 (100.0%)

Total basepairs processed:   506,459,490 bp
Total written (filtered):    477,875,192 bp (94.4%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1423513 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	663	0.0	1	0 0 663
19	7185	0.0	1	0 7030 155
20	1413146	0.0	2	1381832 31000 314
21	1245	0.0	2	0 1177 68
22	1274	0.0	2	0 0 1274

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF14_BR20_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 26.45 s (19 us/read; 3.23 M reads/minute).

=== Summary ===

Total reads processed:               1,423,513
Reads with adapters:                 1,421,330 (99.8%)
Reads written (passing filters):     1,421,330 (99.8%)

Total basepairs processed:   477,875,192 bp
Total written (filtered):    448,732,326 bp (93.9%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1421330 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 2.7%
  C: 33.1%
  G: 0.1%
  T: 64.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1141	0.0	1	0 0 1141
19	10127	0.0	1	0 9935 192
20	1409260	0.0	2	1384123 24215 922
21	801	0.0	2	0 768 33
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF20_BR14_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.26 s (18 us/read; 3.26 M reads/minute).

=== Summary ===

Total reads processed:               1,809,587
Reads with adapters:                 1,808,843 (100.0%)
Reads written (passing filters):     1,808,843 (100.0%)

Total basepairs processed:   647,445,133 bp
Total written (filtered):    611,042,912 bp (94.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1808843 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	3323	0.0	1	0 0 3323
19	39162	0.0	1	0 38678 484
20	1759781	0.0	2	1731598 27855 328
21	5617	0.0	2	0 5534 83
22	960	0.0	2	0 0 960

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF20_BR14_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.92 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               1,808,843
Reads with adapters:                 1,806,545 (99.9%)
Reads written (passing filters):     1,806,545 (99.9%)

Total basepairs processed:   611,042,912 bp
Total written (filtered):    574,144,813 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 1806545 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 90.0%
  C: 1.8%
  G: 1.1%
  T: 7.1%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	769	0.0	1	0 0 769
19	8603	0.0	1	0 8389 214
20	1796191	0.0	2	1756650 38572 969
21	981	0.0	2	0 960 21
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF20_BR24_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.45 s (21 us/read; 2.79 M reads/minute).

=== Summary ===

Total reads processed:               1,556,785
Reads with adapters:                 1,556,152 (100.0%)
Reads written (passing filters):     1,556,152 (100.0%)

Total basepairs processed:   716,882,846 bp
Total written (filtered):    685,505,363 bp (95.6%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1556152 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2812	0.0	1	0 0 2812
19	34056	0.0	1	0 33632 424
20	1513432	0.0	2	1488659 24523 250
21	5048	0.0	2	0 4967 81
22	804	0.0	2	0 0 804

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF20_BR24_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.15 s (21 us/read; 2.82 M reads/minute).

=== Summary ===

Total reads processed:               1,556,152
Reads with adapters:                 1,553,845 (99.9%)
Reads written (passing filters):     1,553,845 (99.9%)

Total basepairs processed:   685,505,363 bp
Total written (filtered):    653,446,757 bp (95.3%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1553845 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.4%
  C: 12.4%
  G: 0.1%
  T: 87.1%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "T" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "T" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1905	0.0	1	0 0 1905
19	20047	0.0	1	0 19381 666
20	1530723	0.0	2	1479140 49598 1985
21	1166	0.0	2	0 1092 74
22	4	0.0	2	0 0 4

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF21_BR13_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 37.80 s (19 us/read; 3.19 M reads/minute).

=== Summary ===

Total reads processed:               2,007,723
Reads with adapters:                 2,006,519 (99.9%)
Reads written (passing filters):     2,006,519 (99.9%)

Total basepairs processed:   724,859,998 bp
Total written (filtered):    684,351,337 bp (94.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 2006519 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5308	0.0	1	0 0 5308
19	55014	0.0	1	0 54137 877
20	1935950	0.0	2	1897451 38006 493
21	8545	0.0	2	0 8345 200
22	1702	0.0	2	0 0 1702

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF21_BR13_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 37.53 s (19 us/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:               2,006,519
Reads with adapters:                 2,003,941 (99.9%)
Reads written (passing filters):     2,003,941 (99.9%)

Total basepairs processed:   684,351,337 bp
Total written (filtered):    643,405,278 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2003941 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 87.7%
  C: 0.3%
  G: 0.5%
  T: 11.5%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	787	0.0	1	0 0 787
19	7599	0.0	1	0 6785 814
20	1994568	0.0	2	1950948 42430 1190
21	987	0.0	2	0 962 25

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF21_BR23_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 32.20 s (21 us/read; 2.85 M reads/minute).

=== Summary ===

Total reads processed:               1,529,473
Reads with adapters:                 1,528,606 (99.9%)
Reads written (passing filters):     1,528,606 (99.9%)

Total basepairs processed:   704,806,393 bp
Total written (filtered):    673,876,841 bp (95.6%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1528606 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4126	0.0	1	0 0 4126
19	42057	0.0	1	0 41344 713
20	1472808	0.0	2	1442565 29821 422
21	6467	0.0	2	0 6342 125
22	3148	0.0	2	0 0 3148

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF21_BR23_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 32.58 s (21 us/read; 2.82 M reads/minute).

=== Summary ===

Total reads processed:               1,528,606
Reads with adapters:                 1,526,640 (99.9%)
Reads written (passing filters):     1,526,640 (99.9%)

Total basepairs processed:   673,876,841 bp
Total written (filtered):    642,509,657 bp (95.3%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1526640 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.2%
  C: 72.6%
  G: 0.1%
  T: 27.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1700	0.0	1	0 0 1700
19	13614	0.0	1	0 13272 342
20	1510044	0.0	2	1465946 42660 1438
21	1282	0.0	2	0 1247 35

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF22_BR12_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.26 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               1,825,258
Reads with adapters:                 1,823,531 (99.9%)
Reads written (passing filters):     1,823,531 (99.9%)

Total basepairs processed:   658,596,237 bp
Total written (filtered):    621,601,885 bp (94.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1823531 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	9066	0.0	1	0 0 9066
19	88550	0.0	1	0 86941 1609
20	1716633	0.0	2	1677371 38510 752
21	8567	0.0	2	0 8389 178
22	715	0.0	2	0 0 715

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF22_BR12_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.24 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               1,823,531
Reads with adapters:                 1,821,348 (99.9%)
Reads written (passing filters):     1,821,348 (99.9%)

Total basepairs processed:   621,601,885 bp
Total written (filtered):    584,443,090 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 1821348 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 96.2%
  C: 0.2%
  G: 0.5%
  T: 3.0%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	837	0.0	1	0 0 837
19	6402	0.0	1	0 5720 682
20	1813133	0.0	2	1643632 165424 4077
21	974	0.0	2	0 952 22
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF22_BR22_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.21 s (21 us/read; 2.80 M reads/minute).

=== Summary ===

Total reads processed:               1,547,480
Reads with adapters:                 1,546,006 (99.9%)
Reads written (passing filters):     1,546,006 (99.9%)

Total basepairs processed:   712,557,320 bp
Total written (filtered):    681,053,052 bp (95.6%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1546006 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	7680	0.0	1	0 0 7680
19	74289	0.0	1	0 72900 1389
20	1455697	0.0	2	1423873 31213 611
21	6390	0.0	2	0 6253 137
22	1950	0.0	2	0 0 1950

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF22_BR22_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 32.45 s (21 us/read; 2.86 M reads/minute).

=== Summary ===

Total reads processed:               1,546,006
Reads with adapters:                 1,544,102 (99.9%)
Reads written (passing filters):     1,544,102 (99.9%)

Total basepairs processed:   681,053,052 bp
Total written (filtered):    649,407,051 bp (95.4%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1544102 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 71.4%
  G: 0.1%
  T: 28.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1704	0.0	1	0 0 1704
19	13233	0.0	1	0 12912 321
20	1528108	0.0	2	1491148 35672 1288
21	1055	0.0	2	0 1025 30
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF23_BR11_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 38.52 s (18 us/read; 3.26 M reads/minute).

=== Summary ===

Total reads processed:               2,090,532
Reads with adapters:                 2,084,873 (99.7%)
Reads written (passing filters):     2,084,873 (99.7%)

Total basepairs processed:   754,566,448 bp
Total written (filtered):    711,023,856 bp (94.2%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 2084873 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	26407	0.0	1	0 0 26407
19	204007	0.0	1	0 199776 4231
20	1789660	0.0	2	1743951 41150 4559
21	55543	0.0	2	0 54304 1239
22	9256	0.0	2	0 0 9256

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF23_BR11_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 39.29 s (19 us/read; 3.18 M reads/minute).

=== Summary ===

Total reads processed:               2,084,873
Reads with adapters:                 2,082,328 (99.9%)
Reads written (passing filters):     2,082,328 (99.9%)

Total basepairs processed:   711,023,856 bp
Total written (filtered):    668,532,915 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2082328 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 91.5%
  C: 0.3%
  G: 0.6%
  T: 7.7%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	859	0.0	1	0 0 859
19	19867	0.0	1	0 19504 363
20	2060699	0.0	2	1818197 237401 5101
21	901	0.0	2	0 828 73
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF23_BR21_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.79 s (21 us/read; 2.85 M reads/minute).

=== Summary ===

Total reads processed:               1,365,455
Reads with adapters:                 1,361,765 (99.7%)
Reads written (passing filters):     1,361,765 (99.7%)

Total basepairs processed:   628,746,323 bp
Total written (filtered):    599,929,264 bp (95.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1361765 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	17783	0.0	1	0 0 17783
19	133346	0.0	1	0 130260 3086
20	1160964	0.0	2	1130909 27109 2946
21	35269	0.0	2	0 34470 799
22	14403	0.0	2	0 0 14403

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF23_BR21_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.84 s (21 us/read; 2.83 M reads/minute).

=== Summary ===

Total reads processed:               1,361,765
Reads with adapters:                 1,360,176 (99.9%)
Reads written (passing filters):     1,360,176 (99.9%)

Total basepairs processed:   599,929,264 bp
Total written (filtered):    572,049,946 bp (95.4%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1360176 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 69.1%
  G: 0.1%
  T: 30.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1488	0.0	1	0 0 1488
19	11666	0.0	1	0 11372 294
20	1345854	0.0	2	1314098 30639 1117
21	1164	0.0	2	0 1137 27
22	4	0.0	2	0 0 4

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF24_BR10_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.36 s (18 us/read; 3.26 M reads/minute).

=== Summary ===

Total reads processed:               2,192,439
Reads with adapters:                 2,191,471 (100.0%)
Reads written (passing filters):     2,191,471 (100.0%)

Total basepairs processed:   789,023,368 bp
Total written (filtered):    744,856,014 bp (94.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 2191471 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1349	0.0	1	0 0 1349
19	14321	0.0	1	0 14059 262
20	2166575	0.0	2	2121977 44110 488
21	7910	0.0	2	0 7750 160
22	1316	0.0	2	0 0 1316

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF24_BR10_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.58 s (19 us/read; 3.16 M reads/minute).

=== Summary ===

Total reads processed:               2,191,471
Reads with adapters:                 2,189,051 (99.9%)
Reads written (passing filters):     2,189,051 (99.9%)

Total basepairs processed:   744,856,014 bp
Total written (filtered):    700,273,641 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2189051 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 91.0%
  C: 1.2%
  G: 1.1%
  T: 6.8%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	788	0.0	1	0 0 788
19	18383	0.0	1	0 18089 294
20	2169190	0.0	2	2128533 39560 1097
21	690	0.0	2	0 624 66

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L001_BF24_BR20_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.19 s (21 us/read; 2.86 M reads/minute).

=== Summary ===

Total reads processed:               1,579,267
Reads with adapters:                 1,578,581 (100.0%)
Reads written (passing filters):     1,578,581 (100.0%)

Total basepairs processed:   727,287,536 bp
Total written (filtered):    695,417,417 bp (95.6%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1578581 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1000	0.0	1	0 0 1000
19	10441	0.0	1	0 10229 212
20	1559919	0.0	2	1527467 32116 336
21	5860	0.0	2	0 5733 127
22	1361	0.0	2	0 0 1361

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF24_BR20_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.27 s (21 us/read; 2.85 M reads/minute).

=== Summary ===

Total reads processed:               1,578,581
Reads with adapters:                 1,577,159 (99.9%)
Reads written (passing filters):     1,577,159 (99.9%)

Total basepairs processed:   695,417,417 bp
Total written (filtered):    663,282,317 bp (95.4%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1577159 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 1.6%
  C: 18.0%
  G: 0.1%
  T: 80.2%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "T" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "T" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1289	0.0	1	0 0 1289
19	12026	0.0	1	0 11804 222
20	1562868	0.0	2	1531296 30265 1307
21	974	0.0	2	0 944 30
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR10_BF14_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 32.21 s (16 us/read; 3.65 M reads/minute).

=== Summary ===

Total reads processed:               1,959,619
Reads with adapters:                 1,958,709 (100.0%)
Reads written (passing filters):     1,958,709 (100.0%)

Total basepairs processed:   502,796,888 bp
Total written (filtered):    463,444,611 bp (92.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 1958709 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4237	0.0	1	0 0 4237
19	56715	0.0	1	0 55846 869
20	1896174	0.0	2	1868282 27599 293
21	1571	0.0	2	0 1534 37
22	12	0.0	2	0 0 12

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR10_BF14_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 31.85 s (16 us/read; 3.69 M reads/minute).

=== Summary ===

Total reads processed:               1,958,709
Reads with adapters:                 1,954,608 (99.8%)
Reads written (passing filters):     1,954,608 (99.8%)

Total basepairs processed:   463,444,611 bp
Total written (filtered):    423,470,747 bp (91.4%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1954608 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 77.3%
  C: 3.3%
  G: 14.7%
  T: 4.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	9378	0.0	1	0 0 9378
19	61272	0.0	1	0 59817 1455
20	1882982	0.0	2	1837910 44106 966
21	974	0.0	2	0 948 26
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR10_BF24_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 35.79 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               1,908,678
Reads with adapters:                 1,907,727 (100.0%)
Reads written (passing filters):     1,907,727 (100.0%)

Total basepairs processed:   683,106,920 bp
Total written (filtered):    644,676,541 bp (94.4%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 1907727 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4098	0.0	1	0 0 4098
19	55184	0.0	1	0 53632 1552
20	1847028	0.0	2	1813867 32838 323
21	1408	0.0	2	0 1310 98
22	9	0.0	2	0 0 9

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR10_BF24_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.36 s (19 us/read; 3.15 M reads/minute).

=== Summary ===

Total reads processed:               1,907,727
Reads with adapters:                 1,904,844 (99.8%)
Reads written (passing filters):     1,904,844 (99.8%)

Total basepairs processed:   644,676,541 bp
Total written (filtered):    605,678,428 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1904844 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 43.6%
  C: 3.5%
  G: 45.1%
  T: 7.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	2439	0.0	1	0 0 2439
19	65008	0.0	1	0 63055 1953
20	1836549	0.0	2	1783420 51935 1194
21	840	0.0	2	0 818 22
22	8	0.0	2	0 0 8

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR11_BF13_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 31.00 s (17 us/read; 3.62 M reads/minute).

=== Summary ===

Total reads processed:               1,871,735
Reads with adapters:                 1,870,797 (99.9%)
Reads written (passing filters):     1,870,797 (99.9%)

Total basepairs processed:   480,705,196 bp
Total written (filtered):    443,107,628 bp (92.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 1870797 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4378	0.0	1	0 0 4378
19	50835	0.0	1	0 50206 629
20	1813864	0.0	2	1758212 54988 664
21	1717	0.0	2	0 1660 57
22	3	0.0	2	0 0 3

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR11_BF13_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 31.03 s (17 us/read; 3.62 M reads/minute).

=== Summary ===

Total reads processed:               1,870,797
Reads with adapters:                 1,869,199 (99.9%)
Reads written (passing filters):     1,869,199 (99.9%)

Total basepairs processed:   443,107,628 bp
Total written (filtered):    405,354,631 bp (91.5%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1869199 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 61.6%
  C: 30.7%
  G: 5.3%
  T: 2.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	718	0.0	1	0 0 718
19	7272	0.0	1	0 7155 117
20	1860402	0.0	2	1830375 29308 719
21	807	0.0	2	0 798 9

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR11_BF23_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.93 s (19 us/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:               1,817,265
Reads with adapters:                 1,816,250 (99.9%)
Reads written (passing filters):     1,816,250 (99.9%)

Total basepairs processed:   656,768,599 bp
Total written (filtered):    620,138,963 bp (94.4%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 1816250 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4537	0.0	1	0 0 4537
19	51470	0.0	1	0 50625 845
20	1758437	0.0	2	1616257 140196 1984
21	1801	0.0	2	0 1615 186
22	5	0.0	2	0 0 5

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR11_BF23_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.76 s (19 us/read; 3.13 M reads/minute).

=== Summary ===

Total reads processed:               1,816,250
Reads with adapters:                 1,814,288 (99.9%)
Reads written (passing filters):     1,814,288 (99.9%)

Total basepairs processed:   620,138,963 bp
Total written (filtered):    583,195,137 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1814288 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 31.7%
  C: 8.1%
  G: 58.4%
  T: 1.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	993	0.0	1	0 0 993
19	8474	0.0	1	0 8119 355
20	1804164	0.0	2	1743153 59696 1315
21	656	0.0	2	0 640 16
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR12_BF12_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 27.35 s (17 us/read; 3.61 M reads/minute).

=== Summary ===

Total reads processed:               1,647,062
Reads with adapters:                 1,646,050 (99.9%)
Reads written (passing filters):     1,646,050 (99.9%)

Total basepairs processed:   423,013,989 bp
Total written (filtered):    389,893,064 bp (92.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 1646050 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4494	0.0	1	0 0 4494
19	53081	0.0	1	0 51688 1393
20	1586739	0.0	2	1549576 36651 512
21	1724	0.0	2	0 1693 31
22	12	0.0	2	0 0 12

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR12_BF12_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 26.88 s (16 us/read; 3.67 M reads/minute).

=== Summary ===

Total reads processed:               1,646,050
Reads with adapters:                 1,644,593 (99.9%)
Reads written (passing filters):     1,644,593 (99.9%)

Total basepairs processed:   389,893,064 bp
Total written (filtered):    356,662,800 bp (91.5%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1644593 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 62.8%
  C: 22.7%
  G: 14.1%
  T: 0.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	643	0.0	1	0 0 643
19	6621	0.0	1	0 6505 116
20	1636663	0.0	2	1603645 32352 666
21	666	0.0	2	0 651 15

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR12_BF22_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 30.55 s (19 us/read; 3.19 M reads/minute).

=== Summary ===

Total reads processed:               1,625,232
Reads with adapters:                 1,624,048 (99.9%)
Reads written (passing filters):     1,624,048 (99.9%)

Total basepairs processed:   587,314,010 bp
Total written (filtered):    554,468,989 bp (94.4%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 1624048 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4662	0.0	1	0 0 4662
19	53439	0.0	1	0 49579 3860
20	1564254	0.0	2	1488343 74670 1241
21	1692	0.0	2	0 1649 43
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR12_BF22_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 31.72 s (20 us/read; 3.07 M reads/minute).

=== Summary ===

Total reads processed:               1,624,048
Reads with adapters:                 1,621,940 (99.9%)
Reads written (passing filters):     1,621,940 (99.9%)

Total basepairs processed:   554,468,989 bp
Total written (filtered):    521,340,609 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1621940 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 6.4%
  C: 25.5%
  G: 68.0%
  T: 0.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1556	0.0	1	0 0 1556
19	24344	0.0	1	0 23634 710
20	1595351	0.0	2	1552643 41799 909
21	686	0.0	2	0 658 28
22	3	0.0	2	0 0 3

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR13_BF11_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 42.00 s (17 us/read; 3.57 M reads/minute).

=== Summary ===

Total reads processed:               2,498,279
Reads with adapters:                 2,490,625 (99.7%)
Reads written (passing filters):     2,490,625 (99.7%)

Total basepairs processed:   641,274,940 bp
Total written (filtered):    589,907,461 bp (92.0%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2490625 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	39701	0.0	1	0 0 39701
19	338204	0.0	1	0 332195 6009
20	2107330	0.0	2	2071184 35261 885
21	5330	0.0	2	0 5234 96
22	60	0.0	2	0 0 60

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR13_BF11_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.68 s (16 us/read; 3.67 M reads/minute).

=== Summary ===

Total reads processed:               2,490,625
Reads with adapters:                 2,488,497 (99.9%)
Reads written (passing filters):     2,488,497 (99.9%)

Total basepairs processed:   589,907,461 bp
Total written (filtered):    539,658,334 bp (91.5%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 2488497 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 65.4%
  C: 21.6%
  G: 9.6%
  T: 3.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1071	0.0	1	0 0 1071
19	16981	0.0	1	0 16749 232
20	2469631	0.0	2	2434498 34356 777
21	814	0.0	2	0 805 9

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR13_BF21_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 37.21 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               1,982,457
Reads with adapters:                 1,973,991 (99.6%)
Reads written (passing filters):     1,973,991 (99.6%)

Total basepairs processed:   715,409,667 bp
Total written (filtered):    673,217,956 bp (94.1%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 1973991 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	32144	0.0	1	0 0 32144
19	280356	0.0	1	0 270001 10355
20	1657183	0.0	2	1622720 33658 805
21	4267	0.0	2	0 4186 81
22	41	0.0	2	0 0 41

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR13_BF21_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 37.05 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               1,973,991
Reads with adapters:                 1,971,351 (99.9%)
Reads written (passing filters):     1,971,351 (99.9%)

Total basepairs processed:   673,217,956 bp
Total written (filtered):    632,904,403 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1971351 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 32.1%
  C: 9.1%
  G: 56.9%
  T: 1.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	799	0.0	1	0 0 799
19	8658	0.0	1	0 8330 328
20	1961115	0.0	2	1917384 42408 1323
21	777	0.0	2	0 666 111
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR14_BF10_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.78 s (16 us/read; 3.66 M reads/minute).

=== Summary ===

Total reads processed:               2,123,572
Reads with adapters:                 2,122,836 (100.0%)
Reads written (passing filters):     2,122,836 (100.0%)

Total basepairs processed:   545,142,044 bp
Total written (filtered):    502,514,121 bp (92.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2122836 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1119	0.0	1	0 0 1119
19	13371	0.0	1	0 13176 195
20	2107369	0.0	2	2070208 36784 377
21	974	0.0	2	0 958 16
22	3	0.0	2	0 0 3

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR14_BF10_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 35.18 s (17 us/read; 3.62 M reads/minute).

=== Summary ===

Total reads processed:               2,122,836
Reads with adapters:                 2,121,229 (99.9%)
Reads written (passing filters):     2,121,229 (99.9%)

Total basepairs processed:   502,514,121 bp
Total written (filtered):    459,718,077 bp (91.5%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 2121229 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 76.5%
  C: 9.8%
  G: 8.6%
  T: 5.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	623	0.0	1	0 0 623
19	10355	0.0	1	0 10241 114
20	2109522	0.0	2	2082240 26709 573
21	727	0.0	2	0 720 7
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L001_BR14_BF20_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.09 s (18 us/read; 3.26 M reads/minute).

=== Summary ===

Total reads processed:               1,959,978
Reads with adapters:                 1,959,219 (100.0%)
Reads written (passing filters):     1,959,219 (100.0%)

Total basepairs processed:   701,497,479 bp
Total written (filtered):    662,057,706 bp (94.4%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 1959219 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1049	0.0	1	0 0 1049
19	12825	0.0	1	0 12595 230
20	1944407	0.0	2	1901871 42074 462
21	934	0.0	2	0 897 37
22	4	0.0	2	0 0 4

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR14_BF20_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.61 s (21 us/read; 2.89 M reads/minute).

=== Summary ===

Total reads processed:               1,959,219
Reads with adapters:                 1,957,306 (99.9%)
Reads written (passing filters):     1,957,306 (99.9%)

Total basepairs processed:   662,057,706 bp
Total written (filtered):    622,275,406 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1957306 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 40.2%
  C: 4.5%
  G: 47.5%
  T: 7.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	605	0.0	1	0 0 605
19	6889	0.0	1	0 6677 212
20	1949200	0.0	2	1911209 37073 918
21	609	0.0	2	0 591 18
22	3	0.0	2	0 0 3

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR20_BF14_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 24.63 s (19 us/read; 3.18 M reads/minute).

=== Summary ===

Total reads processed:               1,304,804
Reads with adapters:                 1,303,247 (99.9%)
Reads written (passing filters):     1,303,247 (99.9%)

Total basepairs processed:   464,043,951 bp
Total written (filtered):    437,507,086 bp (94.3%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1303247 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	7280	0.0	1	0 0 7280
19	65253	0.0	1	0 64264 989
20	1229311	0.0	2	1205427 23648 236
21	1200	0.0	2	0 1179 21
22	203	0.0	2	0 0 203

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR20_BF14_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 24.81 s (19 us/read; 3.15 M reads/minute).

=== Summary ===

Total reads processed:               1,303,247
Reads with adapters:                 1,300,029 (99.8%)
Reads written (passing filters):     1,300,029 (99.8%)

Total basepairs processed:   437,507,086 bp
Total written (filtered):    410,487,358 bp (93.8%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1300029 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 76.2%
  C: 2.1%
  G: 17.4%
  T: 4.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	6335	0.0	1	0 0 6335
19	41015	0.0	1	0 39804 1211
20	1252026	0.0	2	1213496 37612 918
21	651	0.0	2	0 639 12
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR20_BF24_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 30.56 s (21 us/read; 2.84 M reads/minute).

=== Summary ===

Total reads processed:               1,446,303
Reads with adapters:                 1,444,702 (99.9%)
Reads written (passing filters):     1,444,702 (99.9%)

Total basepairs processed:   666,181,397 bp
Total written (filtered):    636,644,724 bp (95.6%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1444702 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	7972	0.0	1	0 0 7972
19	71942	0.0	1	0 70796 1146
20	1363319	0.0	2	1337836 25227 256
21	1351	0.0	2	0 1324 27
22	118	0.0	2	0 0 118

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR20_BF24_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 31.04 s (21 us/read; 2.79 M reads/minute).

=== Summary ===

Total reads processed:               1,444,702
Reads with adapters:                 1,443,053 (99.9%)
Reads written (passing filters):     1,443,053 (99.9%)

Total basepairs processed:   636,644,724 bp
Total written (filtered):    607,126,152 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1443053 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 29.9%
  C: 5.5%
  G: 57.1%
  T: 7.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1863	0.0	1	0 0 1863
19	49678	0.0	1	0 48184 1494
20	1390855	0.0	2	1347080 42502 1273
21	655	0.0	2	0 634 21
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR21_BF13_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 26.80 s (18 us/read; 3.25 M reads/minute).

=== Summary ===

Total reads processed:               1,451,480
Reads with adapters:                 1,449,480 (99.9%)
Reads written (passing filters):     1,449,480 (99.9%)

Total basepairs processed:   516,449,397 bp
Total written (filtered):    486,843,065 bp (94.3%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1449480 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	9333	0.0	1	0 0 9333
19	73904	0.0	1	0 72551 1353
20	1363025	0.0	2	1331236 31441 348
21	2560	0.0	2	0 2515 45
22	658	0.0	2	0 0 658

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR21_BF13_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 27.16 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               1,449,480
Reads with adapters:                 1,447,778 (99.9%)
Reads written (passing filters):     1,447,778 (99.9%)

Total basepairs processed:   486,843,065 bp
Total written (filtered):    457,327,932 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1447778 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 80.6%
  C: 11.5%
  G: 5.9%
  T: 1.9%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	555	0.0	1	0 0 555
19	5755	0.0	1	0 5627 128
20	1440837	0.0	2	1404539 35434 864
21	631	0.0	2	0 616 15

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR21_BF23_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 32.27 s (21 us/read; 2.88 M reads/minute).

=== Summary ===

Total reads processed:               1,549,852
Reads with adapters:                 1,547,784 (99.9%)
Reads written (passing filters):     1,547,784 (99.9%)

Total basepairs processed:   714,156,276 bp
Total written (filtered):    682,350,799 bp (95.5%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1547784 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	10027	0.0	1	0 0 10027
19	79269	0.0	1	0 77824 1445
20	1454882	0.0	2	1420269 34214 399
21	2794	0.0	2	0 2757 37
22	812	0.0	2	0 0 812

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR21_BF23_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 32.38 s (21 us/read; 2.87 M reads/minute).

=== Summary ===

Total reads processed:               1,547,784
Reads with adapters:                 1,546,698 (99.9%)
Reads written (passing filters):     1,546,698 (99.9%)

Total basepairs processed:   682,350,799 bp
Total written (filtered):    651,028,047 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1546698 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 43.2%
  C: 10.6%
  G: 43.4%
  T: 2.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	827	0.0	1	0 0 827
19	7411	0.0	1	0 7108 303
20	1537866	0.0	2	1480177 56123 1566
21	594	0.0	2	0 565 29

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR22_BF12_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 27.24 s (18 us/read; 3.26 M reads/minute).

=== Summary ===

Total reads processed:               1,479,969
Reads with adapters:                 1,477,740 (99.8%)
Reads written (passing filters):     1,477,740 (99.8%)

Total basepairs processed:   526,695,680 bp
Total written (filtered):    496,446,829 bp (94.3%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1477740 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	9415	0.0	1	0 0 9415
19	77066	0.0	1	0 75371 1695
20	1389397	0.0	2	1352376 36495 526
21	1427	0.0	2	0 1389 38
22	435	0.0	2	0 0 435

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR22_BF12_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 27.55 s (19 us/read; 3.22 M reads/minute).

=== Summary ===

Total reads processed:               1,477,740
Reads with adapters:                 1,476,073 (99.9%)
Reads written (passing filters):     1,476,073 (99.9%)

Total basepairs processed:   496,446,829 bp
Total written (filtered):    466,374,420 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1476073 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 93.8%
  C: 3.0%
  G: 3.1%
  T: 0.1%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	551	0.0	1	0 0 551
19	5757	0.0	1	0 5619 138
20	1469151	0.0	2	1435979 32384 788
21	614	0.0	2	0 594 20

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR22_BF22_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 27.01 s (21 us/read; 2.81 M reads/minute).

=== Summary ===

Total reads processed:               1,266,308
Reads with adapters:                 1,264,387 (99.8%)
Reads written (passing filters):     1,264,387 (99.8%)

Total basepairs processed:   583,512,178 bp
Total written (filtered):    557,433,629 bp (95.5%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1264387 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	7938	0.0	1	0 0 7938
19	65141	0.0	1	0 63694 1447
20	1189563	0.0	2	1157942 31199 422
21	1416	0.0	2	0 1373 43
22	329	0.0	2	0 0 329

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR22_BF22_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.71 s (23 us/read; 2.64 M reads/minute).

=== Summary ===

Total reads processed:               1,264,387
Reads with adapters:                 1,263,385 (99.9%)
Reads written (passing filters):     1,263,385 (99.9%)

Total basepairs processed:   557,433,629 bp
Total written (filtered):    531,756,327 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1263385 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 12.4%
  C: 47.5%
  G: 39.9%
  T: 0.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1179	0.0	1	0 0 1179
19	19321	0.0	1	0 18760 561
20	1242365	0.0	2	1208727 32710 928
21	516	0.0	2	0 498 18
22	4	0.0	2	0 0 4

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR23_BF11_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 29.30 s (19 us/read; 3.18 M reads/minute).

=== Summary ===

Total reads processed:               1,554,421
Reads with adapters:                 1,546,331 (99.5%)
Reads written (passing filters):     1,546,331 (99.5%)

Total basepairs processed:   552,950,537 bp
Total written (filtered):    519,455,696 bp (93.9%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1546331 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	35729	0.0	1	0 0 35729
19	218532	0.0	1	0 213894 4638
20	1289823	0.0	2	1244653 44422 748
21	1961	0.0	2	0 1907 54
22	286	0.0	2	0 0 286

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR23_BF11_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 29.21 s (19 us/read; 3.18 M reads/minute).

=== Summary ===

Total reads processed:               1,546,331
Reads with adapters:                 1,544,644 (99.9%)
Reads written (passing filters):     1,544,644 (99.9%)

Total basepairs processed:   519,455,696 bp
Total written (filtered):    488,008,170 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1544644 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 85.8%
  C: 9.4%
  G: 3.3%
  T: 1.5%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	681	0.0	1	0 0 681
19	10604	0.0	1	0 10427 177
20	1532822	0.0	2	1503855 28282 685
21	537	0.0	2	0 528 9

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR23_BF21_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 29.11 s (21 us/read; 2.84 M reads/minute).

=== Summary ===

Total reads processed:               1,377,324
Reads with adapters:                 1,370,035 (99.5%)
Reads written (passing filters):     1,370,035 (99.5%)

Total basepairs processed:   634,489,996 bp
Total written (filtered):    604,010,158 bp (95.2%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1370035 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	31782	0.0	1	0 0 31782
19	194830	0.0	1	0 190705 4125
20	1141375	0.0	2	1101049 39605 721
21	1816	0.0	2	0 1782 34
22	232	0.0	2	0 0 232

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR23_BF21_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 29.00 s (21 us/read; 2.83 M reads/minute).

=== Summary ===

Total reads processed:               1,370,035
Reads with adapters:                 1,369,041 (99.9%)
Reads written (passing filters):     1,369,041 (99.9%)

Total basepairs processed:   604,010,158 bp
Total written (filtered):    576,252,015 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1369041 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 30.9%
  C: 23.9%
  G: 42.2%
  T: 3.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	594	0.0	1	0 0 594
19	6150	0.0	1	0 5923 227
20	1361806	0.0	2	1329685 31086 1035
21	490	0.0	2	0 452 38
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR24_BF10_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.58 s (19 us/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:               1,526,717
Reads with adapters:                 1,525,449 (99.9%)
Reads written (passing filters):     1,525,449 (99.9%)

Total basepairs processed:   543,073,362 bp
Total written (filtered):    512,141,899 bp (94.3%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1525449 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1959	0.0	1	0 0 1959
19	19572	0.0	1	0 18928 644
20	1502187	0.0	2	1459423 42203 561
21	1531	0.0	2	0 1474 57
22	200	0.0	2	0 0 200

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR24_BF10_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.24 s (19 us/read; 3.24 M reads/minute).

=== Summary ===

Total reads processed:               1,525,449
Reads with adapters:                 1,523,874 (99.9%)
Reads written (passing filters):     1,523,874 (99.9%)

Total basepairs processed:   512,141,899 bp
Total written (filtered):    481,144,654 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1523874 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 76.9%
  C: 3.6%
  G: 15.0%
  T: 4.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	491	0.0	1	0 0 491
19	7803	0.0	1	0 7653 150
20	1515089	0.0	2	1488638 25759 692
21	490	0.0	2	0 479 11
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L001_BR24_BF20_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.10 s (21 us/read; 2.82 M reads/minute).

=== Summary ===

Total reads processed:               1,558,642
Reads with adapters:                 1,557,451 (99.9%)
Reads written (passing filters):     1,557,451 (99.9%)

Total basepairs processed:   718,079,059 bp
Total written (filtered):    686,410,467 bp (95.6%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1557451 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2009	0.0	1	0 0 2009
19	20665	0.0	1	0 19928 737
20	1533022	0.0	2	1489024 43450 548
21	1607	0.0	2	0 1550 57
22	148	0.0	2	0 0 148

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR24_BF20_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 32.48 s (21 us/read; 2.88 M reads/minute).

=== Summary ===

Total reads processed:               1,557,451
Reads with adapters:                 1,556,766 (100.0%)
Reads written (passing filters):     1,556,766 (100.0%)

Total basepairs processed:   686,410,467 bp
Total written (filtered):    654,999,638 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1556766 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 31.8%
  C: 7.7%
  G: 54.1%
  T: 6.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	530	0.0	1	0 0 530
19	5659	0.0	1	0 5436 223
20	1550045	0.0	2	1517261 31885 899
21	531	0.0	2	0 519 12
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF10_BR14_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.58 s (16 us/read; 3.65 M reads/minute).

=== Summary ===

Total reads processed:               2,224,481
Reads with adapters:                 2,223,804 (100.0%)
Reads written (passing filters):     2,223,804 (100.0%)

Total basepairs processed:   570,500,833 bp
Total written (filtered):    525,893,498 bp (92.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 2223804 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2933	0.0	1	0 0 2933
19	43331	0.0	1	0 42917 414
20	2171482	0.0	2	2147309 23956 217
21	2995	0.0	2	0 2822 173
22	3063	0.0	2	0 0 3063

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF10_BR14_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.50 s (16 us/read; 3.66 M reads/minute).

=== Summary ===

Total reads processed:               2,223,804
Reads with adapters:                 2,222,442 (99.9%)
Reads written (passing filters):     2,222,442 (99.9%)

Total basepairs processed:   525,893,498 bp
Total written (filtered):    481,135,600 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2222442 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 90.7%
  C: 0.2%
  G: 0.4%
  T: 8.7%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	940	0.0	1	0 0 940
19	10179	0.0	1	0 10029 150
20	2210060	0.0	2	2179343 29931 786
21	1262	0.0	2	0 1250 12
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF10_BR24_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 37.47 s (18 us/read; 3.25 M reads/minute).

=== Summary ===

Total reads processed:               2,029,883
Reads with adapters:                 2,029,155 (100.0%)
Reads written (passing filters):     2,029,155 (100.0%)

Total basepairs processed:   721,827,143 bp
Total written (filtered):    681,025,607 bp (94.3%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 2029155 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2866	0.0	1	0 0 2866
19	41494	0.0	1	0 41054 440
20	1978687	0.0	2	1955168 23293 226
21	2838	0.0	2	0 2652 186
22	3270	0.0	2	0 0 3270

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF10_BR24_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 37.67 s (19 us/read; 3.23 M reads/minute).

=== Summary ===

Total reads processed:               2,029,155
Reads with adapters:                 2,023,987 (99.7%)
Reads written (passing filters):     2,023,987 (99.7%)

Total basepairs processed:   681,025,607 bp
Total written (filtered):    638,854,270 bp (93.8%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 2023987 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.3%
  C: 43.0%
  G: 0.0%
  T: 56.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	2699	0.0	1	0 0 2699
19	26851	0.0	1	0 26214 637
20	1992786	0.0	2	1942644 48172 1970
21	1645	0.0	2	0 1583 62
22	6	0.0	2	0 0 6

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF11_BR13_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 39.72 s (17 us/read; 3.56 M reads/minute).

=== Summary ===

Total reads processed:               2,356,537
Reads with adapters:                 2,355,338 (99.9%)
Reads written (passing filters):     2,355,338 (99.9%)

Total basepairs processed:   604,912,475 bp
Total written (filtered):    557,562,123 bp (92.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 2355338 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5370	0.0	1	0 0 5370
19	61141	0.0	1	0 60362 779
20	2282668	0.0	2	2243084 39141 443
21	3161	0.0	2	0 2942 219
22	2998	0.0	2	0 0 2998

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF11_BR13_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 38.74 s (16 us/read; 3.65 M reads/minute).

=== Summary ===

Total reads processed:               2,355,338
Reads with adapters:                 2,353,786 (99.9%)
Reads written (passing filters):     2,353,786 (99.9%)

Total basepairs processed:   557,562,123 bp
Total written (filtered):    510,127,766 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2353786 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 74.0%
  C: 0.1%
  G: 0.2%
  T: 25.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1022	0.0	1	0 0 1022
19	8750	0.0	1	0 8614 136
20	2342728	0.0	2	2310996 30751 981
21	1284	0.0	2	0 1274 10
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF11_BR23_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 28.87 s (18 us/read; 3.25 M reads/minute).

=== Summary ===

Total reads processed:               1,565,170
Reads with adapters:                 1,564,345 (99.9%)
Reads written (passing filters):     1,564,345 (99.9%)

Total basepairs processed:   556,918,332 bp
Total written (filtered):    525,381,819 bp (94.3%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1564345 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	3745	0.0	1	0 0 3745
19	41294	0.0	1	0 40651 643
20	1515115	0.0	2	1487626 27170 319
21	1987	0.0	2	0 1785 202
22	2204	0.0	2	0 0 2204

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF11_BR23_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 30.78 s (20 us/read; 3.05 M reads/minute).

=== Summary ===

Total reads processed:               1,564,345
Reads with adapters:                 1,560,847 (99.8%)
Reads written (passing filters):     1,560,847 (99.8%)

Total basepairs processed:   525,381,819 bp
Total written (filtered):    493,012,379 bp (93.8%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1560847 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 80.6%
  G: 0.0%
  T: 19.3%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "C" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "C" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1854	0.0	1	0 0 1854
19	14428	0.0	1	0 14180 248
20	1543234	0.0	2	1514576 27518 1140
21	1329	0.0	2	0 1296 33
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF12_BR12_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 39.16 s (16 us/read; 3.66 M reads/minute).

=== Summary ===

Total reads processed:               2,389,803
Reads with adapters:                 2,388,547 (99.9%)
Reads written (passing filters):     2,388,547 (99.9%)

Total basepairs processed:   612,095,648 bp
Total written (filtered):    564,066,750 bp (92.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 2388547 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4921	0.0	1	0 0 4921
19	63322	0.0	1	0 62278 1044
20	2309935	0.0	2	2262578 46654 703
21	9261	0.0	2	0 8997 264
22	1108	0.0	2	0 0 1108

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF12_BR12_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 39.05 s (16 us/read; 3.67 M reads/minute).

=== Summary ===

Total reads processed:               2,388,547
Reads with adapters:                 2,386,990 (99.9%)
Reads written (passing filters):     2,386,990 (99.9%)

Total basepairs processed:   564,066,750 bp
Total written (filtered):    515,970,092 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2386990 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 82.8%
  C: 0.1%
  G: 0.3%
  T: 16.8%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1008	0.0	1	0 0 1008
19	8492	0.0	1	0 8339 153
20	2376273	0.0	2	2333506 41379 1388
21	1217	0.0	2	0 1194 23

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF12_BR22_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.42 s (19 us/read; 3.13 M reads/minute).

=== Summary ===

Total reads processed:               1,798,167
Reads with adapters:                 1,797,073 (99.9%)
Reads written (passing filters):     1,797,073 (99.9%)

Total basepairs processed:   639,514,657 bp
Total written (filtered):    603,233,026 bp (94.3%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1797073 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	3793	0.0	1	0 0 3793
19	47768	0.0	1	0 46898 870
20	1738651	0.0	2	1701287 36770 594
21	4218	0.0	2	0 3968 250
22	2643	0.0	2	0 0 2643

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF12_BR22_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.10 s (19 us/read; 3.16 M reads/minute).

=== Summary ===

Total reads processed:               1,797,073
Reads with adapters:                 1,793,131 (99.8%)
Reads written (passing filters):     1,793,131 (99.8%)

Total basepairs processed:   603,233,026 bp
Total written (filtered):    566,074,396 bp (93.8%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1793131 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 86.3%
  G: 0.0%
  T: 13.7%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "C" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "C" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	2149	0.0	1	0 0 2149
19	15771	0.0	1	0 15460 311
20	1773935	0.0	2	1742544 30001 1390
21	1270	0.0	2	0 1250 20
22	6	0.0	2	0 0 6

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF13_BR11_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 47.69 s (17 us/read; 3.59 M reads/minute).

=== Summary ===

Total reads processed:               2,851,606
Reads with adapters:                 2,847,558 (99.9%)
Reads written (passing filters):     2,847,558 (99.9%)

Total basepairs processed:   730,961,617 bp
Total written (filtered):    673,074,434 bp (92.1%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 2847558 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	25020	0.0	1	0 0 25020
19	217354	0.0	1	0 213311 4043
20	2479951	0.0	2	2432899 42032 5020
21	74897	0.0	2	0 73721 1176
22	50336	0.0	2	0 0 50336

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF13_BR11_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 46.41 s (16 us/read; 3.68 M reads/minute).

=== Summary ===

Total reads processed:               2,847,558
Reads with adapters:                 2,845,772 (99.9%)
Reads written (passing filters):     2,845,772 (99.9%)

Total basepairs processed:   673,074,434 bp
Total written (filtered):    615,762,571 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2845772 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 78.3%
  C: 0.1%
  G: 0.3%
  T: 21.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1071	0.0	1	0 0 1071
19	25743	0.0	1	0 25385 358
20	2817771	0.0	2	2772341 43667 1763
21	1186	0.0	2	0 1162 24
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF13_BR21_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 35.56 s (19 us/read; 3.19 M reads/minute).

=== Summary ===

Total reads processed:               1,888,896
Reads with adapters:                 1,885,848 (99.8%)
Reads written (passing filters):     1,885,848 (99.8%)

Total basepairs processed:   671,554,677 bp
Total written (filtered):    632,822,374 bp (94.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1885848 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	17330	0.0	1	0 0 17330
19	146730	0.0	1	0 143809 2921
20	1638574	0.0	2	1605190 30095 3289
21	45094	0.0	2	0 44262 832
22	38120	0.0	2	0 0 38120

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF13_BR21_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.72 s (19 us/read; 3.08 M reads/minute).

=== Summary ===

Total reads processed:               1,885,848
Reads with adapters:                 1,881,555 (99.8%)
Reads written (passing filters):     1,881,555 (99.8%)

Total basepairs processed:   632,822,374 bp
Total written (filtered):    593,781,199 bp (93.8%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1881555 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 70.8%
  G: 0.0%
  T: 29.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	2142	0.0	1	0 0 2142
19	15608	0.0	1	0 15292 316
20	1862190	0.0	2	1831128 29594 1468
21	1611	0.0	2	0 1580 31
22	4	0.0	2	0 0 4

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF14_BR10_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.66 s (16 us/read; 3.71 M reads/minute).

=== Summary ===

Total reads processed:               2,515,739
Reads with adapters:                 2,515,167 (100.0%)
Reads written (passing filters):     2,515,167 (100.0%)

Total basepairs processed:   645,452,009 bp
Total written (filtered):    595,000,771 bp (92.2%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 2515167 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1251	0.0	1	0 0 1251
19	12309	0.0	1	0 12116 193
20	2496826	0.0	2	2461457 35066 303
21	2276	0.0	2	0 2185 91
22	2505	0.0	2	0 0 2505

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF14_BR10_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.17 s (16 us/read; 3.67 M reads/minute).

=== Summary ===

Total reads processed:               2,515,167
Reads with adapters:                 2,513,896 (99.9%)
Reads written (passing filters):     2,513,896 (99.9%)

Total basepairs processed:   595,000,771 bp
Total written (filtered):    544,442,526 bp (91.5%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2513896 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 92.8%
  C: 0.1%
  G: 0.3%
  T: 6.8%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	828	0.0	1	0 0 828
19	20104	0.0	1	0 19874 230
20	2492134	0.0	2	2464521 26687 926
21	829	0.0	2	0 820 9
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF14_BR20_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.52 s (19 us/read; 3.24 M reads/minute).

=== Summary ===

Total reads processed:               1,807,830
Reads with adapters:                 1,807,418 (100.0%)
Reads written (passing filters):     1,807,418 (100.0%)

Total basepairs processed:   643,040,858 bp
Total written (filtered):    606,752,571 bp (94.4%)

=== Adapter 1 ===

Sequence: ACWGGWTGRACWGTNTAYCC; Type: anchored 5'; Length: 20; Trimmed: 1807418 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	834	0.0	1	0 0 834
19	8724	0.0	1	0 8575 149
20	1794652	0.0	2	1768919 25524 209
21	1578	0.0	2	0 1506 72
22	1630	0.0	2	0 0 1630

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF14_BR20_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.09 s (19 us/read; 3.18 M reads/minute).

=== Summary ===

Total reads processed:               1,807,418
Reads with adapters:                 1,803,999 (99.8%)
Reads written (passing filters):     1,803,999 (99.8%)

Total basepairs processed:   606,752,571 bp
Total written (filtered):    569,545,130 bp (93.9%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1803999 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 2.2%
  C: 33.6%
  G: 0.1%
  T: 64.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1482	0.0	1	0 0 1482
19	12794	0.0	1	0 12625 169
20	1788700	0.0	2	1767003 20319 1378
21	1019	0.0	2	0 988 31
22	4	0.0	2	0 0 4

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF20_BR14_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.88 s (18 us/read; 3.28 M reads/minute).

=== Summary ===

Total reads processed:               2,292,433
Reads with adapters:                 2,291,588 (100.0%)
Reads written (passing filters):     2,291,588 (100.0%)

Total basepairs processed:   820,270,032 bp
Total written (filtered):    774,188,070 bp (94.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 2291588 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	4109	0.0	1	0 0 4109
19	49089	0.0	1	0 48645 444
20	2230874	0.0	2	2206201 24406 267
21	6519	0.0	2	0 6429 90
22	997	0.0	2	0 0 997

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF20_BR14_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 44.80 s (20 us/read; 3.07 M reads/minute).

=== Summary ===

Total reads processed:               2,291,588
Reads with adapters:                 2,287,863 (99.8%)
Reads written (passing filters):     2,287,863 (99.8%)

Total basepairs processed:   774,188,070 bp
Total written (filtered):    727,179,563 bp (93.9%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2287863 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 90.0%
  C: 1.8%
  G: 1.1%
  T: 7.1%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	925	0.0	1	0 0 925
19	10570	0.0	1	0 10390 180
20	2275009	0.0	2	2239629 33995 1385
21	1356	0.0	2	0 1346 10
22	3	0.0	2	0 0 3

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF20_BR24_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 42.08 s (22 us/read; 2.79 M reads/minute).

=== Summary ===

Total reads processed:               1,955,755
Reads with adapters:                 1,955,046 (100.0%)
Reads written (passing filters):     1,955,046 (100.0%)

Total basepairs processed:   900,600,413 bp
Total written (filtered):    861,221,544 bp (95.6%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1955046 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	3576	0.0	1	0 0 3576
19	42517	0.0	1	0 42134 383
20	1902385	0.0	2	1880955 21213 217
21	5657	0.0	2	0 5583 74
22	911	0.0	2	0 0 911

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF20_BR24_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 42.45 s (22 us/read; 2.76 M reads/minute).

=== Summary ===

Total reads processed:               1,955,046
Reads with adapters:                 1,951,303 (99.8%)
Reads written (passing filters):     1,951,303 (99.8%)

Total basepairs processed:   861,221,544 bp
Total written (filtered):    820,592,980 bp (95.3%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1951303 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.2%
  C: 12.7%
  G: 0.1%
  T: 87.1%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "T" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "T" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	2417	0.0	1	0 0 2417
19	25399	0.0	1	0 24762 637
20	1921911	0.0	2	1867485 51319 3107
21	1575	0.0	2	0 1493 82
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF21_BR13_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 47.43 s (19 us/read; 3.22 M reads/minute).

=== Summary ===

Total reads processed:               2,544,527
Reads with adapters:                 2,543,009 (99.9%)
Reads written (passing filters):     2,543,009 (99.9%)

Total basepairs processed:   918,663,571 bp
Total written (filtered):    867,331,757 bp (94.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 2543009 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	6589	0.0	1	0 0 6589
19	69615	0.0	1	0 68878 737
20	2456746	0.0	2	2423246 33071 429
21	8643	0.0	2	0 8499 144
22	1416	0.0	2	0 0 1416

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF21_BR13_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 48.25 s (19 us/read; 3.16 M reads/minute).

=== Summary ===

Total reads processed:               2,543,009
Reads with adapters:                 2,538,796 (99.8%)
Reads written (passing filters):     2,538,796 (99.8%)

Total basepairs processed:   867,331,757 bp
Total written (filtered):    815,130,491 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2538796 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 87.8%
  C: 0.2%
  G: 0.5%
  T: 11.5%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1007	0.0	1	0 0 1007
19	9394	0.0	1	0 8549 845
20	2527052	0.0	2	2489798 35398 1856
21	1341	0.0	2	0 1315 26
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF21_BR23_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.98 s (21 us/read; 2.81 M reads/minute).

=== Summary ===

Total reads processed:               1,915,708
Reads with adapters:                 1,914,573 (99.9%)
Reads written (passing filters):     1,914,573 (99.9%)

Total basepairs processed:   882,778,300 bp
Total written (filtered):    844,019,642 bp (95.6%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1914573 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5252	0.0	1	0 0 5252
19	52746	0.0	1	0 52168 578
20	1846991	0.0	2	1820568 26107 316
21	6830	0.0	2	0 6734 96
22	2754	0.0	2	0 0 2754

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF21_BR23_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.84 s (21 us/read; 2.81 M reads/minute).

=== Summary ===

Total reads processed:               1,914,573
Reads with adapters:                 1,911,526 (99.8%)
Reads written (passing filters):     1,911,526 (99.8%)

Total basepairs processed:   844,019,642 bp
Total written (filtered):    804,487,762 bp (95.3%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1911526 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 72.6%
  G: 0.1%
  T: 27.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	2186	0.0	1	0 0 2186
19	16847	0.0	1	0 16489 358
20	1890819	0.0	2	1851413 37405 2001
21	1672	0.0	2	0 1627 45
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF22_BR12_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 42.99 s (19 us/read; 3.23 M reads/minute).

=== Summary ===

Total reads processed:               2,316,518
Reads with adapters:                 2,314,467 (99.9%)
Reads written (passing filters):     2,314,467 (99.9%)

Total basepairs processed:   835,866,641 bp
Total written (filtered):    788,967,558 bp (94.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 2314467 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	11410	0.0	1	0 0 11410
19	112927	0.0	1	0 111494 1433
20	2180902	0.0	2	2144629 35658 615
21	8573	0.0	2	0 8414 159
22	655	0.0	2	0 0 655

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF22_BR12_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 43.21 s (19 us/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:               2,314,467
Reads with adapters:                 2,310,754 (99.8%)
Reads written (passing filters):     2,310,754 (99.8%)

Total basepairs processed:   788,967,558 bp
Total written (filtered):    741,503,214 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2310754 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 96.2%
  C: 0.2%
  G: 0.6%
  T: 3.0%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1048	0.0	1	0 0 1048
19	8333	0.0	1	0 7726 607
20	2300105	0.0	2	2125012 171063 4030
21	1266	0.0	2	0 1245 21
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF22_BR22_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.99 s (22 us/read; 2.77 M reads/minute).

=== Summary ===

Total reads processed:               1,937,499
Reads with adapters:                 1,935,809 (99.9%)
Reads written (passing filters):     1,935,809 (99.9%)

Total basepairs processed:   892,113,825 bp
Total written (filtered):    852,739,259 bp (95.6%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1935809 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	9304	0.0	1	0 0 9304
19	92824	0.0	1	0 91650 1174
20	1825179	0.0	2	1796501 28184 494
21	6738	0.0	2	0 6612 126
22	1764	0.0	2	0 0 1764

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF22_BR22_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.99 s (22 us/read; 2.77 M reads/minute).

=== Summary ===

Total reads processed:               1,935,809
Reads with adapters:                 1,932,724 (99.8%)
Reads written (passing filters):     1,932,724 (99.8%)

Total basepairs processed:   852,739,259 bp
Total written (filtered):    812,834,676 bp (95.3%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1932724 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 71.4%
  G: 0.1%
  T: 28.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	2190	0.0	1	0 0 2190
19	16384	0.0	1	0 16040 344
20	1912798	0.0	2	1875761 34933 2104
21	1351	0.0	2	0 1330 21
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF23_BR11_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 50.00 s (19 us/read; 3.16 M reads/minute).

=== Summary ===

Total reads processed:               2,634,672
Reads with adapters:                 2,627,973 (99.7%)
Reads written (passing filters):     2,627,973 (99.7%)

Total basepairs processed:   950,996,771 bp
Total written (filtered):    896,272,525 bp (94.2%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 2627973 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	33494	0.0	1	0 0 33494
19	257715	0.0	1	0 253628 4087
20	2257503	0.0	2	2213371 38830 5302
21	68015	0.0	2	0 66844 1171
22	11246	0.0	2	0 0 11246

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF23_BR11_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 49.27 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               2,627,973
Reads with adapters:                 2,623,365 (99.8%)
Reads written (passing filters):     2,623,365 (99.8%)

Total basepairs processed:   896,272,525 bp
Total written (filtered):    842,261,827 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2623365 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 91.5%
  C: 0.2%
  G: 0.6%
  T: 7.7%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1143	0.0	1	0 0 1143
19	24840	0.0	1	0 24418 422
20	2596240	0.0	2	2414906 177218 4116
21	1140	0.0	2	0 1043 97
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF23_BR21_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.00 s (21 us/read; 2.83 M reads/minute).

=== Summary ===

Total reads processed:               1,697,205
Reads with adapters:                 1,692,672 (99.7%)
Reads written (passing filters):     1,692,672 (99.7%)

Total basepairs processed:   781,493,570 bp
Total written (filtered):    745,698,635 bp (95.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1692672 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	22298	0.0	1		0 0 22298
19	164846	0.0	1	0 162057 2789
20	1444815	0.0	2	1416216 25068 3531
21	42895	0.0	2	0 42150 745
22	17818	0.0	2	0 0 17818

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF23_BR21_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 35.82 s (21 us/read; 2.84 M reads/minute).

=== Summary ===

Total reads processed:               1,692,672
Reads with adapters:                 1,690,214 (99.9%)
Reads written (passing filters):     1,690,214 (99.9%)

Total basepairs processed:   745,698,635 bp
Total written (filtered):    710,841,216 bp (95.3%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1690214 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.1%
  C: 69.1%
  G: 0.1%
  T: 30.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1938	0.0	1	0 0 1938
19	14340	0.0	1	0 14026 314
20	1672455	0.0	2	1640176 30644 1635
21	1475	0.0	2	0 1452 23
22	6	0.0	2	0 0 6

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF24_BR10_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 51.19 s (18 us/read; 3.25 M reads/minute).

=== Summary ===

Total reads processed:               2,770,960
Reads with adapters:                 2,769,734 (100.0%)
Reads written (passing filters):     2,769,734 (100.0%)

Total basepairs processed:   997,182,931 bp
Total written (filtered):    941,362,538 bp (94.4%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 2769734 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1695	0.0	1	0 0 1695
19	18009	0.0	1	0 17809 200
20	2740290	0.0	2	2704846 35158 286
21	8521	0.0	2	0 8393 128
22	1219	0.0	2	0 0 1219

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF24_BR10_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 51.67 s (19 us/read; 3.22 M reads/minute).

=== Summary ===

Total reads processed:               2,769,734
Reads with adapters:                 2,765,636 (99.9%)
Reads written (passing filters):     2,765,636 (99.9%)

Total basepairs processed:   941,362,538 bp
Total written (filtered):    884,678,189 bp (94.0%)

=== Adapter 1 ===

Sequence: GCHGGDGCHATYACHATRYT; Type: anchored 3'; Length: 20; Trimmed: 2765636 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 91.3%
  C: 0.9%
  G: 1.1%
  T: 6.8%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1012	0.0	1	0 0 1012
19	23210	0.0	1	0 22900 310
20	2740519	0.0	2	2694065 44577 1877
21	893	0.0	2	0 840 53
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt ../2 PE read merging/BP_rerun_L002_BF24_BR20_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.41 s (21 us/read; 2.85 M reads/minute).

=== Summary ===

Total reads processed:               1,968,003
Reads with adapters:                 1,967,188 (100.0%)
Reads written (passing filters):     1,967,188 (100.0%)

Total basepairs processed:   906,283,390 bp
Total written (filtered):    866,583,763 bp (95.6%)

=== Adapter 1 ===

Sequence: GCHCCHGAYATRGCHTTYCC; Type: anchored 5'; Length: 20; Trimmed: 1967188 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1231	0.0	1	0 0 1231
19	12390	0.0	1	0 12251 139
20	1946046	0.0	2	1920369 25441 236
21	6174	0.0	2	0 6090 84
22	1347	0.0	2	0 0 1347

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF24_BR20_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.89 s (21 us/read; 2.82 M reads/minute).

=== Summary ===

Total reads processed:               1,967,188
Reads with adapters:                 1,964,616 (99.9%)
Reads written (passing filters):     1,964,616 (99.9%)

Total basepairs processed:   866,583,763 bp
Total written (filtered):    826,210,539 bp (95.3%)

=== Adapter 1 ===

Sequence: TGRTTYTTYGGNCAYCCHGA; Type: anchored 3'; Length: 20; Trimmed: 1964616 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 1.3%
  C: 18.3%
  G: 0.1%
  T: 80.3%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "T" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "T" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	1671	0.0	1	0 0 1671
19	14887	0.0	1	0 14637 250
20	1946760	0.0	2	1916765 27775 2220
21	1296	0.0	2	0 1245 51
22	2	0.0	2	0 0 2

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR10_BF14_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.68 s (16 us/read; 3.71 M reads/minute).

=== Summary ===

Total reads processed:               2,514,735
Reads with adapters:                 2,513,589 (100.0%)
Reads written (passing filters):     2,513,589 (100.0%)

Total basepairs processed:   645,223,130 bp
Total written (filtered):    594,731,331 bp (92.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2513589 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5395	0.0	1	0 0 5395
19	72572	0.0	1	0 71823 749
20	2433647	0.0	2	2406263 27133 251
21	1958	0.0	2	0 1930 28
22	17	0.0	2	0 0 17

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR10_BF14_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 42.29 s (17 us/read; 3.57 M reads/minute).

=== Summary ===

Total reads processed:               2,513,589
Reads with adapters:                 2,508,883 (99.8%)
Reads written (passing filters):     2,508,883 (99.8%)

Total basepairs processed:   594,731,331 bp
Total written (filtered):    543,553,505 bp (91.4%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 2508883 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 77.3%
  C: 3.3%
  G: 14.7%
  T: 4.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	12156	0.0	1	0 0 12156
19	78585	0.0	1	0 76872 1713
20	2416852	0.0	2	2363041 52359 1452
21	1290	0.0	2	0 1267 23

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR10_BF24_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 45.70 s (19 us/read; 3.19 M reads/minute).

=== Summary ===

Total reads processed:               2,431,819
Reads with adapters:                 2,430,738 (100.0%)
Reads written (passing filters):     2,430,738 (100.0%)

Total basepairs processed:   870,344,991 bp
Total written (filtered):    821,423,079 bp (94.4%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2430738 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5311	0.0	1	0 0 5311
19	70250	0.0	1	0 69325 925
20	2353278	0.0	2	2323541 29417 320
21	1891	0.0	2	0 1839 52
22	8	0.0	2	0 0 8

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR10_BF24_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 45.52 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:               2,430,738
Reads with adapters:                 2,425,870 (99.8%)
Reads written (passing filters):     2,425,870 (99.8%)

Total basepairs processed:   821,423,079 bp
Total written (filtered):    771,349,091 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 2425870 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 43.5%
  C: 3.5%
  G: 45.1%
  T: 7.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	3147	0.0	1	0 0 3147
19	83082	0.0	1	0 81300 1782
20	2338554	0.0	2	2292242 44879 1433
21	1081	0.0	2	0 1053 28
22	6	0.0	2	0 0 6

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR11_BF13_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.87 s (17 us/read; 3.44 M reads/minute).

=== Summary ===

Total reads processed:               2,402,082
Reads with adapters:                 2,400,946 (100.0%)
Reads written (passing filters):     2,400,946 (100.0%)

Total basepairs processed:   616,906,213 bp
Total written (filtered):    568,671,011 bp (92.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2400946 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5664	0.0	1	0 0 5664
19	64123	0.0	1	0 63503 620
20	2328926	0.0	2	2288378 40144 404
21	2228	0.0	2	0 2173 55
22	5	0.0	2	0 0 5

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR11_BF13_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 39.68 s (17 us/read; 3.63 M reads/minute).

=== Summary ===

Total reads processed:               2,400,946
Reads with adapters:                 2,399,388 (99.9%)
Reads written (passing filters):     2,399,388 (99.9%)

Total basepairs processed:   568,671,011 bp
Total written (filtered):    520,325,746 bp (91.5%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 2399388 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 61.6%
  C: 30.7%
  G: 5.3%
  T: 2.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	938	0.0	1	0 0 938
19	9248	0.0	1	0 9103 145
20	2388176	0.0	2	2355166 31918 1092
21	1024	0.0	2	0 1007 17
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR11_BF23_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 44.05 s (19 us/read; 3.15 M reads/minute).

=== Summary ===

Total reads processed:               2,313,260
Reads with adapters:                 2,312,040 (99.9%)
Reads written (passing filters):     2,312,040 (99.9%)

Total basepairs processed:   836,021,311 bp
Total written (filtered):    789,417,489 bp (94.4%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2312040 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5806	0.0	1	0 0 5806
19	63868	0.0	1	0 63097 771
20	2240218	0.0	2	2161124 78288 806
21	2145	0.0	2	0 2050 95
22	3	0.0	2	0 0 3

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR11_BF23_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 44.28 s (19 us/read; 3.13 M reads/minute).

=== Summary ===

Total reads processed:               2,312,040
Reads with adapters:                 2,308,599 (99.9%)
Reads written (passing filters):     2,308,599 (99.9%)

Total basepairs processed:   789,417,489 bp
Total written (filtered):    742,086,171 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 2308599 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 31.7%
  C: 8.1%
  G: 58.4%
  T: 1.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1239	0.0	1	0 0 1239
19	10875	0.0	1	0 10477 398
20	2295561	0.0	2	2239116 55044 1401
21	922	0.0	2	0 901 21
22	2	0.0	2	0 0 2

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR12_BF12_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.19 s (16 us/read; 3.70 M reads/minute).

=== Summary ===

Total reads processed:               2,108,050
Reads with adapters:                 2,106,767 (99.9%)
Reads written (passing filters):     2,106,767 (99.9%)

Total basepairs processed:   541,390,503 bp
Total written (filtered):    499,005,036 bp (92.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2106767 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5792	0.0	1	0 0 5792
19	68508	0.0	1	0 67393 1115
20	2030289	0.0	2	1987282 42526 481
21	2165	0.0	2	0 2133 32
22	13	0.0	2	0 0 13

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR12_BF12_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.55 s (16 us/read; 3.66 M reads/minute).

=== Summary ===

Total reads processed:               2,106,767
Reads with adapters:                 2,105,468 (99.9%)
Reads written (passing filters):     2,105,468 (99.9%)

Total basepairs processed:   499,005,036 bp
Total written (filtered):    456,596,040 bp (91.5%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 2105468 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 62.8%
  C: 22.6%
  G: 14.1%
  T: 0.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	810	0.0	1	0 0 810
19	8336	0.0	1	0 8175 161
20	2095371	0.0	2	2056785 37577 1009
21	951	0.0	2	0 930 21

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR12_BF22_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 38.28 s (19 us/read; 3.23 M reads/minute).

=== Summary ===

Total reads processed:               2,061,876
Reads with adapters:                 2,060,435 (99.9%)
Reads written (passing filters):     2,060,435 (99.9%)

Total basepairs processed:   745,115,606 bp
Total written (filtered):    703,467,315 bp (94.4%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2060435 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	5987	0.0	1	0 0 5987
19	67916	0.0	1	0 65688 2228
20	1984408	0.0	2	1893652 89644 1112
21	2118	0.0	2	0 2084 34
22	6	0.0	2	0 0 6

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR12_BF22_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 39.15 s (19 us/read; 3.16 M reads/minute).

=== Summary ===

Total reads processed:               2,060,435
Reads with adapters:                 2,056,852 (99.8%)
Reads written (passing filters):     2,056,852 (99.8%)

Total basepairs processed:   703,467,315 bp
Total written (filtered):    661,146,260 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 2056852 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 6.4%
  C: 25.5%
  G: 68.0%
  T: 0.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1981	0.0	1	0 0 1981
19	31267	0.0	1	0 30595 672
20	2022690	0.0	2	1982364 39093 1233
21	907	0.0	2	0 878 29
22	7	0.0	2	0 0 7

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR13_BF11_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 52.05 s (16 us/read; 3.68 M reads/minute).

=== Summary ===

Total reads processed:               3,192,983
Reads with adapters:                 3,183,686 (99.7%)
Reads written (passing filters):     3,183,686 (99.7%)

Total basepairs processed:   819,595,298 bp
Total written (filtered):    754,063,287 bp (92.0%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 3183686 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	50268	0.0	1	0 0 50268
19	432513	0.0	1	0 425682 6831
20	2693998	0.0	2	2656447 36605 946
21	6816	0.0	2	0 6722 94
22	91	0.0	2	0 0 91

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR13_BF11_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 52.22 s (16 us/read; 3.66 M reads/minute).

=== Summary ===

Total reads processed:               3,183,686
Reads with adapters:                 3,181,765 (99.9%)
Reads written (passing filters):     3,181,765 (99.9%)

Total basepairs processed:   754,063,287 bp
Total written (filtered):    690,002,544 bp (91.5%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 3181765 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 65.5%
  C: 21.5%
  G: 9.6%
  T: 3.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1375	0.0	1	0 0 1375
19	21555	0.0	1	0 21288 267
20	3157785	0.0	2	3117750 38689 1346
21	1050	0.0	2	0 1042 8

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR13_BF21_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 47.76 s (19 us/read; 3.15 M reads/minute).

=== Summary ===

Total reads processed:               2,508,587
Reads with adapters:                 2,499,532 (99.6%)
Reads written (passing filters):     2,499,532 (99.6%)

Total basepairs processed:   905,287,398 bp
Total written (filtered):    852,465,816 bp (94.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2499532 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	41720	0.0	1	0 0 41720
19	354179	0.0	1	0 342192 11987
20	2098058	0.0	2	2065424 31785 849
21	5538	0.0	2	0 5462 76
22	37	0.0	2	0 0 37

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR13_BF21_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 47.26 s (19 us/read; 3.17 M reads/minute).

=== Summary ===

Total reads processed:               2,499,532
Reads with adapters:                 2,495,272 (99.8%)
Reads written (passing filters):     2,495,272 (99.8%)

Total basepairs processed:   852,465,816 bp
Total written (filtered):    801,126,327 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 2495272 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 32.2%
  C: 9.0%
  G: 56.9%
  T: 1.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1009	0.0	1	0 0 1009
19	11096	0.0	1	0 10754 342
20	2482178	0.0	2	2442154 38303 1721
21	985	0.0	2	0 860 125
22	4	0.0	2	0 0 4

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR14_BF10_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 44.37 s (16 us/read; 3.65 M reads/minute).

=== Summary ===

Total reads processed:               2,699,994
Reads with adapters:                 2,699,092 (100.0%)
Reads written (passing filters):     2,699,092 (100.0%)

Total basepairs processed:   693,159,321 bp
Total written (filtered):    638,967,416 bp (92.2%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2699092 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1401	0.0	1	0 0 1401
19	16559	0.0	1	0 16345 214
20	2679848	0.0	2	2645207 34403 238
21	1279	0.0	2	0 1258 21
22	5	0.0	2	0 0 5

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR14_BF10_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 45.38 s (17 us/read; 3.57 M reads/minute).

=== Summary ===

Total reads processed:               2,699,092
Reads with adapters:                 2,697,734 (99.9%)
Reads written (passing filters):     2,697,734 (99.9%)

Total basepairs processed:   638,967,416 bp
Total written (filtered):    584,698,800 bp (91.5%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 2697734 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 76.5%
  C: 9.7%
  G: 8.6%
  T: 5.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	758	0.0	1	0 0 758
19	13195	0.0	1	0 13052 143
20	2682892	0.0	2	2654907 27000 985
21	889	0.0	2	0 883 6

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^ARYATDGTRATDGCHCCDGC -o temp.txt ../2 PE read merging/BP_rerun_L002_BR14_BF20_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 45.33 s (18 us/read; 3.27 M reads/minute).

=== Summary ===

Total reads processed:               2,469,104
Reads with adapters:                 2,468,166 (100.0%)
Reads written (passing filters):     2,468,166 (100.0%)

Total basepairs processed:   883,722,667 bp
Total written (filtered):    834,045,997 bp (94.4%)

=== Adapter 1 ===

Sequence: ARYATDGTRATDGCHCCDGC; Type: anchored 5'; Length: 20; Trimmed: 2468166 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	1326	0.0	1	0 0 1326
19	16143	0.0	1	0 15931 212
20	2449568	0.0	2	2413815 35447 306
21	1125	0.0	2	0 1090 35
22	4	0.0	2	0 0 4

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR14_BF20_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 46.08 s (19 us/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:               2,468,166
Reads with adapters:                 2,464,789 (99.9%)
Reads written (passing filters):     2,464,789 (99.9%)

Total basepairs processed:   834,045,997 bp
Total written (filtered):    783,617,509 bp (94.0%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 2464789 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 40.2%
  C: 4.5%
  G: 47.5%
  T: 7.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	767	0.0	1	0 0 767
19	8571	0.0	1	0 8319 252
20	2454600	0.0	2	2420420 32935 1245
21	848	0.0	2	0 819 29
22	3	0.0	2	0 0 3

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR20_BF14_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 30.93 s (19 us/read; 3.22 M reads/minute).

=== Summary ===

Total reads processed:               1,660,717
Reads with adapters:                 1,658,761 (99.9%)
Reads written (passing filters):     1,658,761 (99.9%)

Total basepairs processed:   590,624,405 bp
Total written (filtered):    556,858,260 bp (94.3%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1658761 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	9282	0.0	1	0 0 9282
19	82928	0.0	1	0 82021 907
20	1564833	0.0	2	1542825 21771 237
21	1502	0.0	2	0 1490 12
22	216	0.0	2	0 0 216

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR20_BF14_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 31.97 s (19 us/read; 3.11 M reads/minute).

=== Summary ===

Total reads processed:               1,658,761
Reads with adapters:                 1,654,116 (99.7%)
Reads written (passing filters):     1,654,116 (99.7%)

Total basepairs processed:   556,858,260 bp
Total written (filtered):    522,292,967 bp (93.8%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1654116 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 76.2%
  C: 2.1%
  G: 17.3%
  T: 4.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	7941	0.0	1	0 0 7941
19	52127	0.0	1	0 50924 1203
20	1593268	0.0	2	1556330 35698 1240
21	780	0.0	2	0 757 23

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR20_BF24_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 37.75 s (21 us/read; 2.88 M reads/minute).

=== Summary ===

Total reads processed:               1,811,156
Reads with adapters:                 1,809,216 (99.9%)
Reads written (passing filters):     1,809,216 (99.9%)

Total basepairs processed:   834,239,766 bp
Total written (filtered):    797,281,343 bp (95.6%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1809216 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	10229	0.0	1	0 0 10229
19	90634	0.0	1	0 89691 943
20	1706476	0.0	2	1683361 22915 200
21	1754	0.0	2	0 1734 20
22	123	0.0	2	0 0 123

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR20_BF24_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 39.17 s (22 us/read; 2.77 M reads/minute).

=== Summary ===

Total reads processed:               1,809,216
Reads with adapters:                 1,806,524 (99.9%)
Reads written (passing filters):     1,806,524 (99.9%)

Total basepairs processed:   797,281,343 bp
Total written (filtered):    760,049,245 bp (95.3%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1806524 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 29.9%
  C: 5.6%
  G: 57.0%
  T: 7.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	2331	0.0	1	0 0 2331
19	61643	0.0	1	0 60207 1436
20	1741697	0.0	2	1702548 37421 1728
21	852	0.0	2	0 833 19
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR21_BF13_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.30 s (19 us/read; 3.23 M reads/minute).

=== Summary ===

Total reads processed:               1,845,829
Reads with adapters:                 1,843,334 (99.9%)
Reads written (passing filters):     1,843,334 (99.9%)

Total basepairs processed:   656,772,255 bp
Total written (filtered):    619,141,311 bp (94.3%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1843334 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	11923	0.0	1	0 0 11923
19	94443	0.0	1	0 93272 1171
20	1734720	0.0	2	1706052 28372 296
21	1924	0.0	2	0 1895 29
22	324	0.0	2	0 0 324

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR21_BF13_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 34.40 s (19 us/read; 3.22 M reads/minute).

=== Summary ===

Total reads processed:               1,843,334
Reads with adapters:                 1,840,504 (99.8%)
Reads written (passing filters):     1,840,504 (99.8%)

Total basepairs processed:   619,141,311 bp
Total written (filtered):    581,392,221 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1840504 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 80.8%
  C: 11.4%
  G: 6.0%
  T: 1.9%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	727	0.0	1	0 0 727
19	7248	0.0	1	0 7126 122
20	1831720	0.0	2	1802635 27921 1164
21	808	0.0	2	0 795 13
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR21_BF23_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 40.49 s (21 us/read; 2.88 M reads/minute).

=== Summary ===

Total reads processed:               1,943,942
Reads with adapters:                 1,941,462 (99.9%)
Reads written (passing filters):     1,941,462 (99.9%)

Total basepairs processed:   895,769,958 bp
Total written (filtered):    855,927,211 bp (95.6%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1941462 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	12353	0.0	1	0 0 12353
19	98414	0.0	1	0 97204 1210
20	1828183	0.0	2	1797641 30232 310
21	2174	0.0	2	0 2140 34
22	338	0.0	2	0 0 338

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR21_BF23_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.99 s (22 us/read; 2.77 M reads/minute).

=== Summary ===

Total reads processed:               1,941,462
Reads with adapters:                 1,939,387 (99.9%)
Reads written (passing filters):     1,939,387 (99.9%)

Total basepairs processed:   855,927,211 bp
Total written (filtered):    816,333,503 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1939387 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 43.4%
  C: 10.5%
  G: 43.4%
  T: 2.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1061	0.0	1	0 0 1061
19	9156	0.0	1	0 8820 336
20	1928395	0.0	2	1874583 51889 1923
21	774	0.0	2	0 749 25
22	1	0.0	2	0 0 1

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR22_BF12_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 35.29 s (19 us/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:               1,890,033
Reads with adapters:                 1,887,260 (99.9%)
Reads written (passing filters):     1,887,260 (99.9%)

Total basepairs processed:   672,627,010 bp
Total written (filtered):    634,020,908 bp (94.3%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1887260 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	11832	0.0	1	0 0 11832
19	98018	0.0	1	0 96464 1554
20	1774869	0.0	2	1739159 35247 463
21	1953	0.0	2	0 1912 41
22	588	0.0	2	0 0 588

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR22_BF12_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 35.76 s (19 us/read; 3.17 M reads/minute).

=== Summary ===

Total reads processed:               1,887,260
Reads with adapters:                 1,884,369 (99.8%)
Reads written (passing filters):     1,884,369 (99.8%)

Total basepairs processed:   634,020,908 bp
Total written (filtered):    595,372,637 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1884369 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 93.9%
  C: 2.9%
  G: 3.1%
  T: 0.1%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	700	0.0	1	0 0 700
19	7209	0.0	1	0 7068 141
20	1875611	0.0	2	1843506 31013 1092
21	849	0.0	2	0 827 22

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR22_BF22_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.95 s (21 us/read; 2.82 M reads/minute).

=== Summary ===

Total reads processed:               1,593,233
Reads with adapters:                 1,590,848 (99.9%)
Reads written (passing filters):     1,590,848 (99.9%)

Total basepairs processed:   734,149,148 bp
Total written (filtered):    701,349,852 bp (95.5%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1590848 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	9886	0.0	1	0 0 9886
19	81914	0.0	1	0 80605 1309
20	1496937	0.0	2	1466600 29984 353
21	1668	0.0	2	0 1637 31
22	443	0.0	2	0 0 443

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR22_BF22_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 33.74 s (21 us/read; 2.83 M reads/minute).

=== Summary ===

Total reads processed:               1,590,848
Reads with adapters:                 1,589,010 (99.9%)
Reads written (passing filters):     1,589,010 (99.9%)

Total basepairs processed:   701,349,852 bp
Total written (filtered):    668,803,072 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1589010 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 12.3%
  C: 47.6%
  G: 39.8%
  T: 0.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	1539	0.0	1	0 0 1539
19	24402	0.0	1	0 23865 537
20	1562383	0.0	2	1529169 31863 1351
21	681	0.0	2	0 658 23
22	5	0.0	2	0 0 5

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR23_BF11_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.74 s (19 us/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:               1,967,780
Reads with adapters:                 1,957,791 (99.5%)
Reads written (passing filters):     1,957,791 (99.5%)

Total basepairs processed:   699,994,915 bp
Total written (filtered):    657,676,811 bp (94.0%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1957791 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	45318	0.0	1	0 0 45318
19	275398	0.0	1	0 270806 4592
20	1634240	0.0	2	1597804 35807 629
21	2478	0.0	2	0 2433 45
22	357	0.0	2	0 0 357

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR23_BF11_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 37.36 s (19 us/read; 3.14 M reads/minute).

=== Summary ===

Total reads processed:               1,957,791
Reads with adapters:                 1,954,971 (99.9%)
Reads written (passing filters):     1,954,971 (99.9%)

Total basepairs processed:   657,676,811 bp
Total written (filtered):    617,646,204 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1954971 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 85.9%
  C: 9.4%
  G: 3.3%
  T: 1.4%
  none/other: 0.0%
WARNING:
    The adapter is preceded by "A" extremely often.
    The provided adapter sequence may be incomplete.
    To fix the problem, add "A" to the beginning of the adapter sequence.

Overview of removed sequences
length	count	expect	max.err	error counts
18	835	0.0	1	0 0 835
19	13352	0.0	1	0 13155 197
20	1940122	0.0	2	1914539 24606 977
21	661	0.0	2	0 653 8
22	1	0.0	2	0 0 1

WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR23_BF21_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.75 s (21 us/read; 2.81 M reads/minute).

=== Summary ===

Total reads processed:               1,720,031
Reads with adapters:                 1,711,356 (99.5%)
Reads written (passing filters):     1,711,356 (99.5%)

Total basepairs processed:   792,348,744 bp
Total written (filtered):    754,473,581 bp (95.2%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1711356 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	40223	0.0	1	0 0 40223
19	243838	0.0	1	0 239845 3993
20	1424743	0.0	2	1392493 31720 530
21	2232	0.0	2	0 2195 37
22	320	0.0	2	0 0 320

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR23_BF21_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.53 s (21 us/read; 2.81 M reads/minute).

=== Summary ===

Total reads processed:               1,711,356
Reads with adapters:                 1,709,413 (99.9%)
Reads written (passing filters):     1,709,413 (99.9%)

Total basepairs processed:   754,473,581 bp
Total written (filtered):    719,513,067 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1709413 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 31.0%
  C: 23.9%
  G: 42.2%
  T: 2.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	676	0.0	1	0 0 676
19	7566	0.0	1	0 7327 239
20	1700597	0.0	2	1670379 28639 1579
21	570	0.0	2	0 524 46
22	4	0.0	2	0 0 4

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR24_BF10_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 35.48 s (18 us/read; 3.28 M reads/minute).

=== Summary ===

Total reads processed:               1,942,225
Reads with adapters:                 1,940,648 (99.9%)
Reads written (passing filters):     1,940,648 (99.9%)

Total basepairs processed:   690,876,650 bp
Total written (filtered):    651,538,967 bp (94.3%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1940648 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2438	0.0	1	0 0 2438
19	25317	0.0	1	0 24743 574
20	1910753	0.0	2	1871325 39024 404
21	1900	0.0	2	0 1861 39
22	240	0.0	2	0 0 240

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR24_BF10_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 36.77 s (19 us/read; 3.17 M reads/minute).

=== Summary ===

Total reads processed:               1,940,648
Reads with adapters:                 1,938,042 (99.9%)
Reads written (passing filters):     1,938,042 (99.9%)

Total basepairs processed:   651,538,967 bp
Total written (filtered):    611,913,923 bp (93.9%)

=== Adapter 1 ===

Sequence: GGRTANACWGTYCAWCCWGT; Type: anchored 3'; Length: 20; Trimmed: 1938042 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 77.0%
  C: 3.6%
  G: 15.0%
  T: 4.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	647	0.0	1	0 0 647
19	9941	0.0	1	0 9807 134
20	1926786	0.0	2	1903406 22417 963
21	668	0.0	2	0 655 13

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt ../2 PE read merging/BP_rerun_L002_BR24_BF20_merged.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 43.09 s (22 us/read; 2.71 M reads/minute).

=== Summary ===

Total reads processed:               1,949,795
Reads with adapters:                 1,948,285 (99.9%)
Reads written (passing filters):     1,948,285 (99.9%)

Total basepairs processed:   898,296,626 bp
Total written (filtered):    858,672,479 bp (95.6%)

=== Adapter 1 ===

Sequence: TCDGGRTGNCCRAARAAYCA; Type: anchored 5'; Length: 20; Trimmed: 1948285 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Overview of removed sequences
length	count	expect	max.err	error counts
18	2447	0.0	1	0 0 2447
19	25456	0.0	1	0 24894 562
20	1918212	0.0	2	1878192 39592 428
21	1983	0.0	2	0 1937 46
22	187	0.0	2	0 0 187

This is cutadapt 1.9 with Python 2.7.10
Command line parameters: -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR24_BF20_merged_cut.txt temp.txt -f fastq --discard-untrimmed
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 41.72 s (21 us/read; 2.80 M reads/minute).

=== Summary ===

Total reads processed:               1,948,285
Reads with adapters:                 1,946,800 (99.9%)
Reads written (passing filters):     1,946,800 (99.9%)

Total basepairs processed:   858,672,479 bp
Total written (filtered):    819,114,699 bp (95.4%)

=== Adapter 1 ===

Sequence: GGRAADGCYATRTCDGGDGC; Type: anchored 3'; Length: 20; Trimmed: 1946800 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 31.7%
  C: 7.7%
  G: 54.2%
  T: 6.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
18	644	0.0	1	0 0 644
19	6989	0.0	1	0 6755 234
20	1938500	0.0	2	1907800 29311 1389
21	665	0.0	2	0 648 17
22	2	0.0	2	0 0 2

Vascos-MacBook:~ luckylion$ 
