Run multiqc on untrimmed files
eval "$(/opt/anaconda/anaconda3/bin/conda shell.bash hook)"
conda activate
cd fastqc/trimmed/
multiqc .
/// MultiQC 🔍 | v1.12
| multiqc | Search path : /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/fastqc/trimmed
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 144/144
| fastqc | Found 72 reports
| multiqc | Compressing plot data
| multiqc | Report : multiqc_report.html
| multiqc | Data : multiqc_data
| multiqc | MultiQC complete
# trim adapter sequences
mkdir trim-fastq/
cd raw-data/
for F in *.fastq
do
#strip .fastq and directory structure from each file, then
# add suffice .trim to create output name for each file
results_file="$(basename -a $F)"
# run cutadapt on each file, hard trim first 15 bp, minimum length 20
/home/shared/8TB_HDD_02/mattgeorgephd/.local/bin/cutadapt $F -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o \
/home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/$results_file
done
mkdir: cannot create directory ‘trim-fastq/’: File exists
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D54_S145_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D54_S145_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 19.99 s (9 µs/read; 7.03 M reads/minute).
=== Summary ===
Total reads processed: 2,342,412
Reads with adapters: 792,846 (33.8%)
== Read fate breakdown ==
Reads that were too short: 226,667 (9.7%)
Reads written (passing filters): 2,115,745 (90.3%)
Total basepairs processed: 236,583,612 bp
Total written (filtered): 166,621,075 bp (70.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 719377 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.4%
G: 27.4%
T: 29.6%
none/other: 12.6%
Overview of removed sequences
length count expect max.err error counts
3 58419 36600.2 0 58419
4 23418 9150.0 0 23418
5 12510 2287.5 0 12510
6 8475 571.9 0 8475
7 7068 143.0 0 7068
8 6222 35.7 0 6222
9 6081 35.7 0 6081
10 6300 35.7 0 6300
11 5895 35.7 0 5895
12 6019 35.7 0 6019
13 6199 35.7 0 6199
14 6273 35.7 0 6273
15 6212 35.7 0 6212
16 6446 35.7 0 6446
17 6243 35.7 0 6243
18 6114 35.7 0 6114
19 6204 35.7 0 6204
20 6150 35.7 0 6150
21 6145 35.7 0 6145
22 6015 35.7 0 6015
23 6041 35.7 0 6041
24 5911 35.7 0 5911
25 5970 35.7 0 5970
26 5759 35.7 0 5759
27 6149 35.7 0 6149
28 6369 35.7 0 6369
29 6167 35.7 0 6167
30 6374 35.7 0 6374
31 6814 35.7 0 6814
32 6523 35.7 0 6523
33 6818 35.7 0 6818
34 6751 35.7 0 6751
35 6681 35.7 0 6681
36 6402 35.7 0 6402
37 6548 35.7 0 6548
38 6319 35.7 0 6319
39 6510 35.7 0 6510
40 6156 35.7 0 6156
41 6558 35.7 0 6558
42 6652 35.7 0 6652
43 6548 35.7 0 6548
44 6335 35.7 0 6335
45 6592 35.7 0 6592
46 6668 35.7 0 6668
47 6702 35.7 0 6702
48 6229 35.7 0 6229
49 9362 35.7 0 9362
50 11118 35.7 0 11118
51 6670 35.7 0 6670
52 7096 35.7 0 7096
53 6871 35.7 0 6871
54 6075 35.7 0 6075
55 6448 35.7 0 6448
56 6447 35.7 0 6447
57 6245 35.7 0 6245
58 6922 35.7 0 6922
59 6587 35.7 0 6587
60 6519 35.7 0 6519
61 6678 35.7 0 6678
62 6820 35.7 0 6820
63 6385 35.7 0 6385
64 6406 35.7 0 6406
65 6368 35.7 0 6368
66 6228 35.7 0 6228
67 6162 35.7 0 6162
68 6484 35.7 0 6484
69 5901 35.7 0 5901
70 5466 35.7 0 5466
71 5951 35.7 0 5951
72 5888 35.7 0 5888
73 5679 35.7 0 5679
74 5369 35.7 0 5369
75 5601 35.7 0 5601
76 5557 35.7 0 5557
77 5484 35.7 0 5484
78 5948 35.7 0 5948
79 6961 35.7 0 6961
80 6700 35.7 0 6700
81 7733 35.7 0 7733
82 9512 35.7 0 9512
83 10728 35.7 0 10728
84 11422 35.7 0 11422
85 12031 35.7 0 12031
86 90601 35.7 0 90601
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 22269 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.6%
C: 34.7%
G: 0.0%
T: 32.6%
none/other: 2.2%
Overview of removed sequences
length count expect max.err error counts
3 13024 36600.2 0 13024
4 2733 9150.0 0 2733
5 621 2287.5 0 621
6 203 571.9 0 203
7 169 143.0 0 169
8 131 35.7 0 131
9 133 35.7 0 133
10 114 35.7 0 114
11 113 35.7 0 113
12 95 35.7 0 95
13 102 35.7 0 102
14 86 35.7 0 86
15 78 35.7 0 78
16 96 35.7 0 96
17 72 35.7 0 72
18 80 35.7 0 80
19 66 35.7 0 66
20 77 35.7 0 77
21 75 35.7 0 75
22 70 35.7 0 70
23 82 35.7 0 82
24 90 35.7 0 90
25 97 35.7 0 97
26 99 35.7 0 99
27 86 35.7 0 86
28 84 35.7 0 84
29 85 35.7 0 85
30 82 35.7 0 82
31 81 35.7 0 81
32 75 35.7 0 75
33 88 35.7 0 88
34 90 35.7 0 90
35 67 35.7 0 67
36 81 35.7 0 81
37 84 35.7 0 84
38 78 35.7 0 78
39 64 35.7 0 64
40 64 35.7 0 64
41 75 35.7 0 75
42 97 35.7 0 97
43 76 35.7 0 76
44 64 35.7 0 64
45 92 35.7 0 92
46 74 35.7 0 74
47 74 35.7 0 74
48 66 35.7 0 66
49 62 35.7 0 62
50 66 35.7 0 66
51 62 35.7 0 62
52 70 35.7 0 70
53 73 35.7 0 73
54 73 35.7 0 73
55 68 35.7 0 68
56 73 35.7 0 73
57 54 35.7 0 54
58 63 35.7 0 63
59 62 35.7 0 62
60 70 35.7 0 70
61 56 35.7 0 56
62 56 35.7 0 56
63 53 35.7 0 53
64 52 35.7 0 52
65 30 35.7 0 30
66 44 35.7 0 44
67 53 35.7 0 53
68 34 35.7 0 34
69 34 35.7 0 34
70 45 35.7 0 45
71 39 35.7 0 39
72 27 35.7 0 27
73 22 35.7 0 22
74 24 35.7 0 24
75 30 35.7 0 30
76 25 35.7 0 25
77 18 35.7 0 18
78 14 35.7 0 14
79 13 35.7 0 13
80 12 35.7 0 12
81 12 35.7 0 12
82 8 35.7 0 8
83 19 35.7 0 19
84 26 35.7 0 26
85 15 35.7 0 15
86 479 35.7 0 479
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 51200 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 23.2%
G: 21.2%
T: 19.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 38085 36600.2 0 38085
4 8468 9150.0 0 8468
5 1917 2287.5 0 1917
6 291 571.9 0 291
7 33 143.0 0 33
8 34 143.0 0 34
9 32 143.0 0 32
10 42 143.0 0 42
11 36 143.0 0 36
12 32 143.0 0 32
13 42 143.0 0 42
14 43 143.0 0 43
15 24 143.0 0 24
16 54 143.0 0 54
17 39 143.0 0 39
18 21 143.0 0 21
19 46 143.0 0 46
20 50 143.0 0 50
21 48 143.0 0 48
22 43 143.0 0 43
23 43 143.0 0 43
24 31 143.0 0 31
25 39 143.0 0 39
26 27 143.0 0 27
27 20 143.0 0 20
28 27 143.0 0 27
29 33 143.0 0 33
30 36 143.0 0 36
31 24 143.0 0 24
32 43 143.0 0 43
33 25 143.0 0 25
34 26 143.0 0 26
35 25 143.0 0 25
36 30 143.0 0 30
37 25 143.0 0 25
38 18 143.0 0 18
39 33 143.0 0 33
40 36 143.0 0 36
41 38 143.0 0 38
42 16 143.0 0 16
43 22 143.0 0 22
44 28 143.0 0 28
45 29 143.0 0 29
46 17 143.0 0 17
47 33 143.0 0 33
48 28 143.0 0 28
49 20 143.0 0 20
50 28 143.0 0 28
51 24 143.0 0 24
52 33 143.0 0 33
53 14 143.0 0 14
54 25 143.0 0 25
55 41 143.0 0 41
56 35 143.0 0 35
57 31 143.0 0 31
58 38 143.0 0 38
59 30 143.0 0 30
60 34 143.0 0 34
61 27 143.0 0 27
62 31 143.0 0 31
63 20 143.0 0 20
64 26 143.0 0 26
65 39 143.0 0 39
66 32 143.0 0 32
67 25 143.0 0 25
68 32 143.0 0 32
69 30 143.0 0 30
70 20 143.0 0 20
71 28 143.0 0 28
72 23 143.0 0 23
73 18 143.0 0 18
74 21 143.0 0 21
75 22 143.0 0 22
76 18 143.0 0 18
77 45 143.0 0 45
78 39 143.0 0 39
79 21 143.0 0 21
80 24 143.0 0 24
81 26 143.0 0 26
82 22 143.0 0 22
83 36 143.0 0 36
84 23 143.0 0 23
85 28 143.0 0 28
86 39 143.0 0 39
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D55_S146_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D55_S146_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.25 s (8 µs/read; 7.07 M reads/minute).
=== Summary ===
Total reads processed: 3,091,542
Reads with adapters: 1,054,652 (34.1%)
== Read fate breakdown ==
Reads that were too short: 275,247 (8.9%)
Reads written (passing filters): 2,816,295 (91.1%)
Total basepairs processed: 312,245,742 bp
Total written (filtered): 220,739,484 bp (70.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 934920 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.4%
G: 27.0%
T: 30.5%
none/other: 12.1%
Overview of removed sequences
length count expect max.err error counts
3 75548 48305.3 0 75548
4 33227 12076.3 0 33227
5 16970 3019.1 0 16970
6 11575 754.8 0 11575
7 9336 188.7 0 9336
8 8386 47.2 0 8386
9 8295 47.2 0 8295
10 8229 47.2 0 8229
11 8213 47.2 0 8213
12 8601 47.2 0 8601
13 8160 47.2 0 8160
14 8340 47.2 0 8340
15 8457 47.2 0 8457
16 8501 47.2 0 8501
17 8676 47.2 0 8676
18 8620 47.2 0 8620
19 8608 47.2 0 8608
20 8349 47.2 0 8349
21 8468 47.2 0 8468
22 8419 47.2 0 8419
23 8189 47.2 0 8189
24 8197 47.2 0 8197
25 8177 47.2 0 8177
26 8210 47.2 0 8210
27 8316 47.2 0 8316
28 8595 47.2 0 8595
29 8379 47.2 0 8379
30 8195 47.2 0 8195
31 9084 47.2 0 9084
32 8533 47.2 0 8533
33 9000 47.2 0 9000
34 9001 47.2 0 9001
35 8567 47.2 0 8567
36 8864 47.2 0 8864
37 8509 47.2 0 8509
38 8459 47.2 0 8459
39 8517 47.2 0 8517
40 8417 47.2 0 8417
41 8478 47.2 0 8478
42 8745 47.2 0 8745
43 8573 47.2 0 8573
44 8240 47.2 0 8240
45 8685 47.2 0 8685
46 8999 47.2 0 8999
47 8641 47.2 0 8641
48 8776 47.2 0 8776
49 11412 47.2 0 11412
50 12957 47.2 0 12957
51 9255 47.2 0 9255
52 9724 47.2 0 9724
53 9360 47.2 0 9360
54 8612 47.2 0 8612
55 8975 47.2 0 8975
56 9163 47.2 0 9163
57 8935 47.2 0 8935
58 9440 47.2 0 9440
59 8997 47.2 0 8997
60 9020 47.2 0 9020
61 9364 47.2 0 9364
62 9128 47.2 0 9128
63 8753 47.2 0 8753
64 8706 47.2 0 8706
65 8832 47.2 0 8832
66 8453 47.2 0 8453
67 8315 47.2 0 8315
68 8183 47.2 0 8183
69 7800 47.2 0 7800
70 7363 47.2 0 7363
71 7733 47.2 0 7733
72 7499 47.2 0 7499
73 7273 47.2 0 7273
74 6911 47.2 0 6911
75 6816 47.2 0 6816
76 6622 47.2 0 6622
77 6734 47.2 0 6734
78 6741 47.2 0 6741
79 7581 47.2 0 7581
80 7384 47.2 0 7384
81 8353 47.2 0 8353
82 9926 47.2 0 9926
83 11382 47.2 0 11382
84 12062 47.2 0 12062
85 12694 47.2 0 12694
86 113138 47.2 0 113138
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 55677 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.4%
C: 32.6%
G: 0.0%
T: 39.0%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 14145 48305.3 0 14145
4 3618 12076.3 0 3618
5 1312 3019.1 0 1312
6 839 754.8 0 839
7 733 188.7 0 733
8 769 47.2 0 769
9 730 47.2 0 730
10 688 47.2 0 688
11 696 47.2 0 696
12 687 47.2 0 687
13 658 47.2 0 658
14 650 47.2 0 650
15 576 47.2 0 576
16 605 47.2 0 605
17 571 47.2 0 571
18 614 47.2 0 614
19 686 47.2 0 686
20 530 47.2 0 530
21 541 47.2 0 541
22 548 47.2 0 548
23 512 47.2 0 512
24 601 47.2 0 601
25 641 47.2 0 641
26 557 47.2 0 557
27 499 47.2 0 499
28 556 47.2 0 556
29 552 47.2 0 552
30 554 47.2 0 554
31 568 47.2 0 568
32 531 47.2 0 531
33 598 47.2 0 598
34 569 47.2 0 569
35 547 47.2 0 547
36 523 47.2 0 523
37 567 47.2 0 567
38 535 47.2 0 535
39 547 47.2 0 547
40 539 47.2 0 539
41 486 47.2 0 486
42 529 47.2 0 529
43 523 47.2 0 523
44 516 47.2 0 516
45 510 47.2 0 510
46 506 47.2 0 506
47 528 47.2 0 528
48 467 47.2 0 467
49 492 47.2 0 492
50 488 47.2 0 488
51 478 47.2 0 478
52 502 47.2 0 502
53 482 47.2 0 482
54 446 47.2 0 446
55 434 47.2 0 434
56 465 47.2 0 465
57 425 47.2 0 425
58 462 47.2 0 462
59 402 47.2 0 402
60 405 47.2 0 405
61 350 47.2 0 350
62 323 47.2 0 323
63 339 47.2 0 339
64 328 47.2 0 328
65 315 47.2 0 315
66 285 47.2 0 285
67 252 47.2 0 252
68 241 47.2 0 241
69 223 47.2 0 223
70 207 47.2 0 207
71 186 47.2 0 186
72 161 47.2 0 161
73 143 47.2 0 143
74 142 47.2 0 142
75 105 47.2 0 105
76 99 47.2 0 99
77 80 47.2 0 80
78 92 47.2 0 92
79 70 47.2 0 70
80 63 47.2 0 63
81 37 47.2 0 37
82 57 47.2 0 57
83 52 47.2 0 52
84 54 47.2 0 54
85 58 47.2 0 58
86 1677 47.2 0 1677
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 64055 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 22.5%
G: 20.8%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47289 48305.3 0 47289
4 11373 12076.3 0 11373
5 2074 3019.1 0 2074
6 305 754.8 0 305
7 30 188.7 0 30
8 44 188.7 0 44
9 39 188.7 0 39
10 35 188.7 0 35
11 54 188.7 0 54
12 36 188.7 0 36
13 36 188.7 0 36
14 45 188.7 0 45
15 36 188.7 0 36
16 52 188.7 0 52
17 45 188.7 0 45
18 39 188.7 0 39
19 53 188.7 0 53
20 59 188.7 0 59
21 52 188.7 0 52
22 68 188.7 0 68
23 45 188.7 0 45
24 58 188.7 0 58
25 67 188.7 0 67
26 35 188.7 0 35
27 34 188.7 0 34
28 31 188.7 0 31
29 40 188.7 0 40
30 32 188.7 0 32
31 35 188.7 0 35
32 44 188.7 0 44
33 24 188.7 0 24
34 32 188.7 0 32
35 32 188.7 0 32
36 36 188.7 0 36
37 33 188.7 0 33
38 25 188.7 0 25
39 47 188.7 0 47
40 28 188.7 0 28
41 31 188.7 0 31
42 37 188.7 0 37
43 26 188.7 0 26
44 31 188.7 0 31
45 24 188.7 0 24
46 42 188.7 0 42
47 39 188.7 0 39
48 32 188.7 0 32
49 42 188.7 0 42
50 25 188.7 0 25
51 42 188.7 0 42
52 28 188.7 0 28
53 28 188.7 0 28
54 31 188.7 0 31
55 42 188.7 0 42
56 26 188.7 0 26
57 29 188.7 0 29
58 35 188.7 0 35
59 36 188.7 0 36
60 25 188.7 0 25
61 40 188.7 0 40
62 32 188.7 0 32
63 22 188.7 0 22
64 42 188.7 0 42
65 38 188.7 0 38
66 50 188.7 0 50
67 37 188.7 0 37
68 39 188.7 0 39
69 37 188.7 0 37
70 38 188.7 0 38
71 34 188.7 0 34
72 33 188.7 0 33
73 22 188.7 0 22
74 28 188.7 0 28
75 26 188.7 0 26
76 27 188.7 0 27
77 76 188.7 0 76
78 53 188.7 0 53
79 35 188.7 0 35
80 42 188.7 0 42
81 30 188.7 0 30
82 28 188.7 0 28
83 38 188.7 0 38
84 37 188.7 0 37
85 35 188.7 0 35
86 43 188.7 0 43
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D55_S146_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D55_S146_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.30 s (9 µs/read; 6.95 M reads/minute).
=== Summary ===
Total reads processed: 3,161,076
Reads with adapters: 1,087,468 (34.4%)
== Read fate breakdown ==
Reads that were too short: 289,072 (9.1%)
Reads written (passing filters): 2,872,004 (90.9%)
Total basepairs processed: 319,268,676 bp
Total written (filtered): 224,875,538 bp (70.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 964399 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.5%
G: 26.9%
T: 30.3%
none/other: 12.4%
Overview of removed sequences
length count expect max.err error counts
3 76495 49391.8 0 76495
4 33576 12348.0 0 33576
5 17132 3087.0 0 17132
6 11534 771.7 0 11534
7 9537 192.9 0 9537
8 8203 48.2 0 8203
9 8493 48.2 0 8493
10 8484 48.2 0 8484
11 8565 48.2 0 8565
12 8384 48.2 0 8384
13 8304 48.2 0 8304
14 8761 48.2 0 8761
15 8651 48.2 0 8651
16 8628 48.2 0 8628
17 8742 48.2 0 8742
18 8703 48.2 0 8703
19 8609 48.2 0 8609
20 8456 48.2 0 8456
21 8736 48.2 0 8736
22 8773 48.2 0 8773
23 8203 48.2 0 8203
24 8461 48.2 0 8461
25 8529 48.2 0 8529
26 8385 48.2 0 8385
27 8390 48.2 0 8390
28 8643 48.2 0 8643
29 8702 48.2 0 8702
30 8772 48.2 0 8772
31 9310 48.2 0 9310
32 8814 48.2 0 8814
33 9249 48.2 0 9249
34 8978 48.2 0 8978
35 8861 48.2 0 8861
36 9057 48.2 0 9057
37 8940 48.2 0 8940
38 8528 48.2 0 8528
39 8757 48.2 0 8757
40 8752 48.2 0 8752
41 8811 48.2 0 8811
42 8744 48.2 0 8744
43 8617 48.2 0 8617
44 8741 48.2 0 8741
45 8779 48.2 0 8779
46 9246 48.2 0 9246
47 9106 48.2 0 9106
48 8892 48.2 0 8892
49 11706 48.2 0 11706
50 13168 48.2 0 13168
51 9603 48.2 0 9603
52 10420 48.2 0 10420
53 9783 48.2 0 9783
54 8788 48.2 0 8788
55 9414 48.2 0 9414
56 9542 48.2 0 9542
57 9114 48.2 0 9114
58 9809 48.2 0 9809
59 9482 48.2 0 9482
60 9481 48.2 0 9481
61 9632 48.2 0 9632
62 9364 48.2 0 9364
63 9184 48.2 0 9184
64 9030 48.2 0 9030
65 8986 48.2 0 8986
66 8756 48.2 0 8756
67 8812 48.2 0 8812
68 8523 48.2 0 8523
69 8174 48.2 0 8174
70 7766 48.2 0 7766
71 8163 48.2 0 8163
72 8098 48.2 0 8098
73 7788 48.2 0 7788
74 7097 48.2 0 7097
75 7098 48.2 0 7098
76 6797 48.2 0 6797
77 7091 48.2 0 7091
78 6877 48.2 0 6877
79 7908 48.2 0 7908
80 7584 48.2 0 7584
81 8608 48.2 0 8608
82 10708 48.2 0 10708
83 11754 48.2 0 11754
84 12547 48.2 0 12547
85 13156 48.2 0 13156
86 119555 48.2 0 119555
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 57738 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.8%
C: 32.4%
G: 0.0%
T: 38.8%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 14460 49391.8 0 14460
4 3850 12348.0 0 3850
5 1412 3087.0 0 1412
6 879 771.7 0 879
7 762 192.9 0 762
8 818 48.2 0 818
9 711 48.2 0 711
10 702 48.2 0 702
11 677 48.2 0 677
12 633 48.2 0 633
13 634 48.2 0 634
14 603 48.2 0 603
15 659 48.2 0 659
16 611 48.2 0 611
17 643 48.2 0 643
18 624 48.2 0 624
19 696 48.2 0 696
20 586 48.2 0 586
21 637 48.2 0 637
22 568 48.2 0 568
23 578 48.2 0 578
24 619 48.2 0 619
25 673 48.2 0 673
26 587 48.2 0 587
27 580 48.2 0 580
28 579 48.2 0 579
29 616 48.2 0 616
30 603 48.2 0 603
31 568 48.2 0 568
32 597 48.2 0 597
33 594 48.2 0 594
34 601 48.2 0 601
35 583 48.2 0 583
36 644 48.2 0 644
37 575 48.2 0 575
38 527 48.2 0 527
39 551 48.2 0 551
40 512 48.2 0 512
41 502 48.2 0 502
42 487 48.2 0 487
43 560 48.2 0 560
44 559 48.2 0 559
45 557 48.2 0 557
46 538 48.2 0 538
47 510 48.2 0 510
48 501 48.2 0 501
49 471 48.2 0 471
50 496 48.2 0 496
51 439 48.2 0 439
52 477 48.2 0 477
53 476 48.2 0 476
54 459 48.2 0 459
55 457 48.2 0 457
56 445 48.2 0 445
57 422 48.2 0 422
58 461 48.2 0 461
59 451 48.2 0 451
60 419 48.2 0 419
61 417 48.2 0 417
62 365 48.2 0 365
63 335 48.2 0 335
64 352 48.2 0 352
65 311 48.2 0 311
66 288 48.2 0 288
67 253 48.2 0 253
68 273 48.2 0 273
69 227 48.2 0 227
70 177 48.2 0 177
71 199 48.2 0 199
72 155 48.2 0 155
73 172 48.2 0 172
74 143 48.2 0 143
75 117 48.2 0 117
76 140 48.2 0 140
77 91 48.2 0 91
78 88 48.2 0 88
79 89 48.2 0 89
80 76 48.2 0 76
81 52 48.2 0 52
82 43 48.2 0 43
83 56 48.2 0 56
84 66 48.2 0 66
85 56 48.2 0 56
86 1758 48.2 0 1758
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 65331 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 23.0%
G: 20.9%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47903 49391.8 0 47903
4 11780 12348.0 0 11780
5 2226 3087.0 0 2226
6 302 771.7 0 302
7 26 192.9 0 26
8 40 192.9 0 40
9 36 192.9 0 36
10 46 192.9 0 46
11 48 192.9 0 48
12 44 192.9 0 44
13 48 192.9 0 48
14 51 192.9 0 51
15 28 192.9 0 28
16 50 192.9 0 50
17 44 192.9 0 44
18 35 192.9 0 35
19 58 192.9 0 58
20 47 192.9 0 47
21 55 192.9 0 55
22 69 192.9 0 69
23 54 192.9 0 54
24 41 192.9 0 41
25 64 192.9 0 64
26 55 192.9 0 55
27 44 192.9 0 44
28 40 192.9 0 40
29 44 192.9 0 44
30 29 192.9 0 29
31 44 192.9 0 44
32 36 192.9 0 36
33 36 192.9 0 36
34 40 192.9 0 40
35 22 192.9 0 22
36 38 192.9 0 38
37 37 192.9 0 37
38 28 192.9 0 28
39 49 192.9 0 49
40 44 192.9 0 44
41 38 192.9 0 38
42 30 192.9 0 30
43 42 192.9 0 42
44 31 192.9 0 31
45 34 192.9 0 34
46 36 192.9 0 36
47 32 192.9 0 32
48 34 192.9 0 34
49 39 192.9 0 39
50 34 192.9 0 34
51 38 192.9 0 38
52 34 192.9 0 34
53 44 192.9 0 44
54 38 192.9 0 38
55 22 192.9 0 22
56 33 192.9 0 33
57 31 192.9 0 31
58 46 192.9 0 46
59 35 192.9 0 35
60 36 192.9 0 36
61 49 192.9 0 49
62 35 192.9 0 35
63 26 192.9 0 26
64 28 192.9 0 28
65 33 192.9 0 33
66 35 192.9 0 35
67 45 192.9 0 45
68 35 192.9 0 35
69 28 192.9 0 28
70 46 192.9 0 46
71 31 192.9 0 31
72 31 192.9 0 31
73 34 192.9 0 34
74 40 192.9 0 40
75 31 192.9 0 31
76 28 192.9 0 28
77 75 192.9 0 75
78 55 192.9 0 55
79 26 192.9 0 26
80 29 192.9 0 29
81 33 192.9 0 33
82 33 192.9 0 33
83 35 192.9 0 35
84 36 192.9 0 36
85 26 192.9 0 26
86 40 192.9 0 40
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D56_S136_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D56_S136_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 22.46 s (7 µs/read; 8.30 M reads/minute).
=== Summary ===
Total reads processed: 3,106,123
Reads with adapters: 1,058,535 (34.1%)
== Read fate breakdown ==
Reads that were too short: 273,149 (8.8%)
Reads written (passing filters): 2,832,974 (91.2%)
Total basepairs processed: 313,718,423 bp
Total written (filtered): 222,452,614 bp (70.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 939662 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.5%
G: 28.0%
T: 29.7%
none/other: 12.8%
Overview of removed sequences
length count expect max.err error counts
3 74420 48533.2 0 74420
4 33507 12133.3 0 33507
5 17648 3033.3 0 17648
6 11919 758.3 0 11919
7 9703 189.6 0 9703
8 8465 47.4 0 8465
9 8576 47.4 0 8576
10 8553 47.4 0 8553
11 8327 47.4 0 8327
12 8433 47.4 0 8433
13 8540 47.4 0 8540
14 8823 47.4 0 8823
15 9096 47.4 0 9096
16 8836 47.4 0 8836
17 9127 47.4 0 9127
18 9227 47.4 0 9227
19 8949 47.4 0 8949
20 8831 47.4 0 8831
21 9289 47.4 0 9289
22 8918 47.4 0 8918
23 8358 47.4 0 8358
24 8462 47.4 0 8462
25 8501 47.4 0 8501
26 8217 47.4 0 8217
27 8380 47.4 0 8380
28 8842 47.4 0 8842
29 8731 47.4 0 8731
30 8831 47.4 0 8831
31 8947 47.4 0 8947
32 8858 47.4 0 8858
33 9561 47.4 0 9561
34 8792 47.4 0 8792
35 9671 47.4 0 9671
36 9069 47.4 0 9069
37 8528 47.4 0 8528
38 8933 47.4 0 8933
39 8352 47.4 0 8352
40 8441 47.4 0 8441
41 9171 47.4 0 9171
42 8572 47.4 0 8572
43 9342 47.4 0 9342
44 8500 47.4 0 8500
45 8880 47.4 0 8880
46 10526 47.4 0 10526
47 9059 47.4 0 9059
48 8947 47.4 0 8947
49 12905 47.4 0 12905
50 12608 47.4 0 12608
51 8656 47.4 0 8656
52 10625 47.4 0 10625
53 8925 47.4 0 8925
54 7961 47.4 0 7961
55 8395 47.4 0 8395
56 8551 47.4 0 8551
57 7985 47.4 0 7985
58 8712 47.4 0 8712
59 8459 47.4 0 8459
60 8348 47.4 0 8348
61 8695 47.4 0 8695
62 8223 47.4 0 8223
63 8460 47.4 0 8460
64 7911 47.4 0 7911
65 7693 47.4 0 7693
66 7450 47.4 0 7450
67 7578 47.4 0 7578
68 7243 47.4 0 7243
69 7105 47.4 0 7105
70 6700 47.4 0 6700
71 7342 47.4 0 7342
72 6870 47.4 0 6870
73 6652 47.4 0 6652
74 6372 47.4 0 6372
75 6385 47.4 0 6385
76 6319 47.4 0 6319
77 6415 47.4 0 6415
78 6530 47.4 0 6530
79 7233 47.4 0 7233
80 7024 47.4 0 7024
81 8357 47.4 0 8357
82 10142 47.4 0 10142
83 10821 47.4 0 10821
84 11969 47.4 0 11969
85 12626 47.4 0 12626
86 119759 47.4 0 119759
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 50571 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.4%
C: 32.0%
G: 0.0%
T: 38.1%
none/other: 2.5%
Overview of removed sequences
length count expect max.err error counts
3 15484 48533.2 0 15484
4 3894 12133.3 0 3894
5 1257 3033.3 0 1257
6 706 758.3 0 706
7 640 189.6 0 640
8 632 47.4 0 632
9 622 47.4 0 622
10 533 47.4 0 533
11 534 47.4 0 534
12 531 47.4 0 531
13 540 47.4 0 540
14 497 47.4 0 497
15 525 47.4 0 525
16 466 47.4 0 466
17 454 47.4 0 454
18 534 47.4 0 534
19 524 47.4 0 524
20 462 47.4 0 462
21 469 47.4 0 469
22 457 47.4 0 457
23 439 47.4 0 439
24 466 47.4 0 466
25 509 47.4 0 509
26 489 47.4 0 489
27 449 47.4 0 449
28 455 47.4 0 455
29 434 47.4 0 434
30 463 47.4 0 463
31 461 47.4 0 461
32 415 47.4 0 415
33 473 47.4 0 473
34 467 47.4 0 467
35 456 47.4 0 456
36 456 47.4 0 456
37 439 47.4 0 439
38 457 47.4 0 457
39 439 47.4 0 439
40 427 47.4 0 427
41 448 47.4 0 448
42 410 47.4 0 410
43 419 47.4 0 419
44 395 47.4 0 395
45 445 47.4 0 445
46 435 47.4 0 435
47 459 47.4 0 459
48 436 47.4 0 436
49 394 47.4 0 394
50 371 47.4 0 371
51 364 47.4 0 364
52 377 47.4 0 377
53 387 47.4 0 387
54 386 47.4 0 386
55 375 47.4 0 375
56 368 47.4 0 368
57 424 47.4 0 424
58 385 47.4 0 385
59 350 47.4 0 350
60 371 47.4 0 371
61 297 47.4 0 297
62 303 47.4 0 303
63 263 47.4 0 263
64 266 47.4 0 266
65 246 47.4 0 246
66 213 47.4 0 213
67 194 47.4 0 194
68 178 47.4 0 178
69 172 47.4 0 172
70 148 47.4 0 148
71 151 47.4 0 151
72 106 47.4 0 106
73 119 47.4 0 119
74 101 47.4 0 101
75 66 47.4 0 66
76 81 47.4 0 81
77 64 47.4 0 64
78 51 47.4 0 51
79 33 47.4 0 33
80 52 47.4 0 52
81 44 47.4 0 44
82 44 47.4 0 44
83 49 47.4 0 49
84 65 47.4 0 65
85 47 47.4 0 47
86 1264 47.4 0 1264
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 68302 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.1%
C: 22.5%
G: 21.1%
T: 20.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51427 48533.2 0 51427
4 11511 12133.3 0 11511
5 2031 3033.3 0 2031
6 264 758.3 0 264
7 48 189.6 0 48
8 40 189.6 0 40
9 19 189.6 0 19
10 34 189.6 0 34
11 54 189.6 0 54
12 39 189.6 0 39
13 50 189.6 0 50
14 40 189.6 0 40
15 33 189.6 0 33
16 38 189.6 0 38
17 33 189.6 0 33
18 33 189.6 0 33
19 47 189.6 0 47
20 52 189.6 0 52
21 57 189.6 0 57
22 45 189.6 0 45
23 43 189.6 0 43
24 32 189.6 0 32
25 49 189.6 0 49
26 47 189.6 0 47
27 27 189.6 0 27
28 41 189.6 0 41
29 45 189.6 0 45
30 38 189.6 0 38
31 29 189.6 0 29
32 54 189.6 0 54
33 37 189.6 0 37
34 46 189.6 0 46
35 31 189.6 0 31
36 47 189.6 0 47
37 50 189.6 0 50
38 36 189.6 0 36
39 39 189.6 0 39
40 45 189.6 0 45
41 30 189.6 0 30
42 36 189.6 0 36
43 35 189.6 0 35
44 44 189.6 0 44
45 38 189.6 0 38
46 46 189.6 0 46
47 38 189.6 0 38
48 40 189.6 0 40
49 26 189.6 0 26
50 44 189.6 0 44
51 43 189.6 0 43
52 42 189.6 0 42
53 38 189.6 0 38
54 29 189.6 0 29
55 39 189.6 0 39
56 34 189.6 0 34
57 42 189.6 0 42
58 31 189.6 0 31
59 39 189.6 0 39
60 27 189.6 0 27
61 47 189.6 0 47
62 53 189.6 0 53
63 34 189.6 0 34
64 36 189.6 0 36
65 52 189.6 0 52
66 30 189.6 0 30
67 33 189.6 0 33
68 29 189.6 0 29
69 26 189.6 0 26
70 38 189.6 0 38
71 38 189.6 0 38
72 30 189.6 0 30
73 38 189.6 0 38
74 35 189.6 0 35
75 28 189.6 0 28
76 18 189.6 0 18
77 56 189.6 0 56
78 39 189.6 0 39
79 29 189.6 0 29
80 40 189.6 0 40
81 40 189.6 0 40
82 18 189.6 0 18
83 52 189.6 0 52
84 27 189.6 0 27
85 31 189.6 0 31
86 33 189.6 0 33
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D56_S136_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D56_S136_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 22.72 s (7 µs/read; 8.42 M reads/minute).
=== Summary ===
Total reads processed: 3,187,877
Reads with adapters: 1,093,185 (34.3%)
== Read fate breakdown ==
Reads that were too short: 287,335 (9.0%)
Reads written (passing filters): 2,900,542 (91.0%)
Total basepairs processed: 321,975,577 bp
Total written (filtered): 227,573,723 bp (70.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 970438 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.5%
G: 27.9%
T: 29.5%
none/other: 13.1%
Overview of removed sequences
length count expect max.err error counts
3 75956 49810.6 0 75956
4 33886 12452.6 0 33886
5 17810 3113.2 0 17810
6 12221 778.3 0 12221
7 9656 194.6 0 9656
8 8674 48.6 0 8674
9 8576 48.6 0 8576
10 8833 48.6 0 8833
11 8571 48.6 0 8571
12 8634 48.6 0 8634
13 8711 48.6 0 8711
14 9056 48.6 0 9056
15 9247 48.6 0 9247
16 8955 48.6 0 8955
17 9128 48.6 0 9128
18 9360 48.6 0 9360
19 9058 48.6 0 9058
20 8953 48.6 0 8953
21 9518 48.6 0 9518
22 8805 48.6 0 8805
23 8343 48.6 0 8343
24 8648 48.6 0 8648
25 8729 48.6 0 8729
26 8376 48.6 0 8376
27 8619 48.6 0 8619
28 9008 48.6 0 9008
29 8950 48.6 0 8950
30 9308 48.6 0 9308
31 9079 48.6 0 9079
32 9193 48.6 0 9193
33 9604 48.6 0 9604
34 8826 48.6 0 8826
35 9857 48.6 0 9857
36 9334 48.6 0 9334
37 8827 48.6 0 8827
38 9073 48.6 0 9073
39 8727 48.6 0 8727
40 8694 48.6 0 8694
41 9658 48.6 0 9658
42 8857 48.6 0 8857
43 9530 48.6 0 9530
44 8879 48.6 0 8879
45 9080 48.6 0 9080
46 10845 48.6 0 10845
47 9333 48.6 0 9333
48 9278 48.6 0 9278
49 13114 48.6 0 13114
50 13208 48.6 0 13208
51 9158 48.6 0 9158
52 11076 48.6 0 11076
53 9537 48.6 0 9537
54 8207 48.6 0 8207
55 8671 48.6 0 8671
56 8585 48.6 0 8585
57 8522 48.6 0 8522
58 8909 48.6 0 8909
59 8720 48.6 0 8720
60 8727 48.6 0 8727
61 8862 48.6 0 8862
62 8592 48.6 0 8592
63 8877 48.6 0 8877
64 8198 48.6 0 8198
65 8009 48.6 0 8009
66 8007 48.6 0 8007
67 7697 48.6 0 7697
68 7569 48.6 0 7569
69 7336 48.6 0 7336
70 7191 48.6 0 7191
71 7754 48.6 0 7754
72 7302 48.6 0 7302
73 7011 48.6 0 7011
74 6637 48.6 0 6637
75 6672 48.6 0 6672
76 6494 48.6 0 6494
77 6567 48.6 0 6567
78 6681 48.6 0 6681
79 7674 48.6 0 7674
80 7373 48.6 0 7373
81 8829 48.6 0 8829
82 10741 48.6 0 10741
83 11296 48.6 0 11296
84 12196 48.6 0 12196
85 13394 48.6 0 13394
86 126782 48.6 0 126782
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 52670 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.2%
C: 32.2%
G: 0.0%
T: 38.0%
none/other: 2.5%
Overview of removed sequences
length count expect max.err error counts
3 15935 49810.6 0 15935
4 3777 12452.6 0 3777
5 1300 3113.2 0 1300
6 787 778.3 0 787
7 635 194.6 0 635
8 651 48.6 0 651
9 626 48.6 0 626
10 591 48.6 0 591
11 600 48.6 0 600
12 511 48.6 0 511
13 547 48.6 0 547
14 574 48.6 0 574
15 551 48.6 0 551
16 557 48.6 0 557
17 510 48.6 0 510
18 535 48.6 0 535
19 507 48.6 0 507
20 520 48.6 0 520
21 530 48.6 0 530
22 488 48.6 0 488
23 483 48.6 0 483
24 495 48.6 0 495
25 540 48.6 0 540
26 482 48.6 0 482
27 476 48.6 0 476
28 499 48.6 0 499
29 478 48.6 0 478
30 472 48.6 0 472
31 445 48.6 0 445
32 498 48.6 0 498
33 490 48.6 0 490
34 475 48.6 0 475
35 467 48.6 0 467
36 454 48.6 0 454
37 485 48.6 0 485
38 462 48.6 0 462
39 488 48.6 0 488
40 428 48.6 0 428
41 455 48.6 0 455
42 432 48.6 0 432
43 461 48.6 0 461
44 392 48.6 0 392
45 430 48.6 0 430
46 440 48.6 0 440
47 417 48.6 0 417
48 459 48.6 0 459
49 430 48.6 0 430
50 432 48.6 0 432
51 417 48.6 0 417
52 426 48.6 0 426
53 458 48.6 0 458
54 394 48.6 0 394
55 445 48.6 0 445
56 373 48.6 0 373
57 409 48.6 0 409
58 383 48.6 0 383
59 357 48.6 0 357
60 370 48.6 0 370
61 306 48.6 0 306
62 304 48.6 0 304
63 294 48.6 0 294
64 266 48.6 0 266
65 246 48.6 0 246
66 219 48.6 0 219
67 250 48.6 0 250
68 233 48.6 0 233
69 179 48.6 0 179
70 145 48.6 0 145
71 141 48.6 0 141
72 126 48.6 0 126
73 119 48.6 0 119
74 99 48.6 0 99
75 101 48.6 0 101
76 79 48.6 0 79
77 68 48.6 0 68
78 52 48.6 0 52
79 62 48.6 0 62
80 59 48.6 0 59
81 43 48.6 0 43
82 45 48.6 0 45
83 54 48.6 0 54
84 71 48.6 0 71
85 64 48.6 0 64
86 1316 48.6 0 1316
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 70077 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 22.7%
G: 21.5%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 52712 49810.6 0 52712
4 11632 12452.6 0 11632
5 2102 3113.2 0 2102
6 252 778.3 0 252
7 43 194.6 0 43
8 35 194.6 0 35
9 29 194.6 0 29
10 45 194.6 0 45
11 40 194.6 0 40
12 34 194.6 0 34
13 38 194.6 0 38
14 38 194.6 0 38
15 40 194.6 0 40
16 45 194.6 0 45
17 42 194.6 0 42
18 58 194.6 0 58
19 59 194.6 0 59
20 50 194.6 0 50
21 46 194.6 0 46
22 47 194.6 0 47
23 44 194.6 0 44
24 37 194.6 0 37
25 44 194.6 0 44
26 47 194.6 0 47
27 39 194.6 0 39
28 42 194.6 0 42
29 36 194.6 0 36
30 41 194.6 0 41
31 35 194.6 0 35
32 50 194.6 0 50
33 44 194.6 0 44
34 41 194.6 0 41
35 40 194.6 0 40
36 57 194.6 0 57
37 48 194.6 0 48
38 41 194.6 0 41
39 47 194.6 0 47
40 43 194.6 0 43
41 43 194.6 0 43
42 36 194.6 0 36
43 32 194.6 0 32
44 37 194.6 0 37
45 32 194.6 0 32
46 43 194.6 0 43
47 50 194.6 0 50
48 44 194.6 0 44
49 35 194.6 0 35
50 51 194.6 0 51
51 49 194.6 0 49
52 44 194.6 0 44
53 40 194.6 0 40
54 51 194.6 0 51
55 46 194.6 0 46
56 32 194.6 0 32
57 41 194.6 0 41
58 37 194.6 0 37
59 31 194.6 0 31
60 47 194.6 0 47
61 39 194.6 0 39
62 40 194.6 0 40
63 44 194.6 0 44
64 48 194.6 0 48
65 50 194.6 0 50
66 39 194.6 0 39
67 32 194.6 0 32
68 30 194.6 0 30
69 42 194.6 0 42
70 46 194.6 0 46
71 46 194.6 0 46
72 33 194.6 0 33
73 33 194.6 0 33
74 49 194.6 0 49
75 28 194.6 0 28
76 31 194.6 0 31
77 86 194.6 0 86
78 52 194.6 0 52
79 45 194.6 0 45
80 26 194.6 0 26
81 38 194.6 0 38
82 43 194.6 0 43
83 49 194.6 0 49
84 48 194.6 0 48
85 30 194.6 0 30
86 46 194.6 0 46
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D57_S143_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D57_S143_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 19.56 s (7 µs/read; 8.50 M reads/minute).
=== Summary ===
Total reads processed: 2,771,722
Reads with adapters: 870,006 (31.4%)
== Read fate breakdown ==
Reads that were too short: 234,951 (8.5%)
Reads written (passing filters): 2,536,771 (91.5%)
Total basepairs processed: 279,943,922 bp
Total written (filtered): 201,345,987 bp (71.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 780102 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.2%
G: 27.3%
T: 30.4%
none/other: 12.1%
Overview of removed sequences
length count expect max.err error counts
3 68679 43308.2 0 68679
4 27010 10827.0 0 27010
5 14096 2706.8 0 14096
6 9228 676.7 0 9228
7 7530 169.2 0 7530
8 6523 42.3 0 6523
9 6425 42.3 0 6425
10 6524 42.3 0 6524
11 6625 42.3 0 6625
12 6550 42.3 0 6550
13 6537 42.3 0 6537
14 6771 42.3 0 6771
15 6965 42.3 0 6965
16 6873 42.3 0 6873
17 6857 42.3 0 6857
18 7284 42.3 0 7284
19 6729 42.3 0 6729
20 6717 42.3 0 6717
21 7200 42.3 0 7200
22 6799 42.3 0 6799
23 6350 42.3 0 6350
24 6651 42.3 0 6651
25 6486 42.3 0 6486
26 6325 42.3 0 6325
27 6313 42.3 0 6313
28 7001 42.3 0 7001
29 6845 42.3 0 6845
30 7013 42.3 0 7013
31 7482 42.3 0 7482
32 7562 42.3 0 7562
33 7664 42.3 0 7664
34 7651 42.3 0 7651
35 7628 42.3 0 7628
36 7386 42.3 0 7386
37 7455 42.3 0 7455
38 7159 42.3 0 7159
39 6844 42.3 0 6844
40 6705 42.3 0 6705
41 7120 42.3 0 7120
42 6995 42.3 0 6995
43 7413 42.3 0 7413
44 6748 42.3 0 6748
45 6950 42.3 0 6950
46 8657 42.3 0 8657
47 7272 42.3 0 7272
48 7185 42.3 0 7185
49 11635 42.3 0 11635
50 12222 42.3 0 12222
51 7130 42.3 0 7130
52 9084 42.3 0 9084
53 7549 42.3 0 7549
54 6238 42.3 0 6238
55 6903 42.3 0 6903
56 7034 42.3 0 7034
57 6435 42.3 0 6435
58 7135 42.3 0 7135
59 6669 42.3 0 6669
60 6833 42.3 0 6833
61 7017 42.3 0 7017
62 6714 42.3 0 6714
63 6452 42.3 0 6452
64 6608 42.3 0 6608
65 6533 42.3 0 6533
66 6330 42.3 0 6330
67 6236 42.3 0 6236
68 6404 42.3 0 6404
69 6268 42.3 0 6268
70 5650 42.3 0 5650
71 6281 42.3 0 6281
72 6317 42.3 0 6317
73 5991 42.3 0 5991
74 5636 42.3 0 5636
75 5895 42.3 0 5895
76 5805 42.3 0 5805
77 5675 42.3 0 5675
78 6291 42.3 0 6291
79 7508 42.3 0 7508
80 6736 42.3 0 6736
81 8257 42.3 0 8257
82 9704 42.3 0 9704
83 10473 42.3 0 10473
84 11252 42.3 0 11252
85 11889 42.3 0 11889
86 94531 42.3 0 94531
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28551 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.1%
C: 34.0%
G: 0.0%
T: 33.2%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 16148 43308.2 0 16148
4 3222 10827.0 0 3222
5 795 2706.8 0 795
6 254 676.7 0 254
7 198 169.2 0 198
8 170 42.3 0 170
9 200 42.3 0 200
10 156 42.3 0 156
11 150 42.3 0 150
12 136 42.3 0 136
13 138 42.3 0 138
14 131 42.3 0 131
15 135 42.3 0 135
16 130 42.3 0 130
17 139 42.3 0 139
18 121 42.3 0 121
19 127 42.3 0 127
20 130 42.3 0 130
21 122 42.3 0 122
22 122 42.3 0 122
23 122 42.3 0 122
24 132 42.3 0 132
25 139 42.3 0 139
26 119 42.3 0 119
27 125 42.3 0 125
28 124 42.3 0 124
29 107 42.3 0 107
30 110 42.3 0 110
31 111 42.3 0 111
32 115 42.3 0 115
33 123 42.3 0 123
34 118 42.3 0 118
35 123 42.3 0 123
36 112 42.3 0 112
37 108 42.3 0 108
38 85 42.3 0 85
39 110 42.3 0 110
40 107 42.3 0 107
41 117 42.3 0 117
42 124 42.3 0 124
43 102 42.3 0 102
44 96 42.3 0 96
45 105 42.3 0 105
46 94 42.3 0 94
47 97 42.3 0 97
48 113 42.3 0 113
49 116 42.3 0 116
50 97 42.3 0 97
51 80 42.3 0 80
52 82 42.3 0 82
53 91 42.3 0 91
54 93 42.3 0 93
55 86 42.3 0 86
56 82 42.3 0 82
57 88 42.3 0 88
58 75 42.3 0 75
59 88 42.3 0 88
60 87 42.3 0 87
61 92 42.3 0 92
62 73 42.3 0 73
63 71 42.3 0 71
64 59 42.3 0 59
65 55 42.3 0 55
66 69 42.3 0 69
67 47 42.3 0 47
68 49 42.3 0 49
69 43 42.3 0 43
70 60 42.3 0 60
71 42 42.3 0 42
72 34 42.3 0 34
73 38 42.3 0 38
74 27 42.3 0 27
75 29 42.3 0 29
76 25 42.3 0 25
77 24 42.3 0 24
78 29 42.3 0 29
79 27 42.3 0 27
80 23 42.3 0 23
81 20 42.3 0 20
82 21 42.3 0 21
83 27 42.3 0 27
84 26 42.3 0 26
85 32 42.3 0 32
86 782 42.3 0 782
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61353 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.0%
C: 23.4%
G: 21.0%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45904 43308.2 0 45904
4 9941 10827.0 0 9941
5 2309 2706.8 0 2309
6 378 676.7 0 378
7 27 169.2 0 27
8 30 169.2 0 30
9 28 169.2 0 28
10 39 169.2 0 39
11 30 169.2 0 30
12 34 169.2 0 34
13 38 169.2 0 38
14 25 169.2 0 25
15 29 169.2 0 29
16 29 169.2 0 29
17 49 169.2 0 49
18 38 169.2 0 38
19 39 169.2 0 39
20 41 169.2 0 41
21 38 169.2 0 38
22 24 169.2 0 24
23 32 169.2 0 32
24 30 169.2 0 30
25 46 169.2 0 46
26 24 169.2 0 24
27 29 169.2 0 29
28 33 169.2 0 33
29 38 169.2 0 38
30 32 169.2 0 32
31 27 169.2 0 27
32 36 169.2 0 36
33 40 169.2 0 40
34 23 169.2 0 23
35 29 169.2 0 29
36 27 169.2 0 27
37 37 169.2 0 37
38 40 169.2 0 40
39 38 169.2 0 38
40 29 169.2 0 29
41 29 169.2 0 29
42 31 169.2 0 31
43 26 169.2 0 26
44 37 169.2 0 37
45 32 169.2 0 32
46 29 169.2 0 29
47 63 169.2 0 63
48 30 169.2 0 30
49 43 169.2 0 43
50 48 169.2 0 48
51 36 169.2 0 36
52 33 169.2 0 33
53 36 169.2 0 36
54 33 169.2 0 33
55 30 169.2 0 30
56 24 169.2 0 24
57 31 169.2 0 31
58 42 169.2 0 42
59 40 169.2 0 40
60 38 169.2 0 38
61 23 169.2 0 23
62 43 169.2 0 43
63 51 169.2 0 51
64 37 169.2 0 37
65 42 169.2 0 42
66 39 169.2 0 39
67 34 169.2 0 34
68 40 169.2 0 40
69 25 169.2 0 25
70 43 169.2 0 43
71 40 169.2 0 40
72 26 169.2 0 26
73 29 169.2 0 29
74 24 169.2 0 24
75 26 169.2 0 26
76 23 169.2 0 23
77 80 169.2 0 80
78 48 169.2 0 48
79 29 169.2 0 29
80 33 169.2 0 33
81 38 169.2 0 38
82 46 169.2 0 46
83 38 169.2 0 38
84 43 169.2 0 43
85 48 169.2 0 48
86 34 169.2 0 34
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D57_S143_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D57_S143_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 20.70 s (7 µs/read; 8.21 M reads/minute).
=== Summary ===
Total reads processed: 2,833,849
Reads with adapters: 898,055 (31.7%)
== Read fate breakdown ==
Reads that were too short: 246,349 (8.7%)
Reads written (passing filters): 2,587,500 (91.3%)
Total basepairs processed: 286,218,749 bp
Total written (filtered): 205,181,717 bp (71.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 806295 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.2%
G: 27.3%
T: 30.2%
none/other: 12.3%
Overview of removed sequences
length count expect max.err error counts
3 70030 44278.9 0 70030
4 27663 11069.7 0 27663
5 14607 2767.4 0 14607
6 9350 691.9 0 9350
7 7684 173.0 0 7684
8 6533 43.2 0 6533
9 6588 43.2 0 6588
10 6805 43.2 0 6805
11 6633 43.2 0 6633
12 6650 43.2 0 6650
13 6602 43.2 0 6602
14 7004 43.2 0 7004
15 7006 43.2 0 7006
16 6905 43.2 0 6905
17 7057 43.2 0 7057
18 7294 43.2 0 7294
19 6773 43.2 0 6773
20 6926 43.2 0 6926
21 7312 43.2 0 7312
22 7071 43.2 0 7071
23 6606 43.2 0 6606
24 6973 43.2 0 6973
25 6660 43.2 0 6660
26 6521 43.2 0 6521
27 6565 43.2 0 6565
28 6778 43.2 0 6778
29 7146 43.2 0 7146
30 7248 43.2 0 7248
31 7714 43.2 0 7714
32 7592 43.2 0 7592
33 7992 43.2 0 7992
34 7600 43.2 0 7600
35 7674 43.2 0 7674
36 7503 43.2 0 7503
37 7845 43.2 0 7845
38 7376 43.2 0 7376
39 7150 43.2 0 7150
40 7030 43.2 0 7030
41 7195 43.2 0 7195
42 7275 43.2 0 7275
43 7588 43.2 0 7588
44 7086 43.2 0 7086
45 7196 43.2 0 7196
46 8891 43.2 0 8891
47 7486 43.2 0 7486
48 7278 43.2 0 7278
49 12095 43.2 0 12095
50 13181 43.2 0 13181
51 7386 43.2 0 7386
52 9679 43.2 0 9679
53 7774 43.2 0 7774
54 6441 43.2 0 6441
55 6901 43.2 0 6901
56 7159 43.2 0 7159
57 6740 43.2 0 6740
58 7185 43.2 0 7185
59 6971 43.2 0 6971
60 6861 43.2 0 6861
61 7294 43.2 0 7294
62 6989 43.2 0 6989
63 6773 43.2 0 6773
64 6837 43.2 0 6837
65 6731 43.2 0 6731
66 6698 43.2 0 6698
67 6550 43.2 0 6550
68 6771 43.2 0 6771
69 6432 43.2 0 6432
70 6031 43.2 0 6031
71 6459 43.2 0 6459
72 6488 43.2 0 6488
73 6246 43.2 0 6246
74 5987 43.2 0 5987
75 6254 43.2 0 6254
76 6258 43.2 0 6258
77 6067 43.2 0 6067
78 6690 43.2 0 6690
79 7654 43.2 0 7654
80 7147 43.2 0 7147
81 8602 43.2 0 8602
82 10313 43.2 0 10313
83 10950 43.2 0 10950
84 11856 43.2 0 11856
85 12198 43.2 0 12198
86 99186 43.2 0 99186
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29280 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.9%
C: 34.2%
G: 0.0%
T: 33.2%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 16512 44278.9 0 16512
4 3345 11069.7 0 3345
5 777 2767.4 0 777
6 305 691.9 0 305
7 213 173.0 0 213
8 189 43.2 0 189
9 191 43.2 0 191
10 148 43.2 0 148
11 140 43.2 0 140
12 140 43.2 0 140
13 132 43.2 0 132
14 134 43.2 0 134
15 125 43.2 0 125
16 112 43.2 0 112
17 136 43.2 0 136
18 115 43.2 0 115
19 123 43.2 0 123
20 127 43.2 0 127
21 135 43.2 0 135
22 109 43.2 0 109
23 128 43.2 0 128
24 137 43.2 0 137
25 116 43.2 0 116
26 135 43.2 0 135
27 117 43.2 0 117
28 107 43.2 0 107
29 114 43.2 0 114
30 111 43.2 0 111
31 126 43.2 0 126
32 122 43.2 0 122
33 112 43.2 0 112
34 120 43.2 0 120
35 129 43.2 0 129
36 99 43.2 0 99
37 121 43.2 0 121
38 94 43.2 0 94
39 130 43.2 0 130
40 136 43.2 0 136
41 100 43.2 0 100
42 125 43.2 0 125
43 110 43.2 0 110
44 76 43.2 0 76
45 101 43.2 0 101
46 112 43.2 0 112
47 107 43.2 0 107
48 97 43.2 0 97
49 86 43.2 0 86
50 107 43.2 0 107
51 86 43.2 0 86
52 113 43.2 0 113
53 112 43.2 0 112
54 88 43.2 0 88
55 108 43.2 0 108
56 111 43.2 0 111
57 101 43.2 0 101
58 81 43.2 0 81
59 105 43.2 0 105
60 98 43.2 0 98
61 69 43.2 0 69
62 77 43.2 0 77
63 76 43.2 0 76
64 80 43.2 0 80
65 75 43.2 0 75
66 65 43.2 0 65
67 58 43.2 0 58
68 57 43.2 0 57
69 45 43.2 0 45
70 61 43.2 0 61
71 51 43.2 0 51
72 49 43.2 0 49
73 37 43.2 0 37
74 35 43.2 0 35
75 32 43.2 0 32
76 34 43.2 0 34
77 17 43.2 0 17
78 23 43.2 0 23
79 24 43.2 0 24
80 22 43.2 0 22
81 18 43.2 0 18
82 22 43.2 0 22
83 18 43.2 0 18
84 28 43.2 0 28
85 34 43.2 0 34
86 787 43.2 0 787
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 62480 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.9%
C: 23.3%
G: 20.9%
T: 20.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 46861 44278.9 0 46861
4 10094 11069.7 0 10094
5 2332 2767.4 0 2332
6 395 691.9 0 395
7 31 173.0 0 31
8 32 173.0 0 32
9 31 173.0 0 31
10 30 173.0 0 30
11 46 173.0 0 46
12 21 173.0 0 21
13 31 173.0 0 31
14 34 173.0 0 34
15 36 173.0 0 36
16 38 173.0 0 38
17 30 173.0 0 30
18 22 173.0 0 22
19 39 173.0 0 39
20 35 173.0 0 35
21 28 173.0 0 28
22 30 173.0 0 30
23 27 173.0 0 27
24 37 173.0 0 37
25 36 173.0 0 36
26 28 173.0 0 28
27 34 173.0 0 34
28 31 173.0 0 31
29 27 173.0 0 27
30 34 173.0 0 34
31 33 173.0 0 33
32 39 173.0 0 39
33 29 173.0 0 29
34 29 173.0 0 29
35 26 173.0 0 26
36 36 173.0 0 36
37 41 173.0 0 41
38 32 173.0 0 32
39 27 173.0 0 27
40 37 173.0 0 37
41 39 173.0 0 39
42 36 173.0 0 36
43 21 173.0 0 21
44 52 173.0 0 52
45 26 173.0 0 26
46 33 173.0 0 33
47 45 173.0 0 45
48 34 173.0 0 34
49 31 173.0 0 31
50 37 173.0 0 37
51 37 173.0 0 37
52 37 173.0 0 37
53 23 173.0 0 23
54 40 173.0 0 40
55 48 173.0 0 48
56 25 173.0 0 25
57 27 173.0 0 27
58 36 173.0 0 36
59 38 173.0 0 38
60 41 173.0 0 41
61 33 173.0 0 33
62 49 173.0 0 49
63 29 173.0 0 29
64 39 173.0 0 39
65 46 173.0 0 46
66 41 173.0 0 41
67 44 173.0 0 44
68 26 173.0 0 26
69 32 173.0 0 32
70 34 173.0 0 34
71 46 173.0 0 46
72 35 173.0 0 35
73 28 173.0 0 28
74 31 173.0 0 31
75 34 173.0 0 34
76 24 173.0 0 24
77 84 173.0 0 84
78 41 173.0 0 41
79 34 173.0 0 34
80 39 173.0 0 39
81 38 173.0 0 38
82 23 173.0 0 23
83 30 173.0 0 30
84 48 173.0 0 48
85 42 173.0 0 42
86 45 173.0 0 45
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D58_S144_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D58_S144_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 30.23 s (7 µs/read; 8.15 M reads/minute).
=== Summary ===
Total reads processed: 4,105,518
Reads with adapters: 1,475,952 (36.0%)
== Read fate breakdown ==
Reads that were too short: 339,241 (8.3%)
Reads written (passing filters): 3,766,277 (91.7%)
Total basepairs processed: 414,657,318 bp
Total written (filtered): 291,716,805 bp (70.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1298466 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 32.2%
G: 27.9%
T: 30.4%
none/other: 9.4%
Overview of removed sequences
length count expect max.err error counts
3 98206 64148.7 0 98206
4 45803 16037.2 0 45803
5 24593 4009.3 0 24593
6 16743 1002.3 0 16743
7 13774 250.6 0 13774
8 12568 62.6 0 12568
9 12222 62.6 0 12222
10 12288 62.6 0 12288
11 12130 62.6 0 12130
12 12379 62.6 0 12379
13 12282 62.6 0 12282
14 12670 62.6 0 12670
15 12712 62.6 0 12712
16 12828 62.6 0 12828
17 12850 62.6 0 12850
18 12918 62.6 0 12918
19 12814 62.6 0 12814
20 12762 62.6 0 12762
21 12622 62.6 0 12622
22 12908 62.6 0 12908
23 12455 62.6 0 12455
24 12486 62.6 0 12486
25 12604 62.6 0 12604
26 12330 62.6 0 12330
27 12420 62.6 0 12420
28 13033 62.6 0 13033
29 12885 62.6 0 12885
30 12619 62.6 0 12619
31 13313 62.6 0 13313
32 12826 62.6 0 12826
33 12861 62.6 0 12861
34 13165 62.6 0 13165
35 12799 62.6 0 12799
36 12710 62.6 0 12710
37 13182 62.6 0 13182
38 12712 62.6 0 12712
39 12891 62.6 0 12891
40 12749 62.6 0 12749
41 12659 62.6 0 12659
42 12932 62.6 0 12932
43 12911 62.6 0 12911
44 12238 62.6 0 12238
45 12738 62.6 0 12738
46 12929 62.6 0 12929
47 12777 62.6 0 12777
48 12664 62.6 0 12664
49 16598 62.6 0 16598
50 18537 62.6 0 18537
51 13745 62.6 0 13745
52 14090 62.6 0 14090
53 14178 62.6 0 14178
54 12999 62.6 0 12999
55 13482 62.6 0 13482
56 13332 62.6 0 13332
57 13037 62.6 0 13037
58 13345 62.6 0 13345
59 13232 62.6 0 13232
60 13257 62.6 0 13257
61 13338 62.6 0 13338
62 12959 62.6 0 12959
63 12996 62.6 0 12996
64 12533 62.6 0 12533
65 12809 62.6 0 12809
66 12437 62.6 0 12437
67 12117 62.6 0 12117
68 12173 62.6 0 12173
69 11420 62.6 0 11420
70 10994 62.6 0 10994
71 11079 62.6 0 11079
72 10666 62.6 0 10666
73 10233 62.6 0 10233
74 9553 62.6 0 9553
75 9529 62.6 0 9529
76 9052 62.6 0 9052
77 8883 62.6 0 8883
78 8706 62.6 0 8706
79 9585 62.6 0 9585
80 9211 62.6 0 9211
81 10227 62.6 0 10227
82 12018 62.6 0 12018
83 13859 62.6 0 13859
84 14502 62.6 0 14502
85 15343 62.6 0 15343
86 122452 62.6 0 122452
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 99362 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 23.3%
C: 34.7%
G: 0.0%
T: 39.3%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 18436 64148.7 0 18436
4 5366 16037.2 0 5366
5 2269 4009.3 0 2269
6 1532 1002.3 0 1532
7 1339 250.6 0 1339
8 1412 62.6 0 1412
9 1384 62.6 0 1384
10 1266 62.6 0 1266
11 1321 62.6 0 1321
12 1224 62.6 0 1224
13 1199 62.6 0 1199
14 1240 62.6 0 1240
15 1215 62.6 0 1215
16 1217 62.6 0 1217
17 1255 62.6 0 1255
18 1270 62.6 0 1270
19 1184 62.6 0 1184
20 1171 62.6 0 1171
21 1155 62.6 0 1155
22 1143 62.6 0 1143
23 1178 62.6 0 1178
24 1188 62.6 0 1188
25 1266 62.6 0 1266
26 1187 62.6 0 1187
27 1089 62.6 0 1089
28 1164 62.6 0 1164
29 1166 62.6 0 1166
30 1146 62.6 0 1146
31 1187 62.6 0 1187
32 1115 62.6 0 1115
33 1215 62.6 0 1215
34 1212 62.6 0 1212
35 1159 62.6 0 1159
36 1183 62.6 0 1183
37 1149 62.6 0 1149
38 1118 62.6 0 1118
39 1100 62.6 0 1100
40 1097 62.6 0 1097
41 1082 62.6 0 1082
42 1071 62.6 0 1071
43 1092 62.6 0 1092
44 1026 62.6 0 1026
45 1109 62.6 0 1109
46 1053 62.6 0 1053
47 1086 62.6 0 1086
48 1055 62.6 0 1055
49 1040 62.6 0 1040
50 1035 62.6 0 1035
51 926 62.6 0 926
52 943 62.6 0 943
53 992 62.6 0 992
54 893 62.6 0 893
55 937 62.6 0 937
56 976 62.6 0 976
57 939 62.6 0 939
58 874 62.6 0 874
59 881 62.6 0 881
60 876 62.6 0 876
61 823 62.6 0 823
62 740 62.6 0 740
63 767 62.6 0 767
64 681 62.6 0 681
65 608 62.6 0 608
66 549 62.6 0 549
67 499 62.6 0 499
68 451 62.6 0 451
69 388 62.6 0 388
70 377 62.6 0 377
71 298 62.6 0 298
72 285 62.6 0 285
73 259 62.6 0 259
74 245 62.6 0 245
75 180 62.6 0 180
76 166 62.6 0 166
77 162 62.6 0 162
78 126 62.6 0 126
79 110 62.6 0 110
80 108 62.6 0 108
81 65 62.6 0 65
82 77 62.6 0 77
83 68 62.6 0 68
84 107 62.6 0 107
85 101 62.6 0 101
86 2719 62.6 0 2719
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 78124 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.1%
C: 22.4%
G: 20.0%
T: 21.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 57149 64148.7 0 57149
4 14269 16037.2 0 14269
5 2554 4009.3 0 2554
6 334 1002.3 0 334
7 58 250.6 0 58
8 53 250.6 0 53
9 43 250.6 0 43
10 47 250.6 0 47
11 55 250.6 0 55
12 50 250.6 0 50
13 49 250.6 0 49
14 54 250.6 0 54
15 44 250.6 0 44
16 60 250.6 0 60
17 63 250.6 0 63
18 47 250.6 0 47
19 68 250.6 0 68
20 61 250.6 0 61
21 53 250.6 0 53
22 67 250.6 0 67
23 62 250.6 0 62
24 46 250.6 0 46
25 79 250.6 0 79
26 43 250.6 0 43
27 55 250.6 0 55
28 51 250.6 0 51
29 54 250.6 0 54
30 46 250.6 0 46
31 42 250.6 0 42
32 57 250.6 0 57
33 63 250.6 0 63
34 46 250.6 0 46
35 34 250.6 0 34
36 51 250.6 0 51
37 41 250.6 0 41
38 41 250.6 0 41
39 53 250.6 0 53
40 37 250.6 0 37
41 41 250.6 0 41
42 37 250.6 0 37
43 43 250.6 0 43
44 43 250.6 0 43
45 44 250.6 0 44
46 44 250.6 0 44
47 49 250.6 0 49
48 39 250.6 0 39
49 49 250.6 0 49
50 46 250.6 0 46
51 47 250.6 0 47
52 55 250.6 0 55
53 49 250.6 0 49
54 55 250.6 0 55
55 74 250.6 0 74
56 49 250.6 0 49
57 44 250.6 0 44
58 35 250.6 0 35
59 47 250.6 0 47
60 41 250.6 0 41
61 41 250.6 0 41
62 43 250.6 0 43
63 37 250.6 0 37
64 42 250.6 0 42
65 56 250.6 0 56
66 47 250.6 0 47
67 41 250.6 0 41
68 44 250.6 0 44
69 36 250.6 0 36
70 48 250.6 0 48
71 44 250.6 0 44
72 38 250.6 0 38
73 43 250.6 0 43
74 42 250.6 0 42
75 35 250.6 0 35
76 30 250.6 0 30
77 65 250.6 0 65
78 46 250.6 0 46
79 40 250.6 0 40
80 39 250.6 0 39
81 47 250.6 0 47
82 31 250.6 0 31
83 46 250.6 0 46
84 48 250.6 0 48
85 34 250.6 0 34
86 51 250.6 0 51
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D58_S144_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D58_S144_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 39.46 s (9 µs/read; 6.33 M reads/minute).
=== Summary ===
Total reads processed: 4,164,407
Reads with adapters: 1,515,647 (36.4%)
== Read fate breakdown ==
Reads that were too short: 354,193 (8.5%)
Reads written (passing filters): 3,810,214 (91.5%)
Total basepairs processed: 420,605,107 bp
Total written (filtered): 294,567,849 bp (70.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1334863 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 32.2%
G: 28.0%
T: 30.2%
none/other: 9.6%
Overview of removed sequences
length count expect max.err error counts
3 98723 65068.9 0 98723
4 46438 16267.2 0 46438
5 24861 4066.8 0 24861
6 17010 1016.7 0 17010
7 14005 254.2 0 14005
8 12526 63.5 0 12526
9 12681 63.5 0 12681
10 12591 63.5 0 12591
11 12589 63.5 0 12589
12 12344 63.5 0 12344
13 12696 63.5 0 12696
14 12868 63.5 0 12868
15 12893 63.5 0 12893
16 12861 63.5 0 12861
17 13089 63.5 0 13089
18 13130 63.5 0 13130
19 12893 63.5 0 12893
20 12844 63.5 0 12844
21 13078 63.5 0 13078
22 12992 63.5 0 12992
23 12736 63.5 0 12736
24 12691 63.5 0 12691
25 12877 63.5 0 12877
26 12880 63.5 0 12880
27 12689 63.5 0 12689
28 13103 63.5 0 13103
29 13244 63.5 0 13244
30 13053 63.5 0 13053
31 13398 63.5 0 13398
32 13075 63.5 0 13075
33 12987 63.5 0 12987
34 13385 63.5 0 13385
35 13148 63.5 0 13148
36 13096 63.5 0 13096
37 13229 63.5 0 13229
38 12846 63.5 0 12846
39 13046 63.5 0 13046
40 13226 63.5 0 13226
41 13078 63.5 0 13078
42 13049 63.5 0 13049
43 13439 63.5 0 13439
44 12526 63.5 0 12526
45 13165 63.5 0 13165
46 13269 63.5 0 13269
47 13272 63.5 0 13272
48 13495 63.5 0 13495
49 17204 63.5 0 17204
50 19286 63.5 0 19286
51 14191 63.5 0 14191
52 14438 63.5 0 14438
53 14370 63.5 0 14370
54 13246 63.5 0 13246
55 13916 63.5 0 13916
56 13970 63.5 0 13970
57 13376 63.5 0 13376
58 14103 63.5 0 14103
59 13610 63.5 0 13610
60 13826 63.5 0 13826
61 13832 63.5 0 13832
62 13502 63.5 0 13502
63 13407 63.5 0 13407
64 13160 63.5 0 13160
65 13133 63.5 0 13133
66 12996 63.5 0 12996
67 12769 63.5 0 12769
68 12473 63.5 0 12473
69 12281 63.5 0 12281
70 11533 63.5 0 11533
71 11561 63.5 0 11561
72 11384 63.5 0 11384
73 10636 63.5 0 10636
74 9908 63.5 0 9908
75 9786 63.5 0 9786
76 9321 63.5 0 9321
77 9319 63.5 0 9319
78 9121 63.5 0 9121
79 10006 63.5 0 10006
80 9614 63.5 0 9614
81 10604 63.5 0 10604
82 12452 63.5 0 12452
83 14200 63.5 0 14200
84 14903 63.5 0 14903
85 15799 63.5 0 15799
86 128513 63.5 0 128513
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 101996 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 23.4%
C: 34.8%
G: 0.0%
T: 38.9%
none/other: 2.9%
Overview of removed sequences
length count expect max.err error counts
3 18821 65068.9 0 18821
4 5340 16267.2 0 5340
5 2327 4066.8 0 2327
6 1552 1016.7 0 1552
7 1349 254.2 0 1349
8 1378 63.5 0 1378
9 1403 63.5 0 1403
10 1309 63.5 0 1309
11 1317 63.5 0 1317
12 1297 63.5 0 1297
13 1303 63.5 0 1303
14 1183 63.5 0 1183
15 1219 63.5 0 1219
16 1228 63.5 0 1228
17 1223 63.5 0 1223
18 1290 63.5 0 1290
19 1211 63.5 0 1211
20 1136 63.5 0 1136
21 1219 63.5 0 1219
22 1149 63.5 0 1149
23 1199 63.5 0 1199
24 1172 63.5 0 1172
25 1300 63.5 0 1300
26 1196 63.5 0 1196
27 1162 63.5 0 1162
28 1238 63.5 0 1238
29 1220 63.5 0 1220
30 1206 63.5 0 1206
31 1113 63.5 0 1113
32 1105 63.5 0 1105
33 1231 63.5 0 1231
34 1256 63.5 0 1256
35 1184 63.5 0 1184
36 1148 63.5 0 1148
37 1174 63.5 0 1174
38 1157 63.5 0 1157
39 1101 63.5 0 1101
40 1169 63.5 0 1169
41 1119 63.5 0 1119
42 1137 63.5 0 1137
43 1145 63.5 0 1145
44 1143 63.5 0 1143
45 1107 63.5 0 1107
46 1110 63.5 0 1110
47 1154 63.5 0 1154
48 1142 63.5 0 1142
49 1131 63.5 0 1131
50 1053 63.5 0 1053
51 1033 63.5 0 1033
52 1043 63.5 0 1043
53 1049 63.5 0 1049
54 971 63.5 0 971
55 1007 63.5 0 1007
56 992 63.5 0 992
57 939 63.5 0 939
58 960 63.5 0 960
59 919 63.5 0 919
60 935 63.5 0 935
61 769 63.5 0 769
62 742 63.5 0 742
63 727 63.5 0 727
64 708 63.5 0 708
65 635 63.5 0 635
66 595 63.5 0 595
67 523 63.5 0 523
68 475 63.5 0 475
69 413 63.5 0 413
70 371 63.5 0 371
71 347 63.5 0 347
72 302 63.5 0 302
73 254 63.5 0 254
74 247 63.5 0 247
75 185 63.5 0 185
76 165 63.5 0 165
77 143 63.5 0 143
78 133 63.5 0 133
79 126 63.5 0 126
80 114 63.5 0 114
81 78 63.5 0 78
82 76 63.5 0 76
83 91 63.5 0 91
84 77 63.5 0 77
85 110 63.5 0 110
86 2916 63.5 0 2916
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 78788 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.8%
C: 22.5%
G: 19.9%
T: 21.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 57836 65068.9 0 57836
4 14369 16267.2 0 14369
5 2565 4066.8 0 2565
6 326 1016.7 0 326
7 61 254.2 0 61
8 61 254.2 0 61
9 54 254.2 0 54
10 42 254.2 0 42
11 55 254.2 0 55
12 44 254.2 0 44
13 60 254.2 0 60
14 62 254.2 0 62
15 37 254.2 0 37
16 53 254.2 0 53
17 43 254.2 0 43
18 56 254.2 0 56
19 53 254.2 0 53
20 51 254.2 0 51
21 55 254.2 0 55
22 60 254.2 0 60
23 64 254.2 0 64
24 47 254.2 0 47
25 70 254.2 0 70
26 55 254.2 0 55
27 47 254.2 0 47
28 51 254.2 0 51
29 57 254.2 0 57
30 55 254.2 0 55
31 45 254.2 0 45
32 61 254.2 0 61
33 63 254.2 0 63
34 44 254.2 0 44
35 33 254.2 0 33
36 47 254.2 0 47
37 36 254.2 0 36
38 35 254.2 0 35
39 47 254.2 0 47
40 43 254.2 0 43
41 38 254.2 0 38
42 34 254.2 0 34
43 47 254.2 0 47
44 44 254.2 0 44
45 31 254.2 0 31
46 40 254.2 0 40
47 42 254.2 0 42
48 47 254.2 0 47
49 49 254.2 0 49
50 48 254.2 0 48
51 51 254.2 0 51
52 49 254.2 0 49
53 40 254.2 0 40
54 34 254.2 0 34
55 41 254.2 0 41
56 35 254.2 0 35
57 47 254.2 0 47
58 42 254.2 0 42
59 31 254.2 0 31
60 38 254.2 0 38
61 44 254.2 0 44
62 43 254.2 0 43
63 32 254.2 0 32
64 44 254.2 0 44
65 40 254.2 0 40
66 50 254.2 0 50
67 51 254.2 0 51
68 38 254.2 0 38
69 37 254.2 0 37
70 63 254.2 0 63
71 53 254.2 0 53
72 35 254.2 0 35
73 39 254.2 0 39
74 60 254.2 0 60
75 40 254.2 0 40
76 32 254.2 0 32
77 69 254.2 0 69
78 57 254.2 0 57
79 28 254.2 0 28
80 41 254.2 0 41
81 38 254.2 0 38
82 25 254.2 0 25
83 42 254.2 0 42
84 35 254.2 0 35
85 34 254.2 0 34
86 47 254.2 0 47
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D59_S142_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D59_S142_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 21.66 s (8 µs/read; 7.70 M reads/minute).
=== Summary ===
Total reads processed: 2,779,358
Reads with adapters: 831,414 (29.9%)
== Read fate breakdown ==
Reads that were too short: 208,388 (7.5%)
Reads written (passing filters): 2,570,970 (92.5%)
Total basepairs processed: 280,715,158 bp
Total written (filtered): 204,949,254 bp (73.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 721621 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.8%
G: 27.8%
T: 30.3%
none/other: 12.0%
Overview of removed sequences
length count expect max.err error counts
3 66623 43427.5 0 66623
4 28812 10856.9 0 28812
5 14598 2714.2 0 14598
6 9192 678.6 0 9192
7 7308 169.6 0 7308
8 6459 42.4 0 6459
9 6427 42.4 0 6427
10 6448 42.4 0 6448
11 6272 42.4 0 6272
12 6236 42.4 0 6236
13 6347 42.4 0 6347
14 6478 42.4 0 6478
15 6879 42.4 0 6879
16 7105 42.4 0 7105
17 6702 42.4 0 6702
18 7052 42.4 0 7052
19 6945 42.4 0 6945
20 6451 42.4 0 6451
21 6864 42.4 0 6864
22 6916 42.4 0 6916
23 6469 42.4 0 6469
24 6346 42.4 0 6346
25 6148 42.4 0 6148
26 6187 42.4 0 6187
27 6029 42.4 0 6029
28 6407 42.4 0 6407
29 6549 42.4 0 6549
30 6341 42.4 0 6341
31 6530 42.4 0 6530
32 6456 42.4 0 6456
33 6553 42.4 0 6553
34 6442 42.4 0 6442
35 6466 42.4 0 6466
36 6291 42.4 0 6291
37 6491 42.4 0 6491
38 6160 42.4 0 6160
39 6486 42.4 0 6486
40 6339 42.4 0 6339
41 6251 42.4 0 6251
42 6424 42.4 0 6424
43 6773 42.4 0 6773
44 6264 42.4 0 6264
45 6708 42.4 0 6708
46 6995 42.4 0 6995
47 6696 42.4 0 6696
48 6499 42.4 0 6499
49 8929 42.4 0 8929
50 10213 42.4 0 10213
51 6700 42.4 0 6700
52 6841 42.4 0 6841
53 6755 42.4 0 6755
54 6323 42.4 0 6323
55 6633 42.4 0 6633
56 6602 42.4 0 6602
57 6380 42.4 0 6380
58 6719 42.4 0 6719
59 6429 42.4 0 6429
60 6619 42.4 0 6619
61 6693 42.4 0 6693
62 6483 42.4 0 6483
63 6503 42.4 0 6503
64 6376 42.4 0 6376
65 6178 42.4 0 6178
66 6172 42.4 0 6172
67 6046 42.4 0 6046
68 6041 42.4 0 6041
69 5676 42.4 0 5676
70 5320 42.4 0 5320
71 5788 42.4 0 5788
72 5799 42.4 0 5799
73 5208 42.4 0 5208
74 5080 42.4 0 5080
75 5043 42.4 0 5043
76 4905 42.4 0 4905
77 4875 42.4 0 4875
78 5108 42.4 0 5108
79 5838 42.4 0 5838
80 5556 42.4 0 5556
81 6435 42.4 0 6435
82 7789 42.4 0 7789
83 8464 42.4 0 8464
84 9332 42.4 0 9332
85 9900 42.4 0 9900
86 86456 42.4 0 86456
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 48287 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.8%
C: 33.9%
G: 0.0%
T: 36.4%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 15790 43427.5 0 15790
4 3705 10856.9 0 3705
5 1176 2714.2 0 1176
6 663 678.6 0 663
7 587 169.6 0 587
8 623 42.4 0 623
9 545 42.4 0 545
10 458 42.4 0 458
11 512 42.4 0 512
12 453 42.4 0 453
13 484 42.4 0 484
14 465 42.4 0 465
15 471 42.4 0 471
16 494 42.4 0 494
17 427 42.4 0 427
18 437 42.4 0 437
19 420 42.4 0 420
20 418 42.4 0 418
21 396 42.4 0 396
22 405 42.4 0 405
23 424 42.4 0 424
24 430 42.4 0 430
25 452 42.4 0 452
26 450 42.4 0 450
27 405 42.4 0 405
28 455 42.4 0 455
29 414 42.4 0 414
30 426 42.4 0 426
31 403 42.4 0 403
32 404 42.4 0 404
33 408 42.4 0 408
34 401 42.4 0 401
35 427 42.4 0 427
36 418 42.4 0 418
37 397 42.4 0 397
38 378 42.4 0 378
39 416 42.4 0 416
40 402 42.4 0 402
41 371 42.4 0 371
42 409 42.4 0 409
43 426 42.4 0 426
44 376 42.4 0 376
45 384 42.4 0 384
46 395 42.4 0 395
47 389 42.4 0 389
48 409 42.4 0 409
49 370 42.4 0 370
50 373 42.4 0 373
51 392 42.4 0 392
52 362 42.4 0 362
53 384 42.4 0 384
54 363 42.4 0 363
55 347 42.4 0 347
56 348 42.4 0 348
57 329 42.4 0 329
58 327 42.4 0 327
59 320 42.4 0 320
60 302 42.4 0 302
61 283 42.4 0 283
62 249 42.4 0 249
63 255 42.4 0 255
64 246 42.4 0 246
65 211 42.4 0 211
66 216 42.4 0 216
67 191 42.4 0 191
68 154 42.4 0 154
69 162 42.4 0 162
70 129 42.4 0 129
71 116 42.4 0 116
72 123 42.4 0 123
73 111 42.4 0 111
74 88 42.4 0 88
75 81 42.4 0 81
76 63 42.4 0 63
77 68 42.4 0 68
78 70 42.4 0 70
79 42 42.4 0 42
80 43 42.4 0 43
81 29 42.4 0 29
82 49 42.4 0 49
83 36 42.4 0 36
84 54 42.4 0 54
85 42 42.4 0 42
86 1361 42.4 0 1361
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61506 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 22.5%
G: 20.7%
T: 21.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45411 43427.5 0 45411
4 10727 10856.9 0 10727
5 2068 2714.2 0 2068
6 346 678.6 0 346
7 42 169.6 0 42
8 35 169.6 0 35
9 33 169.6 0 33
10 27 169.6 0 27
11 37 169.6 0 37
12 32 169.6 0 32
13 51 169.6 0 51
14 45 169.6 0 45
15 32 169.6 0 32
16 68 169.6 0 68
17 50 169.6 0 50
18 39 169.6 0 39
19 41 169.6 0 41
20 34 169.6 0 34
21 40 169.6 0 40
22 42 169.6 0 42
23 31 169.6 0 31
24 31 169.6 0 31
25 46 169.6 0 46
26 38 169.6 0 38
27 28 169.6 0 28
28 42 169.6 0 42
29 34 169.6 0 34
30 36 169.6 0 36
31 30 169.6 0 30
32 30 169.6 0 30
33 27 169.6 0 27
34 40 169.6 0 40
35 35 169.6 0 35
36 26 169.6 0 26
37 35 169.6 0 35
38 26 169.6 0 26
39 30 169.6 0 30
40 45 169.6 0 45
41 36 169.6 0 36
42 37 169.6 0 37
43 51 169.6 0 51
44 33 169.6 0 33
45 34 169.6 0 34
46 30 169.6 0 30
47 34 169.6 0 34
48 32 169.6 0 32
49 33 169.6 0 33
50 41 169.6 0 41
51 32 169.6 0 32
52 60 169.6 0 60
53 42 169.6 0 42
54 42 169.6 0 42
55 24 169.6 0 24
56 33 169.6 0 33
57 29 169.6 0 29
58 31 169.6 0 31
59 55 169.6 0 55
60 28 169.6 0 28
61 31 169.6 0 31
62 44 169.6 0 44
63 37 169.6 0 37
64 32 169.6 0 32
65 60 169.6 0 60
66 38 169.6 0 38
67 38 169.6 0 38
68 28 169.6 0 28
69 45 169.6 0 45
70 31 169.6 0 31
71 55 169.6 0 55
72 26 169.6 0 26
73 33 169.6 0 33
74 40 169.6 0 40
75 23 169.6 0 23
76 16 169.6 0 16
77 46 169.6 0 46
78 38 169.6 0 38
79 27 169.6 0 27
80 38 169.6 0 38
81 32 169.6 0 32
82 35 169.6 0 35
83 45 169.6 0 45
84 34 169.6 0 34
85 42 169.6 0 42
86 45 169.6 0 45
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: D59_S142_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/D59_S142_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.53 s (9 µs/read; 6.39 M reads/minute).
=== Summary ===
Total reads processed: 2,827,339
Reads with adapters: 852,725 (30.2%)
== Read fate breakdown ==
Reads that were too short: 217,317 (7.7%)
Reads written (passing filters): 2,610,022 (92.3%)
Total basepairs processed: 285,561,239 bp
Total written (filtered): 207,863,851 bp (72.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 741286 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.8%
G: 27.8%
T: 30.2%
none/other: 12.2%
Overview of removed sequences
length count expect max.err error counts
3 67544 44177.2 0 67544
4 29024 11044.3 0 29024
5 14880 2761.1 0 14880
6 9446 690.3 0 9446
7 7351 172.6 0 7351
8 6397 43.1 0 6397
9 6288 43.1 0 6288
10 6502 43.1 0 6502
11 6445 43.1 0 6445
12 6182 43.1 0 6182
13 6438 43.1 0 6438
14 6603 43.1 0 6603
15 6851 43.1 0 6851
16 7011 43.1 0 7011
17 6799 43.1 0 6799
18 7218 43.1 0 7218
19 7177 43.1 0 7177
20 6721 43.1 0 6721
21 7282 43.1 0 7282
22 7216 43.1 0 7216
23 6548 43.1 0 6548
24 6455 43.1 0 6455
25 6199 43.1 0 6199
26 6182 43.1 0 6182
27 6270 43.1 0 6270
28 6538 43.1 0 6538
29 6492 43.1 0 6492
30 6453 43.1 0 6453
31 6735 43.1 0 6735
32 6286 43.1 0 6286
33 6768 43.1 0 6768
34 6774 43.1 0 6774
35 6678 43.1 0 6678
36 6566 43.1 0 6566
37 6534 43.1 0 6534
38 6265 43.1 0 6265
39 6521 43.1 0 6521
40 6509 43.1 0 6509
41 6432 43.1 0 6432
42 6866 43.1 0 6866
43 6877 43.1 0 6877
44 6526 43.1 0 6526
45 6587 43.1 0 6587
46 6860 43.1 0 6860
47 6764 43.1 0 6764
48 6584 43.1 0 6584
49 9015 43.1 0 9015
50 10419 43.1 0 10419
51 6900 43.1 0 6900
52 7101 43.1 0 7101
53 6987 43.1 0 6987
54 6357 43.1 0 6357
55 6682 43.1 0 6682
56 6852 43.1 0 6852
57 6555 43.1 0 6555
58 7020 43.1 0 7020
59 6687 43.1 0 6687
60 6891 43.1 0 6891
61 7044 43.1 0 7044
62 6921 43.1 0 6921
63 6881 43.1 0 6881
64 6644 43.1 0 6644
65 6588 43.1 0 6588
66 6591 43.1 0 6591
67 6295 43.1 0 6295
68 6318 43.1 0 6318
69 6115 43.1 0 6115
70 5584 43.1 0 5584
71 5944 43.1 0 5944
72 5868 43.1 0 5868
73 5564 43.1 0 5564
74 5155 43.1 0 5155
75 5258 43.1 0 5258
76 5065 43.1 0 5065
77 5135 43.1 0 5135
78 5298 43.1 0 5298
79 6245 43.1 0 6245
80 5852 43.1 0 5852
81 6635 43.1 0 6635
82 8116 43.1 0 8116
83 8894 43.1 0 8894
84 9549 43.1 0 9549
85 10375 43.1 0 10375
86 90242 43.1 0 90242
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 49456 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.6%
C: 34.3%
G: 0.0%
T: 36.5%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 16237 44177.2 0 16237
4 3791 11044.3 0 3791
5 1190 2761.1 0 1190
6 661 690.3 0 661
7 522 172.6 0 522
8 547 43.1 0 547
9 557 43.1 0 557
10 525 43.1 0 525
11 485 43.1 0 485
12 483 43.1 0 483
13 486 43.1 0 486
14 441 43.1 0 441
15 480 43.1 0 480
16 495 43.1 0 495
17 432 43.1 0 432
18 456 43.1 0 456
19 428 43.1 0 428
20 442 43.1 0 442
21 452 43.1 0 452
22 446 43.1 0 446
23 433 43.1 0 433
24 478 43.1 0 478
25 466 43.1 0 466
26 432 43.1 0 432
27 423 43.1 0 423
28 435 43.1 0 435
29 431 43.1 0 431
30 422 43.1 0 422
31 413 43.1 0 413
32 418 43.1 0 418
33 454 43.1 0 454
34 436 43.1 0 436
35 414 43.1 0 414
36 402 43.1 0 402
37 397 43.1 0 397
38 402 43.1 0 402
39 389 43.1 0 389
40 391 43.1 0 391
41 418 43.1 0 418
42 403 43.1 0 403
43 431 43.1 0 431
44 341 43.1 0 341
45 387 43.1 0 387
46 401 43.1 0 401
47 406 43.1 0 406
48 422 43.1 0 422
49 420 43.1 0 420
50 357 43.1 0 357
51 380 43.1 0 380
52 410 43.1 0 410
53 427 43.1 0 427
54 351 43.1 0 351
55 377 43.1 0 377
56 315 43.1 0 315
57 350 43.1 0 350
58 319 43.1 0 319
59 349 43.1 0 349
60 358 43.1 0 358
61 276 43.1 0 276
62 306 43.1 0 306
63 257 43.1 0 257
64 255 43.1 0 255
65 247 43.1 0 247
66 223 43.1 0 223
67 219 43.1 0 219
68 190 43.1 0 190
69 164 43.1 0 164
70 141 43.1 0 141
71 153 43.1 0 153
72 128 43.1 0 128
73 90 43.1 0 90
74 99 43.1 0 99
75 69 43.1 0 69
76 96 43.1 0 96
77 58 43.1 0 58
78 53 43.1 0 53
79 42 43.1 0 42
80 40 43.1 0 40
81 55 43.1 0 55
82 45 43.1 0 45
83 40 43.1 0 40
84 44 43.1 0 44
85 59 43.1 0 59
86 1293 43.1 0 1293
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61983 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 22.5%
G: 20.8%
T: 21.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45747 44177.2 0 45747
4 10732 11044.3 0 10732
5 2191 2761.1 0 2191
6 362 690.3 0 362
7 40 172.6 0 40
8 40 172.6 0 40
9 32 172.6 0 32
10 26 172.6 0 26
11 38 172.6 0 38
12 24 172.6 0 24
13 49 172.6 0 49
14 38 172.6 0 38
15 39 172.6 0 39
16 41 172.6 0 41
17 40 172.6 0 40
18 40 172.6 0 40
19 70 172.6 0 70
20 31 172.6 0 31
21 34 172.6 0 34
22 37 172.6 0 37
23 35 172.6 0 35
24 42 172.6 0 42
25 45 172.6 0 45
26 43 172.6 0 43
27 32 172.6 0 32
28 38 172.6 0 38
29 33 172.6 0 33
30 24 172.6 0 24
31 26 172.6 0 26
32 32 172.6 0 32
33 34 172.6 0 34
34 36 172.6 0 36
35 34 172.6 0 34
36 28 172.6 0 28
37 24 172.6 0 24
38 38 172.6 0 38
39 27 172.6 0 27
40 51 172.6 0 51
41 41 172.6 0 41
42 37 172.6 0 37
43 29 172.6 0 29
44 39 172.6 0 39
45 29 172.6 0 29
46 43 172.6 0 43
47 54 172.6 0 54
48 31 172.6 0 31
49 36 172.6 0 36
50 39 172.6 0 39
51 39 172.6 0 39
52 33 172.6 0 33
53 44 172.6 0 44
54 47 172.6 0 47
55 35 172.6 0 35
56 25 172.6 0 25
57 42 172.6 0 42
58 36 172.6 0 36
59 40 172.6 0 40
60 38 172.6 0 38
61 28 172.6 0 28
62 34 172.6 0 34
63 34 172.6 0 34
64 28 172.6 0 28
65 51 172.6 0 51
66 46 172.6 0 46
67 26 172.6 0 26
68 34 172.6 0 34
69 36 172.6 0 36
70 41 172.6 0 41
71 33 172.6 0 33
72 26 172.6 0 26
73 47 172.6 0 47
74 34 172.6 0 34
75 29 172.6 0 29
76 29 172.6 0 29
77 74 172.6 0 74
78 34 172.6 0 34
79 35 172.6 0 35
80 34 172.6 0 34
81 33 172.6 0 33
82 31 172.6 0 31
83 40 172.6 0 40
84 32 172.6 0 32
85 39 172.6 0 39
86 45 172.6 0 45
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M41_S161_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M41_S161_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.05 s (9 µs/read; 6.52 M reads/minute).
=== Summary ===
Total reads processed: 2,829,039
Reads with adapters: 917,421 (32.4%)
== Read fate breakdown ==
Reads that were too short: 266,530 (9.4%)
Reads written (passing filters): 2,562,509 (90.6%)
Total basepairs processed: 285,732,939 bp
Total written (filtered): 202,608,563 bp (70.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 824043 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.7%
G: 27.9%
T: 28.3%
none/other: 14.1%
Overview of removed sequences
length count expect max.err error counts
3 66329 44203.7 0 66329
4 28518 11050.9 0 28518
5 14003 2762.7 0 14003
6 9470 690.7 0 9470
7 7444 172.7 0 7444
8 6539 43.2 0 6539
9 6497 43.2 0 6497
10 6431 43.2 0 6431
11 6316 43.2 0 6316
12 6410 43.2 0 6410
13 6677 43.2 0 6677
14 6646 43.2 0 6646
15 6723 43.2 0 6723
16 6812 43.2 0 6812
17 6730 43.2 0 6730
18 7104 43.2 0 7104
19 6528 43.2 0 6528
20 6346 43.2 0 6346
21 6874 43.2 0 6874
22 6954 43.2 0 6954
23 6448 43.2 0 6448
24 6548 43.2 0 6548
25 6572 43.2 0 6572
26 6678 43.2 0 6678
27 6716 43.2 0 6716
28 6966 43.2 0 6966
29 7053 43.2 0 7053
30 6679 43.2 0 6679
31 7935 43.2 0 7935
32 7095 43.2 0 7095
33 7359 43.2 0 7359
34 7195 43.2 0 7195
35 7455 43.2 0 7455
36 6938 43.2 0 6938
37 7197 43.2 0 7197
38 6861 43.2 0 6861
39 6972 43.2 0 6972
40 7221 43.2 0 7221
41 7458 43.2 0 7458
42 7627 43.2 0 7627
43 8184 43.2 0 8184
44 7397 43.2 0 7397
45 7585 43.2 0 7585
46 8320 43.2 0 8320
47 7949 43.2 0 7949
48 7453 43.2 0 7453
49 11565 43.2 0 11565
50 13444 43.2 0 13444
51 7878 43.2 0 7878
52 8255 43.2 0 8255
53 8045 43.2 0 8045
54 6952 43.2 0 6952
55 7681 43.2 0 7681
56 7661 43.2 0 7661
57 7424 43.2 0 7424
58 7948 43.2 0 7948
59 7575 43.2 0 7575
60 7582 43.2 0 7582
61 7968 43.2 0 7968
62 7701 43.2 0 7701
63 7929 43.2 0 7929
64 7283 43.2 0 7283
65 7283 43.2 0 7283
66 7052 43.2 0 7052
67 7222 43.2 0 7222
68 7075 43.2 0 7075
69 6818 43.2 0 6818
70 6684 43.2 0 6684
71 7319 43.2 0 7319
72 7179 43.2 0 7179
73 6931 43.2 0 6931
74 6532 43.2 0 6532
75 6595 43.2 0 6595
76 6507 43.2 0 6507
77 6582 43.2 0 6582
78 6536 43.2 0 6536
79 7318 43.2 0 7318
80 6892 43.2 0 6892
81 7946 43.2 0 7946
82 9529 43.2 0 9529
83 10232 43.2 0 10232
84 11373 43.2 0 11373
85 11859 43.2 0 11859
86 116476 43.2 0 116476
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30134 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.0%
C: 29.7%
G: 0.0%
T: 35.1%
none/other: 4.2%
Overview of removed sequences
length count expect max.err error counts
3 14250 44203.7 0 14250
4 3069 11050.9 0 3069
5 860 2762.7 0 860
6 359 690.7 0 359
7 274 172.7 0 274
8 245 43.2 0 245
9 247 43.2 0 247
10 232 43.2 0 232
11 198 43.2 0 198
12 198 43.2 0 198
13 240 43.2 0 240
14 188 43.2 0 188
15 168 43.2 0 168
16 179 43.2 0 179
17 152 43.2 0 152
18 180 43.2 0 180
19 187 43.2 0 187
20 166 43.2 0 166
21 155 43.2 0 155
22 181 43.2 0 181
23 163 43.2 0 163
24 180 43.2 0 180
25 161 43.2 0 161
26 165 43.2 0 165
27 156 43.2 0 156
28 155 43.2 0 155
29 175 43.2 0 175
30 166 43.2 0 166
31 154 43.2 0 154
32 154 43.2 0 154
33 173 43.2 0 173
34 167 43.2 0 167
35 157 43.2 0 157
36 170 43.2 0 170
37 160 43.2 0 160
38 172 43.2 0 172
39 140 43.2 0 140
40 139 43.2 0 139
41 150 43.2 0 150
42 161 43.2 0 161
43 136 43.2 0 136
44 134 43.2 0 134
45 162 43.2 0 162
46 134 43.2 0 134
47 154 43.2 0 154
48 147 43.2 0 147
49 151 43.2 0 151
50 129 43.2 0 129
51 162 43.2 0 162
52 153 43.2 0 153
53 148 43.2 0 148
54 151 43.2 0 151
55 138 43.2 0 138
56 133 43.2 0 133
57 124 43.2 0 124
58 140 43.2 0 140
59 119 43.2 0 119
60 128 43.2 0 128
61 108 43.2 0 108
62 99 43.2 0 99
63 120 43.2 0 120
64 109 43.2 0 109
65 91 43.2 0 91
66 88 43.2 0 88
67 58 43.2 0 58
68 83 43.2 0 83
69 65 43.2 0 65
70 48 43.2 0 48
71 47 43.2 0 47
72 48 43.2 0 48
73 40 43.2 0 40
74 39 43.2 0 39
75 41 43.2 0 41
76 39 43.2 0 39
77 16 43.2 0 16
78 28 43.2 0 28
79 23 43.2 0 23
80 27 43.2 0 27
81 25 43.2 0 25
82 31 43.2 0 31
83 38 43.2 0 38
84 25 43.2 0 25
85 33 43.2 0 33
86 1276 43.2 0 1276
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 63244 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 23.4%
G: 20.7%
T: 19.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47228 44203.7 0 47228
4 10668 11050.9 0 10668
5 2020 2762.7 0 2020
6 268 690.7 0 268
7 25 172.7 0 25
8 38 172.7 0 38
9 29 172.7 0 29
10 45 172.7 0 45
11 31 172.7 0 31
12 38 172.7 0 38
13 31 172.7 0 31
14 31 172.7 0 31
15 32 172.7 0 32
16 35 172.7 0 35
17 40 172.7 0 40
18 35 172.7 0 35
19 59 172.7 0 59
20 64 172.7 0 64
21 43 172.7 0 43
22 38 172.7 0 38
23 27 172.7 0 27
24 29 172.7 0 29
25 41 172.7 0 41
26 41 172.7 0 41
27 27 172.7 0 27
28 40 172.7 0 40
29 37 172.7 0 37
30 28 172.7 0 28
31 37 172.7 0 37
32 39 172.7 0 39
33 54 172.7 0 54
34 29 172.7 0 29
35 41 172.7 0 41
36 37 172.7 0 37
37 29 172.7 0 29
38 33 172.7 0 33
39 32 172.7 0 32
40 40 172.7 0 40
41 35 172.7 0 35
42 30 172.7 0 30
43 35 172.7 0 35
44 34 172.7 0 34
45 26 172.7 0 26
46 22 172.7 0 22
47 35 172.7 0 35
48 34 172.7 0 34
49 43 172.7 0 43
50 30 172.7 0 30
51 31 172.7 0 31
52 43 172.7 0 43
53 26 172.7 0 26
54 31 172.7 0 31
55 52 172.7 0 52
56 34 172.7 0 34
57 50 172.7 0 50
58 41 172.7 0 41
59 34 172.7 0 34
60 29 172.7 0 29
61 32 172.7 0 32
62 33 172.7 0 33
63 27 172.7 0 27
64 40 172.7 0 40
65 41 172.7 0 41
66 42 172.7 0 42
67 42 172.7 0 42
68 38 172.7 0 38
69 32 172.7 0 32
70 48 172.7 0 48
71 37 172.7 0 37
72 31 172.7 0 31
73 50 172.7 0 50
74 43 172.7 0 43
75 23 172.7 0 23
76 27 172.7 0 27
77 114 172.7 0 114
78 91 172.7 0 91
79 43 172.7 0 43
80 37 172.7 0 37
81 44 172.7 0 44
82 30 172.7 0 30
83 52 172.7 0 52
84 41 172.7 0 41
85 35 172.7 0 35
86 37 172.7 0 37
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M41_S161_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M41_S161_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.07 s (9 µs/read; 6.64 M reads/minute).
=== Summary ===
Total reads processed: 2,886,534
Reads with adapters: 944,284 (32.7%)
== Read fate breakdown ==
Reads that were too short: 277,705 (9.6%)
Reads written (passing filters): 2,608,829 (90.4%)
Total basepairs processed: 291,539,934 bp
Total written (filtered): 206,049,968 bp (70.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 848602 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.7%
G: 27.9%
T: 28.0%
none/other: 14.4%
Overview of removed sequences
length count expect max.err error counts
3 67164 45102.1 0 67164
4 28750 11275.5 0 28750
5 14500 2818.9 0 14500
6 9437 704.7 0 9437
7 7496 176.2 0 7496
8 6452 44.0 0 6452
9 6567 44.0 0 6567
10 6621 44.0 0 6621
11 6473 44.0 0 6473
12 6580 44.0 0 6580
13 6554 44.0 0 6554
14 6747 44.0 0 6747
15 6804 44.0 0 6804
16 7035 44.0 0 7035
17 6776 44.0 0 6776
18 6965 44.0 0 6965
19 6697 44.0 0 6697
20 6516 44.0 0 6516
21 6953 44.0 0 6953
22 7063 44.0 0 7063
23 6741 44.0 0 6741
24 6586 44.0 0 6586
25 6612 44.0 0 6612
26 6727 44.0 0 6727
27 6869 44.0 0 6869
28 7103 44.0 0 7103
29 7214 44.0 0 7214
30 7146 44.0 0 7146
31 8028 44.0 0 8028
32 7312 44.0 0 7312
33 7868 44.0 0 7868
34 7628 44.0 0 7628
35 7618 44.0 0 7618
36 7196 44.0 0 7196
37 7675 44.0 0 7675
38 7157 44.0 0 7157
39 7328 44.0 0 7328
40 7522 44.0 0 7522
41 7618 44.0 0 7618
42 7799 44.0 0 7799
43 8410 44.0 0 8410
44 7685 44.0 0 7685
45 7703 44.0 0 7703
46 8339 44.0 0 8339
47 8179 44.0 0 8179
48 7714 44.0 0 7714
49 11898 44.0 0 11898
50 14183 44.0 0 14183
51 8066 44.0 0 8066
52 8525 44.0 0 8525
53 8251 44.0 0 8251
54 7267 44.0 0 7267
55 8040 44.0 0 8040
56 7837 44.0 0 7837
57 7528 44.0 0 7528
58 8074 44.0 0 8074
59 7826 44.0 0 7826
60 7844 44.0 0 7844
61 8180 44.0 0 8180
62 8024 44.0 0 8024
63 8185 44.0 0 8185
64 7557 44.0 0 7557
65 7469 44.0 0 7469
66 7345 44.0 0 7345
67 7337 44.0 0 7337
68 7494 44.0 0 7494
69 7123 44.0 0 7123
70 6752 44.0 0 6752
71 7609 44.0 0 7609
72 7516 44.0 0 7516
73 7075 44.0 0 7075
74 6761 44.0 0 6761
75 6833 44.0 0 6833
76 6620 44.0 0 6620
77 6763 44.0 0 6763
78 6857 44.0 0 6857
79 7660 44.0 0 7660
80 7125 44.0 0 7125
81 8510 44.0 0 8510
82 9963 44.0 0 9963
83 10682 44.0 0 10682
84 11797 44.0 0 11797
85 12149 44.0 0 12149
86 121950 44.0 0 121950
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 31219 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.6%
C: 29.3%
G: 0.0%
T: 35.7%
none/other: 4.4%
Overview of removed sequences
length count expect max.err error counts
3 14337 45102.1 0 14337
4 3214 11275.5 0 3214
5 842 2818.9 0 842
6 347 704.7 0 347
7 282 176.2 0 282
8 262 44.0 0 262
9 265 44.0 0 265
10 229 44.0 0 229
11 210 44.0 0 210
12 203 44.0 0 203
13 199 44.0 0 199
14 199 44.0 0 199
15 205 44.0 0 205
16 187 44.0 0 187
17 151 44.0 0 151
18 211 44.0 0 211
19 188 44.0 0 188
20 198 44.0 0 198
21 171 44.0 0 171
22 171 44.0 0 171
23 176 44.0 0 176
24 206 44.0 0 206
25 195 44.0 0 195
26 204 44.0 0 204
27 170 44.0 0 170
28 172 44.0 0 172
29 173 44.0 0 173
30 190 44.0 0 190
31 180 44.0 0 180
32 139 44.0 0 139
33 184 44.0 0 184
34 211 44.0 0 211
35 168 44.0 0 168
36 133 44.0 0 133
37 176 44.0 0 176
38 168 44.0 0 168
39 159 44.0 0 159
40 156 44.0 0 156
41 158 44.0 0 158
42 171 44.0 0 171
43 142 44.0 0 142
44 139 44.0 0 139
45 165 44.0 0 165
46 164 44.0 0 164
47 149 44.0 0 149
48 164 44.0 0 164
49 143 44.0 0 143
50 139 44.0 0 139
51 150 44.0 0 150
52 151 44.0 0 151
53 147 44.0 0 147
54 158 44.0 0 158
55 142 44.0 0 142
56 164 44.0 0 164
57 147 44.0 0 147
58 135 44.0 0 135
59 145 44.0 0 145
60 146 44.0 0 146
61 128 44.0 0 128
62 130 44.0 0 130
63 105 44.0 0 105
64 112 44.0 0 112
65 99 44.0 0 99
66 109 44.0 0 109
67 78 44.0 0 78
68 84 44.0 0 84
69 77 44.0 0 77
70 58 44.0 0 58
71 74 44.0 0 74
72 70 44.0 0 70
73 57 44.0 0 57
74 47 44.0 0 47
75 35 44.0 0 35
76 34 44.0 0 34
77 28 44.0 0 28
78 37 44.0 0 37
79 38 44.0 0 38
80 20 44.0 0 20
81 18 44.0 0 18
82 28 44.0 0 28
83 41 44.0 0 41
84 50 44.0 0 50
85 52 44.0 0 52
86 1360 44.0 0 1360
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 64463 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 23.5%
G: 20.3%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 48294 45102.1 0 48294
4 10718 11275.5 0 10718
5 2175 2818.9 0 2175
6 306 704.7 0 306
7 15 176.2 0 15
8 29 176.2 0 29
9 25 176.2 0 25
10 19 176.2 0 19
11 28 176.2 0 28
12 26 176.2 0 26
13 47 176.2 0 47
14 37 176.2 0 37
15 39 176.2 0 39
16 31 176.2 0 31
17 43 176.2 0 43
18 31 176.2 0 31
19 59 176.2 0 59
20 38 176.2 0 38
21 35 176.2 0 35
22 44 176.2 0 44
23 54 176.2 0 54
24 29 176.2 0 29
25 45 176.2 0 45
26 33 176.2 0 33
27 29 176.2 0 29
28 38 176.2 0 38
29 47 176.2 0 47
30 26 176.2 0 26
31 38 176.2 0 38
32 35 176.2 0 35
33 39 176.2 0 39
34 33 176.2 0 33
35 34 176.2 0 34
36 44 176.2 0 44
37 36 176.2 0 36
38 42 176.2 0 42
39 33 176.2 0 33
40 41 176.2 0 41
41 26 176.2 0 26
42 52 176.2 0 52
43 33 176.2 0 33
44 34 176.2 0 34
45 34 176.2 0 34
46 29 176.2 0 29
47 39 176.2 0 39
48 29 176.2 0 29
49 28 176.2 0 28
50 38 176.2 0 38
51 37 176.2 0 37
52 26 176.2 0 26
53 39 176.2 0 39
54 30 176.2 0 30
55 35 176.2 0 35
56 36 176.2 0 36
57 38 176.2 0 38
58 41 176.2 0 41
59 39 176.2 0 39
60 30 176.2 0 30
61 24 176.2 0 24
62 18 176.2 0 18
63 37 176.2 0 37
64 42 176.2 0 42
65 53 176.2 0 53
66 38 176.2 0 38
67 30 176.2 0 30
68 44 176.2 0 44
69 32 176.2 0 32
70 35 176.2 0 35
71 50 176.2 0 50
72 28 176.2 0 28
73 31 176.2 0 31
74 31 176.2 0 31
75 30 176.2 0 30
76 32 176.2 0 32
77 114 176.2 0 114
78 73 176.2 0 73
79 31 176.2 0 31
80 37 176.2 0 37
81 31 176.2 0 31
82 31 176.2 0 31
83 52 176.2 0 52
84 42 176.2 0 42
85 38 176.2 0 38
86 51 176.2 0 51
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M42_S169_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M42_S169_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.32 s (10 µs/read; 6.12 M reads/minute).
=== Summary ===
Total reads processed: 2,686,216
Reads with adapters: 866,281 (32.2%)
== Read fate breakdown ==
Reads that were too short: 235,969 (8.8%)
Reads written (passing filters): 2,450,247 (91.2%)
Total basepairs processed: 271,307,816 bp
Total written (filtered): 193,861,921 bp (71.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 776830 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.7%
G: 27.7%
T: 30.1%
none/other: 12.6%
Overview of removed sequences
length count expect max.err error counts
3 63887 41972.1 0 63887
4 26771 10493.0 0 26771
5 14147 2623.3 0 14147
6 9458 655.8 0 9458
7 7733 164.0 0 7733
8 6934 41.0 0 6934
9 6729 41.0 0 6729
10 7023 41.0 0 7023
11 6651 41.0 0 6651
12 6810 41.0 0 6810
13 6842 41.0 0 6842
14 6837 41.0 0 6837
15 7010 41.0 0 7010
16 7008 41.0 0 7008
17 6784 41.0 0 6784
18 6917 41.0 0 6917
19 6755 41.0 0 6755
20 6671 41.0 0 6671
21 6951 41.0 0 6951
22 6724 41.0 0 6724
23 6613 41.0 0 6613
24 6425 41.0 0 6425
25 6525 41.0 0 6525
26 6476 41.0 0 6476
27 6792 41.0 0 6792
28 6953 41.0 0 6953
29 6743 41.0 0 6743
30 6877 41.0 0 6877
31 7605 41.0 0 7605
32 7074 41.0 0 7074
33 7654 41.0 0 7654
34 7688 41.0 0 7688
35 7031 41.0 0 7031
36 6912 41.0 0 6912
37 7098 41.0 0 7098
38 6662 41.0 0 6662
39 6603 41.0 0 6603
40 6894 41.0 0 6894
41 6679 41.0 0 6679
42 7048 41.0 0 7048
43 8356 41.0 0 8356
44 6995 41.0 0 6995
45 7434 41.0 0 7434
46 9063 41.0 0 9063
47 7753 41.0 0 7753
48 7231 41.0 0 7231
49 12690 41.0 0 12690
50 12729 41.0 0 12729
51 7235 41.0 0 7235
52 8102 41.0 0 8102
53 7118 41.0 0 7118
54 6202 41.0 0 6202
55 6572 41.0 0 6572
56 6699 41.0 0 6699
57 6498 41.0 0 6498
58 7010 41.0 0 7010
59 6705 41.0 0 6705
60 6897 41.0 0 6897
61 6841 41.0 0 6841
62 6840 41.0 0 6840
63 6423 41.0 0 6423
64 6257 41.0 0 6257
65 6555 41.0 0 6555
66 6096 41.0 0 6096
67 6163 41.0 0 6163
68 6327 41.0 0 6327
69 5915 41.0 0 5915
70 5573 41.0 0 5573
71 5983 41.0 0 5983
72 6161 41.0 0 6161
73 5769 41.0 0 5769
74 5453 41.0 0 5453
75 5552 41.0 0 5552
76 5672 41.0 0 5672
77 5485 41.0 0 5485
78 6200 41.0 0 6200
79 6968 41.0 0 6968
80 6868 41.0 0 6868
81 8039 41.0 0 8039
82 9579 41.0 0 9579
83 10520 41.0 0 10520
84 11591 41.0 0 11591
85 12238 41.0 0 12238
86 97479 41.0 0 97479
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30348 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.8%
C: 32.1%
G: 0.0%
T: 34.9%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 14191 41972.1 0 14191
4 3181 10493.0 0 3181
5 887 2623.3 0 887
6 317 655.8 0 317
7 269 164.0 0 269
8 278 41.0 0 278
9 224 41.0 0 224
10 244 41.0 0 244
11 257 41.0 0 257
12 217 41.0 0 217
13 197 41.0 0 197
14 201 41.0 0 201
15 188 41.0 0 188
16 180 41.0 0 180
17 183 41.0 0 183
18 214 41.0 0 214
19 189 41.0 0 189
20 201 41.0 0 201
21 157 41.0 0 157
22 180 41.0 0 180
23 183 41.0 0 183
24 176 41.0 0 176
25 190 41.0 0 190
26 159 41.0 0 159
27 169 41.0 0 169
28 174 41.0 0 174
29 178 41.0 0 178
30 148 41.0 0 148
31 172 41.0 0 172
32 171 41.0 0 171
33 165 41.0 0 165
34 192 41.0 0 192
35 171 41.0 0 171
36 161 41.0 0 161
37 180 41.0 0 180
38 184 41.0 0 184
39 151 41.0 0 151
40 158 41.0 0 158
41 160 41.0 0 160
42 189 41.0 0 189
43 165 41.0 0 165
44 153 41.0 0 153
45 160 41.0 0 160
46 162 41.0 0 162
47 173 41.0 0 173
48 154 41.0 0 154
49 131 41.0 0 131
50 143 41.0 0 143
51 126 41.0 0 126
52 143 41.0 0 143
53 154 41.0 0 154
54 136 41.0 0 136
55 136 41.0 0 136
56 151 41.0 0 151
57 115 41.0 0 115
58 132 41.0 0 132
59 125 41.0 0 125
60 125 41.0 0 125
61 117 41.0 0 117
62 108 41.0 0 108
63 100 41.0 0 100
64 103 41.0 0 103
65 84 41.0 0 84
66 85 41.0 0 85
67 77 41.0 0 77
68 77 41.0 0 77
69 66 41.0 0 66
70 69 41.0 0 69
71 51 41.0 0 51
72 58 41.0 0 58
73 38 41.0 0 38
74 51 41.0 0 51
75 47 41.0 0 47
76 29 41.0 0 29
77 28 41.0 0 28
78 22 41.0 0 22
79 22 41.0 0 22
80 24 41.0 0 24
81 25 41.0 0 25
82 23 41.0 0 23
83 36 41.0 0 36
84 36 41.0 0 36
85 40 41.0 0 40
86 962 41.0 0 962
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 59103 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 22.9%
G: 20.6%
T: 21.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44361 41972.1 0 44361
4 9794 10493.0 0 9794
5 2023 2623.3 0 2023
6 320 655.8 0 320
7 19 164.0 0 19
8 27 164.0 0 27
9 19 164.0 0 19
10 21 164.0 0 21
11 40 164.0 0 40
12 37 164.0 0 37
13 35 164.0 0 35
14 53 164.0 0 53
15 39 164.0 0 39
16 45 164.0 0 45
17 32 164.0 0 32
18 30 164.0 0 30
19 45 164.0 0 45
20 38 164.0 0 38
21 32 164.0 0 32
22 52 164.0 0 52
23 32 164.0 0 32
24 31 164.0 0 31
25 41 164.0 0 41
26 39 164.0 0 39
27 34 164.0 0 34
28 31 164.0 0 31
29 46 164.0 0 46
30 36 164.0 0 36
31 28 164.0 0 28
32 54 164.0 0 54
33 22 164.0 0 22
34 27 164.0 0 27
35 16 164.0 0 16
36 29 164.0 0 29
37 22 164.0 0 22
38 28 164.0 0 28
39 35 164.0 0 35
40 16 164.0 0 16
41 29 164.0 0 29
42 30 164.0 0 30
43 31 164.0 0 31
44 29 164.0 0 29
45 27 164.0 0 27
46 32 164.0 0 32
47 29 164.0 0 29
48 27 164.0 0 27
49 29 164.0 0 29
50 34 164.0 0 34
51 36 164.0 0 36
52 33 164.0 0 33
53 19 164.0 0 19
54 43 164.0 0 43
55 28 164.0 0 28
56 30 164.0 0 30
57 30 164.0 0 30
58 36 164.0 0 36
59 22 164.0 0 22
60 42 164.0 0 42
61 41 164.0 0 41
62 44 164.0 0 44
63 30 164.0 0 30
64 27 164.0 0 27
65 34 164.0 0 34
66 29 164.0 0 29
67 38 164.0 0 38
68 33 164.0 0 33
69 35 164.0 0 35
70 36 164.0 0 36
71 23 164.0 0 23
72 27 164.0 0 27
73 30 164.0 0 30
74 32 164.0 0 32
75 12 164.0 0 12
76 21 164.0 0 21
77 72 164.0 0 72
78 47 164.0 0 47
79 21 164.0 0 21
80 27 164.0 0 27
81 38 164.0 0 38
82 30 164.0 0 30
83 23 164.0 0 23
84 36 164.0 0 36
85 34 164.0 0 34
86 38 164.0 0 38
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M42_S169_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M42_S169_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.97 s (9 µs/read; 6.33 M reads/minute).
=== Summary ===
Total reads processed: 2,738,304
Reads with adapters: 893,886 (32.6%)
== Read fate breakdown ==
Reads that were too short: 247,067 (9.0%)
Reads written (passing filters): 2,491,237 (91.0%)
Total basepairs processed: 276,568,704 bp
Total written (filtered): 196,808,635 bp (71.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 802941 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.7%
G: 27.5%
T: 29.8%
none/other: 12.9%
Overview of removed sequences
length count expect max.err error counts
3 64577 42786.0 0 64577
4 27732 10696.5 0 27732
5 14511 2674.1 0 14511
6 9527 668.5 0 9527
7 7877 167.1 0 7877
8 6795 41.8 0 6795
9 6891 41.8 0 6891
10 7032 41.8 0 7032
11 6799 41.8 0 6799
12 6722 41.8 0 6722
13 6934 41.8 0 6934
14 6958 41.8 0 6958
15 7171 41.8 0 7171
16 7301 41.8 0 7301
17 7053 41.8 0 7053
18 7098 41.8 0 7098
19 6961 41.8 0 6961
20 6757 41.8 0 6757
21 6956 41.8 0 6956
22 6994 41.8 0 6994
23 6515 41.8 0 6515
24 6660 41.8 0 6660
25 6745 41.8 0 6745
26 6612 41.8 0 6612
27 6710 41.8 0 6710
28 6924 41.8 0 6924
29 7108 41.8 0 7108
30 6994 41.8 0 6994
31 7835 41.8 0 7835
32 7391 41.8 0 7391
33 8002 41.8 0 8002
34 7902 41.8 0 7902
35 7185 41.8 0 7185
36 7289 41.8 0 7289
37 7198 41.8 0 7198
38 6869 41.8 0 6869
39 6885 41.8 0 6885
40 6996 41.8 0 6996
41 7030 41.8 0 7030
42 7317 41.8 0 7317
43 8623 41.8 0 8623
44 7484 41.8 0 7484
45 7811 41.8 0 7811
46 9209 41.8 0 9209
47 7818 41.8 0 7818
48 7405 41.8 0 7405
49 12901 41.8 0 12901
50 13531 41.8 0 13531
51 7664 41.8 0 7664
52 8495 41.8 0 8495
53 7597 41.8 0 7597
54 6521 41.8 0 6521
55 6982 41.8 0 6982
56 6950 41.8 0 6950
57 6620 41.8 0 6620
58 7454 41.8 0 7454
59 7107 41.8 0 7107
60 6845 41.8 0 6845
61 7028 41.8 0 7028
62 7011 41.8 0 7011
63 6689 41.8 0 6689
64 6750 41.8 0 6750
65 6582 41.8 0 6582
66 6477 41.8 0 6477
67 6477 41.8 0 6477
68 6391 41.8 0 6391
69 6169 41.8 0 6169
70 5785 41.8 0 5785
71 6332 41.8 0 6332
72 6443 41.8 0 6443
73 5945 41.8 0 5945
74 5696 41.8 0 5696
75 5674 41.8 0 5674
76 5932 41.8 0 5932
77 5895 41.8 0 5895
78 6385 41.8 0 6385
79 7348 41.8 0 7348
80 7087 41.8 0 7087
81 8309 41.8 0 8309
82 10014 41.8 0 10014
83 10762 41.8 0 10762
84 11990 41.8 0 11990
85 12633 41.8 0 12633
86 103307 41.8 0 103307
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30835 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.6%
C: 32.5%
G: 0.0%
T: 34.7%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 14423 42786.0 0 14423
4 3124 10696.5 0 3124
5 844 2674.1 0 844
6 337 668.5 0 337
7 292 167.1 0 292
8 255 41.8 0 255
9 271 41.8 0 271
10 251 41.8 0 251
11 215 41.8 0 215
12 212 41.8 0 212
13 204 41.8 0 204
14 192 41.8 0 192
15 185 41.8 0 185
16 211 41.8 0 211
17 193 41.8 0 193
18 184 41.8 0 184
19 185 41.8 0 185
20 164 41.8 0 164
21 176 41.8 0 176
22 187 41.8 0 187
23 169 41.8 0 169
24 184 41.8 0 184
25 177 41.8 0 177
26 175 41.8 0 175
27 177 41.8 0 177
28 173 41.8 0 173
29 191 41.8 0 191
30 183 41.8 0 183
31 170 41.8 0 170
32 165 41.8 0 165
33 169 41.8 0 169
34 147 41.8 0 147
35 203 41.8 0 203
36 189 41.8 0 189
37 170 41.8 0 170
38 188 41.8 0 188
39 167 41.8 0 167
40 160 41.8 0 160
41 173 41.8 0 173
42 186 41.8 0 186
43 181 41.8 0 181
44 151 41.8 0 151
45 178 41.8 0 178
46 164 41.8 0 164
47 177 41.8 0 177
48 150 41.8 0 150
49 147 41.8 0 147
50 156 41.8 0 156
51 166 41.8 0 166
52 153 41.8 0 153
53 159 41.8 0 159
54 154 41.8 0 154
55 148 41.8 0 148
56 143 41.8 0 143
57 118 41.8 0 118
58 134 41.8 0 134
59 111 41.8 0 111
60 148 41.8 0 148
61 123 41.8 0 123
62 113 41.8 0 113
63 120 41.8 0 120
64 114 41.8 0 114
65 66 41.8 0 66
66 93 41.8 0 93
67 91 41.8 0 91
68 75 41.8 0 75
69 73 41.8 0 73
70 76 41.8 0 76
71 79 41.8 0 79
72 54 41.8 0 54
73 64 41.8 0 64
74 49 41.8 0 49
75 44 41.8 0 44
76 21 41.8 0 21
77 20 41.8 0 20
78 28 41.8 0 28
79 26 41.8 0 26
80 19 41.8 0 19
81 19 41.8 0 19
82 30 41.8 0 30
83 24 41.8 0 24
84 30 41.8 0 30
85 27 41.8 0 27
86 998 41.8 0 998
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60110 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 23.4%
G: 20.7%
T: 20.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45097 42786.0 0 45097
4 9927 10696.5 0 9927
5 2102 2674.1 0 2102
6 339 668.5 0 339
7 23 167.1 0 23
8 42 167.1 0 42
9 21 167.1 0 21
10 32 167.1 0 32
11 33 167.1 0 33
12 24 167.1 0 24
13 36 167.1 0 36
14 45 167.1 0 45
15 43 167.1 0 43
16 39 167.1 0 39
17 30 167.1 0 30
18 23 167.1 0 23
19 56 167.1 0 56
20 45 167.1 0 45
21 27 167.1 0 27
22 46 167.1 0 46
23 37 167.1 0 37
24 26 167.1 0 26
25 65 167.1 0 65
26 38 167.1 0 38
27 27 167.1 0 27
28 40 167.1 0 40
29 38 167.1 0 38
30 25 167.1 0 25
31 31 167.1 0 31
32 36 167.1 0 36
33 30 167.1 0 30
34 28 167.1 0 28
35 28 167.1 0 28
36 42 167.1 0 42
37 29 167.1 0 29
38 20 167.1 0 20
39 29 167.1 0 29
40 36 167.1 0 36
41 44 167.1 0 44
42 30 167.1 0 30
43 33 167.1 0 33
44 23 167.1 0 23
45 27 167.1 0 27
46 29 167.1 0 29
47 29 167.1 0 29
48 37 167.1 0 37
49 36 167.1 0 36
50 44 167.1 0 44
51 32 167.1 0 32
52 26 167.1 0 26
53 22 167.1 0 22
54 34 167.1 0 34
55 24 167.1 0 24
56 24 167.1 0 24
57 43 167.1 0 43
58 30 167.1 0 30
59 38 167.1 0 38
60 29 167.1 0 29
61 32 167.1 0 32
62 39 167.1 0 39
63 29 167.1 0 29
64 34 167.1 0 34
65 31 167.1 0 31
66 30 167.1 0 30
67 46 167.1 0 46
68 36 167.1 0 36
69 21 167.1 0 21
70 36 167.1 0 36
71 21 167.1 0 21
72 34 167.1 0 34
73 30 167.1 0 30
74 31 167.1 0 31
75 24 167.1 0 24
76 20 167.1 0 20
77 56 167.1 0 56
78 36 167.1 0 36
79 23 167.1 0 23
80 21 167.1 0 21
81 18 167.1 0 18
82 31 167.1 0 31
83 41 167.1 0 41
84 44 167.1 0 44
85 41 167.1 0 41
86 36 167.1 0 36
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M43_S160_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M43_S160_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.24 s (9 µs/read; 6.36 M reads/minute).
=== Summary ===
Total reads processed: 2,885,609
Reads with adapters: 935,979 (32.4%)
== Read fate breakdown ==
Reads that were too short: 271,353 (9.4%)
Reads written (passing filters): 2,614,256 (90.6%)
Total basepairs processed: 291,446,509 bp
Total written (filtered): 207,039,485 bp (71.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 834109 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.0%
G: 28.7%
T: 25.7%
none/other: 16.5%
Overview of removed sequences
length count expect max.err error counts
3 63715 45087.6 0 63715
4 27621 11271.9 0 27621
5 14648 2818.0 0 14648
6 9910 704.5 0 9910
7 8407 176.1 0 8407
8 7168 44.0 0 7168
9 7291 44.0 0 7291
10 7255 44.0 0 7255
11 7165 44.0 0 7165
12 7109 44.0 0 7109
13 7280 44.0 0 7280
14 7327 44.0 0 7327
15 7369 44.0 0 7369
16 7273 44.0 0 7273
17 7396 44.0 0 7396
18 7492 44.0 0 7492
19 7433 44.0 0 7433
20 7007 44.0 0 7007
21 7407 44.0 0 7407
22 7451 44.0 0 7451
23 7078 44.0 0 7078
24 7150 44.0 0 7150
25 6998 44.0 0 6998
26 7021 44.0 0 7021
27 6906 44.0 0 6906
28 7353 44.0 0 7353
29 7809 44.0 0 7809
30 7257 44.0 0 7257
31 7655 44.0 0 7655
32 7527 44.0 0 7527
33 7566 44.0 0 7566
34 7565 44.0 0 7565
35 7525 44.0 0 7525
36 7229 44.0 0 7229
37 7052 44.0 0 7052
38 6918 44.0 0 6918
39 7100 44.0 0 7100
40 7388 44.0 0 7388
41 6920 44.0 0 6920
42 7331 44.0 0 7331
43 7768 44.0 0 7768
44 7016 44.0 0 7016
45 7204 44.0 0 7204
46 8172 44.0 0 8172
47 7499 44.0 0 7499
48 7311 44.0 0 7311
49 11773 44.0 0 11773
50 14736 44.0 0 14736
51 7995 44.0 0 7995
52 8910 44.0 0 8910
53 8324 44.0 0 8324
54 6694 44.0 0 6694
55 7309 44.0 0 7309
56 7538 44.0 0 7538
57 6751 44.0 0 6751
58 7277 44.0 0 7277
59 6943 44.0 0 6943
60 7041 44.0 0 7041
61 7191 44.0 0 7191
62 7030 44.0 0 7030
63 6709 44.0 0 6709
64 6509 44.0 0 6509
65 6558 44.0 0 6558
66 6262 44.0 0 6262
67 6631 44.0 0 6631
68 6491 44.0 0 6491
69 6154 44.0 0 6154
70 5805 44.0 0 5805
71 6421 44.0 0 6421
72 6554 44.0 0 6554
73 6113 44.0 0 6113
74 5886 44.0 0 5886
75 6044 44.0 0 6044
76 5325 44.0 0 5325
77 5574 44.0 0 5574
78 5807 44.0 0 5807
79 6423 44.0 0 6423
80 6052 44.0 0 6052
81 6903 44.0 0 6903
82 8236 44.0 0 8236
83 9214 44.0 0 9214
84 10365 44.0 0 10365
85 10922 44.0 0 10922
86 137597 44.0 0 137597
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 41388 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.8%
C: 34.7%
G: 0.0%
T: 34.2%
none/other: 2.3%
Overview of removed sequences
length count expect max.err error counts
3 17525 45087.6 0 17525
4 3649 11271.9 0 3649
5 992 2818.0 0 992
6 476 704.5 0 476
7 520 176.1 0 520
8 540 44.0 0 540
9 473 44.0 0 473
10 430 44.0 0 430
11 473 44.0 0 473
12 350 44.0 0 350
13 351 44.0 0 351
14 334 44.0 0 334
15 352 44.0 0 352
16 316 44.0 0 316
17 289 44.0 0 289
18 291 44.0 0 291
19 286 44.0 0 286
20 305 44.0 0 305
21 273 44.0 0 273
22 280 44.0 0 280
23 290 44.0 0 290
24 289 44.0 0 289
25 315 44.0 0 315
26 278 44.0 0 278
27 269 44.0 0 269
28 292 44.0 0 292
29 278 44.0 0 278
30 284 44.0 0 284
31 254 44.0 0 254
32 327 44.0 0 327
33 305 44.0 0 305
34 296 44.0 0 296
35 297 44.0 0 297
36 269 44.0 0 269
37 269 44.0 0 269
38 316 44.0 0 316
39 255 44.0 0 255
40 292 44.0 0 292
41 245 44.0 0 245
42 248 44.0 0 248
43 262 44.0 0 262
44 246 44.0 0 246
45 260 44.0 0 260
46 256 44.0 0 256
47 255 44.0 0 255
48 244 44.0 0 244
49 234 44.0 0 234
50 224 44.0 0 224
51 230 44.0 0 230
52 228 44.0 0 228
53 243 44.0 0 243
54 232 44.0 0 232
55 204 44.0 0 204
56 254 44.0 0 254
57 229 44.0 0 229
58 201 44.0 0 201
59 197 44.0 0 197
60 204 44.0 0 204
61 180 44.0 0 180
62 161 44.0 0 161
63 180 44.0 0 180
64 154 44.0 0 154
65 147 44.0 0 147
66 151 44.0 0 151
67 112 44.0 0 112
68 102 44.0 0 102
69 113 44.0 0 113
70 109 44.0 0 109
71 74 44.0 0 74
72 76 44.0 0 76
73 59 44.0 0 59
74 61 44.0 0 61
75 44 44.0 0 44
76 46 44.0 0 46
77 43 44.0 0 43
78 34 44.0 0 34
79 39 44.0 0 39
80 38 44.0 0 38
81 26 44.0 0 26
82 33 44.0 0 33
83 37 44.0 0 37
84 26 44.0 0 26
85 36 44.0 0 36
86 931 44.0 0 931
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60482 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 23.0%
G: 20.4%
T: 21.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45252 45087.6 0 45252
4 10180 11271.9 0 10180
5 2035 2818.0 0 2035
6 325 704.5 0 325
7 43 176.1 0 43
8 29 176.1 0 29
9 33 176.1 0 33
10 34 176.1 0 34
11 40 176.1 0 40
12 39 176.1 0 39
13 32 176.1 0 32
14 28 176.1 0 28
15 33 176.1 0 33
16 20 176.1 0 20
17 24 176.1 0 24
18 36 176.1 0 36
19 32 176.1 0 32
20 24 176.1 0 24
21 33 176.1 0 33
22 34 176.1 0 34
23 28 176.1 0 28
24 23 176.1 0 23
25 28 176.1 0 28
26 15 176.1 0 15
27 31 176.1 0 31
28 25 176.1 0 25
29 27 176.1 0 27
30 28 176.1 0 28
31 21 176.1 0 21
32 25 176.1 0 25
33 27 176.1 0 27
34 14 176.1 0 14
35 24 176.1 0 24
36 32 176.1 0 32
37 32 176.1 0 32
38 35 176.1 0 35
39 23 176.1 0 23
40 36 176.1 0 36
41 47 176.1 0 47
42 23 176.1 0 23
43 24 176.1 0 24
44 43 176.1 0 43
45 25 176.1 0 25
46 30 176.1 0 30
47 46 176.1 0 46
48 32 176.1 0 32
49 46 176.1 0 46
50 36 176.1 0 36
51 45 176.1 0 45
52 37 176.1 0 37
53 35 176.1 0 35
54 43 176.1 0 43
55 39 176.1 0 39
56 24 176.1 0 24
57 36 176.1 0 36
58 33 176.1 0 33
59 30 176.1 0 30
60 31 176.1 0 31
61 33 176.1 0 33
62 39 176.1 0 39
63 32 176.1 0 32
64 26 176.1 0 26
65 43 176.1 0 43
66 27 176.1 0 27
67 25 176.1 0 25
68 26 176.1 0 26
69 36 176.1 0 36
70 46 176.1 0 46
71 37 176.1 0 37
72 34 176.1 0 34
73 44 176.1 0 44
74 29 176.1 0 29
75 19 176.1 0 19
76 27 176.1 0 27
77 132 176.1 0 132
78 45 176.1 0 45
79 41 176.1 0 41
80 44 176.1 0 44
81 23 176.1 0 23
82 17 176.1 0 17
83 36 176.1 0 36
84 30 176.1 0 30
85 44 176.1 0 44
86 62 176.1 0 62
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M43_S160_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M43_S160_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.73 s (9 µs/read; 6.34 M reads/minute).
=== Summary ===
Total reads processed: 2,931,698
Reads with adapters: 957,763 (32.7%)
== Read fate breakdown ==
Reads that were too short: 283,484 (9.7%)
Reads written (passing filters): 2,648,214 (90.3%)
Total basepairs processed: 296,101,498 bp
Total written (filtered): 209,564,808 bp (70.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 855149 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.9%
G: 28.6%
T: 25.4%
none/other: 17.0%
Overview of removed sequences
length count expect max.err error counts
3 63751 45807.8 0 63751
4 27759 11451.9 0 27759
5 14691 2863.0 0 14691
6 10122 715.7 0 10122
7 8327 178.9 0 8327
8 7130 44.7 0 7130
9 7066 44.7 0 7066
10 7483 44.7 0 7483
11 7256 44.7 0 7256
12 7160 44.7 0 7160
13 7312 44.7 0 7312
14 7583 44.7 0 7583
15 7363 44.7 0 7363
16 7494 44.7 0 7494
17 7502 44.7 0 7502
18 7457 44.7 0 7457
19 7525 44.7 0 7525
20 7233 44.7 0 7233
21 7417 44.7 0 7417
22 7475 44.7 0 7475
23 7207 44.7 0 7207
24 7215 44.7 0 7215
25 7266 44.7 0 7266
26 7117 44.7 0 7117
27 7229 44.7 0 7229
28 7344 44.7 0 7344
29 7703 44.7 0 7703
30 7346 44.7 0 7346
31 7705 44.7 0 7705
32 7796 44.7 0 7796
33 7749 44.7 0 7749
34 7650 44.7 0 7650
35 7801 44.7 0 7801
36 7367 44.7 0 7367
37 7225 44.7 0 7225
38 6909 44.7 0 6909
39 7183 44.7 0 7183
40 7483 44.7 0 7483
41 6882 44.7 0 6882
42 7509 44.7 0 7509
43 7961 44.7 0 7961
44 7181 44.7 0 7181
45 7502 44.7 0 7502
46 8476 44.7 0 8476
47 7806 44.7 0 7806
48 7613 44.7 0 7613
49 12072 44.7 0 12072
50 15330 44.7 0 15330
51 7871 44.7 0 7871
52 9208 44.7 0 9208
53 8663 44.7 0 8663
54 6671 44.7 0 6671
55 7540 44.7 0 7540
56 7667 44.7 0 7667
57 6830 44.7 0 6830
58 7563 44.7 0 7563
59 7142 44.7 0 7142
60 7016 44.7 0 7016
61 7360 44.7 0 7360
62 7281 44.7 0 7281
63 7008 44.7 0 7008
64 6729 44.7 0 6729
65 6753 44.7 0 6753
66 6613 44.7 0 6613
67 6715 44.7 0 6715
68 6575 44.7 0 6575
69 6395 44.7 0 6395
70 6198 44.7 0 6198
71 6806 44.7 0 6806
72 6932 44.7 0 6932
73 6231 44.7 0 6231
74 6015 44.7 0 6015
75 6038 44.7 0 6038
76 5481 44.7 0 5481
77 5688 44.7 0 5688
78 5929 44.7 0 5929
79 6556 44.7 0 6556
80 6268 44.7 0 6268
81 7096 44.7 0 7096
82 8500 44.7 0 8500
83 9431 44.7 0 9431
84 10744 44.7 0 10744
85 11221 44.7 0 11221
86 145682 44.7 0 145682
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 42294 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.4%
C: 34.5%
G: 0.0%
T: 33.6%
none/other: 2.5%
Overview of removed sequences
length count expect max.err error counts
3 17565 45807.8 0 17565
4 3668 11451.9 0 3668
5 1061 2863.0 0 1061
6 555 715.7 0 555
7 567 178.9 0 567
8 592 44.7 0 592
9 516 44.7 0 516
10 477 44.7 0 477
11 422 44.7 0 422
12 383 44.7 0 383
13 355 44.7 0 355
14 354 44.7 0 354
15 312 44.7 0 312
16 299 44.7 0 299
17 307 44.7 0 307
18 359 44.7 0 359
19 284 44.7 0 284
20 295 44.7 0 295
21 274 44.7 0 274
22 269 44.7 0 269
23 300 44.7 0 300
24 278 44.7 0 278
25 319 44.7 0 319
26 316 44.7 0 316
27 279 44.7 0 279
28 319 44.7 0 319
29 292 44.7 0 292
30 288 44.7 0 288
31 290 44.7 0 290
32 312 44.7 0 312
33 307 44.7 0 307
34 326 44.7 0 326
35 284 44.7 0 284
36 277 44.7 0 277
37 286 44.7 0 286
38 269 44.7 0 269
39 261 44.7 0 261
40 261 44.7 0 261
41 279 44.7 0 279
42 301 44.7 0 301
43 276 44.7 0 276
44 255 44.7 0 255
45 262 44.7 0 262
46 255 44.7 0 255
47 245 44.7 0 245
48 237 44.7 0 237
49 281 44.7 0 281
50 243 44.7 0 243
51 236 44.7 0 236
52 233 44.7 0 233
53 274 44.7 0 274
54 237 44.7 0 237
55 238 44.7 0 238
56 263 44.7 0 263
57 219 44.7 0 219
58 212 44.7 0 212
59 211 44.7 0 211
60 204 44.7 0 204
61 178 44.7 0 178
62 167 44.7 0 167
63 162 44.7 0 162
64 163 44.7 0 163
65 151 44.7 0 151
66 132 44.7 0 132
67 127 44.7 0 127
68 118 44.7 0 118
69 103 44.7 0 103
70 90 44.7 0 90
71 88 44.7 0 88
72 79 44.7 0 79
73 78 44.7 0 78
74 62 44.7 0 62
75 52 44.7 0 52
76 42 44.7 0 42
77 60 44.7 0 60
78 36 44.7 0 36
79 39 44.7 0 39
80 28 44.7 0 28
81 27 44.7 0 27
82 37 44.7 0 37
83 27 44.7 0 27
84 35 44.7 0 35
85 35 44.7 0 35
86 1039 44.7 0 1039
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60320 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 23.4%
G: 20.3%
T: 21.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44899 45807.8 0 44899
4 10305 11451.9 0 10305
5 2197 2863.0 0 2197
6 338 715.7 0 338
7 26 178.9 0 26
8 29 178.9 0 29
9 32 178.9 0 32
10 26 178.9 0 26
11 22 178.9 0 22
12 25 178.9 0 25
13 31 178.9 0 31
14 45 178.9 0 45
15 31 178.9 0 31
16 20 178.9 0 20
17 33 178.9 0 33
18 34 178.9 0 34
19 32 178.9 0 32
20 29 178.9 0 29
21 28 178.9 0 28
22 18 178.9 0 18
23 22 178.9 0 22
24 24 178.9 0 24
25 18 178.9 0 18
26 29 178.9 0 29
27 20 178.9 0 20
28 16 178.9 0 16
29 26 178.9 0 26
30 21 178.9 0 21
31 34 178.9 0 34
32 40 178.9 0 40
33 31 178.9 0 31
34 27 178.9 0 27
35 23 178.9 0 23
36 44 178.9 0 44
37 36 178.9 0 36
38 42 178.9 0 42
39 28 178.9 0 28
40 40 178.9 0 40
41 32 178.9 0 32
42 24 178.9 0 24
43 29 178.9 0 29
44 49 178.9 0 49
45 26 178.9 0 26
46 38 178.9 0 38
47 20 178.9 0 20
48 32 178.9 0 32
49 31 178.9 0 31
50 20 178.9 0 20
51 35 178.9 0 35
52 40 178.9 0 40
53 16 178.9 0 16
54 34 178.9 0 34
55 34 178.9 0 34
56 35 178.9 0 35
57 37 178.9 0 37
58 30 178.9 0 30
59 36 178.9 0 36
60 25 178.9 0 25
61 22 178.9 0 22
62 29 178.9 0 29
63 40 178.9 0 40
64 25 178.9 0 25
65 42 178.9 0 42
66 37 178.9 0 37
67 42 178.9 0 42
68 29 178.9 0 29
69 35 178.9 0 35
70 34 178.9 0 34
71 32 178.9 0 32
72 26 178.9 0 26
73 32 178.9 0 32
74 30 178.9 0 30
75 38 178.9 0 38
76 28 178.9 0 28
77 133 178.9 0 133
78 54 178.9 0 54
79 34 178.9 0 34
80 26 178.9 0 26
81 31 178.9 0 31
82 25 178.9 0 25
83 45 178.9 0 45
84 27 178.9 0 27
85 32 178.9 0 32
86 48 178.9 0 48
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M44_S163_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M44_S163_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 22.41 s (10 µs/read; 5.95 M reads/minute).
=== Summary ===
Total reads processed: 2,223,387
Reads with adapters: 646,408 (29.1%)
== Read fate breakdown ==
Reads that were too short: 128,161 (5.8%)
Reads written (passing filters): 2,095,226 (94.2%)
Total basepairs processed: 224,562,087 bp
Total written (filtered): 167,413,601 bp (74.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 567517 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.4%
G: 29.8%
T: 31.0%
none/other: 7.7%
Overview of removed sequences
length count expect max.err error counts
3 56300 34740.4 0 56300
4 24933 8685.1 0 24933
5 13477 2171.3 0 13477
6 8764 542.8 0 8764
7 7105 135.7 0 7105
8 6366 33.9 0 6366
9 6180 33.9 0 6180
10 6430 33.9 0 6430
11 6134 33.9 0 6134
12 6068 33.9 0 6068
13 6169 33.9 0 6169
14 6389 33.9 0 6389
15 6361 33.9 0 6361
16 6246 33.9 0 6246
17 6279 33.9 0 6279
18 6398 33.9 0 6398
19 5997 33.9 0 5997
20 5941 33.9 0 5941
21 6280 33.9 0 6280
22 6439 33.9 0 6439
23 5890 33.9 0 5890
24 6015 33.9 0 6015
25 5814 33.9 0 5814
26 5976 33.9 0 5976
27 5916 33.9 0 5916
28 6086 33.9 0 6086
29 6144 33.9 0 6144
30 5722 33.9 0 5722
31 6163 33.9 0 6163
32 5920 33.9 0 5920
33 6763 33.9 0 6763
34 6251 33.9 0 6251
35 5888 33.9 0 5888
36 5410 33.9 0 5410
37 5410 33.9 0 5410
38 5331 33.9 0 5331
39 5517 33.9 0 5517
40 5535 33.9 0 5535
41 5838 33.9 0 5838
42 5353 33.9 0 5353
43 5369 33.9 0 5369
44 5053 33.9 0 5053
45 5417 33.9 0 5417
46 5370 33.9 0 5370
47 5144 33.9 0 5144
48 5023 33.9 0 5023
49 6344 33.9 0 6344
50 7109 33.9 0 7109
51 5153 33.9 0 5153
52 5006 33.9 0 5006
53 5295 33.9 0 5295
54 4775 33.9 0 4775
55 4777 33.9 0 4777
56 5055 33.9 0 5055
57 4771 33.9 0 4771
58 4952 33.9 0 4952
59 4797 33.9 0 4797
60 4937 33.9 0 4937
61 4651 33.9 0 4651
62 4564 33.9 0 4564
63 4456 33.9 0 4456
64 4339 33.9 0 4339
65 4124 33.9 0 4124
66 4038 33.9 0 4038
67 3767 33.9 0 3767
68 3798 33.9 0 3798
69 3539 33.9 0 3539
70 3227 33.9 0 3227
71 3281 33.9 0 3281
72 3366 33.9 0 3366
73 3109 33.9 0 3109
74 2805 33.9 0 2805
75 2847 33.9 0 2847
76 3210 33.9 0 3210
77 3067 33.9 0 3067
78 3474 33.9 0 3474
79 4118 33.9 0 4118
80 4227 33.9 0 4227
81 5002 33.9 0 5002
82 6190 33.9 0 6190
83 7256 33.9 0 7256
84 7836 33.9 0 7836
85 7738 33.9 0 7738
86 43943 33.9 0 43943
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28318 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.1%
C: 30.2%
G: 0.0%
T: 37.1%
none/other: 3.7%
Overview of removed sequences
length count expect max.err error counts
3 11076 34740.4 0 11076
4 2570 8685.1 0 2570
5 796 2171.3 0 796
6 367 542.8 0 367
7 275 135.7 0 275
8 263 33.9 0 263
9 271 33.9 0 271
10 251 33.9 0 251
11 241 33.9 0 241
12 239 33.9 0 239
13 235 33.9 0 235
14 251 33.9 0 251
15 212 33.9 0 212
16 242 33.9 0 242
17 224 33.9 0 224
18 243 33.9 0 243
19 239 33.9 0 239
20 250 33.9 0 250
21 218 33.9 0 218
22 228 33.9 0 228
23 226 33.9 0 226
24 228 33.9 0 228
25 257 33.9 0 257
26 218 33.9 0 218
27 216 33.9 0 216
28 214 33.9 0 214
29 197 33.9 0 197
30 222 33.9 0 222
31 202 33.9 0 202
32 209 33.9 0 209
33 232 33.9 0 232
34 193 33.9 0 193
35 251 33.9 0 251
36 209 33.9 0 209
37 223 33.9 0 223
38 206 33.9 0 206
39 183 33.9 0 183
40 170 33.9 0 170
41 200 33.9 0 200
42 189 33.9 0 189
43 198 33.9 0 198
44 191 33.9 0 191
45 180 33.9 0 180
46 183 33.9 0 183
47 190 33.9 0 190
48 178 33.9 0 178
49 201 33.9 0 201
50 159 33.9 0 159
51 175 33.9 0 175
52 163 33.9 0 163
53 148 33.9 0 148
54 156 33.9 0 156
55 133 33.9 0 133
56 131 33.9 0 131
57 143 33.9 0 143
58 135 33.9 0 135
59 158 33.9 0 158
60 129 33.9 0 129
61 114 33.9 0 114
62 110 33.9 0 110
63 109 33.9 0 109
64 106 33.9 0 106
65 85 33.9 0 85
66 86 33.9 0 86
67 74 33.9 0 74
68 64 33.9 0 64
69 62 33.9 0 62
70 55 33.9 0 55
71 50 33.9 0 50
72 58 33.9 0 58
73 55 33.9 0 55
74 44 33.9 0 44
75 37 33.9 0 37
76 31 33.9 0 31
77 27 33.9 0 27
78 21 33.9 0 21
79 22 33.9 0 22
80 37 33.9 0 37
81 30 33.9 0 30
82 27 33.9 0 27
83 28 33.9 0 28
84 39 33.9 0 39
85 26 33.9 0 26
86 1034 33.9 0 1034
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 50573 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.0%
C: 23.1%
G: 20.5%
T: 21.3%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
3 37458 34740.4 0 37458
4 8789 8685.1 0 8789
5 1651 2171.3 0 1651
6 187 542.8 0 187
7 39 135.7 0 39
8 44 135.7 0 44
9 20 135.7 0 20
10 31 135.7 0 31
11 42 135.7 0 42
12 28 135.7 0 28
13 47 135.7 0 47
14 48 135.7 0 48
15 37 135.7 0 37
16 48 135.7 0 48
17 29 135.7 0 29
18 30 135.7 0 30
19 57 135.7 0 57
20 39 135.7 0 39
21 33 135.7 0 33
22 55 135.7 0 55
23 32 135.7 0 32
24 31 135.7 0 31
25 79 135.7 0 79
26 39 135.7 0 39
27 33 135.7 0 33
28 37 135.7 0 37
29 39 135.7 0 39
30 22 135.7 0 22
31 30 135.7 0 30
32 56 135.7 0 56
33 34 135.7 0 34
34 22 135.7 0 22
35 20 135.7 0 20
36 23 135.7 0 23
37 28 135.7 0 28
38 22 135.7 0 22
39 32 135.7 0 32
40 25 135.7 0 25
41 22 135.7 0 22
42 36 135.7 0 36
43 28 135.7 0 28
44 20 135.7 0 20
45 25 135.7 0 25
46 24 135.7 0 24
47 25 135.7 0 25
48 28 135.7 0 28
49 37 135.7 0 37
50 40 135.7 0 40
51 33 135.7 0 33
52 34 135.7 0 34
53 13 135.7 0 13
54 28 135.7 0 28
55 39 135.7 0 39
56 24 135.7 0 24
57 24 135.7 0 24
58 23 135.7 0 23
59 13 135.7 0 13
60 25 135.7 0 25
61 21 135.7 0 21
62 38 135.7 0 38
63 21 135.7 0 21
64 29 135.7 0 29
65 41 135.7 0 41
66 26 135.7 0 26
67 40 135.7 0 40
68 37 135.7 0 37
69 22 135.7 0 22
70 33 135.7 0 33
71 24 135.7 0 24
72 23 135.7 0 23
73 29 135.7 0 29
74 18 135.7 0 18
75 13 135.7 0 13
76 30 135.7 0 30
77 46 135.7 0 46
78 28 135.7 0 28
79 23 135.7 0 23
80 25 135.7 0 25
81 29 135.7 0 29
82 24 135.7 0 24
83 30 135.7 0 30
84 26 135.7 0 26
85 18 135.7 0 18
86 22 135.7 0 22
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M44_S163_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M44_S163_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 20.95 s (9 µs/read; 6.47 M reads/minute).
=== Summary ===
Total reads processed: 2,260,353
Reads with adapters: 659,999 (29.2%)
== Read fate breakdown ==
Reads that were too short: 132,356 (5.9%)
Reads written (passing filters): 2,127,997 (94.1%)
Total basepairs processed: 228,295,653 bp
Total written (filtered): 169,939,330 bp (74.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 580041 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.5%
G: 29.9%
T: 30.7%
none/other: 7.9%
Overview of removed sequences
length count expect max.err error counts
3 56847 35318.0 0 56847
4 25188 8829.5 0 25188
5 13465 2207.4 0 13465
6 8862 551.8 0 8862
7 7312 138.0 0 7312
8 6429 34.5 0 6429
9 6350 34.5 0 6350
10 6397 34.5 0 6397
11 6345 34.5 0 6345
12 6017 34.5 0 6017
13 6405 34.5 0 6405
14 6614 34.5 0 6614
15 6555 34.5 0 6555
16 6450 34.5 0 6450
17 6226 34.5 0 6226
18 6650 34.5 0 6650
19 6023 34.5 0 6023
20 5912 34.5 0 5912
21 6316 34.5 0 6316
22 6462 34.5 0 6462
23 6184 34.5 0 6184
24 6066 34.5 0 6066
25 6022 34.5 0 6022
26 6034 34.5 0 6034
27 5995 34.5 0 5995
28 6345 34.5 0 6345
29 6308 34.5 0 6308
30 6071 34.5 0 6071
31 6538 34.5 0 6538
32 6062 34.5 0 6062
33 6900 34.5 0 6900
34 6374 34.5 0 6374
35 5850 34.5 0 5850
36 5621 34.5 0 5621
37 5768 34.5 0 5768
38 5277 34.5 0 5277
39 5546 34.5 0 5546
40 5636 34.5 0 5636
41 5944 34.5 0 5944
42 5514 34.5 0 5514
43 5641 34.5 0 5641
44 5204 34.5 0 5204
45 5326 34.5 0 5326
46 5628 34.5 0 5628
47 5335 34.5 0 5335
48 5111 34.5 0 5111
49 6550 34.5 0 6550
50 7355 34.5 0 7355
51 5340 34.5 0 5340
52 5289 34.5 0 5289
53 5189 34.5 0 5189
54 4814 34.5 0 4814
55 4840 34.5 0 4840
56 4984 34.5 0 4984
57 5019 34.5 0 5019
58 4901 34.5 0 4901
59 4998 34.5 0 4998
60 5000 34.5 0 5000
61 4756 34.5 0 4756
62 4800 34.5 0 4800
63 4378 34.5 0 4378
64 4402 34.5 0 4402
65 4184 34.5 0 4184
66 4199 34.5 0 4199
67 3888 34.5 0 3888
68 3919 34.5 0 3919
69 3630 34.5 0 3630
70 3467 34.5 0 3467
71 3434 34.5 0 3434
72 3458 34.5 0 3458
73 3146 34.5 0 3146
74 2945 34.5 0 2945
75 3089 34.5 0 3089
76 3212 34.5 0 3212
77 3003 34.5 0 3003
78 3473 34.5 0 3473
79 4283 34.5 0 4283
80 4080 34.5 0 4080
81 5041 34.5 0 5041
82 6472 34.5 0 6472
83 7436 34.5 0 7436
84 7998 34.5 0 7998
85 8063 34.5 0 8063
86 45881 34.5 0 45881
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29267 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.4%
C: 30.5%
G: 0.0%
T: 36.3%
none/other: 3.8%
Overview of removed sequences
length count expect max.err error counts
3 11153 35318.0 0 11153
4 2605 8829.5 0 2605
5 791 2207.4 0 791
6 374 551.8 0 374
7 297 138.0 0 297
8 303 34.5 0 303
9 264 34.5 0 264
10 263 34.5 0 263
11 269 34.5 0 269
12 264 34.5 0 264
13 245 34.5 0 245
14 231 34.5 0 231
15 272 34.5 0 272
16 263 34.5 0 263
17 255 34.5 0 255
18 245 34.5 0 245
19 250 34.5 0 250
20 222 34.5 0 222
21 232 34.5 0 232
22 248 34.5 0 248
23 232 34.5 0 232
24 209 34.5 0 209
25 265 34.5 0 265
26 240 34.5 0 240
27 238 34.5 0 238
28 202 34.5 0 202
29 229 34.5 0 229
30 202 34.5 0 202
31 236 34.5 0 236
32 235 34.5 0 235
33 232 34.5 0 232
34 257 34.5 0 257
35 212 34.5 0 212
36 208 34.5 0 208
37 274 34.5 0 274
38 212 34.5 0 212
39 205 34.5 0 205
40 189 34.5 0 189
41 176 34.5 0 176
42 189 34.5 0 189
43 209 34.5 0 209
44 230 34.5 0 230
45 185 34.5 0 185
46 211 34.5 0 211
47 213 34.5 0 213
48 197 34.5 0 197
49 187 34.5 0 187
50 185 34.5 0 185
51 162 34.5 0 162
52 169 34.5 0 169
53 169 34.5 0 169
54 164 34.5 0 164
55 174 34.5 0 174
56 175 34.5 0 175
57 157 34.5 0 157
58 154 34.5 0 154
59 130 34.5 0 130
60 134 34.5 0 134
61 116 34.5 0 116
62 127 34.5 0 127
63 142 34.5 0 142
64 100 34.5 0 100
65 96 34.5 0 96
66 94 34.5 0 94
67 73 34.5 0 73
68 76 34.5 0 76
69 63 34.5 0 63
70 57 34.5 0 57
71 48 34.5 0 48
72 51 34.5 0 51
73 41 34.5 0 41
74 41 34.5 0 41
75 24 34.5 0 24
76 27 34.5 0 27
77 34 34.5 0 34
78 23 34.5 0 23
79 31 34.5 0 31
80 37 34.5 0 37
81 26 34.5 0 26
82 28 34.5 0 28
83 29 34.5 0 29
84 38 34.5 0 38
85 37 34.5 0 37
86 1115 34.5 0 1115
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 50691 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.9%
C: 23.3%
G: 20.2%
T: 21.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 37754 35318.0 0 37754
4 8705 8829.5 0 8705
5 1615 2207.4 0 1615
6 196 551.8 0 196
7 27 138.0 0 27
8 42 138.0 0 42
9 22 138.0 0 22
10 35 138.0 0 35
11 39 138.0 0 39
12 21 138.0 0 21
13 49 138.0 0 49
14 51 138.0 0 51
15 38 138.0 0 38
16 37 138.0 0 37
17 35 138.0 0 35
18 38 138.0 0 38
19 46 138.0 0 46
20 42 138.0 0 42
21 33 138.0 0 33
22 56 138.0 0 56
23 25 138.0 0 25
24 35 138.0 0 35
25 68 138.0 0 68
26 48 138.0 0 48
27 29 138.0 0 29
28 34 138.0 0 34
29 37 138.0 0 37
30 23 138.0 0 23
31 20 138.0 0 20
32 35 138.0 0 35
33 30 138.0 0 30
34 16 138.0 0 16
35 15 138.0 0 15
36 36 138.0 0 36
37 22 138.0 0 22
38 24 138.0 0 24
39 28 138.0 0 28
40 32 138.0 0 32
41 24 138.0 0 24
42 38 138.0 0 38
43 27 138.0 0 27
44 20 138.0 0 20
45 21 138.0 0 21
46 24 138.0 0 24
47 30 138.0 0 30
48 16 138.0 0 16
49 32 138.0 0 32
50 38 138.0 0 38
51 23 138.0 0 23
52 34 138.0 0 34
53 19 138.0 0 19
54 25 138.0 0 25
55 18 138.0 0 18
56 18 138.0 0 18
57 27 138.0 0 27
58 38 138.0 0 38
59 27 138.0 0 27
60 21 138.0 0 21
61 37 138.0 0 37
62 34 138.0 0 34
63 18 138.0 0 18
64 38 138.0 0 38
65 37 138.0 0 37
66 30 138.0 0 30
67 31 138.0 0 31
68 32 138.0 0 32
69 19 138.0 0 19
70 24 138.0 0 24
71 33 138.0 0 33
72 23 138.0 0 23
73 37 138.0 0 37
74 25 138.0 0 25
75 17 138.0 0 17
76 24 138.0 0 24
77 29 138.0 0 29
78 32 138.0 0 32
79 17 138.0 0 17
80 25 138.0 0 25
81 29 138.0 0 29
82 21 138.0 0 21
83 40 138.0 0 40
84 23 138.0 0 23
85 27 138.0 0 27
86 31 138.0 0 31
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M45_S140_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M45_S140_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.96 s (9 µs/read; 6.61 M reads/minute).
=== Summary ===
Total reads processed: 2,858,599
Reads with adapters: 1,087,308 (38.0%)
== Read fate breakdown ==
Reads that were too short: 377,534 (13.2%)
Reads written (passing filters): 2,481,065 (86.8%)
Total basepairs processed: 288,718,499 bp
Total written (filtered): 193,225,801 bp (66.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 997342 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.0%
G: 25.6%
T: 27.5%
none/other: 17.9%
Overview of removed sequences
length count expect max.err error counts
3 65689 44665.6 0 65689
4 28221 11166.4 0 28221
5 15006 2791.6 0 15006
6 10161 697.9 0 10161
7 8246 174.5 0 8246
8 7352 43.6 0 7352
9 7425 43.6 0 7425
10 7593 43.6 0 7593
11 7256 43.6 0 7256
12 7625 43.6 0 7625
13 7516 43.6 0 7516
14 7561 43.6 0 7561
15 7623 43.6 0 7623
16 7950 43.6 0 7950
17 7892 43.6 0 7892
18 7980 43.6 0 7980
19 7471 43.6 0 7471
20 7526 43.6 0 7526
21 7668 43.6 0 7668
22 7751 43.6 0 7751
23 7501 43.6 0 7501
24 7359 43.6 0 7359
25 7553 43.6 0 7553
26 7412 43.6 0 7412
27 7233 43.6 0 7233
28 7939 43.6 0 7939
29 8154 43.6 0 8154
30 7716 43.6 0 7716
31 8825 43.6 0 8825
32 8127 43.6 0 8127
33 8451 43.6 0 8451
34 8390 43.6 0 8390
35 8265 43.6 0 8265
36 8011 43.6 0 8011
37 8680 43.6 0 8680
38 7962 43.6 0 7962
39 7885 43.6 0 7885
40 8020 43.6 0 8020
41 8327 43.6 0 8327
42 8326 43.6 0 8326
43 8698 43.6 0 8698
44 7636 43.6 0 7636
45 8090 43.6 0 8090
46 8468 43.6 0 8468
47 8143 43.6 0 8143
48 8136 43.6 0 8136
49 12288 43.6 0 12288
50 14686 43.6 0 14686
51 8945 43.6 0 8945
52 9461 43.6 0 9461
53 9353 43.6 0 9353
54 8323 43.6 0 8323
55 8927 43.6 0 8927
56 8817 43.6 0 8817
57 8736 43.6 0 8736
58 9501 43.6 0 9501
59 9088 43.6 0 9088
60 9356 43.6 0 9356
61 9391 43.6 0 9391
62 9177 43.6 0 9177
63 9139 43.6 0 9139
64 8958 43.6 0 8958
65 9214 43.6 0 9214
66 8614 43.6 0 8614
67 8746 43.6 0 8746
68 8807 43.6 0 8807
69 8175 43.6 0 8175
70 8065 43.6 0 8065
71 8985 43.6 0 8985
72 8845 43.6 0 8845
73 8230 43.6 0 8230
74 8207 43.6 0 8207
75 8134 43.6 0 8134
76 8016 43.6 0 8016
77 8192 43.6 0 8192
78 8425 43.6 0 8425
79 9965 43.6 0 9965
80 9367 43.6 0 9367
81 11003 43.6 0 11003
82 13866 43.6 0 13866
83 15857 43.6 0 15857
84 17142 43.6 0 17142
85 18058 43.6 0 18058
86 178464 43.6 0 178464
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28679 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.5%
C: 28.3%
G: 0.0%
T: 35.7%
none/other: 4.5%
Overview of removed sequences
length count expect max.err error counts
3 13047 44665.6 0 13047
4 2843 11166.4 0 2843
5 780 2791.6 0 780
6 336 697.9 0 336
7 305 174.5 0 305
8 302 43.6 0 302
9 276 43.6 0 276
10 234 43.6 0 234
11 218 43.6 0 218
12 201 43.6 0 201
13 216 43.6 0 216
14 172 43.6 0 172
15 175 43.6 0 175
16 166 43.6 0 166
17 156 43.6 0 156
18 151 43.6 0 151
19 176 43.6 0 176
20 172 43.6 0 172
21 174 43.6 0 174
22 180 43.6 0 180
23 204 43.6 0 204
24 192 43.6 0 192
25 183 43.6 0 183
26 195 43.6 0 195
27 165 43.6 0 165
28 173 43.6 0 173
29 174 43.6 0 174
30 158 43.6 0 158
31 149 43.6 0 149
32 140 43.6 0 140
33 168 43.6 0 168
34 148 43.6 0 148
35 167 43.6 0 167
36 148 43.6 0 148
37 146 43.6 0 146
38 141 43.6 0 141
39 147 43.6 0 147
40 126 43.6 0 126
41 141 43.6 0 141
42 117 43.6 0 117
43 161 43.6 0 161
44 152 43.6 0 152
45 136 43.6 0 136
46 157 43.6 0 157
47 165 43.6 0 165
48 128 43.6 0 128
49 139 43.6 0 139
50 148 43.6 0 148
51 137 43.6 0 137
52 141 43.6 0 141
53 116 43.6 0 116
54 121 43.6 0 121
55 157 43.6 0 157
56 128 43.6 0 128
57 125 43.6 0 125
58 144 43.6 0 144
59 131 43.6 0 131
60 107 43.6 0 107
61 109 43.6 0 109
62 119 43.6 0 119
63 99 43.6 0 99
64 88 43.6 0 88
65 81 43.6 0 81
66 101 43.6 0 101
67 84 43.6 0 84
68 66 43.6 0 66
69 76 43.6 0 76
70 51 43.6 0 51
71 60 43.6 0 60
72 49 43.6 0 49
73 39 43.6 0 39
74 42 43.6 0 42
75 38 43.6 0 38
76 34 43.6 0 34
77 18 43.6 0 18
78 31 43.6 0 31
79 21 43.6 0 21
80 19 43.6 0 19
81 26 43.6 0 26
82 43 43.6 0 43
83 44 43.6 0 44
84 45 43.6 0 45
85 57 43.6 0 57
86 1284 43.6 0 1284
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61287 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.8%
C: 22.6%
G: 21.6%
T: 18.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45958 44665.6 0 45958
4 10185 11166.4 0 10185
5 1892 2791.6 0 1892
6 267 697.9 0 267
7 24 174.5 0 24
8 51 174.5 0 51
9 24 174.5 0 24
10 34 174.5 0 34
11 39 174.5 0 39
12 27 174.5 0 27
13 34 174.5 0 34
14 52 174.5 0 52
15 38 174.5 0 38
16 50 174.5 0 50
17 37 174.5 0 37
18 37 174.5 0 37
19 64 174.5 0 64
20 47 174.5 0 47
21 27 174.5 0 27
22 57 174.5 0 57
23 27 174.5 0 27
24 30 174.5 0 30
25 56 174.5 0 56
26 57 174.5 0 57
27 47 174.5 0 47
28 40 174.5 0 40
29 29 174.5 0 29
30 43 174.5 0 43
31 25 174.5 0 25
32 43 174.5 0 43
33 42 174.5 0 42
34 27 174.5 0 27
35 33 174.5 0 33
36 28 174.5 0 28
37 30 174.5 0 30
38 39 174.5 0 39
39 26 174.5 0 26
40 40 174.5 0 40
41 32 174.5 0 32
42 24 174.5 0 24
43 18 174.5 0 18
44 33 174.5 0 33
45 28 174.5 0 28
46 27 174.5 0 27
47 45 174.5 0 45
48 27 174.5 0 27
49 46 174.5 0 46
50 40 174.5 0 40
51 31 174.5 0 31
52 36 174.5 0 36
53 26 174.5 0 26
54 30 174.5 0 30
55 31 174.5 0 31
56 33 174.5 0 33
57 36 174.5 0 36
58 37 174.5 0 37
59 28 174.5 0 28
60 30 174.5 0 30
61 31 174.5 0 31
62 38 174.5 0 38
63 28 174.5 0 28
64 36 174.5 0 36
65 26 174.5 0 26
66 26 174.5 0 26
67 21 174.5 0 21
68 27 174.5 0 27
69 27 174.5 0 27
70 36 174.5 0 36
71 25 174.5 0 25
72 34 174.5 0 34
73 28 174.5 0 28
74 39 174.5 0 39
75 26 174.5 0 26
76 17 174.5 0 17
77 169 174.5 0 169
78 102 174.5 0 102
79 37 174.5 0 37
80 43 174.5 0 43
81 41 174.5 0 41
82 36 174.5 0 36
83 37 174.5 0 37
84 39 174.5 0 39
85 25 174.5 0 25
86 49 174.5 0 49
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M45_S140_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M45_S140_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.32 s (9 µs/read; 6.65 M reads/minute).
=== Summary ===
Total reads processed: 2,915,102
Reads with adapters: 1,118,391 (38.4%)
== Read fate breakdown ==
Reads that were too short: 392,670 (13.5%)
Reads written (passing filters): 2,522,432 (86.5%)
Total basepairs processed: 294,425,302 bp
Total written (filtered): 196,263,683 bp (66.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1027273 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.9%
G: 25.6%
T: 27.3%
none/other: 18.2%
Overview of removed sequences
length count expect max.err error counts
3 66756 45548.5 0 66756
4 28620 11387.1 0 28620
5 15220 2846.8 0 15220
6 10515 711.7 0 10515
7 8542 177.9 0 8542
8 7543 44.5 0 7543
9 7607 44.5 0 7607
10 7696 44.5 0 7696
11 7524 44.5 0 7524
12 7826 44.5 0 7826
13 7816 44.5 0 7816
14 7846 44.5 0 7846
15 7858 44.5 0 7858
16 8050 44.5 0 8050
17 8098 44.5 0 8098
18 8037 44.5 0 8037
19 7872 44.5 0 7872
20 7628 44.5 0 7628
21 7988 44.5 0 7988
22 7679 44.5 0 7679
23 7644 44.5 0 7644
24 7686 44.5 0 7686
25 7594 44.5 0 7594
26 7573 44.5 0 7573
27 7528 44.5 0 7528
28 8124 44.5 0 8124
29 8109 44.5 0 8109
30 7824 44.5 0 7824
31 8830 44.5 0 8830
32 8218 44.5 0 8218
33 8368 44.5 0 8368
34 8704 44.5 0 8704
35 8575 44.5 0 8575
36 8322 44.5 0 8322
37 8835 44.5 0 8835
38 7897 44.5 0 7897
39 8017 44.5 0 8017
40 8326 44.5 0 8326
41 8709 44.5 0 8709
42 8529 44.5 0 8529
43 8693 44.5 0 8693
44 7894 44.5 0 7894
45 8284 44.5 0 8284
46 8844 44.5 0 8844
47 8458 44.5 0 8458
48 8468 44.5 0 8468
49 12609 44.5 0 12609
50 15222 44.5 0 15222
51 9300 44.5 0 9300
52 9848 44.5 0 9848
53 9583 44.5 0 9583
54 8375 44.5 0 8375
55 9105 44.5 0 9105
56 9026 44.5 0 9026
57 8956 44.5 0 8956
58 9704 44.5 0 9704
59 9441 44.5 0 9441
60 9531 44.5 0 9531
61 9517 44.5 0 9517
62 9554 44.5 0 9554
63 9306 44.5 0 9306
64 9302 44.5 0 9302
65 9365 44.5 0 9365
66 9036 44.5 0 9036
67 9013 44.5 0 9013
68 9167 44.5 0 9167
69 8685 44.5 0 8685
70 8426 44.5 0 8426
71 9306 44.5 0 9306
72 9352 44.5 0 9352
73 8629 44.5 0 8629
74 8322 44.5 0 8322
75 8483 44.5 0 8483
76 8353 44.5 0 8353
77 8657 44.5 0 8657
78 8718 44.5 0 8718
79 10257 44.5 0 10257
80 9786 44.5 0 9786
81 11533 44.5 0 11533
82 14244 44.5 0 14244
83 16435 44.5 0 16435
84 17570 44.5 0 17570
85 18176 44.5 0 18176
86 186607 44.5 0 186607
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29167 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.5%
C: 28.6%
G: 0.0%
T: 35.3%
none/other: 4.5%
Overview of removed sequences
length count expect max.err error counts
3 13104 45548.5 0 13104
4 2979 11387.1 0 2979
5 682 2846.8 0 682
6 350 711.7 0 350
7 309 177.9 0 309
8 336 44.5 0 336
9 281 44.5 0 281
10 254 44.5 0 254
11 233 44.5 0 233
12 176 44.5 0 176
13 225 44.5 0 225
14 203 44.5 0 203
15 192 44.5 0 192
16 159 44.5 0 159
17 150 44.5 0 150
18 169 44.5 0 169
19 189 44.5 0 189
20 174 44.5 0 174
21 162 44.5 0 162
22 170 44.5 0 170
23 171 44.5 0 171
24 178 44.5 0 178
25 192 44.5 0 192
26 185 44.5 0 185
27 204 44.5 0 204
28 168 44.5 0 168
29 157 44.5 0 157
30 173 44.5 0 173
31 177 44.5 0 177
32 152 44.5 0 152
33 171 44.5 0 171
34 163 44.5 0 163
35 197 44.5 0 197
36 162 44.5 0 162
37 167 44.5 0 167
38 165 44.5 0 165
39 137 44.5 0 137
40 140 44.5 0 140
41 180 44.5 0 180
42 169 44.5 0 169
43 135 44.5 0 135
44 134 44.5 0 134
45 137 44.5 0 137
46 147 44.5 0 147
47 153 44.5 0 153
48 153 44.5 0 153
49 169 44.5 0 169
50 121 44.5 0 121
51 146 44.5 0 146
52 140 44.5 0 140
53 136 44.5 0 136
54 134 44.5 0 134
55 141 44.5 0 141
56 131 44.5 0 131
57 127 44.5 0 127
58 113 44.5 0 113
59 120 44.5 0 120
60 134 44.5 0 134
61 124 44.5 0 124
62 110 44.5 0 110
63 100 44.5 0 100
64 103 44.5 0 103
65 109 44.5 0 109
66 96 44.5 0 96
67 93 44.5 0 93
68 62 44.5 0 62
69 75 44.5 0 75
70 60 44.5 0 60
71 60 44.5 0 60
72 59 44.5 0 59
73 38 44.5 0 38
74 39 44.5 0 39
75 25 44.5 0 25
76 24 44.5 0 24
77 18 44.5 0 18
78 21 44.5 0 21
79 27 44.5 0 27
80 27 44.5 0 27
81 32 44.5 0 32
82 35 44.5 0 35
83 30 44.5 0 30
84 56 44.5 0 56
85 47 44.5 0 47
86 1321 44.5 0 1321
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61951 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.9%
C: 22.6%
G: 21.6%
T: 18.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 46469 45548.5 0 46469
4 10199 11387.1 0 10199
5 1984 2846.8 0 1984
6 265 711.7 0 265
7 33 177.9 0 33
8 41 177.9 0 41
9 36 177.9 0 36
10 37 177.9 0 37
11 46 177.9 0 46
12 24 177.9 0 24
13 43 177.9 0 43
14 54 177.9 0 54
15 48 177.9 0 48
16 43 177.9 0 43
17 43 177.9 0 43
18 42 177.9 0 42
19 66 177.9 0 66
20 53 177.9 0 53
21 49 177.9 0 49
22 52 177.9 0 52
23 41 177.9 0 41
24 27 177.9 0 27
25 58 177.9 0 58
26 65 177.9 0 65
27 35 177.9 0 35
28 50 177.9 0 50
29 28 177.9 0 28
30 42 177.9 0 42
31 30 177.9 0 30
32 54 177.9 0 54
33 35 177.9 0 35
34 28 177.9 0 28
35 38 177.9 0 38
36 35 177.9 0 35
37 28 177.9 0 28
38 30 177.9 0 30
39 46 177.9 0 46
40 32 177.9 0 32
41 28 177.9 0 28
42 40 177.9 0 40
43 30 177.9 0 30
44 23 177.9 0 23
45 26 177.9 0 26
46 22 177.9 0 22
47 30 177.9 0 30
48 34 177.9 0 34
49 44 177.9 0 44
50 33 177.9 0 33
51 36 177.9 0 36
52 41 177.9 0 41
53 27 177.9 0 27
54 30 177.9 0 30
55 49 177.9 0 49
56 29 177.9 0 29
57 27 177.9 0 27
58 25 177.9 0 25
59 31 177.9 0 31
60 25 177.9 0 25
61 36 177.9 0 36
62 25 177.9 0 25
63 30 177.9 0 30
64 37 177.9 0 37
65 41 177.9 0 41
66 21 177.9 0 21
67 21 177.9 0 21
68 26 177.9 0 26
69 31 177.9 0 31
70 44 177.9 0 44
71 37 177.9 0 37
72 33 177.9 0 33
73 23 177.9 0 23
74 17 177.9 0 17
75 26 177.9 0 26
76 32 177.9 0 32
77 157 177.9 0 157
78 75 177.9 0 75
79 41 177.9 0 41
80 31 177.9 0 31
81 36 177.9 0 36
82 24 177.9 0 24
83 37 177.9 0 37
84 37 177.9 0 37
85 35 177.9 0 35
86 39 177.9 0 39
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M46_S141_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M46_S141_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.87 s (9 µs/read; 6.45 M reads/minute).
=== Summary ===
Total reads processed: 2,780,879
Reads with adapters: 921,598 (33.1%)
== Read fate breakdown ==
Reads that were too short: 259,033 (9.3%)
Reads written (passing filters): 2,521,846 (90.7%)
Total basepairs processed: 280,868,779 bp
Total written (filtered): 198,845,167 bp (70.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 820675 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.9%
G: 27.2%
T: 29.4%
none/other: 13.4%
Overview of removed sequences
length count expect max.err error counts
3 62937 43451.2 0 62937
4 27040 10862.8 0 27040
5 14654 2715.7 0 14654
6 9470 678.9 0 9470
7 7853 169.7 0 7853
8 6986 42.4 0 6986
9 7063 42.4 0 7063
10 6882 42.4 0 6882
11 6968 42.4 0 6968
12 6756 42.4 0 6756
13 6899 42.4 0 6899
14 7055 42.4 0 7055
15 7640 42.4 0 7640
16 8085 42.4 0 8085
17 7531 42.4 0 7531
18 8101 42.4 0 8101
19 7971 42.4 0 7971
20 7373 42.4 0 7373
21 8002 42.4 0 8002
22 7882 42.4 0 7882
23 7137 42.4 0 7137
24 6845 42.4 0 6845
25 6707 42.4 0 6707
26 6737 42.4 0 6737
27 6869 42.4 0 6869
28 7267 42.4 0 7267
29 7270 42.4 0 7270
30 6954 42.4 0 6954
31 7890 42.4 0 7890
32 7516 42.4 0 7516
33 7640 42.4 0 7640
34 7683 42.4 0 7683
35 7409 42.4 0 7409
36 7103 42.4 0 7103
37 7677 42.4 0 7677
38 7243 42.4 0 7243
39 7197 42.4 0 7197
40 7296 42.4 0 7296
41 7236 42.4 0 7236
42 7474 42.4 0 7474
43 7597 42.4 0 7597
44 7008 42.4 0 7008
45 7207 42.4 0 7207
46 7499 42.4 0 7499
47 7367 42.4 0 7367
48 7110 42.4 0 7110
49 10865 42.4 0 10865
50 13147 42.4 0 13147
51 7626 42.4 0 7626
52 7968 42.4 0 7968
53 7911 42.4 0 7911
54 6744 42.4 0 6744
55 7222 42.4 0 7222
56 7442 42.4 0 7442
57 7066 42.4 0 7066
58 7466 42.4 0 7466
59 7535 42.4 0 7535
60 7582 42.4 0 7582
61 7672 42.4 0 7672
62 7424 42.4 0 7424
63 7621 42.4 0 7621
64 7347 42.4 0 7347
65 7241 42.4 0 7241
66 7043 42.4 0 7043
67 6890 42.4 0 6890
68 6949 42.4 0 6949
69 6677 42.4 0 6677
70 6264 42.4 0 6264
71 6882 42.4 0 6882
72 6894 42.4 0 6894
73 6545 42.4 0 6545
74 6164 42.4 0 6164
75 6335 42.4 0 6335
76 6078 42.4 0 6078
77 6243 42.4 0 6243
78 6414 42.4 0 6414
79 7258 42.4 0 7258
80 7104 42.4 0 7104
81 8428 42.4 0 8428
82 9853 42.4 0 9853
83 10721 42.4 0 10721
84 11461 42.4 0 11461
85 12264 42.4 0 12264
86 110243 42.4 0 110243
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 43305 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.6%
C: 34.7%
G: 0.0%
T: 36.2%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 15562 43451.2 0 15562
4 3566 10862.8 0 3566
5 1061 2715.7 0 1061
6 565 678.9 0 565
7 480 169.7 0 480
8 469 42.4 0 469
9 453 42.4 0 453
10 412 42.4 0 412
11 416 42.4 0 416
12 420 42.4 0 420
13 394 42.4 0 394
14 373 42.4 0 373
15 406 42.4 0 406
16 368 42.4 0 368
17 360 42.4 0 360
18 352 42.4 0 352
19 360 42.4 0 360
20 367 42.4 0 367
21 334 42.4 0 334
22 339 42.4 0 339
23 334 42.4 0 334
24 380 42.4 0 380
25 408 42.4 0 408
26 336 42.4 0 336
27 351 42.4 0 351
28 363 42.4 0 363
29 339 42.4 0 339
30 341 42.4 0 341
31 335 42.4 0 335
32 328 42.4 0 328
33 357 42.4 0 357
34 329 42.4 0 329
35 360 42.4 0 360
36 326 42.4 0 326
37 340 42.4 0 340
38 332 42.4 0 332
39 316 42.4 0 316
40 338 42.4 0 338
41 325 42.4 0 325
42 305 42.4 0 305
43 356 42.4 0 356
44 322 42.4 0 322
45 310 42.4 0 310
46 330 42.4 0 330
47 336 42.4 0 336
48 334 42.4 0 334
49 291 42.4 0 291
50 320 42.4 0 320
51 281 42.4 0 281
52 303 42.4 0 303
53 261 42.4 0 261
54 322 42.4 0 322
55 281 42.4 0 281
56 339 42.4 0 339
57 291 42.4 0 291
58 276 42.4 0 276
59 270 42.4 0 270
60 259 42.4 0 259
61 253 42.4 0 253
62 242 42.4 0 242
63 242 42.4 0 242
64 233 42.4 0 233
65 170 42.4 0 170
66 165 42.4 0 165
67 186 42.4 0 186
68 145 42.4 0 145
69 145 42.4 0 145
70 118 42.4 0 118
71 111 42.4 0 111
72 98 42.4 0 98
73 79 42.4 0 79
74 99 42.4 0 99
75 66 42.4 0 66
76 62 42.4 0 62
77 51 42.4 0 51
78 41 42.4 0 41
79 38 42.4 0 38
80 41 42.4 0 41
81 36 42.4 0 36
82 34 42.4 0 34
83 38 42.4 0 38
84 56 42.4 0 56
85 54 42.4 0 54
86 1120 42.4 0 1120
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 57618 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 23.0%
G: 19.8%
T: 21.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 42907 43451.2 0 42907
4 9687 10862.8 0 9687
5 1962 2715.7 0 1962
6 410 678.9 0 410
7 21 169.7 0 21
8 28 169.7 0 28
9 11 169.7 0 11
10 35 169.7 0 35
11 30 169.7 0 30
12 25 169.7 0 25
13 39 169.7 0 39
14 28 169.7 0 28
15 40 169.7 0 40
16 39 169.7 0 39
17 32 169.7 0 32
18 28 169.7 0 28
19 49 169.7 0 49
20 44 169.7 0 44
21 29 169.7 0 29
22 21 169.7 0 21
23 24 169.7 0 24
24 31 169.7 0 31
25 30 169.7 0 30
26 29 169.7 0 29
27 34 169.7 0 34
28 25 169.7 0 25
29 29 169.7 0 29
30 33 169.7 0 33
31 37 169.7 0 37
32 33 169.7 0 33
33 36 169.7 0 36
34 30 169.7 0 30
35 28 169.7 0 28
36 40 169.7 0 40
37 37 169.7 0 37
38 40 169.7 0 40
39 17 169.7 0 17
40 48 169.7 0 48
41 34 169.7 0 34
42 32 169.7 0 32
43 29 169.7 0 29
44 34 169.7 0 34
45 23 169.7 0 23
46 25 169.7 0 25
47 39 169.7 0 39
48 31 169.7 0 31
49 31 169.7 0 31
50 35 169.7 0 35
51 37 169.7 0 37
52 25 169.7 0 25
53 35 169.7 0 35
54 32 169.7 0 32
55 20 169.7 0 20
56 36 169.7 0 36
57 41 169.7 0 41
58 39 169.7 0 39
59 27 169.7 0 27
60 23 169.7 0 23
61 28 169.7 0 28
62 34 169.7 0 34
63 36 169.7 0 36
64 26 169.7 0 26
65 40 169.7 0 40
66 32 169.7 0 32
67 42 169.7 0 42
68 34 169.7 0 34
69 28 169.7 0 28
70 40 169.7 0 40
71 44 169.7 0 44
72 21 169.7 0 21
73 33 169.7 0 33
74 38 169.7 0 38
75 24 169.7 0 24
76 40 169.7 0 40
77 84 169.7 0 84
78 39 169.7 0 39
79 28 169.7 0 28
80 38 169.7 0 38
81 31 169.7 0 31
82 37 169.7 0 37
83 30 169.7 0 30
84 43 169.7 0 43
85 40 169.7 0 40
86 34 169.7 0 34
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M46_S141_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M46_S141_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.07 s (10 µs/read; 6.29 M reads/minute).
=== Summary ===
Total reads processed: 2,839,304
Reads with adapters: 950,939 (33.5%)
== Read fate breakdown ==
Reads that were too short: 271,242 (9.6%)
Reads written (passing filters): 2,568,062 (90.4%)
Total basepairs processed: 286,769,704 bp
Total written (filtered): 202,237,466 bp (70.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 848219 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.9%
G: 27.1%
T: 29.2%
none/other: 13.7%
Overview of removed sequences
length count expect max.err error counts
3 64566 44364.1 0 64566
4 27388 11091.0 0 27388
5 14603 2772.8 0 14603
6 9360 693.2 0 9360
7 7965 173.3 0 7965
8 7130 43.3 0 7130
9 6856 43.3 0 6856
10 7258 43.3 0 7258
11 6979 43.3 0 6979
12 7109 43.3 0 7109
13 7055 43.3 0 7055
14 7262 43.3 0 7262
15 7820 43.3 0 7820
16 8275 43.3 0 8275
17 7744 43.3 0 7744
18 8227 43.3 0 8227
19 8103 43.3 0 8103
20 7421 43.3 0 7421
21 8039 43.3 0 8039
22 8279 43.3 0 8279
23 7255 43.3 0 7255
24 7135 43.3 0 7135
25 6898 43.3 0 6898
26 6978 43.3 0 6978
27 7069 43.3 0 7069
28 7191 43.3 0 7191
29 7352 43.3 0 7352
30 7130 43.3 0 7130
31 8011 43.3 0 8011
32 7571 43.3 0 7571
33 7723 43.3 0 7723
34 8148 43.3 0 8148
35 7662 43.3 0 7662
36 7651 43.3 0 7651
37 7871 43.3 0 7871
38 7359 43.3 0 7359
39 7430 43.3 0 7430
40 7501 43.3 0 7501
41 7366 43.3 0 7366
42 7776 43.3 0 7776
43 7774 43.3 0 7774
44 7290 43.3 0 7290
45 7772 43.3 0 7772
46 7752 43.3 0 7752
47 7630 43.3 0 7630
48 7175 43.3 0 7175
49 11362 43.3 0 11362
50 13955 43.3 0 13955
51 7994 43.3 0 7994
52 8254 43.3 0 8254
53 8220 43.3 0 8220
54 7193 43.3 0 7193
55 7597 43.3 0 7597
56 7605 43.3 0 7605
57 7481 43.3 0 7481
58 7953 43.3 0 7953
59 7695 43.3 0 7695
60 7764 43.3 0 7764
61 7780 43.3 0 7780
62 7621 43.3 0 7621
63 7791 43.3 0 7791
64 7485 43.3 0 7485
65 7312 43.3 0 7312
66 7253 43.3 0 7253
67 7313 43.3 0 7313
68 7292 43.3 0 7292
69 7108 43.3 0 7108
70 6738 43.3 0 6738
71 7214 43.3 0 7214
72 7396 43.3 0 7396
73 6482 43.3 0 6482
74 6407 43.3 0 6407
75 6579 43.3 0 6579
76 6421 43.3 0 6421
77 6506 43.3 0 6506
78 6646 43.3 0 6646
79 7696 43.3 0 7696
80 7296 43.3 0 7296
81 8760 43.3 0 8760
82 10190 43.3 0 10190
83 11097 43.3 0 11097
84 12098 43.3 0 12098
85 12512 43.3 0 12512
86 116244 43.3 0 116244
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 44151 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.7%
C: 35.4%
G: 0.0%
T: 35.5%
none/other: 2.4%
Overview of removed sequences
length count expect max.err error counts
3 15799 44364.1 0 15799
4 3612 11091.0 0 3612
5 1047 2772.8 0 1047
6 506 693.2 0 506
7 491 173.3 0 491
8 508 43.3 0 508
9 471 43.3 0 471
10 398 43.3 0 398
11 427 43.3 0 427
12 412 43.3 0 412
13 406 43.3 0 406
14 407 43.3 0 407
15 396 43.3 0 396
16 365 43.3 0 365
17 359 43.3 0 359
18 347 43.3 0 347
19 363 43.3 0 363
20 376 43.3 0 376
21 392 43.3 0 392
22 345 43.3 0 345
23 364 43.3 0 364
24 376 43.3 0 376
25 359 43.3 0 359
26 353 43.3 0 353
27 375 43.3 0 375
28 358 43.3 0 358
29 331 43.3 0 331
30 334 43.3 0 334
31 349 43.3 0 349
32 343 43.3 0 343
33 377 43.3 0 377
34 381 43.3 0 381
35 360 43.3 0 360
36 330 43.3 0 330
37 379 43.3 0 379
38 342 43.3 0 342
39 339 43.3 0 339
40 296 43.3 0 296
41 314 43.3 0 314
42 333 43.3 0 333
43 369 43.3 0 369
44 305 43.3 0 305
45 363 43.3 0 363
46 357 43.3 0 357
47 368 43.3 0 368
48 339 43.3 0 339
49 317 43.3 0 317
50 304 43.3 0 304
51 312 43.3 0 312
52 307 43.3 0 307
53 340 43.3 0 340
54 280 43.3 0 280
55 309 43.3 0 309
56 298 43.3 0 298
57 303 43.3 0 303
58 310 43.3 0 310
59 278 43.3 0 278
60 276 43.3 0 276
61 265 43.3 0 265
62 264 43.3 0 264
63 275 43.3 0 275
64 245 43.3 0 245
65 228 43.3 0 228
66 177 43.3 0 177
67 182 43.3 0 182
68 155 43.3 0 155
69 134 43.3 0 134
70 123 43.3 0 123
71 111 43.3 0 111
72 99 43.3 0 99
73 75 43.3 0 75
74 88 43.3 0 88
75 72 43.3 0 72
76 63 43.3 0 63
77 49 43.3 0 49
78 51 43.3 0 51
79 48 43.3 0 48
80 46 43.3 0 46
81 39 43.3 0 39
82 29 43.3 0 29
83 28 43.3 0 28
84 35 43.3 0 35
85 49 43.3 0 49
86 1066 43.3 0 1066
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 58569 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.1%
C: 23.1%
G: 19.8%
T: 20.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 43423 44364.1 0 43423
4 9882 11091.0 0 9882
5 2117 2772.8 0 2117
6 426 693.2 0 426
7 27 173.3 0 27
8 24 173.3 0 24
9 28 173.3 0 28
10 35 173.3 0 35
11 37 173.3 0 37
12 27 173.3 0 27
13 46 173.3 0 46
14 39 173.3 0 39
15 40 173.3 0 40
16 29 173.3 0 29
17 27 173.3 0 27
18 39 173.3 0 39
19 44 173.3 0 44
20 33 173.3 0 33
21 36 173.3 0 36
22 34 173.3 0 34
23 22 173.3 0 22
24 31 173.3 0 31
25 37 173.3 0 37
26 34 173.3 0 34
27 32 173.3 0 32
28 32 173.3 0 32
29 34 173.3 0 34
30 40 173.3 0 40
31 32 173.3 0 32
32 30 173.3 0 30
33 29 173.3 0 29
34 29 173.3 0 29
35 30 173.3 0 30
36 31 173.3 0 31
37 29 173.3 0 29
38 34 173.3 0 34
39 43 173.3 0 43
40 43 173.3 0 43
41 37 173.3 0 37
42 30 173.3 0 30
43 28 173.3 0 28
44 30 173.3 0 30
45 26 173.3 0 26
46 32 173.3 0 32
47 38 173.3 0 38
48 27 173.3 0 27
49 31 173.3 0 31
50 47 173.3 0 47
51 30 173.3 0 30
52 49 173.3 0 49
53 20 173.3 0 20
54 30 173.3 0 30
55 28 173.3 0 28
56 22 173.3 0 22
57 29 173.3 0 29
58 34 173.3 0 34
59 21 173.3 0 21
60 44 173.3 0 44
61 52 173.3 0 52
62 45 173.3 0 45
63 34 173.3 0 34
64 33 173.3 0 33
65 45 173.3 0 45
66 37 173.3 0 37
67 43 173.3 0 43
68 32 173.3 0 32
69 22 173.3 0 22
70 44 173.3 0 44
71 29 173.3 0 29
72 27 173.3 0 27
73 22 173.3 0 22
74 41 173.3 0 41
75 26 173.3 0 26
76 37 173.3 0 37
77 78 173.3 0 78
78 43 173.3 0 43
79 21 173.3 0 21
80 39 173.3 0 39
81 35 173.3 0 35
82 25 173.3 0 25
83 37 173.3 0 37
84 30 173.3 0 30
85 33 173.3 0 33
86 41 173.3 0 41
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M47_S162_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M47_S162_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.63 s (9 µs/read; 6.40 M reads/minute).
=== Summary ===
Total reads processed: 3,054,784
Reads with adapters: 1,008,825 (33.0%)
== Read fate breakdown ==
Reads that were too short: 280,472 (9.2%)
Reads written (passing filters): 2,774,312 (90.8%)
Total basepairs processed: 308,533,184 bp
Total written (filtered): 219,198,148 bp (71.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 912156 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.7%
G: 28.1%
T: 28.2%
none/other: 14.0%
Overview of removed sequences
length count expect max.err error counts
3 71282 47731.0 0 71282
4 31247 11932.8 0 31247
5 16342 2983.2 0 16342
6 11327 745.8 0 11327
7 9333 186.4 0 9333
8 8157 46.6 0 8157
9 8365 46.6 0 8365
10 8420 46.6 0 8420
11 8346 46.6 0 8346
12 8352 46.6 0 8352
13 8311 46.6 0 8311
14 8248 46.6 0 8248
15 8392 46.6 0 8392
16 8545 46.6 0 8545
17 8426 46.6 0 8426
18 8703 46.6 0 8703
19 8286 46.6 0 8286
20 7936 46.6 0 7936
21 8500 46.6 0 8500
22 8407 46.6 0 8407
23 7824 46.6 0 7824
24 7959 46.6 0 7959
25 7862 46.6 0 7862
26 7788 46.6 0 7788
27 7807 46.6 0 7807
28 8372 46.6 0 8372
29 8094 46.6 0 8094
30 8067 46.6 0 8067
31 9063 46.6 0 9063
32 8392 46.6 0 8392
33 9066 46.6 0 9066
34 8567 46.6 0 8567
35 9024 46.6 0 9024
36 7943 46.6 0 7943
37 8757 46.6 0 8757
38 8084 46.6 0 8084
39 8211 46.6 0 8211
40 8396 46.6 0 8396
41 8905 46.6 0 8905
42 8430 46.6 0 8430
43 9286 46.6 0 9286
44 8230 46.6 0 8230
45 8465 46.6 0 8465
46 9030 46.6 0 9030
47 8511 46.6 0 8511
48 8265 46.6 0 8265
49 12362 46.6 0 12362
50 14854 46.6 0 14854
51 8235 46.6 0 8235
52 8550 46.6 0 8550
53 8609 46.6 0 8609
54 7381 46.6 0 7381
55 7750 46.6 0 7750
56 7710 46.6 0 7710
57 7452 46.6 0 7452
58 7792 46.6 0 7792
59 7739 46.6 0 7739
60 7775 46.6 0 7775
61 7682 46.6 0 7682
62 7609 46.6 0 7609
63 7711 46.6 0 7711
64 7234 46.6 0 7234
65 7241 46.6 0 7241
66 7188 46.6 0 7188
67 7011 46.6 0 7011
68 6895 46.6 0 6895
69 6894 46.6 0 6894
70 6536 46.6 0 6536
71 7006 46.6 0 7006
72 7068 46.6 0 7068
73 6424 46.6 0 6424
74 6375 46.6 0 6375
75 6552 46.6 0 6552
76 6334 46.6 0 6334
77 6208 46.6 0 6208
78 6636 46.6 0 6636
79 7470 46.6 0 7470
80 7358 46.6 0 7358
81 8565 46.6 0 8565
82 10391 46.6 0 10391
83 11213 46.6 0 11213
84 12207 46.6 0 12207
85 13084 46.6 0 13084
86 127732 46.6 0 127732
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29113 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 32.3%
C: 31.5%
G: 0.0%
T: 32.8%
none/other: 3.4%
Overview of removed sequences
length count expect max.err error counts
3 15436 47731.0 0 15436
4 3470 11932.8 0 3470
5 814 2983.2 0 814
6 320 745.8 0 320
7 298 186.4 0 298
8 259 46.6 0 259
9 255 46.6 0 255
10 214 46.6 0 214
11 223 46.6 0 223
12 186 46.6 0 186
13 142 46.6 0 142
14 146 46.6 0 146
15 143 46.6 0 143
16 123 46.6 0 123
17 124 46.6 0 124
18 133 46.6 0 133
19 142 46.6 0 142
20 120 46.6 0 120
21 140 46.6 0 140
22 130 46.6 0 130
23 141 46.6 0 141
24 128 46.6 0 128
25 122 46.6 0 122
26 109 46.6 0 109
27 98 46.6 0 98
28 114 46.6 0 114
29 130 46.6 0 130
30 110 46.6 0 110
31 137 46.6 0 137
32 136 46.6 0 136
33 114 46.6 0 114
34 119 46.6 0 119
35 118 46.6 0 118
36 116 46.6 0 116
37 138 46.6 0 138
38 111 46.6 0 111
39 116 46.6 0 116
40 105 46.6 0 105
41 112 46.6 0 112
42 99 46.6 0 99
43 126 46.6 0 126
44 100 46.6 0 100
45 98 46.6 0 98
46 105 46.6 0 105
47 104 46.6 0 104
48 105 46.6 0 105
49 107 46.6 0 107
50 108 46.6 0 108
51 98 46.6 0 98
52 117 46.6 0 117
53 105 46.6 0 105
54 100 46.6 0 100
55 105 46.6 0 105
56 89 46.6 0 89
57 87 46.6 0 87
58 99 46.6 0 99
59 92 46.6 0 92
60 84 46.6 0 84
61 84 46.6 0 84
62 65 46.6 0 65
63 69 46.6 0 69
64 69 46.6 0 69
65 50 46.6 0 50
66 54 46.6 0 54
67 61 46.6 0 61
68 69 46.6 0 69
69 50 46.6 0 50
70 52 46.6 0 52
71 64 46.6 0 64
72 42 46.6 0 42
73 45 46.6 0 45
74 38 46.6 0 38
75 27 46.6 0 27
76 30 46.6 0 30
77 22 46.6 0 22
78 25 46.6 0 25
79 17 46.6 0 17
80 25 46.6 0 25
81 15 46.6 0 15
82 30 46.6 0 30
83 31 46.6 0 31
84 36 46.6 0 36
85 44 46.6 0 44
86 979 46.6 0 979
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 67556 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 24.1%
G: 20.3%
T: 19.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 49890 47731.0 0 49890
4 11226 11932.8 0 11226
5 2480 2983.2 0 2480
6 336 745.8 0 336
7 29 186.4 0 29
8 56 186.4 0 56
9 43 186.4 0 43
10 39 186.4 0 39
11 54 186.4 0 54
12 45 186.4 0 45
13 74 186.4 0 74
14 57 186.4 0 57
15 75 186.4 0 75
16 86 186.4 0 86
17 55 186.4 0 55
18 57 186.4 0 57
19 81 186.4 0 81
20 46 186.4 0 46
21 56 186.4 0 56
22 60 186.4 0 60
23 48 186.4 0 48
24 39 186.4 0 39
25 78 186.4 0 78
26 63 186.4 0 63
27 21 186.4 0 21
28 60 186.4 0 60
29 51 186.4 0 51
30 40 186.4 0 40
31 34 186.4 0 34
32 57 186.4 0 57
33 35 186.4 0 35
34 68 186.4 0 68
35 42 186.4 0 42
36 45 186.4 0 45
37 71 186.4 0 71
38 55 186.4 0 55
39 41 186.4 0 41
40 61 186.4 0 61
41 57 186.4 0 57
42 40 186.4 0 40
43 33 186.4 0 33
44 40 186.4 0 40
45 32 186.4 0 32
46 39 186.4 0 39
47 25 186.4 0 25
48 49 186.4 0 49
49 40 186.4 0 40
50 45 186.4 0 45
51 40 186.4 0 40
52 41 186.4 0 41
53 33 186.4 0 33
54 40 186.4 0 40
55 39 186.4 0 39
56 37 186.4 0 37
57 39 186.4 0 39
58 34 186.4 0 34
59 35 186.4 0 35
60 36 186.4 0 36
61 24 186.4 0 24
62 43 186.4 0 43
63 33 186.4 0 33
64 40 186.4 0 40
65 35 186.4 0 35
66 42 186.4 0 42
67 49 186.4 0 49
68 45 186.4 0 45
69 38 186.4 0 38
70 47 186.4 0 47
71 43 186.4 0 43
72 35 186.4 0 35
73 25 186.4 0 25
74 37 186.4 0 37
75 30 186.4 0 30
76 25 186.4 0 25
77 84 186.4 0 84
78 42 186.4 0 42
79 23 186.4 0 23
80 32 186.4 0 32
81 25 186.4 0 25
82 41 186.4 0 41
83 49 186.4 0 49
84 41 186.4 0 41
85 44 186.4 0 44
86 56 186.4 0 56
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M47_S162_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M47_S162_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.95 s (9 µs/read; 6.48 M reads/minute).
=== Summary ===
Total reads processed: 3,125,352
Reads with adapters: 1,042,126 (33.3%)
== Read fate breakdown ==
Reads that were too short: 295,293 (9.4%)
Reads written (passing filters): 2,830,059 (90.6%)
Total basepairs processed: 315,660,552 bp
Total written (filtered): 223,381,460 bp (70.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 943415 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.6%
G: 28.1%
T: 28.0%
none/other: 14.3%
Overview of removed sequences
length count expect max.err error counts
3 72278 48833.6 0 72278
4 31737 12208.4 0 31737
5 16985 3052.1 0 16985
6 11480 763.0 0 11480
7 9630 190.8 0 9630
8 8471 47.7 0 8471
9 8622 47.7 0 8622
10 8510 47.7 0 8510
11 8552 47.7 0 8552
12 8459 47.7 0 8459
13 8490 47.7 0 8490
14 8602 47.7 0 8602
15 8529 47.7 0 8529
16 8557 47.7 0 8557
17 8465 47.7 0 8465
18 8629 47.7 0 8629
19 8455 47.7 0 8455
20 8058 47.7 0 8058
21 8380 47.7 0 8380
22 8640 47.7 0 8640
23 7918 47.7 0 7918
24 7982 47.7 0 7982
25 7936 47.7 0 7936
26 7874 47.7 0 7874
27 8098 47.7 0 8098
28 8136 47.7 0 8136
29 8481 47.7 0 8481
30 8268 47.7 0 8268
31 9416 47.7 0 9416
32 8452 47.7 0 8452
33 9259 47.7 0 9259
34 9085 47.7 0 9085
35 9212 47.7 0 9212
36 8113 47.7 0 8113
37 8889 47.7 0 8889
38 8587 47.7 0 8587
39 8467 47.7 0 8467
40 8638 47.7 0 8638
41 9215 47.7 0 9215
42 8990 47.7 0 8990
43 9788 47.7 0 9788
44 8526 47.7 0 8526
45 8829 47.7 0 8829
46 9227 47.7 0 9227
47 8595 47.7 0 8595
48 8360 47.7 0 8360
49 13056 47.7 0 13056
50 15461 47.7 0 15461
51 8634 47.7 0 8634
52 8942 47.7 0 8942
53 8813 47.7 0 8813
54 7612 47.7 0 7612
55 8014 47.7 0 8014
56 8099 47.7 0 8099
57 7699 47.7 0 7699
58 8096 47.7 0 8096
59 7865 47.7 0 7865
60 8018 47.7 0 8018
61 7965 47.7 0 7965
62 8096 47.7 0 8096
63 8001 47.7 0 8001
64 7537 47.7 0 7537
65 7502 47.7 0 7502
66 7316 47.7 0 7316
67 7288 47.7 0 7288
68 7311 47.7 0 7311
69 7346 47.7 0 7346
70 6564 47.7 0 6564
71 7356 47.7 0 7356
72 7570 47.7 0 7570
73 6967 47.7 0 6967
74 6716 47.7 0 6716
75 6897 47.7 0 6897
76 6334 47.7 0 6334
77 6657 47.7 0 6657
78 7147 47.7 0 7147
79 8117 47.7 0 8117
80 7555 47.7 0 7555
81 8999 47.7 0 8999
82 10905 47.7 0 10905
83 11694 47.7 0 11694
84 13031 47.7 0 13031
85 13618 47.7 0 13618
86 134747 47.7 0 134747
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29630 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 32.8%
C: 31.7%
G: 0.0%
T: 32.2%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 15700 48833.6 0 15700
4 3494 12208.4 0 3494
5 807 3052.1 0 807
6 320 763.0 0 320
7 311 190.8 0 311
8 280 47.7 0 280
9 265 47.7 0 265
10 208 47.7 0 208
11 195 47.7 0 195
12 165 47.7 0 165
13 191 47.7 0 191
14 148 47.7 0 148
15 153 47.7 0 153
16 141 47.7 0 141
17 140 47.7 0 140
18 121 47.7 0 121
19 132 47.7 0 132
20 132 47.7 0 132
21 130 47.7 0 130
22 162 47.7 0 162
23 119 47.7 0 119
24 156 47.7 0 156
25 154 47.7 0 154
26 143 47.7 0 143
27 122 47.7 0 122
28 139 47.7 0 139
29 121 47.7 0 121
30 137 47.7 0 137
31 95 47.7 0 95
32 126 47.7 0 126
33 127 47.7 0 127
34 134 47.7 0 134
35 113 47.7 0 113
36 107 47.7 0 107
37 98 47.7 0 98
38 114 47.7 0 114
39 98 47.7 0 98
40 123 47.7 0 123
41 89 47.7 0 89
42 113 47.7 0 113
43 115 47.7 0 115
44 101 47.7 0 101
45 126 47.7 0 126
46 102 47.7 0 102
47 119 47.7 0 119
48 112 47.7 0 112
49 111 47.7 0 111
50 112 47.7 0 112
51 88 47.7 0 88
52 88 47.7 0 88
53 84 47.7 0 84
54 94 47.7 0 94
55 98 47.7 0 98
56 110 47.7 0 110
57 103 47.7 0 103
58 111 47.7 0 111
59 95 47.7 0 95
60 95 47.7 0 95
61 106 47.7 0 106
62 89 47.7 0 89
63 85 47.7 0 85
64 94 47.7 0 94
65 65 47.7 0 65
66 72 47.7 0 72
67 55 47.7 0 55
68 57 47.7 0 57
69 68 47.7 0 68
70 50 47.7 0 50
71 41 47.7 0 41
72 43 47.7 0 43
73 39 47.7 0 39
74 30 47.7 0 30
75 37 47.7 0 37
76 16 47.7 0 16
77 21 47.7 0 21
78 21 47.7 0 21
79 18 47.7 0 18
80 28 47.7 0 28
81 19 47.7 0 19
82 24 47.7 0 24
83 23 47.7 0 23
84 47 47.7 0 47
85 35 47.7 0 35
86 960 47.7 0 960
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69081 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.3%
C: 23.5%
G: 20.4%
T: 19.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51058 48833.6 0 51058
4 11522 12208.4 0 11522
5 2465 3052.1 0 2465
6 333 763.0 0 333
7 28 190.8 0 28
8 42 190.8 0 42
9 40 190.8 0 40
10 35 190.8 0 35
11 53 190.8 0 53
12 33 190.8 0 33
13 74 190.8 0 74
14 81 190.8 0 81
15 43 190.8 0 43
16 85 190.8 0 85
17 59 190.8 0 59
18 60 190.8 0 60
19 97 190.8 0 97
20 45 190.8 0 45
21 56 190.8 0 56
22 47 190.8 0 47
23 38 190.8 0 38
24 34 190.8 0 34
25 66 190.8 0 66
26 53 190.8 0 53
27 47 190.8 0 47
28 46 190.8 0 46
29 65 190.8 0 65
30 51 190.8 0 51
31 38 190.8 0 38
32 55 190.8 0 55
33 53 190.8 0 53
34 56 190.8 0 56
35 40 190.8 0 40
36 61 190.8 0 61
37 60 190.8 0 60
38 67 190.8 0 67
39 42 190.8 0 42
40 64 190.8 0 64
41 40 190.8 0 40
42 48 190.8 0 48
43 34 190.8 0 34
44 41 190.8 0 41
45 38 190.8 0 38
46 41 190.8 0 41
47 29 190.8 0 29
48 44 190.8 0 44
49 42 190.8 0 42
50 34 190.8 0 34
51 67 190.8 0 67
52 45 190.8 0 45
53 42 190.8 0 42
54 56 190.8 0 56
55 29 190.8 0 29
56 27 190.8 0 27
57 37 190.8 0 37
58 44 190.8 0 44
59 35 190.8 0 35
60 37 190.8 0 37
61 36 190.8 0 36
62 47 190.8 0 47
63 30 190.8 0 30
64 34 190.8 0 34
65 52 190.8 0 52
66 38 190.8 0 38
67 41 190.8 0 41
68 35 190.8 0 35
69 45 190.8 0 45
70 38 190.8 0 38
71 52 190.8 0 52
72 34 190.8 0 34
73 40 190.8 0 40
74 45 190.8 0 45
75 28 190.8 0 28
76 28 190.8 0 28
77 80 190.8 0 80
78 48 190.8 0 48
79 32 190.8 0 32
80 35 190.8 0 35
81 40 190.8 0 40
82 35 190.8 0 35
83 51 190.8 0 51
84 46 190.8 0 46
85 43 190.8 0 43
86 46 190.8 0 46
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M48_S137_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M48_S137_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.31 s (10 µs/read; 6.28 M reads/minute).
=== Summary ===
Total reads processed: 2,546,006
Reads with adapters: 847,042 (33.3%)
== Read fate breakdown ==
Reads that were too short: 276,762 (10.9%)
Reads written (passing filters): 2,269,244 (89.1%)
Total basepairs processed: 257,146,606 bp
Total written (filtered): 179,538,292 bp (69.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 756210 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.8%
G: 26.3%
T: 28.4%
none/other: 16.6%
Overview of removed sequences
length count expect max.err error counts
3 57757 39781.3 0 57757
4 24787 9945.3 0 24787
5 12422 2486.3 0 12422
6 8039 621.6 0 8039
7 6251 155.4 0 6251
8 5487 38.8 0 5487
9 5399 38.8 0 5399
10 5436 38.8 0 5436
11 5339 38.8 0 5339
12 5402 38.8 0 5402
13 5538 38.8 0 5538
14 5677 38.8 0 5677
15 5875 38.8 0 5875
16 5949 38.8 0 5949
17 5911 38.8 0 5911
18 5947 38.8 0 5947
19 5714 38.8 0 5714
20 5679 38.8 0 5679
21 5957 38.8 0 5957
22 5808 38.8 0 5808
23 5633 38.8 0 5633
24 5604 38.8 0 5604
25 5753 38.8 0 5753
26 5513 38.8 0 5513
27 5658 38.8 0 5658
28 6049 38.8 0 6049
29 6110 38.8 0 6110
30 5728 38.8 0 5728
31 6214 38.8 0 6214
32 6136 38.8 0 6136
33 6142 38.8 0 6142
34 6014 38.8 0 6014
35 6200 38.8 0 6200
36 5910 38.8 0 5910
37 5664 38.8 0 5664
38 5839 38.8 0 5839
39 6041 38.8 0 6041
40 6063 38.8 0 6063
41 6188 38.8 0 6188
42 6199 38.8 0 6199
43 6280 38.8 0 6280
44 5862 38.8 0 5862
45 6306 38.8 0 6306
46 6553 38.8 0 6553
47 6279 38.8 0 6279
48 6189 38.8 0 6189
49 9667 38.8 0 9667
50 11120 38.8 0 11120
51 6881 38.8 0 6881
52 7552 38.8 0 7552
53 7347 38.8 0 7347
54 6419 38.8 0 6419
55 6712 38.8 0 6712
56 7028 38.8 0 7028
57 6572 38.8 0 6572
58 7137 38.8 0 7137
59 7130 38.8 0 7130
60 7144 38.8 0 7144
61 7340 38.8 0 7340
62 6892 38.8 0 6892
63 6788 38.8 0 6788
64 6985 38.8 0 6985
65 6775 38.8 0 6775
66 6595 38.8 0 6595
67 6549 38.8 0 6549
68 6584 38.8 0 6584
69 6455 38.8 0 6455
70 6210 38.8 0 6210
71 6888 38.8 0 6888
72 6876 38.8 0 6876
73 6396 38.8 0 6396
74 6033 38.8 0 6033
75 6133 38.8 0 6133
76 6105 38.8 0 6105
77 6396 38.8 0 6396
78 6313 38.8 0 6313
79 7328 38.8 0 7328
80 7049 38.8 0 7049
81 8413 38.8 0 8413
82 10649 38.8 0 10649
83 12014 38.8 0 12014
84 12610 38.8 0 12610
85 13243 38.8 0 13243
86 125381 38.8 0 125381
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34697 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.8%
C: 30.7%
G: 0.0%
T: 36.6%
none/other: 3.9%
Overview of removed sequences
length count expect max.err error counts
3 13414 39781.3 0 13414
4 2962 9945.3 0 2962
5 899 2486.3 0 899
6 392 621.6 0 392
7 330 155.4 0 330
8 360 38.8 0 360
9 316 38.8 0 316
10 323 38.8 0 323
11 316 38.8 0 316
12 274 38.8 0 274
13 259 38.8 0 259
14 246 38.8 0 246
15 253 38.8 0 253
16 255 38.8 0 255
17 248 38.8 0 248
18 279 38.8 0 279
19 290 38.8 0 290
20 263 38.8 0 263
21 266 38.8 0 266
22 281 38.8 0 281
23 280 38.8 0 280
24 308 38.8 0 308
25 335 38.8 0 335
26 285 38.8 0 285
27 276 38.8 0 276
28 264 38.8 0 264
29 256 38.8 0 256
30 257 38.8 0 257
31 258 38.8 0 258
32 240 38.8 0 240
33 259 38.8 0 259
34 286 38.8 0 286
35 238 38.8 0 238
36 243 38.8 0 243
37 244 38.8 0 244
38 237 38.8 0 237
39 231 38.8 0 231
40 227 38.8 0 227
41 215 38.8 0 215
42 237 38.8 0 237
43 237 38.8 0 237
44 239 38.8 0 239
45 237 38.8 0 237
46 208 38.8 0 208
47 230 38.8 0 230
48 260 38.8 0 260
49 201 38.8 0 201
50 211 38.8 0 211
51 239 38.8 0 239
52 242 38.8 0 242
53 219 38.8 0 219
54 198 38.8 0 198
55 220 38.8 0 220
56 207 38.8 0 207
57 219 38.8 0 219
58 180 38.8 0 180
59 207 38.8 0 207
60 197 38.8 0 197
61 141 38.8 0 141
62 170 38.8 0 170
63 179 38.8 0 179
64 163 38.8 0 163
65 128 38.8 0 128
66 123 38.8 0 123
67 102 38.8 0 102
68 107 38.8 0 107
69 89 38.8 0 89
70 83 38.8 0 83
71 77 38.8 0 77
72 76 38.8 0 76
73 60 38.8 0 60
74 54 38.8 0 54
75 59 38.8 0 59
76 48 38.8 0 48
77 34 38.8 0 34
78 29 38.8 0 29
79 40 38.8 0 40
80 32 38.8 0 32
81 21 38.8 0 21
82 38 38.8 0 38
83 33 38.8 0 33
84 49 38.8 0 49
85 46 38.8 0 46
86 1363 38.8 0 1363
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 56135 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.8%
C: 22.7%
G: 20.9%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41942 39781.3 0 41942
4 9703 9945.3 0 9703
5 1738 2486.3 0 1738
6 291 621.6 0 291
7 23 155.4 0 23
8 24 155.4 0 24
9 21 155.4 0 21
10 24 155.4 0 24
11 21 155.4 0 21
12 23 155.4 0 23
13 36 155.4 0 36
14 32 155.4 0 32
15 24 155.4 0 24
16 30 155.4 0 30
17 23 155.4 0 23
18 31 155.4 0 31
19 34 155.4 0 34
20 25 155.4 0 25
21 34 155.4 0 34
22 38 155.4 0 38
23 29 155.4 0 29
24 18 155.4 0 18
25 28 155.4 0 28
26 40 155.4 0 40
27 26 155.4 0 26
28 22 155.4 0 22
29 37 155.4 0 37
30 46 155.4 0 46
31 17 155.4 0 17
32 38 155.4 0 38
33 31 155.4 0 31
34 26 155.4 0 26
35 22 155.4 0 22
36 31 155.4 0 31
37 41 155.4 0 41
38 26 155.4 0 26
39 16 155.4 0 16
40 33 155.4 0 33
41 40 155.4 0 40
42 20 155.4 0 20
43 23 155.4 0 23
44 38 155.4 0 38
45 33 155.4 0 33
46 18 155.4 0 18
47 27 155.4 0 27
48 31 155.4 0 31
49 22 155.4 0 22
50 32 155.4 0 32
51 30 155.4 0 30
52 37 155.4 0 37
53 30 155.4 0 30
54 30 155.4 0 30
55 26 155.4 0 26
56 26 155.4 0 26
57 26 155.4 0 26
58 40 155.4 0 40
59 31 155.4 0 31
60 25 155.4 0 25
61 21 155.4 0 21
62 33 155.4 0 33
63 36 155.4 0 36
64 29 155.4 0 29
65 45 155.4 0 45
66 45 155.4 0 45
67 22 155.4 0 22
68 25 155.4 0 25
69 21 155.4 0 21
70 34 155.4 0 34
71 28 155.4 0 28
72 24 155.4 0 24
73 32 155.4 0 32
74 29 155.4 0 29
75 18 155.4 0 18
76 33 155.4 0 33
77 96 155.4 0 96
78 59 155.4 0 59
79 36 155.4 0 36
80 42 155.4 0 42
81 35 155.4 0 35
82 25 155.4 0 25
83 30 155.4 0 30
84 31 155.4 0 31
85 34 155.4 0 34
86 43 155.4 0 43
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M48_S137_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M48_S137_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.14 s (9 µs/read; 6.50 M reads/minute).
=== Summary ===
Total reads processed: 2,613,840
Reads with adapters: 876,566 (33.5%)
== Read fate breakdown ==
Reads that were too short: 290,264 (11.1%)
Reads written (passing filters): 2,323,576 (88.9%)
Total basepairs processed: 263,997,840 bp
Total written (filtered): 183,678,133 bp (69.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 783507 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.8%
G: 26.1%
T: 28.2%
none/other: 16.9%
Overview of removed sequences
length count expect max.err error counts
3 58466 40841.2 0 58466
4 25195 10210.3 0 25195
5 12703 2552.6 0 12703
6 8111 638.1 0 8111
7 6341 159.5 0 6341
8 5554 39.9 0 5554
9 5798 39.9 0 5798
10 5517 39.9 0 5517
11 5410 39.9 0 5410
12 5771 39.9 0 5771
13 5772 39.9 0 5772
14 5851 39.9 0 5851
15 5987 39.9 0 5987
16 5888 39.9 0 5888
17 5934 39.9 0 5934
18 6117 39.9 0 6117
19 5938 39.9 0 5938
20 5871 39.9 0 5871
21 6090 39.9 0 6090
22 5798 39.9 0 5798
23 5842 39.9 0 5842
24 5858 39.9 0 5858
25 5735 39.9 0 5735
26 5734 39.9 0 5734
27 5779 39.9 0 5779
28 6222 39.9 0 6222
29 6248 39.9 0 6248
30 6033 39.9 0 6033
31 6434 39.9 0 6434
32 6104 39.9 0 6104
33 6467 39.9 0 6467
34 6290 39.9 0 6290
35 6175 39.9 0 6175
36 6058 39.9 0 6058
37 6061 39.9 0 6061
38 5941 39.9 0 5941
39 6125 39.9 0 6125
40 6170 39.9 0 6170
41 6269 39.9 0 6269
42 6319 39.9 0 6319
43 6365 39.9 0 6365
44 5971 39.9 0 5971
45 6442 39.9 0 6442
46 6828 39.9 0 6828
47 6705 39.9 0 6705
48 6527 39.9 0 6527
49 10072 39.9 0 10072
50 12063 39.9 0 12063
51 7182 39.9 0 7182
52 7948 39.9 0 7948
53 7504 39.9 0 7504
54 6361 39.9 0 6361
55 7147 39.9 0 7147
56 7284 39.9 0 7284
57 6969 39.9 0 6969
58 7390 39.9 0 7390
59 7262 39.9 0 7262
60 7369 39.9 0 7369
61 7317 39.9 0 7317
62 7379 39.9 0 7379
63 7104 39.9 0 7104
64 7246 39.9 0 7246
65 7206 39.9 0 7206
66 6819 39.9 0 6819
67 6867 39.9 0 6867
68 6853 39.9 0 6853
69 6672 39.9 0 6672
70 6436 39.9 0 6436
71 7107 39.9 0 7107
72 7208 39.9 0 7208
73 6708 39.9 0 6708
74 6435 39.9 0 6435
75 6196 39.9 0 6196
76 6223 39.9 0 6223
77 6735 39.9 0 6735
78 6623 39.9 0 6623
79 7717 39.9 0 7717
80 7560 39.9 0 7560
81 8866 39.9 0 8866
82 10781 39.9 0 10781
83 12284 39.9 0 12284
84 13325 39.9 0 13325
85 13932 39.9 0 13932
86 132543 39.9 0 132543
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35436 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.5%
C: 30.7%
G: 0.0%
T: 37.2%
none/other: 3.6%
Overview of removed sequences
length count expect max.err error counts
3 13707 40841.2 0 13707
4 2990 10210.3 0 2990
5 915 2552.6 0 915
6 467 638.1 0 467
7 359 159.5 0 359
8 363 39.9 0 363
9 307 39.9 0 307
10 339 39.9 0 339
11 299 39.9 0 299
12 289 39.9 0 289
13 312 39.9 0 312
14 307 39.9 0 307
15 269 39.9 0 269
16 270 39.9 0 270
17 277 39.9 0 277
18 285 39.9 0 285
19 293 39.9 0 293
20 281 39.9 0 281
21 263 39.9 0 263
22 293 39.9 0 293
23 325 39.9 0 325
24 284 39.9 0 284
25 298 39.9 0 298
26 265 39.9 0 265
27 282 39.9 0 282
28 280 39.9 0 280
29 281 39.9 0 281
30 240 39.9 0 240
31 231 39.9 0 231
32 212 39.9 0 212
33 283 39.9 0 283
34 253 39.9 0 253
35 277 39.9 0 277
36 231 39.9 0 231
37 252 39.9 0 252
38 243 39.9 0 243
39 247 39.9 0 247
40 239 39.9 0 239
41 265 39.9 0 265
42 251 39.9 0 251
43 222 39.9 0 222
44 229 39.9 0 229
45 225 39.9 0 225
46 225 39.9 0 225
47 255 39.9 0 255
48 219 39.9 0 219
49 207 39.9 0 207
50 258 39.9 0 258
51 221 39.9 0 221
52 216 39.9 0 216
53 226 39.9 0 226
54 216 39.9 0 216
55 213 39.9 0 213
56 201 39.9 0 201
57 190 39.9 0 190
58 212 39.9 0 212
59 201 39.9 0 201
60 187 39.9 0 187
61 194 39.9 0 194
62 167 39.9 0 167
63 148 39.9 0 148
64 140 39.9 0 140
65 150 39.9 0 150
66 136 39.9 0 136
67 146 39.9 0 146
68 127 39.9 0 127
69 124 39.9 0 124
70 86 39.9 0 86
71 96 39.9 0 96
72 71 39.9 0 71
73 80 39.9 0 80
74 60 39.9 0 60
75 43 39.9 0 43
76 48 39.9 0 48
77 38 39.9 0 38
78 35 39.9 0 35
79 26 39.9 0 26
80 30 39.9 0 30
81 24 39.9 0 24
82 28 39.9 0 28
83 30 39.9 0 30
84 39 39.9 0 39
85 31 39.9 0 31
86 1292 39.9 0 1292
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 57623 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.8%
C: 22.5%
G: 21.1%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 42855 40841.2 0 42855
4 9922 10210.3 0 9922
5 1932 2552.6 0 1932
6 282 638.1 0 282
7 21 159.5 0 21
8 36 159.5 0 36
9 17 159.5 0 17
10 18 159.5 0 18
11 28 159.5 0 28
12 19 159.5 0 19
13 44 159.5 0 44
14 37 159.5 0 37
15 46 159.5 0 46
16 29 159.5 0 29
17 25 159.5 0 25
18 39 159.5 0 39
19 38 159.5 0 38
20 41 159.5 0 41
21 23 159.5 0 23
22 40 159.5 0 40
23 38 159.5 0 38
24 22 159.5 0 22
25 33 159.5 0 33
26 37 159.5 0 37
27 22 159.5 0 22
28 23 159.5 0 23
29 33 159.5 0 33
30 30 159.5 0 30
31 25 159.5 0 25
32 36 159.5 0 36
33 35 159.5 0 35
34 23 159.5 0 23
35 19 159.5 0 19
36 22 159.5 0 22
37 32 159.5 0 32
38 36 159.5 0 36
39 36 159.5 0 36
40 29 159.5 0 29
41 34 159.5 0 34
42 29 159.5 0 29
43 45 159.5 0 45
44 44 159.5 0 44
45 23 159.5 0 23
46 25 159.5 0 25
47 44 159.5 0 44
48 33 159.5 0 33
49 28 159.5 0 28
50 37 159.5 0 37
51 39 159.5 0 39
52 43 159.5 0 43
53 28 159.5 0 28
54 32 159.5 0 32
55 27 159.5 0 27
56 21 159.5 0 21
57 30 159.5 0 30
58 36 159.5 0 36
59 26 159.5 0 26
60 35 159.5 0 35
61 28 159.5 0 28
62 42 159.5 0 42
63 30 159.5 0 30
64 36 159.5 0 36
65 34 159.5 0 34
66 32 159.5 0 32
67 23 159.5 0 23
68 44 159.5 0 44
69 24 159.5 0 24
70 15 159.5 0 15
71 26 159.5 0 26
72 31 159.5 0 31
73 25 159.5 0 25
74 18 159.5 0 18
75 28 159.5 0 28
76 32 159.5 0 32
77 98 159.5 0 98
78 72 159.5 0 72
79 39 159.5 0 39
80 27 159.5 0 27
81 27 159.5 0 27
82 22 159.5 0 22
83 44 159.5 0 44
84 41 159.5 0 41
85 52 159.5 0 52
86 51 159.5 0 51
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M49_S139_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M49_S139_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 29.41 s (9 µs/read; 6.98 M reads/minute).
=== Summary ===
Total reads processed: 3,419,960
Reads with adapters: 1,099,780 (32.2%)
== Read fate breakdown ==
Reads that were too short: 291,255 (8.5%)
Reads written (passing filters): 3,128,705 (91.5%)
Total basepairs processed: 345,415,960 bp
Total written (filtered): 247,497,541 bp (71.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 978419 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.3%
G: 27.2%
T: 31.0%
none/other: 11.5%
Overview of removed sequences
length count expect max.err error counts
3 80354 53436.9 0 80354
4 33660 13359.2 0 33660
5 18468 3339.8 0 18468
6 11966 835.0 0 11966
7 9779 208.7 0 9779
8 8466 52.2 0 8466
9 8464 52.2 0 8464
10 8540 52.2 0 8540
11 8581 52.2 0 8581
12 8484 52.2 0 8484
13 8397 52.2 0 8397
14 8769 52.2 0 8769
15 9667 52.2 0 9667
16 10045 52.2 0 10045
17 9546 52.2 0 9546
18 9988 52.2 0 9988
19 10076 52.2 0 10076
20 9016 52.2 0 9016
21 10138 52.2 0 10138
22 10540 52.2 0 10540
23 8860 52.2 0 8860
24 8408 52.2 0 8408
25 8038 52.2 0 8038
26 8129 52.2 0 8129
27 8296 52.2 0 8296
28 8666 52.2 0 8666
29 8772 52.2 0 8772
30 8472 52.2 0 8472
31 9406 52.2 0 9406
32 8838 52.2 0 8838
33 9294 52.2 0 9294
34 9326 52.2 0 9326
35 8913 52.2 0 8913
36 8812 52.2 0 8812
37 9183 52.2 0 9183
38 8467 52.2 0 8467
39 8841 52.2 0 8841
40 8764 52.2 0 8764
41 8660 52.2 0 8660
42 9124 52.2 0 9124
43 9157 52.2 0 9157
44 8629 52.2 0 8629
45 8760 52.2 0 8760
46 9062 52.2 0 9062
47 8965 52.2 0 8965
48 8608 52.2 0 8608
49 12274 52.2 0 12274
50 14290 52.2 0 14290
51 9090 52.2 0 9090
52 9534 52.2 0 9534
53 9252 52.2 0 9252
54 8216 52.2 0 8216
55 8642 52.2 0 8642
56 8856 52.2 0 8856
57 8323 52.2 0 8323
58 9364 52.2 0 9364
59 8722 52.2 0 8722
60 8922 52.2 0 8922
61 9284 52.2 0 9284
62 9202 52.2 0 9202
63 8762 52.2 0 8762
64 8913 52.2 0 8913
65 8857 52.2 0 8857
66 8560 52.2 0 8560
67 8475 52.2 0 8475
68 8826 52.2 0 8826
69 8173 52.2 0 8173
70 7834 52.2 0 7834
71 8184 52.2 0 8184
72 7998 52.2 0 7998
73 7703 52.2 0 7703
74 7282 52.2 0 7282
75 7402 52.2 0 7402
76 7592 52.2 0 7592
77 7542 52.2 0 7542
78 7763 52.2 0 7763
79 9272 52.2 0 9272
80 8410 52.2 0 8410
81 9789 52.2 0 9789
82 12152 52.2 0 12152
83 12703 52.2 0 12703
84 13706 52.2 0 13706
85 14588 52.2 0 14588
86 112568 52.2 0 112568
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 47105 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.9%
C: 34.5%
G: 0.0%
T: 35.4%
none/other: 2.1%
Overview of removed sequences
length count expect max.err error counts
3 19278 53436.9 0 19278
4 4501 13359.2 0 4501
5 1258 3339.8 0 1258
6 526 835.0 0 526
7 450 208.7 0 450
8 416 52.2 0 416
9 422 52.2 0 422
10 410 52.2 0 410
11 393 52.2 0 393
12 396 52.2 0 396
13 391 52.2 0 391
14 353 52.2 0 353
15 402 52.2 0 402
16 347 52.2 0 347
17 381 52.2 0 381
18 364 52.2 0 364
19 345 52.2 0 345
20 336 52.2 0 336
21 319 52.2 0 319
22 349 52.2 0 349
23 374 52.2 0 374
24 300 52.2 0 300
25 358 52.2 0 358
26 345 52.2 0 345
27 312 52.2 0 312
28 332 52.2 0 332
29 289 52.2 0 289
30 340 52.2 0 340
31 304 52.2 0 304
32 340 52.2 0 340
33 328 52.2 0 328
34 356 52.2 0 356
35 326 52.2 0 326
36 334 52.2 0 334
37 326 52.2 0 326
38 320 52.2 0 320
39 314 52.2 0 314
40 325 52.2 0 325
41 346 52.2 0 346
42 364 52.2 0 364
43 353 52.2 0 353
44 302 52.2 0 302
45 309 52.2 0 309
46 314 52.2 0 314
47 301 52.2 0 301
48 312 52.2 0 312
49 280 52.2 0 280
50 312 52.2 0 312
51 316 52.2 0 316
52 269 52.2 0 269
53 287 52.2 0 287
54 273 52.2 0 273
55 289 52.2 0 289
56 290 52.2 0 290
57 230 52.2 0 230
58 289 52.2 0 289
59 252 52.2 0 252
60 270 52.2 0 270
61 234 52.2 0 234
62 204 52.2 0 204
63 208 52.2 0 208
64 185 52.2 0 185
65 208 52.2 0 208
66 148 52.2 0 148
67 159 52.2 0 159
68 142 52.2 0 142
69 139 52.2 0 139
70 108 52.2 0 108
71 97 52.2 0 97
72 95 52.2 0 95
73 76 52.2 0 76
74 69 52.2 0 69
75 60 52.2 0 60
76 45 52.2 0 45
77 44 52.2 0 44
78 50 52.2 0 50
79 44 52.2 0 44
80 46 52.2 0 46
81 36 52.2 0 36
82 36 52.2 0 36
83 56 52.2 0 56
84 50 52.2 0 50
85 54 52.2 0 54
86 994 52.2 0 994
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 74256 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.8%
C: 22.6%
G: 20.2%
T: 21.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 55335 53436.9 0 55335
4 12448 13359.2 0 12448
5 2607 3339.8 0 2607
6 405 835.0 0 405
7 33 208.7 0 33
8 37 208.7 0 37
9 27 208.7 0 27
10 41 208.7 0 41
11 46 208.7 0 46
12 40 208.7 0 40
13 43 208.7 0 43
14 38 208.7 0 38
15 38 208.7 0 38
16 51 208.7 0 51
17 44 208.7 0 44
18 30 208.7 0 30
19 55 208.7 0 55
20 34 208.7 0 34
21 49 208.7 0 49
22 55 208.7 0 55
23 20 208.7 0 20
24 41 208.7 0 41
25 45 208.7 0 45
26 43 208.7 0 43
27 41 208.7 0 41
28 37 208.7 0 37
29 32 208.7 0 32
30 28 208.7 0 28
31 38 208.7 0 38
32 47 208.7 0 47
33 47 208.7 0 47
34 38 208.7 0 38
35 38 208.7 0 38
36 44 208.7 0 44
37 44 208.7 0 44
38 42 208.7 0 42
39 40 208.7 0 40
40 32 208.7 0 32
41 49 208.7 0 49
42 44 208.7 0 44
43 52 208.7 0 52
44 40 208.7 0 40
45 27 208.7 0 27
46 32 208.7 0 32
47 51 208.7 0 51
48 38 208.7 0 38
49 45 208.7 0 45
50 61 208.7 0 61
51 72 208.7 0 72
52 47 208.7 0 47
53 40 208.7 0 40
54 48 208.7 0 48
55 50 208.7 0 50
56 45 208.7 0 45
57 37 208.7 0 37
58 55 208.7 0 55
59 45 208.7 0 45
60 49 208.7 0 49
61 38 208.7 0 38
62 50 208.7 0 50
63 38 208.7 0 38
64 38 208.7 0 38
65 71 208.7 0 71
66 48 208.7 0 48
67 43 208.7 0 43
68 57 208.7 0 57
69 48 208.7 0 48
70 30 208.7 0 30
71 66 208.7 0 66
72 32 208.7 0 32
73 23 208.7 0 23
74 53 208.7 0 53
75 29 208.7 0 29
76 31 208.7 0 31
77 53 208.7 0 53
78 46 208.7 0 46
79 42 208.7 0 42
80 43 208.7 0 43
81 48 208.7 0 48
82 39 208.7 0 39
83 45 208.7 0 45
84 57 208.7 0 57
85 56 208.7 0 56
86 52 208.7 0 52
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M49_S139_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M49_S139_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 32.86 s (9 µs/read; 6.40 M reads/minute).
=== Summary ===
Total reads processed: 3,508,070
Reads with adapters: 1,134,929 (32.4%)
== Read fate breakdown ==
Reads that were too short: 304,420 (8.7%)
Reads written (passing filters): 3,203,650 (91.3%)
Total basepairs processed: 354,315,070 bp
Total written (filtered): 253,235,541 bp (71.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1011013 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.4%
G: 27.2%
T: 30.8%
none/other: 11.6%
Overview of removed sequences
length count expect max.err error counts
3 82023 54813.6 0 82023
4 34437 13703.4 0 34437
5 19140 3425.8 0 19140
6 12118 856.5 0 12118
7 9835 214.1 0 9835
8 8644 53.5 0 8644
9 8616 53.5 0 8616
10 8774 53.5 0 8774
11 8726 53.5 0 8726
12 8562 53.5 0 8562
13 8602 53.5 0 8602
14 9164 53.5 0 9164
15 9836 53.5 0 9836
16 10337 53.5 0 10337
17 9571 53.5 0 9571
18 10107 53.5 0 10107
19 10180 53.5 0 10180
20 9250 53.5 0 9250
21 10225 53.5 0 10225
22 10590 53.5 0 10590
23 9168 53.5 0 9168
24 8537 53.5 0 8537
25 8448 53.5 0 8448
26 8516 53.5 0 8516
27 8549 53.5 0 8549
28 8873 53.5 0 8873
29 8828 53.5 0 8828
30 8978 53.5 0 8978
31 9497 53.5 0 9497
32 9080 53.5 0 9080
33 9729 53.5 0 9729
34 9336 53.5 0 9336
35 9233 53.5 0 9233
36 9048 53.5 0 9048
37 9538 53.5 0 9538
38 8758 53.5 0 8758
39 9068 53.5 0 9068
40 9125 53.5 0 9125
41 8921 53.5 0 8921
42 9573 53.5 0 9573
43 9389 53.5 0 9389
44 8845 53.5 0 8845
45 9062 53.5 0 9062
46 9234 53.5 0 9234
47 9238 53.5 0 9238
48 9063 53.5 0 9063
49 12724 53.5 0 12724
50 15027 53.5 0 15027
51 9342 53.5 0 9342
52 9688 53.5 0 9688
53 9157 53.5 0 9157
54 8689 53.5 0 8689
55 9308 53.5 0 9308
56 9171 53.5 0 9171
57 8888 53.5 0 8888
58 9697 53.5 0 9697
59 9390 53.5 0 9390
60 9258 53.5 0 9258
61 9589 53.5 0 9589
62 9449 53.5 0 9449
63 9163 53.5 0 9163
64 9127 53.5 0 9127
65 9122 53.5 0 9122
66 8931 53.5 0 8931
67 8887 53.5 0 8887
68 8969 53.5 0 8969
69 8654 53.5 0 8654
70 7976 53.5 0 7976
71 8649 53.5 0 8649
72 8583 53.5 0 8583
73 8151 53.5 0 8151
74 7802 53.5 0 7802
75 7833 53.5 0 7833
76 7905 53.5 0 7905
77 7664 53.5 0 7664
78 8270 53.5 0 8270
79 9497 53.5 0 9497
80 8987 53.5 0 8987
81 10460 53.5 0 10460
82 12587 53.5 0 12587
83 13093 53.5 0 13093
84 14393 53.5 0 14393
85 15076 53.5 0 15076
86 117486 53.5 0 117486
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 48057 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.6%
C: 35.0%
G: 0.0%
T: 35.1%
none/other: 2.3%
Overview of removed sequences
length count expect max.err error counts
3 19496 54813.6 0 19496
4 4563 13703.4 0 4563
5 1197 3425.8 0 1197
6 515 856.5 0 515
7 488 214.1 0 488
8 436 53.5 0 436
9 443 53.5 0 443
10 457 53.5 0 457
11 419 53.5 0 419
12 379 53.5 0 379
13 419 53.5 0 419
14 387 53.5 0 387
15 377 53.5 0 377
16 391 53.5 0 391
17 340 53.5 0 340
18 339 53.5 0 339
19 365 53.5 0 365
20 380 53.5 0 380
21 347 53.5 0 347
22 363 53.5 0 363
23 351 53.5 0 351
24 328 53.5 0 328
25 376 53.5 0 376
26 347 53.5 0 347
27 331 53.5 0 331
28 393 53.5 0 393
29 358 53.5 0 358
30 318 53.5 0 318
31 363 53.5 0 363
32 314 53.5 0 314
33 342 53.5 0 342
34 346 53.5 0 346
35 341 53.5 0 341
36 346 53.5 0 346
37 320 53.5 0 320
38 337 53.5 0 337
39 329 53.5 0 329
40 341 53.5 0 341
41 329 53.5 0 329
42 315 53.5 0 315
43 300 53.5 0 300
44 352 53.5 0 352
45 304 53.5 0 304
46 317 53.5 0 317
47 308 53.5 0 308
48 332 53.5 0 332
49 321 53.5 0 321
50 281 53.5 0 281
51 261 53.5 0 261
52 288 53.5 0 288
53 331 53.5 0 331
54 275 53.5 0 275
55 260 53.5 0 260
56 279 53.5 0 279
57 264 53.5 0 264
58 244 53.5 0 244
59 250 53.5 0 250
60 241 53.5 0 241
61 253 53.5 0 253
62 235 53.5 0 235
63 223 53.5 0 223
64 207 53.5 0 207
65 193 53.5 0 193
66 195 53.5 0 195
67 163 53.5 0 163
68 148 53.5 0 148
69 141 53.5 0 141
70 128 53.5 0 128
71 111 53.5 0 111
72 93 53.5 0 93
73 86 53.5 0 86
74 85 53.5 0 85
75 61 53.5 0 61
76 55 53.5 0 55
77 62 53.5 0 62
78 48 53.5 0 48
79 47 53.5 0 47
80 29 53.5 0 29
81 38 53.5 0 38
82 45 53.5 0 45
83 49 53.5 0 49
84 60 53.5 0 60
85 63 53.5 0 63
86 1105 53.5 0 1105
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 75859 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 22.5%
G: 20.6%
T: 21.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 56516 54813.6 0 56516
4 12696 13703.4 0 12696
5 2710 3425.8 0 2710
6 418 856.5 0 418
7 34 214.1 0 34
8 36 214.1 0 36
9 32 214.1 0 32
10 34 214.1 0 34
11 47 214.1 0 47
12 37 214.1 0 37
13 40 214.1 0 40
14 38 214.1 0 38
15 42 214.1 0 42
16 45 214.1 0 45
17 53 214.1 0 53
18 41 214.1 0 41
19 44 214.1 0 44
20 38 214.1 0 38
21 32 214.1 0 32
22 40 214.1 0 40
23 41 214.1 0 41
24 37 214.1 0 37
25 61 214.1 0 61
26 54 214.1 0 54
27 44 214.1 0 44
28 39 214.1 0 39
29 41 214.1 0 41
30 30 214.1 0 30
31 43 214.1 0 43
32 57 214.1 0 57
33 37 214.1 0 37
34 31 214.1 0 31
35 36 214.1 0 36
36 56 214.1 0 56
37 61 214.1 0 61
38 40 214.1 0 40
39 38 214.1 0 38
40 57 214.1 0 57
41 40 214.1 0 40
42 50 214.1 0 50
43 44 214.1 0 44
44 46 214.1 0 46
45 39 214.1 0 39
46 42 214.1 0 42
47 56 214.1 0 56
48 39 214.1 0 39
49 45 214.1 0 45
50 54 214.1 0 54
51 46 214.1 0 46
52 38 214.1 0 38
53 43 214.1 0 43
54 60 214.1 0 60
55 46 214.1 0 46
56 33 214.1 0 33
57 44 214.1 0 44
58 55 214.1 0 55
59 46 214.1 0 46
60 42 214.1 0 42
61 43 214.1 0 43
62 46 214.1 0 46
63 36 214.1 0 36
64 52 214.1 0 52
65 69 214.1 0 69
66 48 214.1 0 48
67 51 214.1 0 51
68 41 214.1 0 41
69 37 214.1 0 37
70 32 214.1 0 32
71 40 214.1 0 40
72 31 214.1 0 31
73 36 214.1 0 36
74 46 214.1 0 46
75 35 214.1 0 35
76 32 214.1 0 32
77 64 214.1 0 64
78 57 214.1 0 57
79 43 214.1 0 43
80 40 214.1 0 40
81 44 214.1 0 44
82 38 214.1 0 38
83 62 214.1 0 62
84 45 214.1 0 45
85 58 214.1 0 58
86 49 214.1 0 49
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M89_S138_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M89_S138_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 34.04 s (10 µs/read; 6.09 M reads/minute).
=== Summary ===
Total reads processed: 3,456,947
Reads with adapters: 1,264,916 (36.6%)
== Read fate breakdown ==
Reads that were too short: 359,151 (10.4%)
Reads written (passing filters): 3,097,796 (89.6%)
Total basepairs processed: 349,151,647 bp
Total written (filtered): 240,296,370 bp (68.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1126237 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.1%
G: 26.2%
T: 29.0%
none/other: 13.7%
Overview of removed sequences
length count expect max.err error counts
3 79775 54014.8 0 79775
4 36067 13503.7 0 36067
5 18839 3375.9 0 18839
6 12445 844.0 0 12445
7 10091 211.0 0 10091
8 9241 52.7 0 9241
9 9061 52.7 0 9061
10 9173 52.7 0 9173
11 9049 52.7 0 9049
12 9062 52.7 0 9062
13 9094 52.7 0 9094
14 9372 52.7 0 9372
15 9418 52.7 0 9418
16 9753 52.7 0 9753
17 9432 52.7 0 9432
18 9855 52.7 0 9855
19 9550 52.7 0 9550
20 9496 52.7 0 9496
21 9691 52.7 0 9691
22 9601 52.7 0 9601
23 9500 52.7 0 9500
24 9363 52.7 0 9363
25 9712 52.7 0 9712
26 9282 52.7 0 9282
27 9486 52.7 0 9486
28 10108 52.7 0 10108
29 10148 52.7 0 10148
30 9863 52.7 0 9863
31 10392 52.7 0 10392
32 10047 52.7 0 10047
33 10064 52.7 0 10064
34 10004 52.7 0 10004
35 10029 52.7 0 10029
36 10141 52.7 0 10141
37 10177 52.7 0 10177
38 9827 52.7 0 9827
39 9926 52.7 0 9926
40 10245 52.7 0 10245
41 10312 52.7 0 10312
42 10210 52.7 0 10210
43 10673 52.7 0 10673
44 10112 52.7 0 10112
45 10849 52.7 0 10849
46 11374 52.7 0 11374
47 10476 52.7 0 10476
48 10768 52.7 0 10768
49 13937 52.7 0 13937
50 14367 52.7 0 14367
51 11396 52.7 0 11396
52 11966 52.7 0 11966
53 11102 52.7 0 11102
54 10840 52.7 0 10840
55 11368 52.7 0 11368
56 11289 52.7 0 11289
57 11217 52.7 0 11217
58 11737 52.7 0 11737
59 11371 52.7 0 11371
60 11491 52.7 0 11491
61 11799 52.7 0 11799
62 11699 52.7 0 11699
63 11489 52.7 0 11489
64 11346 52.7 0 11346
65 11484 52.7 0 11484
66 11488 52.7 0 11488
67 10925 52.7 0 10925
68 10827 52.7 0 10827
69 10434 52.7 0 10434
70 10323 52.7 0 10323
71 10843 52.7 0 10843
72 10318 52.7 0 10318
73 10382 52.7 0 10382
74 9312 52.7 0 9312
75 8948 52.7 0 8948
76 8940 52.7 0 8940
77 9396 52.7 0 9396
78 8484 52.7 0 8484
79 9825 52.7 0 9825
80 8854 52.7 0 8854
81 9610 52.7 0 9610
82 11650 52.7 0 11650
83 13049 52.7 0 13049
84 13638 52.7 0 13638
85 14204 52.7 0 14204
86 153736 52.7 0 153736
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 69191 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 24.5%
C: 33.4%
G: 0.0%
T: 39.6%
none/other: 2.5%
Overview of removed sequences
length count expect max.err error counts
3 14769 54014.8 0 14769
4 4132 13503.7 0 4132
5 1712 3375.9 0 1712
6 1038 844.0 0 1038
7 1029 211.0 0 1029
8 963 52.7 0 963
9 952 52.7 0 952
10 883 52.7 0 883
11 939 52.7 0 939
12 868 52.7 0 868
13 840 52.7 0 840
14 863 52.7 0 863
15 782 52.7 0 782
16 827 52.7 0 827
17 759 52.7 0 759
18 772 52.7 0 772
19 784 52.7 0 784
20 823 52.7 0 823
21 758 52.7 0 758
22 738 52.7 0 738
23 765 52.7 0 765
24 772 52.7 0 772
25 767 52.7 0 767
26 770 52.7 0 770
27 721 52.7 0 721
28 760 52.7 0 760
29 770 52.7 0 770
30 746 52.7 0 746
31 663 52.7 0 663
32 726 52.7 0 726
33 779 52.7 0 779
34 769 52.7 0 769
35 769 52.7 0 769
36 748 52.7 0 748
37 739 52.7 0 739
38 690 52.7 0 690
39 733 52.7 0 733
40 715 52.7 0 715
41 685 52.7 0 685
42 773 52.7 0 773
43 748 52.7 0 748
44 665 52.7 0 665
45 699 52.7 0 699
46 721 52.7 0 721
47 719 52.7 0 719
48 725 52.7 0 725
49 646 52.7 0 646
50 690 52.7 0 690
51 654 52.7 0 654
52 657 52.7 0 657
53 684 52.7 0 684
54 601 52.7 0 601
55 646 52.7 0 646
56 623 52.7 0 623
57 617 52.7 0 617
58 616 52.7 0 616
59 589 52.7 0 589
60 541 52.7 0 541
61 529 52.7 0 529
62 482 52.7 0 482
63 497 52.7 0 497
64 420 52.7 0 420
65 431 52.7 0 431
66 360 52.7 0 360
67 331 52.7 0 331
68 291 52.7 0 291
69 289 52.7 0 289
70 229 52.7 0 229
71 234 52.7 0 234
72 214 52.7 0 214
73 198 52.7 0 198
74 154 52.7 0 154
75 111 52.7 0 111
76 115 52.7 0 115
77 90 52.7 0 90
78 101 52.7 0 101
79 81 52.7 0 81
80 84 52.7 0 84
81 57 52.7 0 57
82 59 52.7 0 59
83 61 52.7 0 61
84 51 52.7 0 51
85 73 52.7 0 73
86 1717 52.7 0 1717
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69488 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.3%
C: 22.6%
G: 20.6%
T: 20.4%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51274 54014.8 0 51274
4 12182 13503.7 0 12182
5 2184 3375.9 0 2184
6 265 844.0 0 265
7 41 211.0 0 41
8 50 211.0 0 50
9 35 211.0 0 35
10 49 211.0 0 49
11 42 211.0 0 42
12 38 211.0 0 38
13 60 211.0 0 60
14 58 211.0 0 58
15 37 211.0 0 37
16 41 211.0 0 41
17 48 211.0 0 48
18 43 211.0 0 43
19 51 211.0 0 51
20 52 211.0 0 52
21 43 211.0 0 43
22 33 211.0 0 33
23 39 211.0 0 39
24 37 211.0 0 37
25 64 211.0 0 64
26 62 211.0 0 62
27 50 211.0 0 50
28 37 211.0 0 37
29 43 211.0 0 43
30 40 211.0 0 40
31 42 211.0 0 42
32 70 211.0 0 70
33 45 211.0 0 45
34 42 211.0 0 42
35 47 211.0 0 47
36 42 211.0 0 42
37 40 211.0 0 40
38 48 211.0 0 48
39 56 211.0 0 56
40 48 211.0 0 48
41 51 211.0 0 51
42 41 211.0 0 41
43 55 211.0 0 55
44 33 211.0 0 33
45 37 211.0 0 37
46 35 211.0 0 35
47 43 211.0 0 43
48 52 211.0 0 52
49 43 211.0 0 43
50 36 211.0 0 36
51 56 211.0 0 56
52 41 211.0 0 41
53 31 211.0 0 31
54 47 211.0 0 47
55 35 211.0 0 35
56 27 211.0 0 27
57 21 211.0 0 21
58 58 211.0 0 58
59 45 211.0 0 45
60 41 211.0 0 41
61 50 211.0 0 50
62 42 211.0 0 42
63 43 211.0 0 43
64 41 211.0 0 41
65 56 211.0 0 56
66 37 211.0 0 37
67 42 211.0 0 42
68 36 211.0 0 36
69 45 211.0 0 45
70 70 211.0 0 70
71 43 211.0 0 43
72 34 211.0 0 34
73 48 211.0 0 48
74 45 211.0 0 45
75 31 211.0 0 31
76 38 211.0 0 38
77 113 211.0 0 113
78 56 211.0 0 56
79 30 211.0 0 30
80 35 211.0 0 35
81 43 211.0 0 43
82 27 211.0 0 27
83 53 211.0 0 53
84 48 211.0 0 48
85 33 211.0 0 33
86 43 211.0 0 43
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M89_S138_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M89_S138_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 31.82 s (9 µs/read; 6.62 M reads/minute).
=== Summary ===
Total reads processed: 3,511,895
Reads with adapters: 1,295,877 (36.9%)
== Read fate breakdown ==
Reads that were too short: 374,549 (10.7%)
Reads written (passing filters): 3,137,346 (89.3%)
Total basepairs processed: 354,701,395 bp
Total written (filtered): 243,090,589 bp (68.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1154333 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.1%
G: 26.2%
T: 28.8%
none/other: 14.0%
Overview of removed sequences
length count expect max.err error counts
3 80276 54873.4 0 80276
4 36810 13718.3 0 36810
5 18783 3429.6 0 18783
6 12668 857.4 0 12668
7 10264 214.3 0 10264
8 9057 53.6 0 9057
9 9058 53.6 0 9058
10 9135 53.6 0 9135
11 9290 53.6 0 9290
12 8913 53.6 0 8913
13 9073 53.6 0 9073
14 9627 53.6 0 9627
15 9640 53.6 0 9640
16 9919 53.6 0 9919
17 9667 53.6 0 9667
18 9785 53.6 0 9785
19 9668 53.6 0 9668
20 9614 53.6 0 9614
21 9818 53.6 0 9818
22 9854 53.6 0 9854
23 9532 53.6 0 9532
24 9596 53.6 0 9596
25 9479 53.6 0 9479
26 9529 53.6 0 9529
27 9959 53.6 0 9959
28 9970 53.6 0 9970
29 10166 53.6 0 10166
30 10174 53.6 0 10174
31 10414 53.6 0 10414
32 10095 53.6 0 10095
33 10254 53.6 0 10254
34 9929 53.6 0 9929
35 10166 53.6 0 10166
36 10380 53.6 0 10380
37 10053 53.6 0 10053
38 10038 53.6 0 10038
39 10212 53.6 0 10212
40 10335 53.6 0 10335
41 10698 53.6 0 10698
42 10455 53.6 0 10455
43 10946 53.6 0 10946
44 10411 53.6 0 10411
45 11080 53.6 0 11080
46 11571 53.6 0 11571
47 10941 53.6 0 10941
48 11176 53.6 0 11176
49 14026 53.6 0 14026
50 14823 53.6 0 14823
51 11690 53.6 0 11690
52 12221 53.6 0 12221
53 11453 53.6 0 11453
54 11222 53.6 0 11222
55 11511 53.6 0 11511
56 11535 53.6 0 11535
57 11512 53.6 0 11512
58 12147 53.6 0 12147
59 11928 53.6 0 11928
60 11805 53.6 0 11805
61 12084 53.6 0 12084
62 11998 53.6 0 11998
63 11671 53.6 0 11671
64 11868 53.6 0 11868
65 12015 53.6 0 12015
66 11591 53.6 0 11591
67 11655 53.6 0 11655
68 11151 53.6 0 11151
69 11061 53.6 0 11061
70 10529 53.6 0 10529
71 11237 53.6 0 11237
72 10597 53.6 0 10597
73 10820 53.6 0 10820
74 9610 53.6 0 9610
75 9332 53.6 0 9332
76 9451 53.6 0 9451
77 9681 53.6 0 9681
78 9132 53.6 0 9132
79 10030 53.6 0 10030
80 9119 53.6 0 9119
81 9893 53.6 0 9893
82 11855 53.6 0 11855
83 13598 53.6 0 13598
84 14230 53.6 0 14230
85 14535 53.6 0 14535
86 161239 53.6 0 161239
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 71602 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.1%
C: 33.1%
G: 0.0%
T: 39.2%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 14907 54873.4 0 14907
4 4174 13718.3 0 4174
5 1654 3429.6 0 1654
6 1062 857.4 0 1062
7 1030 214.3 0 1030
8 1100 53.6 0 1100
9 1055 53.6 0 1055
10 964 53.6 0 964
11 910 53.6 0 910
12 908 53.6 0 908
13 885 53.6 0 885
14 816 53.6 0 816
15 888 53.6 0 888
16 772 53.6 0 772
17 824 53.6 0 824
18 829 53.6 0 829
19 847 53.6 0 847
20 766 53.6 0 766
21 825 53.6 0 825
22 811 53.6 0 811
23 776 53.6 0 776
24 838 53.6 0 838
25 839 53.6 0 839
26 757 53.6 0 757
27 731 53.6 0 731
28 805 53.6 0 805
29 733 53.6 0 733
30 760 53.6 0 760
31 728 53.6 0 728
32 750 53.6 0 750
33 808 53.6 0 808
34 776 53.6 0 776
35 749 53.6 0 749
36 817 53.6 0 817
37 804 53.6 0 804
38 755 53.6 0 755
39 715 53.6 0 715
40 820 53.6 0 820
41 762 53.6 0 762
42 746 53.6 0 746
43 778 53.6 0 778
44 767 53.6 0 767
45 699 53.6 0 699
46 724 53.6 0 724
47 730 53.6 0 730
48 711 53.6 0 711
49 684 53.6 0 684
50 705 53.6 0 705
51 694 53.6 0 694
52 658 53.6 0 658
53 685 53.6 0 685
54 659 53.6 0 659
55 656 53.6 0 656
56 658 53.6 0 658
57 662 53.6 0 662
58 634 53.6 0 634
59 612 53.6 0 612
60 603 53.6 0 603
61 586 53.6 0 586
62 497 53.6 0 497
63 517 53.6 0 517
64 494 53.6 0 494
65 463 53.6 0 463
66 378 53.6 0 378
67 350 53.6 0 350
68 305 53.6 0 305
69 319 53.6 0 319
70 284 53.6 0 284
71 230 53.6 0 230
72 236 53.6 0 236
73 197 53.6 0 197
74 172 53.6 0 172
75 146 53.6 0 146
76 119 53.6 0 119
77 100 53.6 0 100
78 96 53.6 0 96
79 79 53.6 0 79
80 72 53.6 0 72
81 51 53.6 0 51
82 55 53.6 0 55
83 63 53.6 0 63
84 57 53.6 0 57
85 84 53.6 0 84
86 1837 53.6 0 1837
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69942 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.4%
C: 22.8%
G: 20.1%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51518 54873.4 0 51518
4 12420 13718.3 0 12420
5 2195 3429.6 0 2195
6 228 857.4 0 228
7 46 214.3 0 46
8 37 214.3 0 37
9 27 214.3 0 27
10 48 214.3 0 48
11 46 214.3 0 46
12 28 214.3 0 28
13 46 214.3 0 46
14 54 214.3 0 54
15 33 214.3 0 33
16 50 214.3 0 50
17 43 214.3 0 43
18 40 214.3 0 40
19 47 214.3 0 47
20 38 214.3 0 38
21 41 214.3 0 41
22 42 214.3 0 42
23 55 214.3 0 55
24 30 214.3 0 30
25 57 214.3 0 57
26 48 214.3 0 48
27 43 214.3 0 43
28 57 214.3 0 57
29 56 214.3 0 56
30 47 214.3 0 47
31 41 214.3 0 41
32 61 214.3 0 61
33 42 214.3 0 42
34 41 214.3 0 41
35 38 214.3 0 38
36 47 214.3 0 47
37 49 214.3 0 49
38 41 214.3 0 41
39 40 214.3 0 40
40 39 214.3 0 39
41 46 214.3 0 46
42 55 214.3 0 55
43 48 214.3 0 48
44 44 214.3 0 44
45 37 214.3 0 37
46 22 214.3 0 22
47 43 214.3 0 43
48 49 214.3 0 49
49 31 214.3 0 31
50 37 214.3 0 37
51 58 214.3 0 58
52 43 214.3 0 43
53 39 214.3 0 39
54 33 214.3 0 33
55 46 214.3 0 46
56 33 214.3 0 33
57 43 214.3 0 43
58 53 214.3 0 53
59 54 214.3 0 54
60 51 214.3 0 51
61 48 214.3 0 48
62 46 214.3 0 46
63 45 214.3 0 45
64 38 214.3 0 38
65 53 214.3 0 53
66 46 214.3 0 46
67 34 214.3 0 34
68 45 214.3 0 45
69 55 214.3 0 55
70 45 214.3 0 45
71 48 214.3 0 48
72 37 214.3 0 37
73 38 214.3 0 38
74 53 214.3 0 53
75 36 214.3 0 36
76 38 214.3 0 38
77 110 214.3 0 110
78 60 214.3 0 60
79 34 214.3 0 34
80 29 214.3 0 29
81 42 214.3 0 42
82 46 214.3 0 46
83 54 214.3 0 54
84 48 214.3 0 48
85 38 214.3 0 38
86 52 214.3 0 52
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M90_S147_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M90_S147_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.90 s (10 µs/read; 5.98 M reads/minute).
=== Summary ===
Total reads processed: 2,380,635
Reads with adapters: 756,979 (31.8%)
== Read fate breakdown ==
Reads that were too short: 224,382 (9.4%)
Reads written (passing filters): 2,156,253 (90.6%)
Total basepairs processed: 240,444,135 bp
Total written (filtered): 171,091,547 bp (71.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 675434 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.4%
G: 27.1%
T: 29.4%
none/other: 14.0%
Overview of removed sequences
length count expect max.err error counts
3 55025 37197.4 0 55025
4 22740 9299.4 0 22740
5 11658 2324.8 0 11658
6 7657 581.2 0 7657
7 6178 145.3 0 6178
8 5332 36.3 0 5332
9 5313 36.3 0 5313
10 5438 36.3 0 5438
11 5190 36.3 0 5190
12 5345 36.3 0 5345
13 5474 36.3 0 5474
14 5434 36.3 0 5434
15 5489 36.3 0 5489
16 5689 36.3 0 5689
17 5555 36.3 0 5555
18 5445 36.3 0 5445
19 5475 36.3 0 5475
20 5431 36.3 0 5431
21 5386 36.3 0 5386
22 5288 36.3 0 5288
23 5288 36.3 0 5288
24 5319 36.3 0 5319
25 5255 36.3 0 5255
26 5421 36.3 0 5421
27 5337 36.3 0 5337
28 5573 36.3 0 5573
29 5696 36.3 0 5696
30 5459 36.3 0 5459
31 6077 36.3 0 6077
32 5971 36.3 0 5971
33 5977 36.3 0 5977
34 6051 36.3 0 6051
35 5929 36.3 0 5929
36 5854 36.3 0 5854
37 5965 36.3 0 5965
38 5700 36.3 0 5700
39 5827 36.3 0 5827
40 5844 36.3 0 5844
41 5531 36.3 0 5531
42 5986 36.3 0 5986
43 6218 36.3 0 6218
44 5723 36.3 0 5723
45 5979 36.3 0 5979
46 6186 36.3 0 6186
47 6188 36.3 0 6188
48 5689 36.3 0 5689
49 8889 36.3 0 8889
50 10706 36.3 0 10706
51 6082 36.3 0 6082
52 6531 36.3 0 6531
53 6571 36.3 0 6571
54 5643 36.3 0 5643
55 5974 36.3 0 5974
56 6120 36.3 0 6120
57 5766 36.3 0 5766
58 6518 36.3 0 6518
59 6228 36.3 0 6228
60 6240 36.3 0 6240
61 6494 36.3 0 6494
62 6231 36.3 0 6231
63 6233 36.3 0 6233
64 6207 36.3 0 6207
65 6225 36.3 0 6225
66 5937 36.3 0 5937
67 5992 36.3 0 5992
68 6078 36.3 0 6078
69 5739 36.3 0 5739
70 5619 36.3 0 5619
71 6094 36.3 0 6094
72 5986 36.3 0 5986
73 5880 36.3 0 5880
74 5385 36.3 0 5385
75 5676 36.3 0 5676
76 5483 36.3 0 5483
77 5559 36.3 0 5559
78 5840 36.3 0 5840
79 6513 36.3 0 6513
80 5958 36.3 0 5958
81 6983 36.3 0 6983
82 8455 36.3 0 8455
83 9409 36.3 0 9409
84 10274 36.3 0 10274
85 10518 36.3 0 10518
86 94813 36.3 0 94813
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28031 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.5%
C: 33.5%
G: 0.0%
T: 34.5%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 13289 37197.4 0 13289
4 2981 9299.4 0 2981
5 739 2324.8 0 739
6 330 581.2 0 330
7 277 145.3 0 277
8 245 36.3 0 245
9 221 36.3 0 221
10 209 36.3 0 209
11 202 36.3 0 202
12 166 36.3 0 166
13 198 36.3 0 198
14 162 36.3 0 162
15 176 36.3 0 176
16 185 36.3 0 185
17 155 36.3 0 155
18 177 36.3 0 177
19 166 36.3 0 166
20 177 36.3 0 177
21 159 36.3 0 159
22 151 36.3 0 151
23 161 36.3 0 161
24 168 36.3 0 168
25 174 36.3 0 174
26 164 36.3 0 164
27 128 36.3 0 128
28 164 36.3 0 164
29 158 36.3 0 158
30 156 36.3 0 156
31 156 36.3 0 156
32 144 36.3 0 144
33 154 36.3 0 154
34 160 36.3 0 160
35 151 36.3 0 151
36 140 36.3 0 140
37 140 36.3 0 140
38 126 36.3 0 126
39 139 36.3 0 139
40 145 36.3 0 145
41 182 36.3 0 182
42 149 36.3 0 149
43 123 36.3 0 123
44 121 36.3 0 121
45 150 36.3 0 150
46 141 36.3 0 141
47 161 36.3 0 161
48 163 36.3 0 163
49 170 36.3 0 170
50 140 36.3 0 140
51 125 36.3 0 125
52 136 36.3 0 136
53 138 36.3 0 138
54 126 36.3 0 126
55 124 36.3 0 124
56 134 36.3 0 134
57 121 36.3 0 121
58 129 36.3 0 129
59 128 36.3 0 128
60 128 36.3 0 128
61 116 36.3 0 116
62 124 36.3 0 124
63 101 36.3 0 101
64 128 36.3 0 128
65 85 36.3 0 85
66 76 36.3 0 76
67 81 36.3 0 81
68 79 36.3 0 79
69 75 36.3 0 75
70 65 36.3 0 65
71 43 36.3 0 43
72 50 36.3 0 50
73 47 36.3 0 47
74 33 36.3 0 33
75 38 36.3 0 38
76 33 36.3 0 33
77 26 36.3 0 26
78 28 36.3 0 28
79 27 36.3 0 27
80 15 36.3 0 15
81 25 36.3 0 25
82 22 36.3 0 22
83 26 36.3 0 26
84 43 36.3 0 43
85 44 36.3 0 44
86 719 36.3 0 719
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 53514 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.7%
C: 23.0%
G: 21.8%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 40184 37197.4 0 40184
4 8754 9299.4 0 8754
5 1936 2324.8 0 1936
6 280 581.2 0 280
7 24 145.3 0 24
8 30 145.3 0 30
9 25 145.3 0 25
10 31 145.3 0 31
11 38 145.3 0 38
12 30 145.3 0 30
13 37 145.3 0 37
14 24 145.3 0 24
15 30 145.3 0 30
16 42 145.3 0 42
17 36 145.3 0 36
18 31 145.3 0 31
19 36 145.3 0 36
20 30 145.3 0 30
21 32 145.3 0 32
22 30 145.3 0 30
23 35 145.3 0 35
24 34 145.3 0 34
25 28 145.3 0 28
26 26 145.3 0 26
27 20 145.3 0 20
28 25 145.3 0 25
29 26 145.3 0 26
30 22 145.3 0 22
31 25 145.3 0 25
32 34 145.3 0 34
33 34 145.3 0 34
34 26 145.3 0 26
35 33 145.3 0 33
36 21 145.3 0 21
37 32 145.3 0 32
38 24 145.3 0 24
39 23 145.3 0 23
40 24 145.3 0 24
41 35 145.3 0 35
42 28 145.3 0 28
43 21 145.3 0 21
44 26 145.3 0 26
45 25 145.3 0 25
46 16 145.3 0 16
47 24 145.3 0 24
48 29 145.3 0 29
49 39 145.3 0 39
50 22 145.3 0 22
51 28 145.3 0 28
52 34 145.3 0 34
53 21 145.3 0 21
54 32 145.3 0 32
55 27 145.3 0 27
56 22 145.3 0 22
57 39 145.3 0 39
58 23 145.3 0 23
59 31 145.3 0 31
60 29 145.3 0 29
61 27 145.3 0 27
62 47 145.3 0 47
63 43 145.3 0 43
64 27 145.3 0 27
65 28 145.3 0 28
66 30 145.3 0 30
67 32 145.3 0 32
68 32 145.3 0 32
69 27 145.3 0 27
70 24 145.3 0 24
71 33 145.3 0 33
72 20 145.3 0 20
73 20 145.3 0 20
74 34 145.3 0 34
75 20 145.3 0 20
76 15 145.3 0 15
77 61 145.3 0 61
78 43 145.3 0 43
79 28 145.3 0 28
80 29 145.3 0 29
81 30 145.3 0 30
82 26 145.3 0 26
83 37 145.3 0 37
84 35 145.3 0 35
85 34 145.3 0 34
86 29 145.3 0 29
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: M90_S147_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/M90_S147_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 22.63 s (9 µs/read; 6.42 M reads/minute).
=== Summary ===
Total reads processed: 2,421,977
Reads with adapters: 778,274 (32.1%)
== Read fate breakdown ==
Reads that were too short: 235,999 (9.7%)
Reads written (passing filters): 2,185,978 (90.3%)
Total basepairs processed: 244,619,677 bp
Total written (filtered): 173,304,665 bp (70.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 695181 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.4%
G: 27.0%
T: 29.2%
none/other: 14.3%
Overview of removed sequences
length count expect max.err error counts
3 55223 37843.4 0 55223
4 22991 9460.8 0 22991
5 11888 2365.2 0 11888
6 7537 591.3 0 7537
7 6173 147.8 0 6173
8 5422 37.0 0 5422
9 5332 37.0 0 5332
10 5436 37.0 0 5436
11 5335 37.0 0 5335
12 5272 37.0 0 5272
13 5630 37.0 0 5630
14 5589 37.0 0 5589
15 5490 37.0 0 5490
16 5698 37.0 0 5698
17 5461 37.0 0 5461
18 5741 37.0 0 5741
19 5534 37.0 0 5534
20 5394 37.0 0 5394
21 5685 37.0 0 5685
22 5533 37.0 0 5533
23 5323 37.0 0 5323
24 5297 37.0 0 5297
25 5181 37.0 0 5181
26 5466 37.0 0 5466
27 5374 37.0 0 5374
28 5805 37.0 0 5805
29 5769 37.0 0 5769
30 5553 37.0 0 5553
31 6269 37.0 0 6269
32 5992 37.0 0 5992
33 6131 37.0 0 6131
34 6100 37.0 0 6100
35 5976 37.0 0 5976
36 5949 37.0 0 5949
37 6252 37.0 0 6252
38 5619 37.0 0 5619
39 6018 37.0 0 6018
40 5929 37.0 0 5929
41 5909 37.0 0 5909
42 6171 37.0 0 6171
43 6481 37.0 0 6481
44 5893 37.0 0 5893
45 6165 37.0 0 6165
46 6322 37.0 0 6322
47 6206 37.0 0 6206
48 6145 37.0 0 6145
49 8981 37.0 0 8981
50 11131 37.0 0 11131
51 6304 37.0 0 6304
52 6621 37.0 0 6621
53 6796 37.0 0 6796
54 5621 37.0 0 5621
55 6236 37.0 0 6236
56 6331 37.0 0 6331
57 6159 37.0 0 6159
58 6599 37.0 0 6599
59 6251 37.0 0 6251
60 6367 37.0 0 6367
61 6583 37.0 0 6583
62 6571 37.0 0 6571
63 6432 37.0 0 6432
64 6408 37.0 0 6408
65 6305 37.0 0 6305
66 5976 37.0 0 5976
67 6314 37.0 0 6314
68 6406 37.0 0 6406
69 6027 37.0 0 6027
70 5854 37.0 0 5854
71 6644 37.0 0 6644
72 6335 37.0 0 6335
73 6206 37.0 0 6206
74 6000 37.0 0 6000
75 5942 37.0 0 5942
76 5640 37.0 0 5640
77 5835 37.0 0 5835
78 6013 37.0 0 6013
79 6932 37.0 0 6932
80 6386 37.0 0 6386
81 7205 37.0 0 7205
82 8821 37.0 0 8821
83 10011 37.0 0 10011
84 10665 37.0 0 10665
85 11097 37.0 0 11097
86 99517 37.0 0 99517
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28672 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.1%
C: 33.6%
G: 0.0%
T: 34.6%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 13655 37843.4 0 13655
4 2956 9460.8 0 2956
5 737 2365.2 0 737
6 277 591.3 0 277
7 252 147.8 0 252
8 238 37.0 0 238
9 254 37.0 0 254
10 203 37.0 0 203
11 205 37.0 0 205
12 197 37.0 0 197
13 186 37.0 0 186
14 180 37.0 0 180
15 191 37.0 0 191
16 160 37.0 0 160
17 180 37.0 0 180
18 156 37.0 0 156
19 158 37.0 0 158
20 192 37.0 0 192
21 169 37.0 0 169
22 156 37.0 0 156
23 181 37.0 0 181
24 190 37.0 0 190
25 173 37.0 0 173
26 151 37.0 0 151
27 166 37.0 0 166
28 177 37.0 0 177
29 175 37.0 0 175
30 158 37.0 0 158
31 143 37.0 0 143
32 140 37.0 0 140
33 186 37.0 0 186
34 160 37.0 0 160
35 145 37.0 0 145
36 153 37.0 0 153
37 147 37.0 0 147
38 139 37.0 0 139
39 158 37.0 0 158
40 178 37.0 0 178
41 154 37.0 0 154
42 154 37.0 0 154
43 159 37.0 0 159
44 165 37.0 0 165
45 146 37.0 0 146
46 161 37.0 0 161
47 158 37.0 0 158
48 147 37.0 0 147
49 134 37.0 0 134
50 145 37.0 0 145
51 122 37.0 0 122
52 150 37.0 0 150
53 138 37.0 0 138
54 148 37.0 0 148
55 100 37.0 0 100
56 133 37.0 0 133
57 144 37.0 0 144
58 133 37.0 0 133
59 136 37.0 0 136
60 133 37.0 0 133
61 125 37.0 0 125
62 106 37.0 0 106
63 94 37.0 0 94
64 101 37.0 0 101
65 103 37.0 0 103
66 103 37.0 0 103
67 90 37.0 0 90
68 76 37.0 0 76
69 80 37.0 0 80
70 52 37.0 0 52
71 55 37.0 0 55
72 38 37.0 0 38
73 49 37.0 0 49
74 43 37.0 0 43
75 36 37.0 0 36
76 34 37.0 0 34
77 21 37.0 0 21
78 20 37.0 0 20
79 26 37.0 0 26
80 24 37.0 0 24
81 20 37.0 0 20
82 39 37.0 0 39
83 19 37.0 0 19
84 31 37.0 0 31
85 32 37.0 0 32
86 773 37.0 0 773
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 54421 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.0%
C: 23.2%
G: 22.0%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 40741 37843.4 0 40741
4 9066 9460.8 0 9066
5 1905 2365.2 0 1905
6 283 591.3 0 283
7 29 147.8 0 29
8 33 147.8 0 33
9 25 147.8 0 25
10 29 147.8 0 29
11 39 147.8 0 39
12 26 147.8 0 26
13 40 147.8 0 40
14 32 147.8 0 32
15 28 147.8 0 28
16 32 147.8 0 32
17 37 147.8 0 37
18 24 147.8 0 24
19 42 147.8 0 42
20 36 147.8 0 36
21 30 147.8 0 30
22 29 147.8 0 29
23 23 147.8 0 23
24 35 147.8 0 35
25 37 147.8 0 37
26 43 147.8 0 43
27 29 147.8 0 29
28 27 147.8 0 27
29 35 147.8 0 35
30 43 147.8 0 43
31 23 147.8 0 23
32 39 147.8 0 39
33 26 147.8 0 26
34 22 147.8 0 22
35 32 147.8 0 32
36 29 147.8 0 29
37 26 147.8 0 26
38 27 147.8 0 27
39 36 147.8 0 36
40 24 147.8 0 24
41 37 147.8 0 37
42 24 147.8 0 24
43 34 147.8 0 34
44 28 147.8 0 28
45 29 147.8 0 29
46 22 147.8 0 22
47 28 147.8 0 28
48 29 147.8 0 29
49 22 147.8 0 22
50 25 147.8 0 25
51 29 147.8 0 29
52 36 147.8 0 36
53 21 147.8 0 21
54 33 147.8 0 33
55 34 147.8 0 34
56 28 147.8 0 28
57 26 147.8 0 26
58 45 147.8 0 45
59 25 147.8 0 25
60 35 147.8 0 35
61 22 147.8 0 22
62 24 147.8 0 24
63 31 147.8 0 31
64 40 147.8 0 40
65 32 147.8 0 32
66 29 147.8 0 29
67 30 147.8 0 30
68 25 147.8 0 25
69 15 147.8 0 15
70 34 147.8 0 34
71 29 147.8 0 29
72 25 147.8 0 25
73 19 147.8 0 19
74 24 147.8 0 24
75 36 147.8 0 36
76 11 147.8 0 11
77 72 147.8 0 72
78 39 147.8 0 39
79 16 147.8 0 16
80 30 147.8 0 30
81 23 147.8 0 23
82 26 147.8 0 26
83 44 147.8 0 44
84 28 147.8 0 28
85 31 147.8 0 31
86 34 147.8 0 34
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N41_S164_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N41_S164_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.67 s (9 µs/read; 6.52 M reads/minute).
=== Summary ===
Total reads processed: 2,680,915
Reads with adapters: 936,316 (34.9%)
== Read fate breakdown ==
Reads that were too short: 277,935 (10.4%)
Reads written (passing filters): 2,402,980 (89.6%)
Total basepairs processed: 270,772,415 bp
Total written (filtered): 188,395,822 bp (69.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 849033 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.7%
G: 27.4%
T: 28.8%
none/other: 14.1%
Overview of removed sequences
length count expect max.err error counts
3 61076 41889.3 0 61076
4 26238 10472.3 0 26238
5 13810 2618.1 0 13810
6 9905 654.5 0 9905
7 7806 163.6 0 7806
8 6805 40.9 0 6805
9 7025 40.9 0 7025
10 7263 40.9 0 7263
11 6927 40.9 0 6927
12 6896 40.9 0 6896
13 7080 40.9 0 7080
14 7145 40.9 0 7145
15 7263 40.9 0 7263
16 7227 40.9 0 7227
17 7309 40.9 0 7309
18 7516 40.9 0 7516
19 7374 40.9 0 7374
20 6916 40.9 0 6916
21 7342 40.9 0 7342
22 7269 40.9 0 7269
23 6972 40.9 0 6972
24 6895 40.9 0 6895
25 6954 40.9 0 6954
26 7135 40.9 0 7135
27 7211 40.9 0 7211
28 7314 40.9 0 7314
29 7584 40.9 0 7584
30 7259 40.9 0 7259
31 8037 40.9 0 8037
32 7624 40.9 0 7624
33 8271 40.9 0 8271
34 7944 40.9 0 7944
35 7653 40.9 0 7653
36 7448 40.9 0 7448
37 7323 40.9 0 7323
38 7137 40.9 0 7137
39 6987 40.9 0 6987
40 7306 40.9 0 7306
41 7424 40.9 0 7424
42 7653 40.9 0 7653
43 8352 40.9 0 8352
44 7472 40.9 0 7472
45 7983 40.9 0 7983
46 8749 40.9 0 8749
47 8230 40.9 0 8230
48 7772 40.9 0 7772
49 12928 40.9 0 12928
50 14664 40.9 0 14664
51 8090 40.9 0 8090
52 8850 40.9 0 8850
53 8182 40.9 0 8182
54 7093 40.9 0 7093
55 7713 40.9 0 7713
56 7676 40.9 0 7676
57 7363 40.9 0 7363
58 8095 40.9 0 8095
59 7677 40.9 0 7677
60 7745 40.9 0 7745
61 7871 40.9 0 7871
62 7569 40.9 0 7569
63 7264 40.9 0 7264
64 7427 40.9 0 7427
65 7322 40.9 0 7322
66 7083 40.9 0 7083
67 7019 40.9 0 7019
68 7191 40.9 0 7191
69 6959 40.9 0 6959
70 6655 40.9 0 6655
71 7392 40.9 0 7392
72 7601 40.9 0 7601
73 6959 40.9 0 6959
74 6740 40.9 0 6740
75 6824 40.9 0 6824
76 6710 40.9 0 6710
77 6898 40.9 0 6898
78 6871 40.9 0 6871
79 8109 40.9 0 8109
80 7532 40.9 0 7532
81 8849 40.9 0 8849
82 10339 40.9 0 10339
83 11507 40.9 0 11507
84 12511 40.9 0 12511
85 13035 40.9 0 13035
86 119839 40.9 0 119839
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27836 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.7%
C: 30.5%
G: 0.0%
T: 34.3%
none/other: 3.4%
Overview of removed sequences
length count expect max.err error counts
3 13632 41889.3 0 13632
4 2962 10472.3 0 2962
5 842 2618.1 0 842
6 334 654.5 0 334
7 289 163.6 0 289
8 239 40.9 0 239
9 240 40.9 0 240
10 202 40.9 0 202
11 181 40.9 0 181
12 176 40.9 0 176
13 185 40.9 0 185
14 144 40.9 0 144
15 140 40.9 0 140
16 165 40.9 0 165
17 154 40.9 0 154
18 139 40.9 0 139
19 140 40.9 0 140
20 155 40.9 0 155
21 161 40.9 0 161
22 127 40.9 0 127
23 156 40.9 0 156
24 152 40.9 0 152
25 123 40.9 0 123
26 138 40.9 0 138
27 147 40.9 0 147
28 141 40.9 0 141
29 120 40.9 0 120
30 133 40.9 0 133
31 157 40.9 0 157
32 143 40.9 0 143
33 158 40.9 0 158
34 132 40.9 0 132
35 136 40.9 0 136
36 142 40.9 0 142
37 139 40.9 0 139
38 142 40.9 0 142
39 133 40.9 0 133
40 122 40.9 0 122
41 131 40.9 0 131
42 148 40.9 0 148
43 126 40.9 0 126
44 128 40.9 0 128
45 126 40.9 0 126
46 122 40.9 0 122
47 136 40.9 0 136
48 128 40.9 0 128
49 124 40.9 0 124
50 129 40.9 0 129
51 117 40.9 0 117
52 124 40.9 0 124
53 122 40.9 0 122
54 132 40.9 0 132
55 120 40.9 0 120
56 133 40.9 0 133
57 130 40.9 0 130
58 113 40.9 0 113
59 90 40.9 0 90
60 101 40.9 0 101
61 102 40.9 0 102
62 89 40.9 0 89
63 87 40.9 0 87
64 81 40.9 0 81
65 76 40.9 0 76
66 66 40.9 0 66
67 73 40.9 0 73
68 63 40.9 0 63
69 59 40.9 0 59
70 59 40.9 0 59
71 46 40.9 0 46
72 48 40.9 0 48
73 50 40.9 0 50
74 28 40.9 0 28
75 31 40.9 0 31
76 26 40.9 0 26
77 34 40.9 0 34
78 31 40.9 0 31
79 31 40.9 0 31
80 26 40.9 0 26
81 29 40.9 0 29
82 26 40.9 0 26
83 36 40.9 0 36
84 40 40.9 0 40
85 41 40.9 0 41
86 957 40.9 0 957
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 59447 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.5%
C: 23.6%
G: 21.3%
T: 19.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44836 41889.3 0 44836
4 9684 10472.3 0 9684
5 1899 2618.1 0 1899
6 264 654.5 0 264
7 28 163.6 0 28
8 32 163.6 0 32
9 21 163.6 0 21
10 38 163.6 0 38
11 30 163.6 0 30
12 28 163.6 0 28
13 45 163.6 0 45
14 55 163.6 0 55
15 29 163.6 0 29
16 44 163.6 0 44
17 39 163.6 0 39
18 37 163.6 0 37
19 58 163.6 0 58
20 52 163.6 0 52
21 27 163.6 0 27
22 40 163.6 0 40
23 29 163.6 0 29
24 35 163.6 0 35
25 53 163.6 0 53
26 35 163.6 0 35
27 34 163.6 0 34
28 43 163.6 0 43
29 45 163.6 0 45
30 39 163.6 0 39
31 30 163.6 0 30
32 50 163.6 0 50
33 44 163.6 0 44
34 26 163.6 0 26
35 32 163.6 0 32
36 26 163.6 0 26
37 34 163.6 0 34
38 44 163.6 0 44
39 19 163.6 0 19
40 35 163.6 0 35
41 42 163.6 0 42
42 22 163.6 0 22
43 36 163.6 0 36
44 30 163.6 0 30
45 17 163.6 0 17
46 31 163.6 0 31
47 24 163.6 0 24
48 24 163.6 0 24
49 50 163.6 0 50
50 32 163.6 0 32
51 44 163.6 0 44
52 42 163.6 0 42
53 23 163.6 0 23
54 28 163.6 0 28
55 36 163.6 0 36
56 25 163.6 0 25
57 32 163.6 0 32
58 44 163.6 0 44
59 35 163.6 0 35
60 28 163.6 0 28
61 30 163.6 0 30
62 28 163.6 0 28
63 35 163.6 0 35
64 23 163.6 0 23
65 53 163.6 0 53
66 33 163.6 0 33
67 37 163.6 0 37
68 25 163.6 0 25
69 30 163.6 0 30
70 42 163.6 0 42
71 37 163.6 0 37
72 28 163.6 0 28
73 34 163.6 0 34
74 28 163.6 0 28
75 26 163.6 0 26
76 23 163.6 0 23
77 75 163.6 0 75
78 51 163.6 0 51
79 19 163.6 0 19
80 25 163.6 0 25
81 25 163.6 0 25
82 28 163.6 0 28
83 30 163.6 0 30
84 27 163.6 0 27
85 33 163.6 0 33
86 38 163.6 0 38
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N41_S164_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N41_S164_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.38 s (9 µs/read; 6.46 M reads/minute).
=== Summary ===
Total reads processed: 2,732,931
Reads with adapters: 962,116 (35.2%)
== Read fate breakdown ==
Reads that were too short: 289,822 (10.6%)
Reads written (passing filters): 2,443,109 (89.4%)
Total basepairs processed: 276,026,031 bp
Total written (filtered): 191,409,222 bp (69.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 872488 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.8%
G: 27.3%
T: 28.5%
none/other: 14.4%
Overview of removed sequences
length count expect max.err error counts
3 62027 42702.0 0 62027
4 27035 10675.5 0 27035
5 13939 2668.9 0 13939
6 9855 667.2 0 9855
7 8120 166.8 0 8120
8 6891 41.7 0 6891
9 7060 41.7 0 7060
10 7107 41.7 0 7107
11 7104 41.7 0 7104
12 6964 41.7 0 6964
13 7189 41.7 0 7189
14 7297 41.7 0 7297
15 7375 41.7 0 7375
16 7310 41.7 0 7310
17 7337 41.7 0 7337
18 7717 41.7 0 7717
19 7425 41.7 0 7425
20 7117 41.7 0 7117
21 7504 41.7 0 7504
22 7334 41.7 0 7334
23 7020 41.7 0 7020
24 7121 41.7 0 7121
25 7000 41.7 0 7000
26 7168 41.7 0 7168
27 7339 41.7 0 7339
28 7575 41.7 0 7575
29 7482 41.7 0 7482
30 7388 41.7 0 7388
31 8200 41.7 0 8200
32 7639 41.7 0 7639
33 8359 41.7 0 8359
34 8142 41.7 0 8142
35 7885 41.7 0 7885
36 7537 41.7 0 7537
37 7482 41.7 0 7482
38 7089 41.7 0 7089
39 7385 41.7 0 7385
40 7277 41.7 0 7277
41 7632 41.7 0 7632
42 7776 41.7 0 7776
43 8747 41.7 0 8747
44 7842 41.7 0 7842
45 8262 41.7 0 8262
46 9009 41.7 0 9009
47 8396 41.7 0 8396
48 7881 41.7 0 7881
49 13416 41.7 0 13416
50 15353 41.7 0 15353
51 8503 41.7 0 8503
52 8898 41.7 0 8898
53 8462 41.7 0 8462
54 7319 41.7 0 7319
55 7965 41.7 0 7965
56 7955 41.7 0 7955
57 7587 41.7 0 7587
58 8257 41.7 0 8257
59 7874 41.7 0 7874
60 7699 41.7 0 7699
61 8055 41.7 0 8055
62 7959 41.7 0 7959
63 7420 41.7 0 7420
64 7420 41.7 0 7420
65 7485 41.7 0 7485
66 7181 41.7 0 7181
67 7322 41.7 0 7322
68 7499 41.7 0 7499
69 7126 41.7 0 7126
70 6856 41.7 0 6856
71 7775 41.7 0 7775
72 7786 41.7 0 7786
73 7326 41.7 0 7326
74 7082 41.7 0 7082
75 7157 41.7 0 7157
76 7045 41.7 0 7045
77 7273 41.7 0 7273
78 7268 41.7 0 7268
79 7987 41.7 0 7987
80 7782 41.7 0 7782
81 9178 41.7 0 9178
82 10744 41.7 0 10744
83 11863 41.7 0 11863
84 13038 41.7 0 13038
85 13635 41.7 0 13635
86 125598 41.7 0 125598
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29124 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.6%
C: 30.0%
G: 0.0%
T: 34.9%
none/other: 3.6%
Overview of removed sequences
length count expect max.err error counts
3 14040 42702.0 0 14040
4 3117 10675.5 0 3117
5 786 2668.9 0 786
6 336 667.2 0 336
7 267 166.8 0 267
8 271 41.7 0 271
9 257 41.7 0 257
10 192 41.7 0 192
11 210 41.7 0 210
12 200 41.7 0 200
13 176 41.7 0 176
14 165 41.7 0 165
15 151 41.7 0 151
16 171 41.7 0 171
17 136 41.7 0 136
18 179 41.7 0 179
19 158 41.7 0 158
20 163 41.7 0 163
21 154 41.7 0 154
22 154 41.7 0 154
23 162 41.7 0 162
24 189 41.7 0 189
25 166 41.7 0 166
26 164 41.7 0 164
27 142 41.7 0 142
28 159 41.7 0 159
29 158 41.7 0 158
30 158 41.7 0 158
31 142 41.7 0 142
32 141 41.7 0 141
33 152 41.7 0 152
34 157 41.7 0 157
35 149 41.7 0 149
36 155 41.7 0 155
37 176 41.7 0 176
38 149 41.7 0 149
39 153 41.7 0 153
40 145 41.7 0 145
41 136 41.7 0 136
42 126 41.7 0 126
43 155 41.7 0 155
44 129 41.7 0 129
45 146 41.7 0 146
46 147 41.7 0 147
47 147 41.7 0 147
48 146 41.7 0 146
49 129 41.7 0 129
50 160 41.7 0 160
51 124 41.7 0 124
52 137 41.7 0 137
53 129 41.7 0 129
54 132 41.7 0 132
55 127 41.7 0 127
56 111 41.7 0 111
57 132 41.7 0 132
58 123 41.7 0 123
59 119 41.7 0 119
60 108 41.7 0 108
61 109 41.7 0 109
62 84 41.7 0 84
63 86 41.7 0 86
64 71 41.7 0 71
65 84 41.7 0 84
66 92 41.7 0 92
67 80 41.7 0 80
68 74 41.7 0 74
69 59 41.7 0 59
70 54 41.7 0 54
71 45 41.7 0 45
72 48 41.7 0 48
73 40 41.7 0 40
74 40 41.7 0 40
75 45 41.7 0 45
76 26 41.7 0 26
77 27 41.7 0 27
78 25 41.7 0 25
79 30 41.7 0 30
80 27 41.7 0 27
81 19 41.7 0 19
82 39 41.7 0 39
83 31 41.7 0 31
84 40 41.7 0 40
85 52 41.7 0 52
86 1034 41.7 0 1034
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60504 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 23.2%
G: 21.2%
T: 19.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45849 42702.0 0 45849
4 9766 10675.5 0 9766
5 1906 2668.9 0 1906
6 270 667.2 0 270
7 31 166.8 0 31
8 42 166.8 0 42
9 29 166.8 0 29
10 43 166.8 0 43
11 53 166.8 0 53
12 27 166.8 0 27
13 28 166.8 0 28
14 44 166.8 0 44
15 32 166.8 0 32
16 30 166.8 0 30
17 57 166.8 0 57
18 43 166.8 0 43
19 43 166.8 0 43
20 31 166.8 0 31
21 33 166.8 0 33
22 58 166.8 0 58
23 38 166.8 0 38
24 29 166.8 0 29
25 53 166.8 0 53
26 40 166.8 0 40
27 29 166.8 0 29
28 34 166.8 0 34
29 38 166.8 0 38
30 23 166.8 0 23
31 22 166.8 0 22
32 43 166.8 0 43
33 42 166.8 0 42
34 17 166.8 0 17
35 32 166.8 0 32
36 32 166.8 0 32
37 44 166.8 0 44
38 33 166.8 0 33
39 26 166.8 0 26
40 30 166.8 0 30
41 40 166.8 0 40
42 16 166.8 0 16
43 40 166.8 0 40
44 42 166.8 0 42
45 28 166.8 0 28
46 32 166.8 0 32
47 29 166.8 0 29
48 29 166.8 0 29
49 35 166.8 0 35
50 31 166.8 0 31
51 42 166.8 0 42
52 37 166.8 0 37
53 27 166.8 0 27
54 35 166.8 0 35
55 37 166.8 0 37
56 26 166.8 0 26
57 32 166.8 0 32
58 35 166.8 0 35
59 26 166.8 0 26
60 40 166.8 0 40
61 27 166.8 0 27
62 34 166.8 0 34
63 29 166.8 0 29
64 32 166.8 0 32
65 31 166.8 0 31
66 25 166.8 0 25
67 32 166.8 0 32
68 39 166.8 0 39
69 26 166.8 0 26
70 23 166.8 0 23
71 40 166.8 0 40
72 27 166.8 0 27
73 26 166.8 0 26
74 17 166.8 0 17
75 26 166.8 0 26
76 23 166.8 0 23
77 76 166.8 0 76
78 41 166.8 0 41
79 30 166.8 0 30
80 29 166.8 0 29
81 30 166.8 0 30
82 24 166.8 0 24
83 25 166.8 0 25
84 31 166.8 0 31
85 40 166.8 0 40
86 42 166.8 0 42
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N42_S167_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N42_S167_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.50 s (9 µs/read; 6.45 M reads/minute).
=== Summary ===
Total reads processed: 2,632,381
Reads with adapters: 926,860 (35.2%)
== Read fate breakdown ==
Reads that were too short: 260,617 (9.9%)
Reads written (passing filters): 2,371,764 (90.1%)
Total basepairs processed: 265,870,481 bp
Total written (filtered): 185,537,645 bp (69.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 843916 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.7%
G: 27.1%
T: 30.7%
none/other: 12.5%
Overview of removed sequences
length count expect max.err error counts
3 62242 41131.0 0 62242
4 26887 10282.7 0 26887
5 14684 2570.7 0 14684
6 10120 642.7 0 10120
7 8252 160.7 0 8252
8 7424 40.2 0 7424
9 7325 40.2 0 7325
10 7546 40.2 0 7546
11 7221 40.2 0 7221
12 7263 40.2 0 7263
13 7502 40.2 0 7502
14 7312 40.2 0 7312
15 8024 40.2 0 8024
16 7952 40.2 0 7952
17 7814 40.2 0 7814
18 8096 40.2 0 8096
19 7960 40.2 0 7960
20 7455 40.2 0 7455
21 7999 40.2 0 7999
22 7977 40.2 0 7977
23 7578 40.2 0 7578
24 7103 40.2 0 7103
25 6912 40.2 0 6912
26 7045 40.2 0 7045
27 7041 40.2 0 7041
28 7351 40.2 0 7351
29 7351 40.2 0 7351
30 7233 40.2 0 7233
31 7651 40.2 0 7651
32 7302 40.2 0 7302
33 7723 40.2 0 7723
34 7661 40.2 0 7661
35 8042 40.2 0 8042
36 7487 40.2 0 7487
37 8052 40.2 0 8052
38 7706 40.2 0 7706
39 7457 40.2 0 7457
40 7747 40.2 0 7747
41 8272 40.2 0 8272
42 8092 40.2 0 8092
43 9378 40.2 0 9378
44 8197 40.2 0 8197
45 8423 40.2 0 8423
46 9371 40.2 0 9371
47 8686 40.2 0 8686
48 7850 40.2 0 7850
49 11958 40.2 0 11958
50 12718 40.2 0 12718
51 7972 40.2 0 7972
52 7895 40.2 0 7895
53 7827 40.2 0 7827
54 7097 40.2 0 7097
55 7597 40.2 0 7597
56 7418 40.2 0 7418
57 7346 40.2 0 7346
58 7803 40.2 0 7803
59 7626 40.2 0 7626
60 7452 40.2 0 7452
61 7711 40.2 0 7711
62 7773 40.2 0 7773
63 7353 40.2 0 7353
64 7326 40.2 0 7326
65 7580 40.2 0 7580
66 7240 40.2 0 7240
67 7391 40.2 0 7391
68 7281 40.2 0 7281
69 6959 40.2 0 6959
70 6650 40.2 0 6650
71 7061 40.2 0 7061
72 7049 40.2 0 7049
73 6788 40.2 0 6788
74 6177 40.2 0 6177
75 6565 40.2 0 6565
76 6397 40.2 0 6397
77 6016 40.2 0 6016
78 7052 40.2 0 7052
79 8214 40.2 0 8214
80 7494 40.2 0 7494
81 8761 40.2 0 8761
82 10380 40.2 0 10380
83 11300 40.2 0 11300
84 12284 40.2 0 12284
85 13233 40.2 0 13233
86 105406 40.2 0 105406
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29037 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.8%
C: 34.2%
G: 0.0%
T: 35.3%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 13279 41131.0 0 13279
4 3090 10282.7 0 3090
5 855 2570.7 0 855
6 407 642.7 0 407
7 267 160.7 0 267
8 264 40.2 0 264
9 218 40.2 0 218
10 230 40.2 0 230
11 207 40.2 0 207
12 183 40.2 0 183
13 173 40.2 0 173
14 174 40.2 0 174
15 170 40.2 0 170
16 186 40.2 0 186
17 167 40.2 0 167
18 196 40.2 0 196
19 204 40.2 0 204
20 178 40.2 0 178
21 156 40.2 0 156
22 161 40.2 0 161
23 169 40.2 0 169
24 169 40.2 0 169
25 202 40.2 0 202
26 189 40.2 0 189
27 170 40.2 0 170
28 200 40.2 0 200
29 165 40.2 0 165
30 199 40.2 0 199
31 162 40.2 0 162
32 174 40.2 0 174
33 210 40.2 0 210
34 156 40.2 0 156
35 154 40.2 0 154
36 177 40.2 0 177
37 141 40.2 0 141
38 182 40.2 0 182
39 154 40.2 0 154
40 124 40.2 0 124
41 154 40.2 0 154
42 152 40.2 0 152
43 163 40.2 0 163
44 165 40.2 0 165
45 164 40.2 0 164
46 166 40.2 0 166
47 149 40.2 0 149
48 151 40.2 0 151
49 136 40.2 0 136
50 169 40.2 0 169
51 143 40.2 0 143
52 145 40.2 0 145
53 161 40.2 0 161
54 160 40.2 0 160
55 155 40.2 0 155
56 122 40.2 0 122
57 130 40.2 0 130
58 132 40.2 0 132
59 127 40.2 0 127
60 114 40.2 0 114
61 116 40.2 0 116
62 116 40.2 0 116
63 116 40.2 0 116
64 102 40.2 0 102
65 86 40.2 0 86
66 90 40.2 0 90
67 86 40.2 0 86
68 73 40.2 0 73
69 72 40.2 0 72
70 64 40.2 0 64
71 58 40.2 0 58
72 48 40.2 0 48
73 51 40.2 0 51
74 41 40.2 0 41
75 41 40.2 0 41
76 30 40.2 0 30
77 28 40.2 0 28
78 26 40.2 0 26
79 30 40.2 0 30
80 32 40.2 0 32
81 23 40.2 0 23
82 22 40.2 0 22
83 27 40.2 0 27
84 30 40.2 0 30
85 36 40.2 0 36
86 773 40.2 0 773
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 53907 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.0%
C: 23.6%
G: 20.6%
T: 20.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 40408 41131.0 0 40408
4 8818 10282.7 0 8818
5 1875 2570.7 0 1875
6 244 642.7 0 244
7 30 160.7 0 30
8 41 160.7 0 41
9 28 160.7 0 28
10 27 160.7 0 27
11 37 160.7 0 37
12 34 160.7 0 34
13 37 160.7 0 37
14 44 160.7 0 44
15 45 160.7 0 45
16 46 160.7 0 46
17 36 160.7 0 36
18 30 160.7 0 30
19 56 160.7 0 56
20 49 160.7 0 49
21 26 160.7 0 26
22 55 160.7 0 55
23 28 160.7 0 28
24 37 160.7 0 37
25 51 160.7 0 51
26 31 160.7 0 31
27 40 160.7 0 40
28 39 160.7 0 39
29 33 160.7 0 33
30 43 160.7 0 43
31 38 160.7 0 38
32 42 160.7 0 42
33 30 160.7 0 30
34 30 160.7 0 30
35 28 160.7 0 28
36 31 160.7 0 31
37 17 160.7 0 17
38 28 160.7 0 28
39 29 160.7 0 29
40 38 160.7 0 38
41 26 160.7 0 26
42 16 160.7 0 16
43 15 160.7 0 15
44 30 160.7 0 30
45 26 160.7 0 26
46 38 160.7 0 38
47 21 160.7 0 21
48 32 160.7 0 32
49 21 160.7 0 21
50 47 160.7 0 47
51 31 160.7 0 31
52 28 160.7 0 28
53 30 160.7 0 30
54 30 160.7 0 30
55 28 160.7 0 28
56 28 160.7 0 28
57 31 160.7 0 31
58 34 160.7 0 34
59 34 160.7 0 34
60 25 160.7 0 25
61 33 160.7 0 33
62 32 160.7 0 32
63 39 160.7 0 39
64 18 160.7 0 18
65 28 160.7 0 28
66 39 160.7 0 39
67 34 160.7 0 34
68 28 160.7 0 28
69 27 160.7 0 27
70 26 160.7 0 26
71 33 160.7 0 33
72 18 160.7 0 18
73 25 160.7 0 25
74 24 160.7 0 24
75 25 160.7 0 25
76 23 160.7 0 23
77 51 160.7 0 51
78 29 160.7 0 29
79 26 160.7 0 26
80 31 160.7 0 31
81 15 160.7 0 15
82 28 160.7 0 28
83 41 160.7 0 41
84 25 160.7 0 25
85 28 160.7 0 28
86 31 160.7 0 31
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N42_S167_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N42_S167_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.35 s (9 µs/read; 6.35 M reads/minute).
=== Summary ===
Total reads processed: 2,681,110
Reads with adapters: 951,567 (35.5%)
== Read fate breakdown ==
Reads that were too short: 271,217 (10.1%)
Reads written (passing filters): 2,409,893 (89.9%)
Total basepairs processed: 270,792,110 bp
Total written (filtered): 188,295,579 bp (69.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 867083 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.9%
G: 27.0%
T: 30.3%
none/other: 12.8%
Overview of removed sequences
length count expect max.err error counts
3 62498 41892.3 0 62498
4 27083 10473.1 0 27083
5 14952 2618.3 0 14952
6 10229 654.6 0 10229
7 8327 163.6 0 8327
8 7338 40.9 0 7338
9 7604 40.9 0 7604
10 7450 40.9 0 7450
11 7369 40.9 0 7369
12 7505 40.9 0 7505
13 7406 40.9 0 7406
14 7475 40.9 0 7475
15 7997 40.9 0 7997
16 8121 40.9 0 8121
17 7965 40.9 0 7965
18 8220 40.9 0 8220
19 7978 40.9 0 7978
20 7598 40.9 0 7598
21 8237 40.9 0 8237
22 8243 40.9 0 8243
23 7517 40.9 0 7517
24 7477 40.9 0 7477
25 7302 40.9 0 7302
26 7081 40.9 0 7081
27 7193 40.9 0 7193
28 7425 40.9 0 7425
29 7451 40.9 0 7451
30 7458 40.9 0 7458
31 8024 40.9 0 8024
32 7675 40.9 0 7675
33 7891 40.9 0 7891
34 7794 40.9 0 7794
35 8185 40.9 0 8185
36 7648 40.9 0 7648
37 8130 40.9 0 8130
38 7749 40.9 0 7749
39 7673 40.9 0 7673
40 7720 40.9 0 7720
41 8542 40.9 0 8542
42 8075 40.9 0 8075
43 9518 40.9 0 9518
44 8715 40.9 0 8715
45 8617 40.9 0 8617
46 9387 40.9 0 9387
47 8959 40.9 0 8959
48 8278 40.9 0 8278
49 12575 40.9 0 12575
50 13232 40.9 0 13232
51 8247 40.9 0 8247
52 8310 40.9 0 8310
53 8206 40.9 0 8206
54 7432 40.9 0 7432
55 7695 40.9 0 7695
56 7819 40.9 0 7819
57 7381 40.9 0 7381
58 7973 40.9 0 7973
59 7718 40.9 0 7718
60 7580 40.9 0 7580
61 8043 40.9 0 8043
62 7946 40.9 0 7946
63 7661 40.9 0 7661
64 7829 40.9 0 7829
65 7925 40.9 0 7925
66 7562 40.9 0 7562
67 7573 40.9 0 7573
68 7416 40.9 0 7416
69 7094 40.9 0 7094
70 6909 40.9 0 6909
71 7214 40.9 0 7214
72 7014 40.9 0 7014
73 7092 40.9 0 7092
74 6503 40.9 0 6503
75 6640 40.9 0 6640
76 6658 40.9 0 6658
77 6572 40.9 0 6572
78 7209 40.9 0 7209
79 8402 40.9 0 8402
80 7724 40.9 0 7724
81 8894 40.9 0 8894
82 10764 40.9 0 10764
83 11874 40.9 0 11874
84 13111 40.9 0 13111
85 13667 40.9 0 13667
86 110540 40.9 0 110540
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29545 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.1%
C: 33.2%
G: 0.0%
T: 36.0%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 13475 41892.3 0 13475
4 3126 10473.1 0 3126
5 796 2618.3 0 796
6 373 654.6 0 373
7 262 163.6 0 262
8 272 40.9 0 272
9 246 40.9 0 246
10 235 40.9 0 235
11 217 40.9 0 217
12 185 40.9 0 185
13 228 40.9 0 228
14 168 40.9 0 168
15 212 40.9 0 212
16 185 40.9 0 185
17 164 40.9 0 164
18 210 40.9 0 210
19 181 40.9 0 181
20 182 40.9 0 182
21 190 40.9 0 190
22 178 40.9 0 178
23 141 40.9 0 141
24 188 40.9 0 188
25 178 40.9 0 178
26 182 40.9 0 182
27 186 40.9 0 186
28 187 40.9 0 187
29 172 40.9 0 172
30 186 40.9 0 186
31 185 40.9 0 185
32 172 40.9 0 172
33 203 40.9 0 203
34 170 40.9 0 170
35 189 40.9 0 189
36 150 40.9 0 150
37 185 40.9 0 185
38 161 40.9 0 161
39 156 40.9 0 156
40 145 40.9 0 145
41 162 40.9 0 162
42 142 40.9 0 142
43 170 40.9 0 170
44 149 40.9 0 149
45 153 40.9 0 153
46 151 40.9 0 151
47 157 40.9 0 157
48 148 40.9 0 148
49 160 40.9 0 160
50 145 40.9 0 145
51 140 40.9 0 140
52 150 40.9 0 150
53 146 40.9 0 146
54 151 40.9 0 151
55 166 40.9 0 166
56 151 40.9 0 151
57 134 40.9 0 134
58 148 40.9 0 148
59 135 40.9 0 135
60 131 40.9 0 131
61 100 40.9 0 100
62 110 40.9 0 110
63 114 40.9 0 114
64 113 40.9 0 113
65 80 40.9 0 80
66 91 40.9 0 91
67 84 40.9 0 84
68 83 40.9 0 83
69 73 40.9 0 73
70 63 40.9 0 63
71 58 40.9 0 58
72 58 40.9 0 58
73 48 40.9 0 48
74 51 40.9 0 51
75 44 40.9 0 44
76 44 40.9 0 44
77 33 40.9 0 33
78 35 40.9 0 35
79 33 40.9 0 33
80 28 40.9 0 28
81 22 40.9 0 22
82 39 40.9 0 39
83 27 40.9 0 27
84 41 40.9 0 41
85 37 40.9 0 37
86 826 40.9 0 826
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 54939 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.1%
C: 23.3%
G: 20.9%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 40965 41892.3 0 40965
4 9223 10473.1 0 9223
5 1880 2618.3 0 1880
6 260 654.6 0 260
7 33 163.6 0 33
8 35 163.6 0 35
9 44 163.6 0 44
10 28 163.6 0 28
11 31 163.6 0 31
12 43 163.6 0 43
13 46 163.6 0 46
14 35 163.6 0 35
15 42 163.6 0 42
16 48 163.6 0 48
17 44 163.6 0 44
18 60 163.6 0 60
19 48 163.6 0 48
20 39 163.6 0 39
21 36 163.6 0 36
22 46 163.6 0 46
23 32 163.6 0 32
24 30 163.6 0 30
25 50 163.6 0 50
26 32 163.6 0 32
27 32 163.6 0 32
28 46 163.6 0 46
29 22 163.6 0 22
30 30 163.6 0 30
31 23 163.6 0 23
32 27 163.6 0 27
33 29 163.6 0 29
34 34 163.6 0 34
35 24 163.6 0 24
36 28 163.6 0 28
37 32 163.6 0 32
38 18 163.6 0 18
39 32 163.6 0 32
40 26 163.6 0 26
41 23 163.6 0 23
42 44 163.6 0 44
43 33 163.6 0 33
44 23 163.6 0 23
45 28 163.6 0 28
46 33 163.6 0 33
47 36 163.6 0 36
48 43 163.6 0 43
49 23 163.6 0 23
50 35 163.6 0 35
51 30 163.6 0 30
52 38 163.6 0 38
53 14 163.6 0 14
54 24 163.6 0 24
55 32 163.6 0 32
56 34 163.6 0 34
57 31 163.6 0 31
58 25 163.6 0 25
59 36 163.6 0 36
60 22 163.6 0 22
61 28 163.6 0 28
62 23 163.6 0 23
63 24 163.6 0 24
64 37 163.6 0 37
65 35 163.6 0 35
66 32 163.6 0 32
67 25 163.6 0 25
68 32 163.6 0 32
69 21 163.6 0 21
70 34 163.6 0 34
71 36 163.6 0 36
72 25 163.6 0 25
73 27 163.6 0 27
74 20 163.6 0 20
75 23 163.6 0 23
76 22 163.6 0 22
77 62 163.6 0 62
78 41 163.6 0 41
79 32 163.6 0 32
80 24 163.6 0 24
81 26 163.6 0 26
82 28 163.6 0 28
83 49 163.6 0 49
84 25 163.6 0 25
85 21 163.6 0 21
86 47 163.6 0 47
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N43_S165_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N43_S165_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.92 s (9 µs/read; 6.48 M reads/minute).
=== Summary ===
Total reads processed: 3,121,412
Reads with adapters: 1,097,877 (35.2%)
== Read fate breakdown ==
Reads that were too short: 307,524 (9.9%)
Reads written (passing filters): 2,813,888 (90.1%)
Total basepairs processed: 315,262,612 bp
Total written (filtered): 220,348,272 bp (69.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 993165 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.1%
G: 27.2%
T: 28.8%
none/other: 12.9%
Overview of removed sequences
length count expect max.err error counts
3 78098 48772.1 0 78098
4 32350 12193.0 0 32350
5 16786 3048.3 0 16786
6 11881 762.1 0 11881
7 9762 190.5 0 9762
8 8669 47.6 0 8669
9 8679 47.6 0 8679
10 8729 47.6 0 8729
11 8479 47.6 0 8479
12 8676 47.6 0 8676
13 8930 47.6 0 8930
14 9084 47.6 0 9084
15 9173 47.6 0 9173
16 9239 47.6 0 9239
17 9235 47.6 0 9235
18 9346 47.6 0 9346
19 8976 47.6 0 8976
20 8918 47.6 0 8918
21 9360 47.6 0 9360
22 9033 47.6 0 9033
23 8435 47.6 0 8435
24 8449 47.6 0 8449
25 8310 47.6 0 8310
26 8395 47.6 0 8395
27 8552 47.6 0 8552
28 8876 47.6 0 8876
29 8852 47.6 0 8852
30 8647 47.6 0 8647
31 9459 47.6 0 9459
32 8776 47.6 0 8776
33 9297 47.6 0 9297
34 9094 47.6 0 9094
35 9006 47.6 0 9006
36 8581 47.6 0 8581
37 8865 47.6 0 8865
38 8377 47.6 0 8377
39 8943 47.6 0 8943
40 9317 47.6 0 9317
41 9011 47.6 0 9011
42 9275 47.6 0 9275
43 9623 47.6 0 9623
44 8706 47.6 0 8706
45 9125 47.6 0 9125
46 8863 47.6 0 8863
47 9157 47.6 0 9157
48 8852 47.6 0 8852
49 13169 47.6 0 13169
50 16008 47.6 0 16008
51 9552 47.6 0 9552
52 9878 47.6 0 9878
53 9812 47.6 0 9812
54 8696 47.6 0 8696
55 9278 47.6 0 9278
56 9072 47.6 0 9072
57 8833 47.6 0 8833
58 9500 47.6 0 9500
59 9112 47.6 0 9112
60 9029 47.6 0 9029
61 9160 47.6 0 9160
62 8979 47.6 0 8979
63 8596 47.6 0 8596
64 8879 47.6 0 8879
65 8528 47.6 0 8528
66 8511 47.6 0 8511
67 8533 47.6 0 8533
68 8550 47.6 0 8550
69 8286 47.6 0 8286
70 7880 47.6 0 7880
71 8365 47.6 0 8365
72 8591 47.6 0 8591
73 7943 47.6 0 7943
74 7680 47.6 0 7680
75 8001 47.6 0 8001
76 7682 47.6 0 7682
77 7734 47.6 0 7734
78 7812 47.6 0 7812
79 8895 47.6 0 8895
80 8405 47.6 0 8405
81 9183 47.6 0 9183
82 11300 47.6 0 11300
83 12797 47.6 0 12797
84 13946 47.6 0 13946
85 14714 47.6 0 14714
86 128030 47.6 0 128030
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38130 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.3%
C: 32.3%
G: 0.0%
T: 35.5%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 15169 48772.1 0 15169
4 3607 12193.0 0 3607
5 1021 3048.3 0 1021
6 536 762.1 0 536
7 386 190.5 0 386
8 411 47.6 0 411
9 392 47.6 0 392
10 340 47.6 0 340
11 386 47.6 0 386
12 320 47.6 0 320
13 298 47.6 0 298
14 304 47.6 0 304
15 317 47.6 0 317
16 273 47.6 0 273
17 280 47.6 0 280
18 328 47.6 0 328
19 264 47.6 0 264
20 286 47.6 0 286
21 279 47.6 0 279
22 246 47.6 0 246
23 288 47.6 0 288
24 280 47.6 0 280
25 299 47.6 0 299
26 265 47.6 0 265
27 263 47.6 0 263
28 288 47.6 0 288
29 254 47.6 0 254
30 261 47.6 0 261
31 252 47.6 0 252
32 256 47.6 0 256
33 251 47.6 0 251
34 256 47.6 0 256
35 237 47.6 0 237
36 237 47.6 0 237
37 268 47.6 0 268
38 243 47.6 0 243
39 247 47.6 0 247
40 258 47.6 0 258
41 274 47.6 0 274
42 258 47.6 0 258
43 259 47.6 0 259
44 236 47.6 0 236
45 251 47.6 0 251
46 247 47.6 0 247
47 228 47.6 0 228
48 226 47.6 0 226
49 205 47.6 0 205
50 239 47.6 0 239
51 236 47.6 0 236
52 223 47.6 0 223
53 225 47.6 0 225
54 226 47.6 0 226
55 232 47.6 0 232
56 214 47.6 0 214
57 224 47.6 0 224
58 207 47.6 0 207
59 200 47.6 0 200
60 224 47.6 0 224
61 203 47.6 0 203
62 156 47.6 0 156
63 192 47.6 0 192
64 156 47.6 0 156
65 148 47.6 0 148
66 131 47.6 0 131
67 112 47.6 0 112
68 120 47.6 0 120
69 111 47.6 0 111
70 106 47.6 0 106
71 75 47.6 0 75
72 89 47.6 0 89
73 69 47.6 0 69
74 79 47.6 0 79
75 52 47.6 0 52
76 42 47.6 0 42
77 36 47.6 0 36
78 41 47.6 0 41
79 35 47.6 0 35
80 38 47.6 0 38
81 37 47.6 0 37
82 39 47.6 0 39
83 41 47.6 0 41
84 60 47.6 0 60
85 56 47.6 0 56
86 1126 47.6 0 1126
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 66582 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 23.4%
G: 21.0%
T: 19.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 49738 48772.1 0 49738
4 11153 12193.0 0 11153
5 2232 3048.3 0 2232
6 298 762.1 0 298
7 36 190.5 0 36
8 45 190.5 0 45
9 40 190.5 0 40
10 39 190.5 0 39
11 28 190.5 0 28
12 36 190.5 0 36
13 43 190.5 0 43
14 48 190.5 0 48
15 46 190.5 0 46
16 43 190.5 0 43
17 61 190.5 0 61
18 39 190.5 0 39
19 72 190.5 0 72
20 41 190.5 0 41
21 40 190.5 0 40
22 53 190.5 0 53
23 26 190.5 0 26
24 32 190.5 0 32
25 67 190.5 0 67
26 52 190.5 0 52
27 40 190.5 0 40
28 31 190.5 0 31
29 38 190.5 0 38
30 31 190.5 0 31
31 43 190.5 0 43
32 48 190.5 0 48
33 43 190.5 0 43
34 34 190.5 0 34
35 38 190.5 0 38
36 46 190.5 0 46
37 42 190.5 0 42
38 36 190.5 0 36
39 39 190.5 0 39
40 35 190.5 0 35
41 44 190.5 0 44
42 30 190.5 0 30
43 19 190.5 0 19
44 36 190.5 0 36
45 30 190.5 0 30
46 18 190.5 0 18
47 28 190.5 0 28
48 30 190.5 0 30
49 41 190.5 0 41
50 37 190.5 0 37
51 34 190.5 0 34
52 46 190.5 0 46
53 36 190.5 0 36
54 41 190.5 0 41
55 30 190.5 0 30
56 40 190.5 0 40
57 42 190.5 0 42
58 43 190.5 0 43
59 26 190.5 0 26
60 37 190.5 0 37
61 42 190.5 0 42
62 29 190.5 0 29
63 24 190.5 0 24
64 41 190.5 0 41
65 41 190.5 0 41
66 32 190.5 0 32
67 53 190.5 0 53
68 41 190.5 0 41
69 34 190.5 0 34
70 39 190.5 0 39
71 42 190.5 0 42
72 47 190.5 0 47
73 43 190.5 0 43
74 43 190.5 0 43
75 25 190.5 0 25
76 31 190.5 0 31
77 62 190.5 0 62
78 44 190.5 0 44
79 18 190.5 0 18
80 33 190.5 0 33
81 41 190.5 0 41
82 36 190.5 0 36
83 51 190.5 0 51
84 50 190.5 0 50
85 35 190.5 0 35
86 65 190.5 0 65
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N43_S165_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N43_S165_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 29.89 s (9 µs/read; 6.36 M reads/minute).
=== Summary ===
Total reads processed: 3,165,991
Reads with adapters: 1,121,198 (35.4%)
== Read fate breakdown ==
Reads that were too short: 317,772 (10.0%)
Reads written (passing filters): 2,848,219 (90.0%)
Total basepairs processed: 319,765,091 bp
Total written (filtered): 222,783,259 bp (69.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1015997 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.1%
G: 27.3%
T: 28.5%
none/other: 13.2%
Overview of removed sequences
length count expect max.err error counts
3 78881 49468.6 0 78881
4 32498 12367.2 0 32498
5 17101 3091.8 0 17101
6 11784 772.9 0 11784
7 9873 193.2 0 9873
8 8717 48.3 0 8717
9 8655 48.3 0 8655
10 9010 48.3 0 9010
11 8533 48.3 0 8533
12 8948 48.3 0 8948
13 8698 48.3 0 8698
14 9271 48.3 0 9271
15 9368 48.3 0 9368
16 9324 48.3 0 9324
17 9509 48.3 0 9509
18 9387 48.3 0 9387
19 9113 48.3 0 9113
20 9131 48.3 0 9131
21 9080 48.3 0 9080
22 9119 48.3 0 9119
23 8585 48.3 0 8585
24 8833 48.3 0 8833
25 8580 48.3 0 8580
26 8442 48.3 0 8442
27 8470 48.3 0 8470
28 9132 48.3 0 9132
29 8991 48.3 0 8991
30 8606 48.3 0 8606
31 9676 48.3 0 9676
32 9083 48.3 0 9083
33 9491 48.3 0 9491
34 9434 48.3 0 9434
35 9034 48.3 0 9034
36 8845 48.3 0 8845
37 9069 48.3 0 9069
38 8723 48.3 0 8723
39 8992 48.3 0 8992
40 9527 48.3 0 9527
41 9202 48.3 0 9202
42 9455 48.3 0 9455
43 9730 48.3 0 9730
44 8828 48.3 0 8828
45 9003 48.3 0 9003
46 9207 48.3 0 9207
47 9414 48.3 0 9414
48 9244 48.3 0 9244
49 13299 48.3 0 13299
50 16249 48.3 0 16249
51 9577 48.3 0 9577
52 10473 48.3 0 10473
53 10156 48.3 0 10156
54 8870 48.3 0 8870
55 9466 48.3 0 9466
56 9328 48.3 0 9328
57 9107 48.3 0 9107
58 9701 48.3 0 9701
59 9300 48.3 0 9300
60 9513 48.3 0 9513
61 9470 48.3 0 9470
62 9335 48.3 0 9335
63 8881 48.3 0 8881
64 9105 48.3 0 9105
65 9063 48.3 0 9063
66 8903 48.3 0 8903
67 8880 48.3 0 8880
68 8690 48.3 0 8690
69 8405 48.3 0 8405
70 7852 48.3 0 7852
71 8800 48.3 0 8800
72 8794 48.3 0 8794
73 7835 48.3 0 7835
74 8037 48.3 0 8037
75 8277 48.3 0 8277
76 7830 48.3 0 7830
77 7847 48.3 0 7847
78 8034 48.3 0 8034
79 9487 48.3 0 9487
80 8643 48.3 0 8643
81 9534 48.3 0 9534
82 11557 48.3 0 11557
83 13406 48.3 0 13406
84 14342 48.3 0 14342
85 14783 48.3 0 14783
86 133572 48.3 0 133572
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38187 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.8%
C: 32.5%
G: 0.0%
T: 35.7%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 15090 49468.6 0 15090
4 3360 12367.2 0 3360
5 1058 3091.8 0 1058
6 492 772.9 0 492
7 401 193.2 0 401
8 404 48.3 0 404
9 373 48.3 0 373
10 358 48.3 0 358
11 322 48.3 0 322
12 335 48.3 0 335
13 330 48.3 0 330
14 325 48.3 0 325
15 319 48.3 0 319
16 299 48.3 0 299
17 279 48.3 0 279
18 274 48.3 0 274
19 273 48.3 0 273
20 267 48.3 0 267
21 281 48.3 0 281
22 269 48.3 0 269
23 326 48.3 0 326
24 299 48.3 0 299
25 299 48.3 0 299
26 317 48.3 0 317
27 250 48.3 0 250
28 268 48.3 0 268
29 274 48.3 0 274
30 262 48.3 0 262
31 276 48.3 0 276
32 233 48.3 0 233
33 263 48.3 0 263
34 270 48.3 0 270
35 275 48.3 0 275
36 277 48.3 0 277
37 279 48.3 0 279
38 236 48.3 0 236
39 239 48.3 0 239
40 246 48.3 0 246
41 249 48.3 0 249
42 273 48.3 0 273
43 274 48.3 0 274
44 250 48.3 0 250
45 226 48.3 0 226
46 272 48.3 0 272
47 267 48.3 0 267
48 265 48.3 0 265
49 223 48.3 0 223
50 242 48.3 0 242
51 215 48.3 0 215
52 264 48.3 0 264
53 242 48.3 0 242
54 217 48.3 0 217
55 226 48.3 0 226
56 235 48.3 0 235
57 209 48.3 0 209
58 226 48.3 0 226
59 206 48.3 0 206
60 213 48.3 0 213
61 186 48.3 0 186
62 184 48.3 0 184
63 194 48.3 0 194
64 146 48.3 0 146
65 132 48.3 0 132
66 123 48.3 0 123
67 145 48.3 0 145
68 133 48.3 0 133
69 121 48.3 0 121
70 100 48.3 0 100
71 86 48.3 0 86
72 85 48.3 0 85
73 86 48.3 0 86
74 68 48.3 0 68
75 70 48.3 0 70
76 41 48.3 0 41
77 31 48.3 0 31
78 34 48.3 0 34
79 39 48.3 0 39
80 26 48.3 0 26
81 27 48.3 0 27
82 45 48.3 0 45
83 37 48.3 0 37
84 47 48.3 0 47
85 50 48.3 0 50
86 1159 48.3 0 1159
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 67014 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 23.4%
G: 21.1%
T: 19.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 50018 49468.6 0 50018
4 11258 12367.2 0 11258
5 2208 3091.8 0 2208
6 299 772.9 0 299
7 41 193.2 0 41
8 41 193.2 0 41
9 33 193.2 0 33
10 39 193.2 0 39
11 54 193.2 0 54
12 45 193.2 0 45
13 39 193.2 0 39
14 54 193.2 0 54
15 41 193.2 0 41
16 39 193.2 0 39
17 49 193.2 0 49
18 44 193.2 0 44
19 87 193.2 0 87
20 51 193.2 0 51
21 42 193.2 0 42
22 61 193.2 0 61
23 40 193.2 0 40
24 42 193.2 0 42
25 61 193.2 0 61
26 40 193.2 0 40
27 22 193.2 0 22
28 50 193.2 0 50
29 40 193.2 0 40
30 42 193.2 0 42
31 41 193.2 0 41
32 46 193.2 0 46
33 42 193.2 0 42
34 39 193.2 0 39
35 47 193.2 0 47
36 32 193.2 0 32
37 29 193.2 0 29
38 46 193.2 0 46
39 35 193.2 0 35
40 38 193.2 0 38
41 52 193.2 0 52
42 44 193.2 0 44
43 37 193.2 0 37
44 41 193.2 0 41
45 23 193.2 0 23
46 50 193.2 0 50
47 28 193.2 0 28
48 22 193.2 0 22
49 25 193.2 0 25
50 37 193.2 0 37
51 36 193.2 0 36
52 32 193.2 0 32
53 38 193.2 0 38
54 40 193.2 0 40
55 44 193.2 0 44
56 39 193.2 0 39
57 36 193.2 0 36
58 59 193.2 0 59
59 34 193.2 0 34
60 40 193.2 0 40
61 44 193.2 0 44
62 36 193.2 0 36
63 34 193.2 0 34
64 34 193.2 0 34
65 52 193.2 0 52
66 45 193.2 0 45
67 41 193.2 0 41
68 24 193.2 0 24
69 29 193.2 0 29
70 47 193.2 0 47
71 36 193.2 0 36
72 37 193.2 0 37
73 32 193.2 0 32
74 38 193.2 0 38
75 35 193.2 0 35
76 25 193.2 0 25
77 72 193.2 0 72
78 55 193.2 0 55
79 23 193.2 0 23
80 35 193.2 0 35
81 29 193.2 0 29
82 32 193.2 0 32
83 40 193.2 0 40
84 32 193.2 0 32
85 38 193.2 0 38
86 37 193.2 0 37
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N44_S171_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N44_S171_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.06 s (10 µs/read; 6.08 M reads/minute).
=== Summary ===
Total reads processed: 2,743,971
Reads with adapters: 904,878 (33.0%)
== Read fate breakdown ==
Reads that were too short: 255,370 (9.3%)
Reads written (passing filters): 2,488,601 (90.7%)
Total basepairs processed: 277,141,071 bp
Total written (filtered): 196,610,761 bp (70.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 811100 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.8%
G: 27.6%
T: 29.1%
none/other: 13.4%
Overview of removed sequences
length count expect max.err error counts
3 64048 42874.5 0 64048
4 27927 10718.6 0 27927
5 14552 2679.7 0 14552
6 9786 669.9 0 9786
7 7964 167.5 0 7964
8 7038 41.9 0 7038
9 7192 41.9 0 7192
10 7048 41.9 0 7048
11 7197 41.9 0 7197
12 6919 41.9 0 6919
13 7151 41.9 0 7151
14 7241 41.9 0 7241
15 7412 41.9 0 7412
16 7416 41.9 0 7416
17 7282 41.9 0 7282
18 7419 41.9 0 7419
19 7092 41.9 0 7092
20 6967 41.9 0 6967
21 7161 41.9 0 7161
22 7116 41.9 0 7116
23 6849 41.9 0 6849
24 6898 41.9 0 6898
25 6891 41.9 0 6891
26 6807 41.9 0 6807
27 6907 41.9 0 6907
28 7314 41.9 0 7314
29 7406 41.9 0 7406
30 7322 41.9 0 7322
31 7689 41.9 0 7689
32 7477 41.9 0 7477
33 8005 41.9 0 8005
34 7831 41.9 0 7831
35 7448 41.9 0 7448
36 7197 41.9 0 7197
37 7327 41.9 0 7327
38 6712 41.9 0 6712
39 6853 41.9 0 6853
40 7194 41.9 0 7194
41 7123 41.9 0 7123
42 7337 41.9 0 7337
43 7235 41.9 0 7235
44 6796 41.9 0 6796
45 7024 41.9 0 7024
46 7412 41.9 0 7412
47 7229 41.9 0 7229
48 7019 41.9 0 7019
49 10634 41.9 0 10634
50 13057 41.9 0 13057
51 7675 41.9 0 7675
52 8351 41.9 0 8351
53 7961 41.9 0 7961
54 6907 41.9 0 6907
55 7158 41.9 0 7158
56 7190 41.9 0 7190
57 6784 41.9 0 6784
58 7521 41.9 0 7521
59 7407 41.9 0 7407
60 7155 41.9 0 7155
61 7355 41.9 0 7355
62 7123 41.9 0 7123
63 6661 41.9 0 6661
64 6897 41.9 0 6897
65 6918 41.9 0 6918
66 6560 41.9 0 6560
67 6605 41.9 0 6605
68 6411 41.9 0 6411
69 6274 41.9 0 6274
70 6099 41.9 0 6099
71 6557 41.9 0 6557
72 6754 41.9 0 6754
73 6413 41.9 0 6413
74 6171 41.9 0 6171
75 6182 41.9 0 6182
76 5828 41.9 0 5828
77 6324 41.9 0 6324
78 6349 41.9 0 6349
79 7227 41.9 0 7227
80 6908 41.9 0 6908
81 8577 41.9 0 8577
82 10121 41.9 0 10121
83 10624 41.9 0 10624
84 12048 41.9 0 12048
85 12146 41.9 0 12146
86 108938 41.9 0 108938
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34097 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.2%
C: 31.8%
G: 0.0%
T: 35.7%
none/other: 3.3%
Overview of removed sequences
length count expect max.err error counts
3 14898 42874.5 0 14898
4 3162 10718.6 0 3162
5 855 2679.7 0 855
6 416 669.9 0 416
7 342 167.5 0 342
8 333 41.9 0 333
9 303 41.9 0 303
10 298 41.9 0 298
11 283 41.9 0 283
12 264 41.9 0 264
13 266 41.9 0 266
14 243 41.9 0 243
15 239 41.9 0 239
16 248 41.9 0 248
17 204 41.9 0 204
18 236 41.9 0 236
19 250 41.9 0 250
20 235 41.9 0 235
21 225 41.9 0 225
22 206 41.9 0 206
23 195 41.9 0 195
24 217 41.9 0 217
25 253 41.9 0 253
26 225 41.9 0 225
27 228 41.9 0 228
28 213 41.9 0 213
29 246 41.9 0 246
30 226 41.9 0 226
31 176 41.9 0 176
32 224 41.9 0 224
33 218 41.9 0 218
34 246 41.9 0 246
35 227 41.9 0 227
36 227 41.9 0 227
37 218 41.9 0 218
38 210 41.9 0 210
39 216 41.9 0 216
40 205 41.9 0 205
41 177 41.9 0 177
42 205 41.9 0 205
43 219 41.9 0 219
44 185 41.9 0 185
45 202 41.9 0 202
46 212 41.9 0 212
47 215 41.9 0 215
48 193 41.9 0 193
49 183 41.9 0 183
50 191 41.9 0 191
51 185 41.9 0 185
52 177 41.9 0 177
53 173 41.9 0 173
54 167 41.9 0 167
55 177 41.9 0 177
56 178 41.9 0 178
57 180 41.9 0 180
58 173 41.9 0 173
59 172 41.9 0 172
60 158 41.9 0 158
61 136 41.9 0 136
62 132 41.9 0 132
63 113 41.9 0 113
64 134 41.9 0 134
65 115 41.9 0 115
66 110 41.9 0 110
67 128 41.9 0 128
68 115 41.9 0 115
69 80 41.9 0 80
70 84 41.9 0 84
71 80 41.9 0 80
72 68 41.9 0 68
73 69 41.9 0 69
74 52 41.9 0 52
75 57 41.9 0 57
76 29 41.9 0 29
77 29 41.9 0 29
78 39 41.9 0 39
79 19 41.9 0 19
80 34 41.9 0 34
81 23 41.9 0 23
82 27 41.9 0 27
83 26 41.9 0 26
84 30 41.9 0 30
85 44 41.9 0 44
86 1126 41.9 0 1126
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 59681 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 23.4%
G: 20.6%
T: 20.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44841 42874.5 0 44841
4 9907 10718.6 0 9907
5 2012 2679.7 0 2012
6 285 669.9 0 285
7 22 167.5 0 22
8 48 167.5 0 48
9 26 167.5 0 26
10 23 167.5 0 23
11 46 167.5 0 46
12 32 167.5 0 32
13 39 167.5 0 39
14 53 167.5 0 53
15 22 167.5 0 22
16 36 167.5 0 36
17 33 167.5 0 33
18 22 167.5 0 22
19 57 167.5 0 57
20 39 167.5 0 39
21 41 167.5 0 41
22 51 167.5 0 51
23 31 167.5 0 31
24 36 167.5 0 36
25 43 167.5 0 43
26 34 167.5 0 34
27 36 167.5 0 36
28 40 167.5 0 40
29 32 167.5 0 32
30 38 167.5 0 38
31 24 167.5 0 24
32 53 167.5 0 53
33 37 167.5 0 37
34 24 167.5 0 24
35 25 167.5 0 25
36 32 167.5 0 32
37 25 167.5 0 25
38 25 167.5 0 25
39 38 167.5 0 38
40 25 167.5 0 25
41 29 167.5 0 29
42 30 167.5 0 30
43 29 167.5 0 29
44 30 167.5 0 30
45 29 167.5 0 29
46 25 167.5 0 25
47 30 167.5 0 30
48 41 167.5 0 41
49 21 167.5 0 21
50 27 167.5 0 27
51 28 167.5 0 28
52 35 167.5 0 35
53 17 167.5 0 17
54 27 167.5 0 27
55 38 167.5 0 38
56 18 167.5 0 18
57 35 167.5 0 35
58 34 167.5 0 34
59 37 167.5 0 37
60 31 167.5 0 31
61 24 167.5 0 24
62 39 167.5 0 39
63 29 167.5 0 29
64 30 167.5 0 30
65 42 167.5 0 42
66 38 167.5 0 38
67 33 167.5 0 33
68 23 167.5 0 23
69 36 167.5 0 36
70 31 167.5 0 31
71 32 167.5 0 32
72 34 167.5 0 34
73 20 167.5 0 20
74 25 167.5 0 25
75 24 167.5 0 24
76 19 167.5 0 19
77 74 167.5 0 74
78 49 167.5 0 49
79 31 167.5 0 31
80 23 167.5 0 23
81 31 167.5 0 31
82 29 167.5 0 29
83 40 167.5 0 40
84 26 167.5 0 26
85 34 167.5 0 34
86 41 167.5 0 41
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N44_S171_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N44_S171_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.33 s (9 µs/read; 6.37 M reads/minute).
=== Summary ===
Total reads processed: 2,797,165
Reads with adapters: 932,234 (33.3%)
== Read fate breakdown ==
Reads that were too short: 267,239 (9.6%)
Reads written (passing filters): 2,529,926 (90.4%)
Total basepairs processed: 282,513,665 bp
Total written (filtered): 199,622,635 bp (70.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 836498 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.8%
G: 27.5%
T: 28.9%
none/other: 13.7%
Overview of removed sequences
length count expect max.err error counts
3 64387 43705.7 0 64387
4 28250 10926.4 0 28250
5 14987 2731.6 0 14987
6 10157 682.9 0 10157
7 8074 170.7 0 8074
8 7180 42.7 0 7180
9 7154 42.7 0 7154
10 7409 42.7 0 7409
11 7298 42.7 0 7298
12 7255 42.7 0 7255
13 7151 42.7 0 7151
14 7482 42.7 0 7482
15 7458 42.7 0 7458
16 7512 42.7 0 7512
17 7352 42.7 0 7352
18 7458 42.7 0 7458
19 7206 42.7 0 7206
20 7131 42.7 0 7131
21 7448 42.7 0 7448
22 7205 42.7 0 7205
23 6878 42.7 0 6878
24 7061 42.7 0 7061
25 7153 42.7 0 7153
26 6889 42.7 0 6889
27 7162 42.7 0 7162
28 7619 42.7 0 7619
29 7467 42.7 0 7467
30 7322 42.7 0 7322
31 7912 42.7 0 7912
32 7447 42.7 0 7447
33 8343 42.7 0 8343
34 7965 42.7 0 7965
35 7678 42.7 0 7678
36 7371 42.7 0 7371
37 7311 42.7 0 7311
38 6984 42.7 0 6984
39 7285 42.7 0 7285
40 7343 42.7 0 7343
41 7354 42.7 0 7354
42 7478 42.7 0 7478
43 7364 42.7 0 7364
44 6794 42.7 0 6794
45 7278 42.7 0 7278
46 7661 42.7 0 7661
47 7329 42.7 0 7329
48 7285 42.7 0 7285
49 11014 42.7 0 11014
50 13624 42.7 0 13624
51 7913 42.7 0 7913
52 8635 42.7 0 8635
53 8029 42.7 0 8029
54 7147 42.7 0 7147
55 7516 42.7 0 7516
56 7415 42.7 0 7415
57 7449 42.7 0 7449
58 8001 42.7 0 8001
59 7519 42.7 0 7519
60 7307 42.7 0 7307
61 7663 42.7 0 7663
62 7368 42.7 0 7368
63 7140 42.7 0 7140
64 7150 42.7 0 7150
65 7049 42.7 0 7049
66 7010 42.7 0 7010
67 6937 42.7 0 6937
68 6814 42.7 0 6814
69 6672 42.7 0 6672
70 6327 42.7 0 6327
71 6995 42.7 0 6995
72 7120 42.7 0 7120
73 6654 42.7 0 6654
74 6334 42.7 0 6334
75 6378 42.7 0 6378
76 6231 42.7 0 6231
77 6272 42.7 0 6272
78 6543 42.7 0 6543
79 7554 42.7 0 7554
80 7219 42.7 0 7219
81 8937 42.7 0 8937
82 10417 42.7 0 10417
83 11034 42.7 0 11034
84 12264 42.7 0 12264
85 12633 42.7 0 12633
86 114927 42.7 0 114927
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34783 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.8%
C: 32.1%
G: 0.0%
T: 35.7%
none/other: 3.4%
Overview of removed sequences
length count expect max.err error counts
3 15211 43705.7 0 15211
4 3110 10926.4 0 3110
5 888 2731.6 0 888
6 413 682.9 0 413
7 359 170.7 0 359
8 365 42.7 0 365
9 323 42.7 0 323
10 290 42.7 0 290
11 284 42.7 0 284
12 250 42.7 0 250
13 260 42.7 0 260
14 237 42.7 0 237
15 233 42.7 0 233
16 243 42.7 0 243
17 217 42.7 0 217
18 233 42.7 0 233
19 234 42.7 0 234
20 245 42.7 0 245
21 226 42.7 0 226
22 214 42.7 0 214
23 199 42.7 0 199
24 236 42.7 0 236
25 247 42.7 0 247
26 250 42.7 0 250
27 185 42.7 0 185
28 225 42.7 0 225
29 213 42.7 0 213
30 226 42.7 0 226
31 227 42.7 0 227
32 230 42.7 0 230
33 214 42.7 0 214
34 229 42.7 0 229
35 222 42.7 0 222
36 218 42.7 0 218
37 198 42.7 0 198
38 187 42.7 0 187
39 211 42.7 0 211
40 247 42.7 0 247
41 222 42.7 0 222
42 204 42.7 0 204
43 186 42.7 0 186
44 198 42.7 0 198
45 234 42.7 0 234
46 202 42.7 0 202
47 210 42.7 0 210
48 197 42.7 0 197
49 203 42.7 0 203
50 211 42.7 0 211
51 202 42.7 0 202
52 213 42.7 0 213
53 209 42.7 0 209
54 185 42.7 0 185
55 181 42.7 0 181
56 214 42.7 0 214
57 162 42.7 0 162
58 175 42.7 0 175
59 162 42.7 0 162
60 158 42.7 0 158
61 139 42.7 0 139
62 154 42.7 0 154
63 136 42.7 0 136
64 129 42.7 0 129
65 135 42.7 0 135
66 114 42.7 0 114
67 108 42.7 0 108
68 103 42.7 0 103
69 101 42.7 0 101
70 88 42.7 0 88
71 86 42.7 0 86
72 77 42.7 0 77
73 53 42.7 0 53
74 64 42.7 0 64
75 53 42.7 0 53
76 39 42.7 0 39
77 23 42.7 0 23
78 27 42.7 0 27
79 31 42.7 0 31
80 33 42.7 0 33
81 27 42.7 0 27
82 29 42.7 0 29
83 36 42.7 0 36
84 39 42.7 0 39
85 49 42.7 0 49
86 1183 42.7 0 1183
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60953 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 23.3%
G: 20.5%
T: 21.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45756 43705.7 0 45756
4 10155 10926.4 0 10155
5 1931 2731.6 0 1931
6 316 682.9 0 316
7 38 170.7 0 38
8 35 170.7 0 35
9 30 170.7 0 30
10 25 170.7 0 25
11 44 170.7 0 44
12 39 170.7 0 39
13 36 170.7 0 36
14 49 170.7 0 49
15 29 170.7 0 29
16 36 170.7 0 36
17 49 170.7 0 49
18 40 170.7 0 40
19 60 170.7 0 60
20 49 170.7 0 49
21 40 170.7 0 40
22 37 170.7 0 37
23 32 170.7 0 32
24 24 170.7 0 24
25 41 170.7 0 41
26 35 170.7 0 35
27 32 170.7 0 32
28 55 170.7 0 55
29 43 170.7 0 43
30 29 170.7 0 29
31 31 170.7 0 31
32 39 170.7 0 39
33 40 170.7 0 40
34 26 170.7 0 26
35 18 170.7 0 18
36 31 170.7 0 31
37 24 170.7 0 24
38 40 170.7 0 40
39 39 170.7 0 39
40 27 170.7 0 27
41 23 170.7 0 23
42 29 170.7 0 29
43 39 170.7 0 39
44 31 170.7 0 31
45 30 170.7 0 30
46 33 170.7 0 33
47 31 170.7 0 31
48 30 170.7 0 30
49 33 170.7 0 33
50 31 170.7 0 31
51 39 170.7 0 39
52 40 170.7 0 40
53 29 170.7 0 29
54 38 170.7 0 38
55 32 170.7 0 32
56 30 170.7 0 30
57 38 170.7 0 38
58 25 170.7 0 25
59 31 170.7 0 31
60 25 170.7 0 25
61 30 170.7 0 30
62 37 170.7 0 37
63 21 170.7 0 21
64 27 170.7 0 27
65 37 170.7 0 37
66 36 170.7 0 36
67 27 170.7 0 27
68 42 170.7 0 42
69 20 170.7 0 20
70 25 170.7 0 25
71 29 170.7 0 29
72 22 170.7 0 22
73 48 170.7 0 48
74 36 170.7 0 36
75 22 170.7 0 22
76 29 170.7 0 29
77 70 170.7 0 70
78 36 170.7 0 36
79 29 170.7 0 29
80 37 170.7 0 37
81 38 170.7 0 38
82 43 170.7 0 43
83 41 170.7 0 41
84 52 170.7 0 52
85 36 170.7 0 36
86 46 170.7 0 46
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N45_S166_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N45_S166_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.51 s (9 µs/read; 6.42 M reads/minute).
=== Summary ===
Total reads processed: 2,943,200
Reads with adapters: 974,042 (33.1%)
== Read fate breakdown ==
Reads that were too short: 296,752 (10.1%)
Reads written (passing filters): 2,646,448 (89.9%)
Total basepairs processed: 297,263,200 bp
Total written (filtered): 209,369,964 bp (70.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 877957 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.1%
G: 27.6%
T: 27.5%
none/other: 15.8%
Overview of removed sequences
length count expect max.err error counts
3 66814 45987.5 0 66814
4 28819 11496.9 0 28819
5 14979 2874.2 0 14979
6 10151 718.6 0 10151
7 8055 179.6 0 8055
8 7235 44.9 0 7235
9 7235 44.9 0 7235
10 7236 44.9 0 7236
11 7126 44.9 0 7126
12 7240 44.9 0 7240
13 7305 44.9 0 7305
14 7487 44.9 0 7487
15 7440 44.9 0 7440
16 7583 44.9 0 7583
17 7469 44.9 0 7469
18 7645 44.9 0 7645
19 7527 44.9 0 7527
20 7235 44.9 0 7235
21 7327 44.9 0 7327
22 7652 44.9 0 7652
23 6960 44.9 0 6960
24 7146 44.9 0 7146
25 7208 44.9 0 7208
26 7077 44.9 0 7077
27 7249 44.9 0 7249
28 7510 44.9 0 7510
29 7581 44.9 0 7581
30 7239 44.9 0 7239
31 7750 44.9 0 7750
32 7328 44.9 0 7328
33 7833 44.9 0 7833
34 7557 44.9 0 7557
35 8064 44.9 0 8064
36 7147 44.9 0 7147
37 7337 44.9 0 7337
38 7219 44.9 0 7219
39 7367 44.9 0 7367
40 7538 44.9 0 7538
41 7881 44.9 0 7881
42 7705 44.9 0 7705
43 8519 44.9 0 8519
44 7639 44.9 0 7639
45 7843 44.9 0 7843
46 8555 44.9 0 8555
47 8267 44.9 0 8267
48 7537 44.9 0 7537
49 12033 44.9 0 12033
50 14476 44.9 0 14476
51 7843 44.9 0 7843
52 8377 44.9 0 8377
53 8333 44.9 0 8333
54 7002 44.9 0 7002
55 7561 44.9 0 7561
56 7668 44.9 0 7668
57 6993 44.9 0 6993
58 7771 44.9 0 7771
59 7688 44.9 0 7688
60 7518 44.9 0 7518
61 7801 44.9 0 7801
62 7843 44.9 0 7843
63 7288 44.9 0 7288
64 7095 44.9 0 7095
65 7045 44.9 0 7045
66 6991 44.9 0 6991
67 7128 44.9 0 7128
68 7072 44.9 0 7072
69 6915 44.9 0 6915
70 6631 44.9 0 6631
71 7446 44.9 0 7446
72 7554 44.9 0 7554
73 7103 44.9 0 7103
74 7078 44.9 0 7078
75 7022 44.9 0 7022
76 6615 44.9 0 6615
77 6966 44.9 0 6966
78 6921 44.9 0 6921
79 7946 44.9 0 7946
80 7569 44.9 0 7569
81 8554 44.9 0 8554
82 10032 44.9 0 10032
83 11234 44.9 0 11234
84 12403 44.9 0 12403
85 12728 44.9 0 12728
86 139098 44.9 0 139098
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 31483 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.6%
C: 31.6%
G: 0.0%
T: 33.1%
none/other: 3.8%
Overview of removed sequences
length count expect max.err error counts
3 15968 45987.5 0 15968
4 3281 11496.9 0 3281
5 842 2874.2 0 842
6 327 718.6 0 327
7 342 179.6 0 342
8 349 44.9 0 349
9 315 44.9 0 315
10 285 44.9 0 285
11 272 44.9 0 272
12 215 44.9 0 215
13 198 44.9 0 198
14 186 44.9 0 186
15 191 44.9 0 191
16 177 44.9 0 177
17 167 44.9 0 167
18 181 44.9 0 181
19 179 44.9 0 179
20 158 44.9 0 158
21 144 44.9 0 144
22 158 44.9 0 158
23 175 44.9 0 175
24 180 44.9 0 180
25 150 44.9 0 150
26 155 44.9 0 155
27 134 44.9 0 134
28 145 44.9 0 145
29 144 44.9 0 144
30 141 44.9 0 141
31 140 44.9 0 140
32 135 44.9 0 135
33 143 44.9 0 143
34 167 44.9 0 167
35 151 44.9 0 151
36 138 44.9 0 138
37 155 44.9 0 155
38 126 44.9 0 126
39 125 44.9 0 125
40 142 44.9 0 142
41 125 44.9 0 125
42 135 44.9 0 135
43 127 44.9 0 127
44 140 44.9 0 140
45 118 44.9 0 118
46 146 44.9 0 146
47 118 44.9 0 118
48 135 44.9 0 135
49 148 44.9 0 148
50 118 44.9 0 118
51 106 44.9 0 106
52 125 44.9 0 125
53 125 44.9 0 125
54 94 44.9 0 94
55 107 44.9 0 107
56 112 44.9 0 112
57 101 44.9 0 101
58 104 44.9 0 104
59 103 44.9 0 103
60 105 44.9 0 105
61 103 44.9 0 103
62 109 44.9 0 109
63 102 44.9 0 102
64 91 44.9 0 91
65 88 44.9 0 88
66 73 44.9 0 73
67 69 44.9 0 69
68 63 44.9 0 63
69 61 44.9 0 61
70 58 44.9 0 58
71 56 44.9 0 56
72 46 44.9 0 46
73 31 44.9 0 31
74 35 44.9 0 35
75 41 44.9 0 41
76 18 44.9 0 18
77 13 44.9 0 13
78 19 44.9 0 19
79 26 44.9 0 26
80 36 44.9 0 36
81 26 44.9 0 26
82 36 44.9 0 36
83 31 44.9 0 31
84 46 44.9 0 46
85 42 44.9 0 42
86 1191 44.9 0 1191
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 64602 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.1%
C: 24.2%
G: 20.3%
T: 20.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 48453 45987.5 0 48453
4 10464 11496.9 0 10464
5 2178 2874.2 0 2178
6 304 718.6 0 304
7 33 179.6 0 33
8 42 179.6 0 42
9 48 179.6 0 48
10 39 179.6 0 39
11 41 179.6 0 41
12 37 179.6 0 37
13 39 179.6 0 39
14 59 179.6 0 59
15 42 179.6 0 42
16 40 179.6 0 40
17 52 179.6 0 52
18 48 179.6 0 48
19 63 179.6 0 63
20 53 179.6 0 53
21 43 179.6 0 43
22 51 179.6 0 51
23 30 179.6 0 30
24 40 179.6 0 40
25 56 179.6 0 56
26 36 179.6 0 36
27 27 179.6 0 27
28 53 179.6 0 53
29 38 179.6 0 38
30 40 179.6 0 40
31 44 179.6 0 44
32 35 179.6 0 35
33 61 179.6 0 61
34 24 179.6 0 24
35 39 179.6 0 39
36 31 179.6 0 31
37 33 179.6 0 33
38 30 179.6 0 30
39 45 179.6 0 45
40 32 179.6 0 32
41 54 179.6 0 54
42 39 179.6 0 39
43 33 179.6 0 33
44 35 179.6 0 35
45 39 179.6 0 39
46 24 179.6 0 24
47 33 179.6 0 33
48 28 179.6 0 28
49 35 179.6 0 35
50 43 179.6 0 43
51 46 179.6 0 46
52 43 179.6 0 43
53 45 179.6 0 45
54 42 179.6 0 42
55 32 179.6 0 32
56 31 179.6 0 31
57 45 179.6 0 45
58 41 179.6 0 41
59 30 179.6 0 30
60 27 179.6 0 27
61 41 179.6 0 41
62 32 179.6 0 32
63 41 179.6 0 41
64 33 179.6 0 33
65 44 179.6 0 44
66 50 179.6 0 50
67 35 179.6 0 35
68 40 179.6 0 40
69 36 179.6 0 36
70 51 179.6 0 51
71 51 179.6 0 51
72 33 179.6 0 33
73 36 179.6 0 36
74 40 179.6 0 40
75 28 179.6 0 28
76 18 179.6 0 18
77 97 179.6 0 97
78 68 179.6 0 68
79 32 179.6 0 32
80 24 179.6 0 24
81 22 179.6 0 22
82 26 179.6 0 26
83 37 179.6 0 37
84 53 179.6 0 53
85 25 179.6 0 25
86 41 179.6 0 41
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N45_S166_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N45_S166_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.97 s (9 µs/read; 6.65 M reads/minute).
=== Summary ===
Total reads processed: 2,990,947
Reads with adapters: 998,276 (33.4%)
== Read fate breakdown ==
Reads that were too short: 309,570 (10.4%)
Reads written (passing filters): 2,681,377 (89.6%)
Total basepairs processed: 302,085,647 bp
Total written (filtered): 211,926,858 bp (70.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 900752 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.0%
G: 27.4%
T: 27.3%
none/other: 16.3%
Overview of removed sequences
length count expect max.err error counts
3 67031 46733.5 0 67031
4 28690 11683.4 0 28690
5 15274 2920.8 0 15274
6 10258 730.2 0 10258
7 8101 182.6 0 8101
8 7219 45.6 0 7219
9 7450 45.6 0 7450
10 7413 45.6 0 7413
11 7120 45.6 0 7120
12 7374 45.6 0 7374
13 7248 45.6 0 7248
14 7524 45.6 0 7524
15 7795 45.6 0 7795
16 7562 45.6 0 7562
17 7633 45.6 0 7633
18 7812 45.6 0 7812
19 7604 45.6 0 7604
20 7351 45.6 0 7351
21 7403 45.6 0 7403
22 7504 45.6 0 7504
23 7055 45.6 0 7055
24 7262 45.6 0 7262
25 7071 45.6 0 7071
26 7132 45.6 0 7132
27 7187 45.6 0 7187
28 7503 45.6 0 7503
29 7760 45.6 0 7760
30 7241 45.6 0 7241
31 7957 45.6 0 7957
32 7550 45.6 0 7550
33 8012 45.6 0 8012
34 7820 45.6 0 7820
35 8069 45.6 0 8069
36 7170 45.6 0 7170
37 7493 45.6 0 7493
38 7535 45.6 0 7535
39 7520 45.6 0 7520
40 7739 45.6 0 7739
41 8189 45.6 0 8189
42 7942 45.6 0 7942
43 8765 45.6 0 8765
44 7810 45.6 0 7810
45 8091 45.6 0 8091
46 8805 45.6 0 8805
47 8257 45.6 0 8257
48 7653 45.6 0 7653
49 12375 45.6 0 12375
50 14951 45.6 0 14951
51 8162 45.6 0 8162
52 8609 45.6 0 8609
53 8521 45.6 0 8521
54 7088 45.6 0 7088
55 7781 45.6 0 7781
56 7764 45.6 0 7764
57 7465 45.6 0 7465
58 7900 45.6 0 7900
59 7938 45.6 0 7938
60 7979 45.6 0 7979
61 7994 45.6 0 7994
62 7718 45.6 0 7718
63 7523 45.6 0 7523
64 7729 45.6 0 7729
65 7422 45.6 0 7422
66 7155 45.6 0 7155
67 7482 45.6 0 7482
68 7229 45.6 0 7229
69 7077 45.6 0 7077
70 6727 45.6 0 6727
71 7581 45.6 0 7581
72 7700 45.6 0 7700
73 7360 45.6 0 7360
74 7114 45.6 0 7114
75 7471 45.6 0 7471
76 6966 45.6 0 6966
77 7175 45.6 0 7175
78 7125 45.6 0 7125
79 8136 45.6 0 8136
80 7741 45.6 0 7741
81 8817 45.6 0 8817
82 10367 45.6 0 10367
83 11601 45.6 0 11601
84 12705 45.6 0 12705
85 13401 45.6 0 13401
86 146949 45.6 0 146949
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 31787 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.5%
C: 31.5%
G: 0.0%
T: 33.2%
none/other: 3.8%
Overview of removed sequences
length count expect max.err error counts
3 16169 46733.5 0 16169
4 3224 11683.4 0 3224
5 842 2920.8 0 842
6 314 730.2 0 314
7 311 182.6 0 311
8 344 45.6 0 344
9 302 45.6 0 302
10 282 45.6 0 282
11 268 45.6 0 268
12 225 45.6 0 225
13 189 45.6 0 189
14 156 45.6 0 156
15 188 45.6 0 188
16 171 45.6 0 171
17 174 45.6 0 174
18 162 45.6 0 162
19 164 45.6 0 164
20 160 45.6 0 160
21 162 45.6 0 162
22 171 45.6 0 171
23 157 45.6 0 157
24 151 45.6 0 151
25 155 45.6 0 155
26 147 45.6 0 147
27 119 45.6 0 119
28 160 45.6 0 160
29 157 45.6 0 157
30 162 45.6 0 162
31 144 45.6 0 144
32 176 45.6 0 176
33 145 45.6 0 145
34 163 45.6 0 163
35 151 45.6 0 151
36 135 45.6 0 135
37 145 45.6 0 145
38 130 45.6 0 130
39 163 45.6 0 163
40 114 45.6 0 114
41 137 45.6 0 137
42 137 45.6 0 137
43 122 45.6 0 122
44 142 45.6 0 142
45 137 45.6 0 137
46 159 45.6 0 159
47 131 45.6 0 131
48 112 45.6 0 112
49 126 45.6 0 126
50 148 45.6 0 148
51 126 45.6 0 126
52 135 45.6 0 135
53 132 45.6 0 132
54 121 45.6 0 121
55 138 45.6 0 138
56 91 45.6 0 91
57 91 45.6 0 91
58 120 45.6 0 120
59 113 45.6 0 113
60 121 45.6 0 121
61 107 45.6 0 107
62 103 45.6 0 103
63 114 45.6 0 114
64 86 45.6 0 86
65 92 45.6 0 92
66 91 45.6 0 91
67 69 45.6 0 69
68 68 45.6 0 68
69 66 45.6 0 66
70 62 45.6 0 62
71 49 45.6 0 49
72 49 45.6 0 49
73 50 45.6 0 50
74 35 45.6 0 35
75 33 45.6 0 33
76 17 45.6 0 17
77 22 45.6 0 22
78 21 45.6 0 21
79 31 45.6 0 31
80 29 45.6 0 29
81 26 45.6 0 26
82 31 45.6 0 31
83 35 45.6 0 35
84 49 45.6 0 49
85 62 45.6 0 62
86 1199 45.6 0 1199
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 65737 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.1%
C: 24.1%
G: 20.2%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 48990 46733.5 0 48990
4 10742 11683.4 0 10742
5 2344 2920.8 0 2344
6 354 730.2 0 354
7 32 182.6 0 32
8 38 182.6 0 38
9 38 182.6 0 38
10 34 182.6 0 34
11 51 182.6 0 51
12 51 182.6 0 51
13 49 182.6 0 49
14 48 182.6 0 48
15 36 182.6 0 36
16 41 182.6 0 41
17 40 182.6 0 40
18 37 182.6 0 37
19 75 182.6 0 75
20 42 182.6 0 42
21 30 182.6 0 30
22 54 182.6 0 54
23 32 182.6 0 32
24 51 182.6 0 51
25 61 182.6 0 61
26 34 182.6 0 34
27 33 182.6 0 33
28 48 182.6 0 48
29 34 182.6 0 34
30 33 182.6 0 33
31 42 182.6 0 42
32 45 182.6 0 45
33 39 182.6 0 39
34 35 182.6 0 35
35 30 182.6 0 30
36 40 182.6 0 40
37 28 182.6 0 28
38 49 182.6 0 49
39 51 182.6 0 51
40 45 182.6 0 45
41 33 182.6 0 33
42 25 182.6 0 25
43 32 182.6 0 32
44 36 182.6 0 36
45 36 182.6 0 36
46 26 182.6 0 26
47 44 182.6 0 44
48 50 182.6 0 50
49 33 182.6 0 33
50 37 182.6 0 37
51 48 182.6 0 48
52 45 182.6 0 45
53 20 182.6 0 20
54 53 182.6 0 53
55 26 182.6 0 26
56 53 182.6 0 53
57 31 182.6 0 31
58 50 182.6 0 50
59 44 182.6 0 44
60 48 182.6 0 48
61 41 182.6 0 41
62 48 182.6 0 48
63 47 182.6 0 47
64 35 182.6 0 35
65 47 182.6 0 47
66 50 182.6 0 50
67 38 182.6 0 38
68 28 182.6 0 28
69 34 182.6 0 34
70 43 182.6 0 43
71 45 182.6 0 45
72 26 182.6 0 26
73 43 182.6 0 43
74 31 182.6 0 31
75 26 182.6 0 26
76 28 182.6 0 28
77 117 182.6 0 117
78 57 182.6 0 57
79 35 182.6 0 35
80 37 182.6 0 37
81 37 182.6 0 37
82 35 182.6 0 35
83 41 182.6 0 41
84 36 182.6 0 36
85 53 182.6 0 53
86 53 182.6 0 53
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N46_S170_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N46_S170_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.32 s (9 µs/read; 6.51 M reads/minute).
=== Summary ===
Total reads processed: 2,854,813
Reads with adapters: 955,330 (33.5%)
== Read fate breakdown ==
Reads that were too short: 274,800 (9.6%)
Reads written (passing filters): 2,580,013 (90.4%)
Total basepairs processed: 288,336,113 bp
Total written (filtered): 203,511,774 bp (70.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 866076 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.6%
G: 27.8%
T: 28.6%
none/other: 13.9%
Overview of removed sequences
length count expect max.err error counts
3 66250 44606.5 0 66250
4 28638 11151.6 0 28638
5 14925 2787.9 0 14925
6 9994 697.0 0 9994
7 8303 174.2 0 8303
8 7330 43.6 0 7330
9 7418 43.6 0 7418
10 7354 43.6 0 7354
11 7246 43.6 0 7246
12 7164 43.6 0 7164
13 7456 43.6 0 7456
14 7276 43.6 0 7276
15 8103 43.6 0 8103
16 8462 43.6 0 8462
17 7752 43.6 0 7752
18 8203 43.6 0 8203
19 8189 43.6 0 8189
20 7455 43.6 0 7455
21 8169 43.6 0 8169
22 8287 43.6 0 8287
23 7324 43.6 0 7324
24 7175 43.6 0 7175
25 7293 43.6 0 7293
26 7284 43.6 0 7284
27 7150 43.6 0 7150
28 7669 43.6 0 7669
29 7435 43.6 0 7435
30 7350 43.6 0 7350
31 8673 43.6 0 8673
32 7812 43.6 0 7812
33 8578 43.6 0 8578
34 8425 43.6 0 8425
35 8387 43.6 0 8387
36 7606 43.6 0 7606
37 8519 43.6 0 8519
38 7720 43.6 0 7720
39 7280 43.6 0 7280
40 7472 43.6 0 7472
41 8234 43.6 0 8234
42 7884 43.6 0 7884
43 9202 43.6 0 9202
44 8009 43.6 0 8009
45 7885 43.6 0 7885
46 8890 43.6 0 8890
47 8331 43.6 0 8331
48 7446 43.6 0 7446
49 12993 43.6 0 12993
50 15075 43.6 0 15075
51 7770 43.6 0 7770
52 8087 43.6 0 8087
53 7796 43.6 0 7796
54 6894 43.6 0 6894
55 7127 43.6 0 7127
56 7437 43.6 0 7437
57 6925 43.6 0 6925
58 7470 43.6 0 7470
59 7335 43.6 0 7335
60 7354 43.6 0 7354
61 7499 43.6 0 7499
62 7277 43.6 0 7277
63 6979 43.6 0 6979
64 6987 43.6 0 6987
65 7261 43.6 0 7261
66 6698 43.6 0 6698
67 6952 43.6 0 6952
68 7041 43.6 0 7041
69 6430 43.6 0 6430
70 6119 43.6 0 6119
71 6949 43.6 0 6949
72 6829 43.6 0 6829
73 6582 43.6 0 6582
74 6338 43.6 0 6338
75 6501 43.6 0 6501
76 6503 43.6 0 6503
77 6591 43.6 0 6591
78 6759 43.6 0 6759
79 8045 43.6 0 8045
80 7318 43.6 0 7318
81 8689 43.6 0 8689
82 10564 43.6 0 10564
83 11360 43.6 0 11360
84 12637 43.6 0 12637
85 13274 43.6 0 13274
86 120624 43.6 0 120624
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27530 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.1%
C: 31.0%
G: 0.0%
T: 33.7%
none/other: 4.2%
Overview of removed sequences
length count expect max.err error counts
3 14481 44606.5 0 14481
4 3065 11151.6 0 3065
5 762 2787.9 0 762
6 262 697.0 0 262
7 213 174.2 0 213
8 233 43.6 0 233
9 222 43.6 0 222
10 184 43.6 0 184
11 183 43.6 0 183
12 181 43.6 0 181
13 131 43.6 0 131
14 146 43.6 0 146
15 151 43.6 0 151
16 160 43.6 0 160
17 110 43.6 0 110
18 134 43.6 0 134
19 121 43.6 0 121
20 122 43.6 0 122
21 117 43.6 0 117
22 105 43.6 0 105
23 123 43.6 0 123
24 111 43.6 0 111
25 138 43.6 0 138
26 122 43.6 0 122
27 112 43.6 0 112
28 117 43.6 0 117
29 114 43.6 0 114
30 129 43.6 0 129
31 99 43.6 0 99
32 123 43.6 0 123
33 108 43.6 0 108
34 114 43.6 0 114
35 121 43.6 0 121
36 115 43.6 0 115
37 93 43.6 0 93
38 108 43.6 0 108
39 99 43.6 0 99
40 112 43.6 0 112
41 126 43.6 0 126
42 113 43.6 0 113
43 113 43.6 0 113
44 97 43.6 0 97
45 110 43.6 0 110
46 115 43.6 0 115
47 112 43.6 0 112
48 140 43.6 0 140
49 104 43.6 0 104
50 109 43.6 0 109
51 101 43.6 0 101
52 104 43.6 0 104
53 117 43.6 0 117
54 98 43.6 0 98
55 103 43.6 0 103
56 90 43.6 0 90
57 98 43.6 0 98
58 83 43.6 0 83
59 96 43.6 0 96
60 98 43.6 0 98
61 87 43.6 0 87
62 68 43.6 0 68
63 72 43.6 0 72
64 73 43.6 0 73
65 50 43.6 0 50
66 43 43.6 0 43
67 62 43.6 0 62
68 78 43.6 0 78
69 37 43.6 0 37
70 47 43.6 0 47
71 40 43.6 0 40
72 49 43.6 0 49
73 36 43.6 0 36
74 31 43.6 0 31
75 27 43.6 0 27
76 27 43.6 0 27
77 23 43.6 0 23
78 22 43.6 0 22
79 23 43.6 0 23
80 23 43.6 0 23
81 17 43.6 0 17
82 23 43.6 0 23
83 39 43.6 0 39
84 35 43.6 0 35
85 66 43.6 0 66
86 1164 43.6 0 1164
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61724 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.5%
C: 23.4%
G: 20.8%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45840 44606.5 0 45840
4 10342 11151.6 0 10342
5 2272 2787.9 0 2272
6 296 697.0 0 296
7 26 174.2 0 26
8 41 174.2 0 41
9 34 174.2 0 34
10 28 174.2 0 28
11 46 174.2 0 46
12 27 174.2 0 27
13 43 174.2 0 43
14 51 174.2 0 51
15 29 174.2 0 29
16 42 174.2 0 42
17 39 174.2 0 39
18 41 174.2 0 41
19 50 174.2 0 50
20 52 174.2 0 52
21 34 174.2 0 34
22 37 174.2 0 37
23 26 174.2 0 26
24 27 174.2 0 27
25 49 174.2 0 49
26 38 174.2 0 38
27 41 174.2 0 41
28 29 174.2 0 29
29 37 174.2 0 37
30 52 174.2 0 52
31 26 174.2 0 26
32 43 174.2 0 43
33 44 174.2 0 44
34 31 174.2 0 31
35 26 174.2 0 26
36 37 174.2 0 37
37 18 174.2 0 18
38 28 174.2 0 28
39 52 174.2 0 52
40 43 174.2 0 43
41 29 174.2 0 29
42 28 174.2 0 28
43 44 174.2 0 44
44 33 174.2 0 33
45 39 174.2 0 39
46 26 174.2 0 26
47 25 174.2 0 25
48 26 174.2 0 26
49 41 174.2 0 41
50 26 174.2 0 26
51 43 174.2 0 43
52 43 174.2 0 43
53 33 174.2 0 33
54 35 174.2 0 35
55 27 174.2 0 27
56 32 174.2 0 32
57 40 174.2 0 40
58 36 174.2 0 36
59 22 174.2 0 22
60 33 174.2 0 33
61 36 174.2 0 36
62 36 174.2 0 36
63 26 174.2 0 26
64 31 174.2 0 31
65 51 174.2 0 51
66 40 174.2 0 40
67 36 174.2 0 36
68 22 174.2 0 22
69 41 174.2 0 41
70 36 174.2 0 36
71 36 174.2 0 36
72 26 174.2 0 26
73 39 174.2 0 39
74 31 174.2 0 31
75 22 174.2 0 22
76 27 174.2 0 27
77 81 174.2 0 81
78 52 174.2 0 52
79 34 174.2 0 34
80 36 174.2 0 36
81 48 174.2 0 48
82 39 174.2 0 39
83 56 174.2 0 56
84 51 174.2 0 51
85 53 174.2 0 53
86 60 174.2 0 60
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N46_S170_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N46_S170_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.10 s (9 µs/read; 6.42 M reads/minute).
=== Summary ===
Total reads processed: 2,901,042
Reads with adapters: 982,371 (33.9%)
== Read fate breakdown ==
Reads that were too short: 288,687 (10.0%)
Reads written (passing filters): 2,612,355 (90.0%)
Total basepairs processed: 293,005,242 bp
Total written (filtered): 205,802,675 bp (70.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 891923 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.6%
G: 27.6%
T: 28.4%
none/other: 14.4%
Overview of removed sequences
length count expect max.err error counts
3 66220 45328.8 0 66220
4 28819 11332.2 0 28819
5 15186 2833.0 0 15186
6 10410 708.3 0 10410
7 8412 177.1 0 8412
8 7382 44.3 0 7382
9 7468 44.3 0 7468
10 7532 44.3 0 7532
11 7637 44.3 0 7637
12 7252 44.3 0 7252
13 7609 44.3 0 7609
14 7481 44.3 0 7481
15 8014 44.3 0 8014
16 8406 44.3 0 8406
17 8078 44.3 0 8078
18 8410 44.3 0 8410
19 8287 44.3 0 8287
20 7648 44.3 0 7648
21 8273 44.3 0 8273
22 8508 44.3 0 8508
23 7381 44.3 0 7381
24 7195 44.3 0 7195
25 7473 44.3 0 7473
26 7072 44.3 0 7072
27 7204 44.3 0 7204
28 7739 44.3 0 7739
29 7661 44.3 0 7661
30 7521 44.3 0 7521
31 8621 44.3 0 8621
32 8024 44.3 0 8024
33 8722 44.3 0 8722
34 8425 44.3 0 8425
35 8457 44.3 0 8457
36 7671 44.3 0 7671
37 8548 44.3 0 8548
38 7871 44.3 0 7871
39 7664 44.3 0 7664
40 7707 44.3 0 7707
41 8571 44.3 0 8571
42 8360 44.3 0 8360
43 9123 44.3 0 9123
44 7955 44.3 0 7955
45 8076 44.3 0 8076
46 9234 44.3 0 9234
47 8375 44.3 0 8375
48 7726 44.3 0 7726
49 13698 44.3 0 13698
50 15257 44.3 0 15257
51 8170 44.3 0 8170
52 8377 44.3 0 8377
53 8220 44.3 0 8220
54 7125 44.3 0 7125
55 7584 44.3 0 7584
56 7575 44.3 0 7575
57 7078 44.3 0 7078
58 7800 44.3 0 7800
59 7746 44.3 0 7746
60 7506 44.3 0 7506
61 7658 44.3 0 7658
62 7640 44.3 0 7640
63 7261 44.3 0 7261
64 7318 44.3 0 7318
65 7310 44.3 0 7310
66 7087 44.3 0 7087
67 7243 44.3 0 7243
68 7220 44.3 0 7220
69 6833 44.3 0 6833
70 6528 44.3 0 6528
71 7173 44.3 0 7173
72 7288 44.3 0 7288
73 6896 44.3 0 6896
74 6636 44.3 0 6636
75 6701 44.3 0 6701
76 6701 44.3 0 6701
77 6658 44.3 0 6658
78 7036 44.3 0 7036
79 8235 44.3 0 8235
80 7770 44.3 0 7770
81 9105 44.3 0 9105
82 11006 44.3 0 11006
83 12345 44.3 0 12345
84 13168 44.3 0 13168
85 13529 44.3 0 13529
86 128034 44.3 0 128034
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27972 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.6%
C: 30.3%
G: 0.0%
T: 34.0%
none/other: 4.1%
Overview of removed sequences
length count expect max.err error counts
3 14687 45328.8 0 14687
4 3082 11332.2 0 3082
5 751 2833.0 0 751
6 265 708.3 0 265
7 255 177.1 0 255
8 234 44.3 0 234
9 200 44.3 0 200
10 202 44.3 0 202
11 213 44.3 0 213
12 177 44.3 0 177
13 171 44.3 0 171
14 149 44.3 0 149
15 170 44.3 0 170
16 116 44.3 0 116
17 137 44.3 0 137
18 118 44.3 0 118
19 114 44.3 0 114
20 136 44.3 0 136
21 128 44.3 0 128
22 108 44.3 0 108
23 138 44.3 0 138
24 125 44.3 0 125
25 131 44.3 0 131
26 125 44.3 0 125
27 118 44.3 0 118
28 131 44.3 0 131
29 123 44.3 0 123
30 106 44.3 0 106
31 101 44.3 0 101
32 119 44.3 0 119
33 145 44.3 0 145
34 133 44.3 0 133
35 134 44.3 0 134
36 108 44.3 0 108
37 118 44.3 0 118
38 132 44.3 0 132
39 113 44.3 0 113
40 119 44.3 0 119
41 102 44.3 0 102
42 125 44.3 0 125
43 95 44.3 0 95
44 110 44.3 0 110
45 124 44.3 0 124
46 95 44.3 0 95
47 126 44.3 0 126
48 113 44.3 0 113
49 111 44.3 0 111
50 118 44.3 0 118
51 113 44.3 0 113
52 101 44.3 0 101
53 107 44.3 0 107
54 98 44.3 0 98
55 98 44.3 0 98
56 88 44.3 0 88
57 99 44.3 0 99
58 113 44.3 0 113
59 88 44.3 0 88
60 72 44.3 0 72
61 95 44.3 0 95
62 74 44.3 0 74
63 84 44.3 0 84
64 72 44.3 0 72
65 75 44.3 0 75
66 65 44.3 0 65
67 50 44.3 0 50
68 51 44.3 0 51
69 51 44.3 0 51
70 28 44.3 0 28
71 45 44.3 0 45
72 52 44.3 0 52
73 41 44.3 0 41
74 22 44.3 0 22
75 23 44.3 0 23
76 20 44.3 0 20
77 16 44.3 0 16
78 30 44.3 0 30
79 20 44.3 0 20
80 19 44.3 0 19
81 27 44.3 0 27
82 23 44.3 0 23
83 34 44.3 0 34
84 41 44.3 0 41
85 48 44.3 0 48
86 1138 44.3 0 1138
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 62476 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 23.5%
G: 20.9%
T: 20.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 46661 45328.8 0 46661
4 10328 11332.2 0 10328
5 2188 2833.0 0 2188
6 288 708.3 0 288
7 29 177.1 0 29
8 57 177.1 0 57
9 31 177.1 0 31
10 40 177.1 0 40
11 42 177.1 0 42
12 33 177.1 0 33
13 39 177.1 0 39
14 39 177.1 0 39
15 39 177.1 0 39
16 35 177.1 0 35
17 31 177.1 0 31
18 37 177.1 0 37
19 69 177.1 0 69
20 46 177.1 0 46
21 28 177.1 0 28
22 42 177.1 0 42
23 31 177.1 0 31
24 42 177.1 0 42
25 42 177.1 0 42
26 34 177.1 0 34
27 35 177.1 0 35
28 36 177.1 0 36
29 42 177.1 0 42
30 35 177.1 0 35
31 22 177.1 0 22
32 47 177.1 0 47
33 36 177.1 0 36
34 19 177.1 0 19
35 32 177.1 0 32
36 42 177.1 0 42
37 38 177.1 0 38
38 41 177.1 0 41
39 35 177.1 0 35
40 41 177.1 0 41
41 35 177.1 0 35
42 34 177.1 0 34
43 36 177.1 0 36
44 40 177.1 0 40
45 21 177.1 0 21
46 31 177.1 0 31
47 30 177.1 0 30
48 22 177.1 0 22
49 42 177.1 0 42
50 41 177.1 0 41
51 32 177.1 0 32
52 57 177.1 0 57
53 25 177.1 0 25
54 34 177.1 0 34
55 34 177.1 0 34
56 42 177.1 0 42
57 29 177.1 0 29
58 45 177.1 0 45
59 44 177.1 0 44
60 31 177.1 0 31
61 35 177.1 0 35
62 47 177.1 0 47
63 27 177.1 0 27
64 31 177.1 0 31
65 40 177.1 0 40
66 36 177.1 0 36
67 29 177.1 0 29
68 36 177.1 0 36
69 30 177.1 0 30
70 41 177.1 0 41
71 38 177.1 0 38
72 35 177.1 0 35
73 44 177.1 0 44
74 23 177.1 0 23
75 31 177.1 0 31
76 26 177.1 0 26
77 75 177.1 0 75
78 51 177.1 0 51
79 38 177.1 0 38
80 51 177.1 0 51
81 45 177.1 0 45
82 33 177.1 0 33
83 52 177.1 0 52
84 35 177.1 0 35
85 49 177.1 0 49
86 41 177.1 0 41
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N47_S168_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N47_S168_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.63 s (10 µs/read; 6.29 M reads/minute).
=== Summary ===
Total reads processed: 2,687,815
Reads with adapters: 776,008 (28.9%)
== Read fate breakdown ==
Reads that were too short: 150,235 (5.6%)
Reads written (passing filters): 2,537,580 (94.4%)
Total basepairs processed: 271,469,315 bp
Total written (filtered): 202,452,330 bp (74.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 685848 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 36.1%
G: 30.3%
T: 27.3%
none/other: 6.2%
Overview of removed sequences
length count expect max.err error counts
3 68236 41997.1 0 68236
4 27920 10499.3 0 27920
5 14794 2624.8 0 14794
6 9777 656.2 0 9777
7 7854 164.1 0 7854
8 6819 41.0 0 6819
9 6933 41.0 0 6933
10 7012 41.0 0 7012
11 6878 41.0 0 6878
12 6895 41.0 0 6895
13 6797 41.0 0 6797
14 6982 41.0 0 6982
15 8135 41.0 0 8135
16 8328 41.0 0 8328
17 7456 41.0 0 7456
18 8438 41.0 0 8438
19 8271 41.0 0 8271
20 6817 41.0 0 6817
21 8350 41.0 0 8350
22 8271 41.0 0 8271
23 6693 41.0 0 6693
24 6417 41.0 0 6417
25 6348 41.0 0 6348
26 6189 41.0 0 6189
27 6195 41.0 0 6195
28 6789 41.0 0 6789
29 6314 41.0 0 6314
30 6243 41.0 0 6243
31 7839 41.0 0 7839
32 6540 41.0 0 6540
33 7110 41.0 0 7110
34 7560 41.0 0 7560
35 6678 41.0 0 6678
36 6513 41.0 0 6513
37 7899 41.0 0 7899
38 6451 41.0 0 6451
39 6686 41.0 0 6686
40 6816 41.0 0 6816
41 6633 41.0 0 6633
42 7259 41.0 0 7259
43 8677 41.0 0 8677
44 6867 41.0 0 6867
45 7314 41.0 0 7314
46 7862 41.0 0 7862
47 6865 41.0 0 6865
48 6556 41.0 0 6556
49 13767 41.0 0 13767
50 10542 41.0 0 10542
51 6338 41.0 0 6338
52 6563 41.0 0 6563
53 6097 41.0 0 6097
54 5618 41.0 0 5618
55 5685 41.0 0 5685
56 5876 41.0 0 5876
57 5587 41.0 0 5587
58 5978 41.0 0 5978
59 5640 41.0 0 5640
60 5726 41.0 0 5726
61 5861 41.0 0 5861
62 5940 41.0 0 5940
63 5444 41.0 0 5444
64 5570 41.0 0 5570
65 5659 41.0 0 5659
66 5443 41.0 0 5443
67 5441 41.0 0 5441
68 5648 41.0 0 5648
69 5204 41.0 0 5204
70 5063 41.0 0 5063
71 5539 41.0 0 5539
72 5330 41.0 0 5330
73 5427 41.0 0 5427
74 4870 41.0 0 4870
75 4914 41.0 0 4914
76 4938 41.0 0 4938
77 4628 41.0 0 4628
78 5051 41.0 0 5051
79 5447 41.0 0 5447
80 4862 41.0 0 4862
81 5802 41.0 0 5802
82 6255 41.0 0 6255
83 6615 41.0 0 6615
84 7259 41.0 0 7259
85 7205 41.0 0 7205
86 42740 41.0 0 42740
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 25845 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.2%
C: 31.0%
G: 0.0%
T: 34.8%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 15255 41997.1 0 15255
4 3465 10499.3 0 3465
5 775 2624.8 0 775
6 258 656.2 0 258
7 123 164.1 0 123
8 104 41.0 0 104
9 97 41.0 0 97
10 85 41.0 0 85
11 88 41.0 0 88
12 80 41.0 0 80
13 81 41.0 0 81
14 78 41.0 0 78
15 90 41.0 0 90
16 64 41.0 0 64
17 75 41.0 0 75
18 70 41.0 0 70
19 80 41.0 0 80
20 99 41.0 0 99
21 90 41.0 0 90
22 100 41.0 0 100
23 88 41.0 0 88
24 76 41.0 0 76
25 90 41.0 0 90
26 80 41.0 0 80
27 85 41.0 0 85
28 86 41.0 0 86
29 88 41.0 0 88
30 84 41.0 0 84
31 86 41.0 0 86
32 102 41.0 0 102
33 95 41.0 0 95
34 65 41.0 0 65
35 80 41.0 0 80
36 72 41.0 0 72
37 98 41.0 0 98
38 91 41.0 0 91
39 84 41.0 0 84
40 108 41.0 0 108
41 93 41.0 0 93
42 102 41.0 0 102
43 118 41.0 0 118
44 100 41.0 0 100
45 97 41.0 0 97
46 109 41.0 0 109
47 73 41.0 0 73
48 71 41.0 0 71
49 61 41.0 0 61
50 79 41.0 0 79
51 61 41.0 0 61
52 60 41.0 0 60
53 59 41.0 0 59
54 62 41.0 0 62
55 67 41.0 0 67
56 56 41.0 0 56
57 69 41.0 0 69
58 55 41.0 0 55
59 66 41.0 0 66
60 63 41.0 0 63
61 59 41.0 0 59
62 65 41.0 0 65
63 61 41.0 0 61
64 48 41.0 0 48
65 43 41.0 0 43
66 44 41.0 0 44
67 41 41.0 0 41
68 40 41.0 0 40
69 34 41.0 0 34
70 45 41.0 0 45
71 28 41.0 0 28
72 31 41.0 0 31
73 31 41.0 0 31
74 26 41.0 0 26
75 22 41.0 0 22
76 19 41.0 0 19
77 14 41.0 0 14
78 13 41.0 0 13
79 20 41.0 0 20
80 19 41.0 0 19
81 25 41.0 0 25
82 18 41.0 0 18
83 31 41.0 0 31
84 27 41.0 0 27
85 24 41.0 0 24
86 781 41.0 0 781
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 64315 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 23.7%
G: 20.7%
T: 19.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 48210 41997.1 0 48210
4 10730 10499.3 0 10730
5 2141 2624.8 0 2141
6 308 656.2 0 308
7 32 164.1 0 32
8 28 164.1 0 28
9 29 164.1 0 29
10 31 164.1 0 31
11 31 164.1 0 31
12 50 164.1 0 50
13 35 164.1 0 35
14 30 164.1 0 30
15 44 164.1 0 44
16 34 164.1 0 34
17 45 164.1 0 45
18 39 164.1 0 39
19 38 164.1 0 38
20 31 164.1 0 31
21 45 164.1 0 45
22 41 164.1 0 41
23 44 164.1 0 44
24 31 164.1 0 31
25 60 164.1 0 60
26 36 164.1 0 36
27 36 164.1 0 36
28 31 164.1 0 31
29 27 164.1 0 27
30 25 164.1 0 25
31 29 164.1 0 29
32 38 164.1 0 38
33 30 164.1 0 30
34 38 164.1 0 38
35 33 164.1 0 33
36 38 164.1 0 38
37 34 164.1 0 34
38 28 164.1 0 28
39 43 164.1 0 43
40 28 164.1 0 28
41 40 164.1 0 40
42 35 164.1 0 35
43 41 164.1 0 41
44 44 164.1 0 44
45 31 164.1 0 31
46 24 164.1 0 24
47 31 164.1 0 31
48 37 164.1 0 37
49 37 164.1 0 37
50 22 164.1 0 22
51 34 164.1 0 34
52 49 164.1 0 49
53 26 164.1 0 26
54 37 164.1 0 37
55 47 164.1 0 47
56 31 164.1 0 31
57 43 164.1 0 43
58 53 164.1 0 53
59 40 164.1 0 40
60 30 164.1 0 30
61 37 164.1 0 37
62 61 164.1 0 61
63 55 164.1 0 55
64 45 164.1 0 45
65 36 164.1 0 36
66 40 164.1 0 40
67 29 164.1 0 29
68 33 164.1 0 33
69 19 164.1 0 19
70 42 164.1 0 42
71 40 164.1 0 40
72 25 164.1 0 25
73 36 164.1 0 36
74 41 164.1 0 41
75 28 164.1 0 28
76 22 164.1 0 22
77 31 164.1 0 31
78 45 164.1 0 45
79 29 164.1 0 29
80 34 164.1 0 34
81 36 164.1 0 36
82 38 164.1 0 38
83 44 164.1 0 44
84 46 164.1 0 46
85 36 164.1 0 36
86 54 164.1 0 54
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N47_S168_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N47_S168_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.93 s (9 µs/read; 6.34 M reads/minute).
=== Summary ===
Total reads processed: 2,738,632
Reads with adapters: 795,939 (29.1%)
== Read fate breakdown ==
Reads that were too short: 157,441 (5.7%)
Reads written (passing filters): 2,581,191 (94.3%)
Total basepairs processed: 276,601,832 bp
Total written (filtered): 205,755,118 bp (74.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 704060 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 36.2%
G: 30.3%
T: 27.1%
none/other: 6.4%
Overview of removed sequences
length count expect max.err error counts
3 68319 42791.1 0 68319
4 27728 10697.8 0 27728
5 14970 2674.4 0 14970
6 9713 668.6 0 9713
7 8155 167.2 0 8155
8 6903 41.8 0 6903
9 6987 41.8 0 6987
10 7175 41.8 0 7175
11 6967 41.8 0 6967
12 6927 41.8 0 6927
13 6929 41.8 0 6929
14 6973 41.8 0 6973
15 8222 41.8 0 8222
16 8780 41.8 0 8780
17 7474 41.8 0 7474
18 8574 41.8 0 8574
19 8350 41.8 0 8350
20 6987 41.8 0 6987
21 8660 41.8 0 8660
22 8626 41.8 0 8626
23 6868 41.8 0 6868
24 6482 41.8 0 6482
25 6632 41.8 0 6632
26 6353 41.8 0 6353
27 6287 41.8 0 6287
28 6894 41.8 0 6894
29 6498 41.8 0 6498
30 6561 41.8 0 6561
31 7770 41.8 0 7770
32 6621 41.8 0 6621
33 7324 41.8 0 7324
34 7934 41.8 0 7934
35 6776 41.8 0 6776
36 6752 41.8 0 6752
37 7981 41.8 0 7981
38 6599 41.8 0 6599
39 6907 41.8 0 6907
40 7045 41.8 0 7045
41 6695 41.8 0 6695
42 7409 41.8 0 7409
43 9092 41.8 0 9092
44 7030 41.8 0 7030
45 7322 41.8 0 7322
46 8139 41.8 0 8139
47 6921 41.8 0 6921
48 6750 41.8 0 6750
49 14189 41.8 0 14189
50 10960 41.8 0 10960
51 6645 41.8 0 6645
52 6749 41.8 0 6749
53 6314 41.8 0 6314
54 5663 41.8 0 5663
55 5984 41.8 0 5984
56 5993 41.8 0 5993
57 5834 41.8 0 5834
58 6337 41.8 0 6337
59 5951 41.8 0 5951
60 5732 41.8 0 5732
61 6261 41.8 0 6261
62 6056 41.8 0 6056
63 5736 41.8 0 5736
64 5676 41.8 0 5676
65 5877 41.8 0 5877
66 5638 41.8 0 5638
67 5628 41.8 0 5628
68 6036 41.8 0 6036
69 5376 41.8 0 5376
70 5433 41.8 0 5433
71 5837 41.8 0 5837
72 5571 41.8 0 5571
73 5441 41.8 0 5441
74 5137 41.8 0 5137
75 5126 41.8 0 5126
76 5308 41.8 0 5308
77 4883 41.8 0 4883
78 5264 41.8 0 5264
79 5808 41.8 0 5808
80 5078 41.8 0 5078
81 5851 41.8 0 5851
82 6563 41.8 0 6563
83 7139 41.8 0 7139
84 7481 41.8 0 7481
85 7463 41.8 0 7463
86 44981 41.8 0 44981
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 26262 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.3%
C: 31.5%
G: 0.0%
T: 35.2%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 15329 42791.1 0 15329
4 3489 10697.8 0 3489
5 855 2674.4 0 855
6 240 668.6 0 240
7 110 167.2 0 110
8 107 41.8 0 107
9 84 41.8 0 84
10 96 41.8 0 96
11 90 41.8 0 90
12 78 41.8 0 78
13 75 41.8 0 75
14 77 41.8 0 77
15 105 41.8 0 105
16 98 41.8 0 98
17 77 41.8 0 77
18 87 41.8 0 87
19 89 41.8 0 89
20 78 41.8 0 78
21 90 41.8 0 90
22 106 41.8 0 106
23 101 41.8 0 101
24 84 41.8 0 84
25 108 41.8 0 108
26 96 41.8 0 96
27 71 41.8 0 71
28 95 41.8 0 95
29 113 41.8 0 113
30 62 41.8 0 62
31 84 41.8 0 84
32 70 41.8 0 70
33 85 41.8 0 85
34 92 41.8 0 92
35 86 41.8 0 86
36 83 41.8 0 83
37 101 41.8 0 101
38 96 41.8 0 96
39 90 41.8 0 90
40 148 41.8 0 148
41 95 41.8 0 95
42 72 41.8 0 72
43 129 41.8 0 129
44 85 41.8 0 85
45 77 41.8 0 77
46 111 41.8 0 111
47 74 41.8 0 74
48 86 41.8 0 86
49 63 41.8 0 63
50 61 41.8 0 61
51 86 41.8 0 86
52 74 41.8 0 74
53 81 41.8 0 81
54 56 41.8 0 56
55 78 41.8 0 78
56 62 41.8 0 62
57 77 41.8 0 77
58 74 41.8 0 74
59 65 41.8 0 65
60 77 41.8 0 77
61 68 41.8 0 68
62 66 41.8 0 66
63 47 41.8 0 47
64 41 41.8 0 41
65 45 41.8 0 45
66 47 41.8 0 47
67 46 41.8 0 46
68 50 41.8 0 50
69 56 41.8 0 56
70 39 41.8 0 39
71 31 41.8 0 31
72 36 41.8 0 36
73 32 41.8 0 32
74 28 41.8 0 28
75 20 41.8 0 20
76 26 41.8 0 26
77 17 41.8 0 17
78 18 41.8 0 18
79 19 41.8 0 19
80 17 41.8 0 17
81 20 41.8 0 20
82 18 41.8 0 18
83 29 41.8 0 29
84 27 41.8 0 27
85 21 41.8 0 21
86 790 41.8 0 790
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 65617 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 23.5%
G: 21.2%
T: 19.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 48992 42791.1 0 48992
4 11028 10697.8 0 11028
5 2333 2674.4 0 2333
6 312 668.6 0 312
7 35 167.2 0 35
8 42 167.2 0 42
9 32 167.2 0 32
10 47 167.2 0 47
11 42 167.2 0 42
12 39 167.2 0 39
13 31 167.2 0 31
14 44 167.2 0 44
15 39 167.2 0 39
16 44 167.2 0 44
17 33 167.2 0 33
18 40 167.2 0 40
19 45 167.2 0 45
20 38 167.2 0 38
21 29 167.2 0 29
22 38 167.2 0 38
23 24 167.2 0 24
24 27 167.2 0 27
25 52 167.2 0 52
26 32 167.2 0 32
27 46 167.2 0 46
28 31 167.2 0 31
29 19 167.2 0 19
30 38 167.2 0 38
31 38 167.2 0 38
32 36 167.2 0 36
33 39 167.2 0 39
34 39 167.2 0 39
35 32 167.2 0 32
36 47 167.2 0 47
37 30 167.2 0 30
38 32 167.2 0 32
39 39 167.2 0 39
40 38 167.2 0 38
41 42 167.2 0 42
42 39 167.2 0 39
43 36 167.2 0 36
44 35 167.2 0 35
45 31 167.2 0 31
46 18 167.2 0 18
47 23 167.2 0 23
48 34 167.2 0 34
49 40 167.2 0 40
50 39 167.2 0 39
51 39 167.2 0 39
52 55 167.2 0 55
53 36 167.2 0 36
54 42 167.2 0 42
55 48 167.2 0 48
56 33 167.2 0 33
57 44 167.2 0 44
58 47 167.2 0 47
59 46 167.2 0 46
60 36 167.2 0 36
61 28 167.2 0 28
62 43 167.2 0 43
63 33 167.2 0 33
64 33 167.2 0 33
65 53 167.2 0 53
66 45 167.2 0 45
67 40 167.2 0 40
68 28 167.2 0 28
69 35 167.2 0 35
70 28 167.2 0 28
71 44 167.2 0 44
72 35 167.2 0 35
73 30 167.2 0 30
74 37 167.2 0 37
75 40 167.2 0 40
76 33 167.2 0 33
77 39 167.2 0 39
78 27 167.2 0 27
79 24 167.2 0 24
80 30 167.2 0 30
81 40 167.2 0 40
82 28 167.2 0 28
83 44 167.2 0 44
84 34 167.2 0 34
85 44 167.2 0 44
86 37 167.2 0 37
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N48_S194_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N48_S194_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 21.91 s (10 µs/read; 6.06 M reads/minute).
=== Summary ===
Total reads processed: 2,212,373
Reads with adapters: 682,273 (30.8%)
== Read fate breakdown ==
Reads that were too short: 182,182 (8.2%)
Reads written (passing filters): 2,030,191 (91.8%)
Total basepairs processed: 223,449,673 bp
Total written (filtered): 161,435,690 bp (72.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 600226 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.3%
G: 27.9%
T: 28.9%
none/other: 12.8%
Overview of removed sequences
length count expect max.err error counts
3 52909 34568.3 0 52909
4 22573 8642.1 0 22573
5 11319 2160.5 0 11319
6 7156 540.1 0 7156
7 5881 135.0 0 5881
8 4997 33.8 0 4997
9 4967 33.8 0 4967
10 5128 33.8 0 5128
11 5169 33.8 0 5169
12 4972 33.8 0 4972
13 5136 33.8 0 5136
14 5225 33.8 0 5225
15 5331 33.8 0 5331
16 5790 33.8 0 5790
17 5404 33.8 0 5404
18 5493 33.8 0 5493
19 5560 33.8 0 5560
20 5303 33.8 0 5303
21 5402 33.8 0 5402
22 5678 33.8 0 5678
23 5113 33.8 0 5113
24 5136 33.8 0 5136
25 5266 33.8 0 5266
26 5238 33.8 0 5238
27 5074 33.8 0 5074
28 5323 33.8 0 5323
29 5537 33.8 0 5537
30 5398 33.8 0 5398
31 5676 33.8 0 5676
32 5212 33.8 0 5212
33 5453 33.8 0 5453
34 5376 33.8 0 5376
35 5412 33.8 0 5412
36 5136 33.8 0 5136
37 5345 33.8 0 5345
38 5111 33.8 0 5111
39 5226 33.8 0 5226
40 5198 33.8 0 5198
41 5252 33.8 0 5252
42 5443 33.8 0 5443
43 5437 33.8 0 5437
44 5111 33.8 0 5111
45 5208 33.8 0 5208
46 5455 33.8 0 5455
47 5387 33.8 0 5387
48 5476 33.8 0 5476
49 7500 33.8 0 7500
50 8810 33.8 0 8810
51 5550 33.8 0 5550
52 5804 33.8 0 5804
53 5677 33.8 0 5677
54 5167 33.8 0 5167
55 5452 33.8 0 5452
56 5354 33.8 0 5354
57 5183 33.8 0 5183
58 5712 33.8 0 5712
59 5536 33.8 0 5536
60 5522 33.8 0 5522
61 5426 33.8 0 5426
62 5520 33.8 0 5520
63 5436 33.8 0 5436
64 5224 33.8 0 5224
65 5241 33.8 0 5241
66 5208 33.8 0 5208
67 5085 33.8 0 5085
68 5151 33.8 0 5151
69 4975 33.8 0 4975
70 4689 33.8 0 4689
71 5282 33.8 0 5282
72 5204 33.8 0 5204
73 4774 33.8 0 4774
74 4715 33.8 0 4715
75 4717 33.8 0 4717
76 4357 33.8 0 4357
77 4743 33.8 0 4743
78 4445 33.8 0 4445
79 5001 33.8 0 5001
80 4690 33.8 0 4690
81 5625 33.8 0 5625
82 6278 33.8 0 6278
83 7065 33.8 0 7065
84 7907 33.8 0 7907
85 7766 33.8 0 7766
86 77043 33.8 0 77043
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 32124 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.5%
C: 31.9%
G: 0.0%
T: 36.6%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 11035 34568.3 0 11035
4 2503 8642.1 0 2503
5 828 2160.5 0 828
6 441 540.1 0 441
7 345 135.0 0 345
8 400 33.8 0 400
9 339 33.8 0 339
10 312 33.8 0 312
11 325 33.8 0 325
12 334 33.8 0 334
13 361 33.8 0 361
14 286 33.8 0 286
15 281 33.8 0 281
16 308 33.8 0 308
17 273 33.8 0 273
18 299 33.8 0 299
19 278 33.8 0 278
20 281 33.8 0 281
21 235 33.8 0 235
22 252 33.8 0 252
23 243 33.8 0 243
24 305 33.8 0 305
25 286 33.8 0 286
26 307 33.8 0 307
27 269 33.8 0 269
28 279 33.8 0 279
29 274 33.8 0 274
30 251 33.8 0 251
31 270 33.8 0 270
32 289 33.8 0 289
33 267 33.8 0 267
34 265 33.8 0 265
35 255 33.8 0 255
36 266 33.8 0 266
37 264 33.8 0 264
38 237 33.8 0 237
39 239 33.8 0 239
40 235 33.8 0 235
41 235 33.8 0 235
42 235 33.8 0 235
43 247 33.8 0 247
44 235 33.8 0 235
45 239 33.8 0 239
46 264 33.8 0 264
47 259 33.8 0 259
48 225 33.8 0 225
49 226 33.8 0 226
50 231 33.8 0 231
51 232 33.8 0 232
52 240 33.8 0 240
53 206 33.8 0 206
54 233 33.8 0 233
55 226 33.8 0 226
56 192 33.8 0 192
57 218 33.8 0 218
58 183 33.8 0 183
59 192 33.8 0 192
60 215 33.8 0 215
61 187 33.8 0 187
62 176 33.8 0 176
63 165 33.8 0 165
64 162 33.8 0 162
65 143 33.8 0 143
66 112 33.8 0 112
67 133 33.8 0 133
68 125 33.8 0 125
69 106 33.8 0 106
70 100 33.8 0 100
71 76 33.8 0 76
72 92 33.8 0 92
73 61 33.8 0 61
74 63 33.8 0 63
75 51 33.8 0 51
76 55 33.8 0 55
77 24 33.8 0 24
78 34 33.8 0 34
79 28 33.8 0 28
80 35 33.8 0 35
81 38 33.8 0 38
82 37 33.8 0 37
83 33 33.8 0 33
84 34 33.8 0 34
85 53 33.8 0 53
86 951 33.8 0 951
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 49923 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 23.0%
G: 20.8%
T: 20.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 37341 34568.3 0 37341
4 8573 8642.1 0 8573
5 1624 2160.5 0 1624
6 225 540.1 0 225
7 27 135.0 0 27
8 26 135.0 0 26
9 20 135.0 0 20
10 20 135.0 0 20
11 27 135.0 0 27
12 25 135.0 0 25
13 32 135.0 0 32
14 27 135.0 0 27
15 27 135.0 0 27
16 35 135.0 0 35
17 32 135.0 0 32
18 25 135.0 0 25
19 45 135.0 0 45
20 41 135.0 0 41
21 29 135.0 0 29
22 34 135.0 0 34
23 26 135.0 0 26
24 25 135.0 0 25
25 38 135.0 0 38
26 36 135.0 0 36
27 16 135.0 0 16
28 21 135.0 0 21
29 35 135.0 0 35
30 36 135.0 0 36
31 23 135.0 0 23
32 26 135.0 0 26
33 40 135.0 0 40
34 13 135.0 0 13
35 27 135.0 0 27
36 34 135.0 0 34
37 28 135.0 0 28
38 20 135.0 0 20
39 29 135.0 0 29
40 30 135.0 0 30
41 17 135.0 0 17
42 27 135.0 0 27
43 22 135.0 0 22
44 22 135.0 0 22
45 28 135.0 0 28
46 20 135.0 0 20
47 21 135.0 0 21
48 23 135.0 0 23
49 22 135.0 0 22
50 33 135.0 0 33
51 25 135.0 0 25
52 25 135.0 0 25
53 23 135.0 0 23
54 24 135.0 0 24
55 26 135.0 0 26
56 30 135.0 0 30
57 35 135.0 0 35
58 20 135.0 0 20
59 24 135.0 0 24
60 18 135.0 0 18
61 32 135.0 0 32
62 19 135.0 0 19
63 25 135.0 0 25
64 28 135.0 0 28
65 27 135.0 0 27
66 28 135.0 0 28
67 24 135.0 0 24
68 34 135.0 0 34
69 28 135.0 0 28
70 21 135.0 0 21
71 31 135.0 0 31
72 24 135.0 0 24
73 18 135.0 0 18
74 26 135.0 0 26
75 22 135.0 0 22
76 13 135.0 0 13
77 50 135.0 0 50
78 40 135.0 0 40
79 38 135.0 0 38
80 20 135.0 0 20
81 24 135.0 0 24
82 19 135.0 0 19
83 25 135.0 0 25
84 22 135.0 0 22
85 33 135.0 0 33
86 29 135.0 0 29
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N48_S194_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N48_S194_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 21.35 s (10 µs/read; 6.31 M reads/minute).
=== Summary ===
Total reads processed: 2,246,548
Reads with adapters: 697,932 (31.1%)
== Read fate breakdown ==
Reads that were too short: 189,252 (8.4%)
Reads written (passing filters): 2,057,296 (91.6%)
Total basepairs processed: 226,901,348 bp
Total written (filtered): 163,472,536 bp (72.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 614080 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.3%
G: 27.8%
T: 28.7%
none/other: 13.1%
Overview of removed sequences
length count expect max.err error counts
3 53155 35102.3 0 53155
4 22976 8775.6 0 22976
5 11375 2193.9 0 11375
6 6973 548.5 0 6973
7 6058 137.1 0 6058
8 5030 34.3 0 5030
9 5094 34.3 0 5094
10 5163 34.3 0 5163
11 5184 34.3 0 5184
12 5054 34.3 0 5054
13 5209 34.3 0 5209
14 5265 34.3 0 5265
15 5523 34.3 0 5523
16 5677 34.3 0 5677
17 5543 34.3 0 5543
18 5554 34.3 0 5554
19 5633 34.3 0 5633
20 5345 34.3 0 5345
21 5550 34.3 0 5550
22 5626 34.3 0 5626
23 5239 34.3 0 5239
24 5307 34.3 0 5307
25 5458 34.3 0 5458
26 5345 34.3 0 5345
27 5101 34.3 0 5101
28 5588 34.3 0 5588
29 5531 34.3 0 5531
30 5349 34.3 0 5349
31 5672 34.3 0 5672
32 5448 34.3 0 5448
33 5719 34.3 0 5719
34 5442 34.3 0 5442
35 5643 34.3 0 5643
36 5176 34.3 0 5176
37 5378 34.3 0 5378
38 5013 34.3 0 5013
39 5212 34.3 0 5212
40 5248 34.3 0 5248
41 5420 34.3 0 5420
42 5447 34.3 0 5447
43 5575 34.3 0 5575
44 5256 34.3 0 5256
45 5369 34.3 0 5369
46 5755 34.3 0 5755
47 5428 34.3 0 5428
48 5425 34.3 0 5425
49 7563 34.3 0 7563
50 9224 34.3 0 9224
51 5779 34.3 0 5779
52 5919 34.3 0 5919
53 5771 34.3 0 5771
54 5307 34.3 0 5307
55 5559 34.3 0 5559
56 5402 34.3 0 5402
57 5467 34.3 0 5467
58 5603 34.3 0 5603
59 5562 34.3 0 5562
60 5653 34.3 0 5653
61 5637 34.3 0 5637
62 5578 34.3 0 5578
63 5671 34.3 0 5671
64 5551 34.3 0 5551
65 5416 34.3 0 5416
66 5366 34.3 0 5366
67 5310 34.3 0 5310
68 5214 34.3 0 5214
69 5083 34.3 0 5083
70 4749 34.3 0 4749
71 5508 34.3 0 5508
72 5364 34.3 0 5364
73 5033 34.3 0 5033
74 4931 34.3 0 4931
75 4674 34.3 0 4674
76 4664 34.3 0 4664
77 4978 34.3 0 4978
78 4621 34.3 0 4621
79 5261 34.3 0 5261
80 4932 34.3 0 4932
81 5504 34.3 0 5504
82 6531 34.3 0 6531
83 7220 34.3 0 7220
84 8190 34.3 0 8190
85 8128 34.3 0 8128
86 80626 34.3 0 80626
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 33313 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.8%
C: 32.2%
G: 0.0%
T: 36.2%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 11374 35102.3 0 11374
4 2529 8775.6 0 2529
5 819 2193.9 0 819
6 384 548.5 0 384
7 364 137.1 0 364
8 416 34.3 0 416
9 394 34.3 0 394
10 360 34.3 0 360
11 325 34.3 0 325
12 350 34.3 0 350
13 336 34.3 0 336
14 317 34.3 0 317
15 341 34.3 0 341
16 272 34.3 0 272
17 307 34.3 0 307
18 311 34.3 0 311
19 292 34.3 0 292
20 273 34.3 0 273
21 264 34.3 0 264
22 270 34.3 0 270
23 297 34.3 0 297
24 259 34.3 0 259
25 300 34.3 0 300
26 287 34.3 0 287
27 304 34.3 0 304
28 278 34.3 0 278
29 272 34.3 0 272
30 279 34.3 0 279
31 246 34.3 0 246
32 271 34.3 0 271
33 316 34.3 0 316
34 258 34.3 0 258
35 258 34.3 0 258
36 288 34.3 0 288
37 267 34.3 0 267
38 251 34.3 0 251
39 246 34.3 0 246
40 295 34.3 0 295
41 263 34.3 0 263
42 269 34.3 0 269
43 291 34.3 0 291
44 251 34.3 0 251
45 245 34.3 0 245
46 234 34.3 0 234
47 271 34.3 0 271
48 249 34.3 0 249
49 268 34.3 0 268
50 247 34.3 0 247
51 245 34.3 0 245
52 253 34.3 0 253
53 258 34.3 0 258
54 226 34.3 0 226
55 239 34.3 0 239
56 234 34.3 0 234
57 229 34.3 0 229
58 236 34.3 0 236
59 205 34.3 0 205
60 194 34.3 0 194
61 204 34.3 0 204
62 175 34.3 0 175
63 175 34.3 0 175
64 176 34.3 0 176
65 149 34.3 0 149
66 151 34.3 0 151
67 140 34.3 0 140
68 121 34.3 0 121
69 104 34.3 0 104
70 104 34.3 0 104
71 91 34.3 0 91
72 77 34.3 0 77
73 63 34.3 0 63
74 34 34.3 0 34
75 57 34.3 0 57
76 47 34.3 0 47
77 31 34.3 0 31
78 38 34.3 0 38
79 28 34.3 0 28
80 38 34.3 0 38
81 29 34.3 0 29
82 37 34.3 0 37
83 36 34.3 0 36
84 40 34.3 0 40
85 51 34.3 0 51
86 940 34.3 0 940
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 50539 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.3%
C: 23.1%
G: 20.3%
T: 20.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 37638 35102.3 0 37638
4 8828 8775.6 0 8828
5 1669 2193.9 0 1669
6 207 548.5 0 207
7 22 137.1 0 22
8 19 137.1 0 19
9 15 137.1 0 15
10 32 137.1 0 32
11 24 137.1 0 24
12 19 137.1 0 19
13 27 137.1 0 27
14 31 137.1 0 31
15 27 137.1 0 27
16 28 137.1 0 28
17 37 137.1 0 37
18 35 137.1 0 35
19 37 137.1 0 37
20 24 137.1 0 24
21 44 137.1 0 44
22 39 137.1 0 39
23 32 137.1 0 32
24 27 137.1 0 27
25 34 137.1 0 34
26 30 137.1 0 30
27 21 137.1 0 21
28 28 137.1 0 28
29 32 137.1 0 32
30 23 137.1 0 23
31 28 137.1 0 28
32 35 137.1 0 35
33 29 137.1 0 29
34 24 137.1 0 24
35 17 137.1 0 17
36 35 137.1 0 35
37 30 137.1 0 30
38 18 137.1 0 18
39 30 137.1 0 30
40 29 137.1 0 29
41 22 137.1 0 22
42 18 137.1 0 18
43 20 137.1 0 20
44 20 137.1 0 20
45 27 137.1 0 27
46 23 137.1 0 23
47 26 137.1 0 26
48 23 137.1 0 23
49 24 137.1 0 24
50 28 137.1 0 28
51 28 137.1 0 28
52 28 137.1 0 28
53 20 137.1 0 20
54 16 137.1 0 16
55 25 137.1 0 25
56 19 137.1 0 19
57 27 137.1 0 27
58 20 137.1 0 20
59 25 137.1 0 25
60 15 137.1 0 15
61 27 137.1 0 27
62 22 137.1 0 22
63 24 137.1 0 24
64 34 137.1 0 34
65 28 137.1 0 28
66 21 137.1 0 21
67 38 137.1 0 38
68 34 137.1 0 34
69 29 137.1 0 29
70 37 137.1 0 37
71 35 137.1 0 35
72 27 137.1 0 27
73 22 137.1 0 22
74 31 137.1 0 31
75 19 137.1 0 19
76 16 137.1 0 16
77 78 137.1 0 78
78 30 137.1 0 30
79 29 137.1 0 29
80 26 137.1 0 26
81 20 137.1 0 20
82 37 137.1 0 37
83 29 137.1 0 29
84 30 137.1 0 30
85 29 137.1 0 29
86 29 137.1 0 29
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N49_S185_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N49_S185_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.02 s (9 µs/read; 6.42 M reads/minute).
=== Summary ===
Total reads processed: 2,464,125
Reads with adapters: 802,542 (32.6%)
== Read fate breakdown ==
Reads that were too short: 213,194 (8.7%)
Reads written (passing filters): 2,250,931 (91.3%)
Total basepairs processed: 248,876,625 bp
Total written (filtered): 177,951,675 bp (71.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 711545 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.4%
G: 27.6%
T: 29.1%
none/other: 13.0%
Overview of removed sequences
length count expect max.err error counts
3 58656 38502.0 0 58656
4 25350 9625.5 0 25350
5 13747 2406.4 0 13747
6 8905 601.6 0 8905
7 7167 150.4 0 7167
8 6423 37.6 0 6423
9 6576 37.6 0 6576
10 6551 37.6 0 6551
11 6307 37.6 0 6307
12 6364 37.6 0 6364
13 6631 37.6 0 6631
14 6575 37.6 0 6575
15 6670 37.6 0 6670
16 7014 37.6 0 7014
17 6640 37.6 0 6640
18 6754 37.6 0 6754
19 6541 37.6 0 6541
20 6536 37.6 0 6536
21 6606 37.6 0 6606
22 6701 37.6 0 6701
23 6359 37.6 0 6359
24 6219 37.6 0 6219
25 6509 37.6 0 6509
26 6252 37.6 0 6252
27 6307 37.6 0 6307
28 6401 37.6 0 6401
29 6442 37.6 0 6442
30 6402 37.6 0 6402
31 6891 37.6 0 6891
32 6548 37.6 0 6548
33 7293 37.6 0 7293
34 6936 37.6 0 6936
35 6518 37.6 0 6518
36 6520 37.6 0 6520
37 6978 37.6 0 6978
38 6278 37.6 0 6278
39 6557 37.6 0 6557
40 6417 37.6 0 6417
41 6189 37.6 0 6189
42 6541 37.6 0 6541
43 6538 37.6 0 6538
44 6168 37.6 0 6168
45 6472 37.6 0 6472
46 6382 37.6 0 6382
47 6208 37.6 0 6208
48 6084 37.6 0 6084
49 8518 37.6 0 8518
50 9993 37.6 0 9993
51 6649 37.6 0 6649
52 6795 37.6 0 6795
53 6666 37.6 0 6666
54 6176 37.6 0 6176
55 6302 37.6 0 6302
56 6267 37.6 0 6267
57 6233 37.6 0 6233
58 6557 37.6 0 6557
59 6392 37.6 0 6392
60 6412 37.6 0 6412
61 6300 37.6 0 6300
62 6306 37.6 0 6306
63 6204 37.6 0 6204
64 6193 37.6 0 6193
65 6238 37.6 0 6238
66 6048 37.6 0 6048
67 6129 37.6 0 6129
68 5811 37.6 0 5811
69 5683 37.6 0 5683
70 5371 37.6 0 5371
71 5714 37.6 0 5714
72 5674 37.6 0 5674
73 5397 37.6 0 5397
74 5014 37.6 0 5014
75 4861 37.6 0 4861
76 4921 37.6 0 4921
77 5043 37.6 0 5043
78 4923 37.6 0 4923
79 5852 37.6 0 5852
80 5580 37.6 0 5580
81 6144 37.6 0 6144
82 7769 37.6 0 7769
83 8751 37.6 0 8751
84 9626 37.6 0 9626
85 9809 37.6 0 9809
86 92101 37.6 0 92101
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35951 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.4%
C: 32.5%
G: 0.0%
T: 37.4%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 12420 38502.0 0 12420
4 2890 9625.5 0 2890
5 967 2406.4 0 967
6 452 601.6 0 452
7 438 150.4 0 438
8 444 37.6 0 444
9 355 37.6 0 355
10 346 37.6 0 346
11 377 37.6 0 377
12 349 37.6 0 349
13 341 37.6 0 341
14 349 37.6 0 349
15 339 37.6 0 339
16 320 37.6 0 320
17 287 37.6 0 287
18 335 37.6 0 335
19 332 37.6 0 332
20 305 37.6 0 305
21 302 37.6 0 302
22 288 37.6 0 288
23 317 37.6 0 317
24 321 37.6 0 321
25 330 37.6 0 330
26 293 37.6 0 293
27 302 37.6 0 302
28 315 37.6 0 315
29 316 37.6 0 316
30 283 37.6 0 283
31 300 37.6 0 300
32 297 37.6 0 297
33 346 37.6 0 346
34 281 37.6 0 281
35 280 37.6 0 280
36 261 37.6 0 261
37 287 37.6 0 287
38 267 37.6 0 267
39 289 37.6 0 289
40 312 37.6 0 312
41 280 37.6 0 280
42 300 37.6 0 300
43 286 37.6 0 286
44 238 37.6 0 238
45 280 37.6 0 280
46 256 37.6 0 256
47 254 37.6 0 254
48 262 37.6 0 262
49 258 37.6 0 258
50 267 37.6 0 267
51 223 37.6 0 223
52 229 37.6 0 229
53 233 37.6 0 233
54 224 37.6 0 224
55 266 37.6 0 266
56 231 37.6 0 231
57 246 37.6 0 246
58 226 37.6 0 226
59 209 37.6 0 209
60 247 37.6 0 247
61 213 37.6 0 213
62 161 37.6 0 161
63 182 37.6 0 182
64 202 37.6 0 202
65 153 37.6 0 153
66 149 37.6 0 149
67 135 37.6 0 135
68 122 37.6 0 122
69 115 37.6 0 115
70 108 37.6 0 108
71 104 37.6 0 104
72 104 37.6 0 104
73 69 37.6 0 69
74 78 37.6 0 78
75 53 37.6 0 53
76 47 37.6 0 47
77 40 37.6 0 40
78 36 37.6 0 36
79 30 37.6 0 30
80 34 37.6 0 34
81 41 37.6 0 41
82 33 37.6 0 33
83 41 37.6 0 41
84 39 37.6 0 39
85 50 37.6 0 50
86 964 37.6 0 964
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 55046 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 22.8%
G: 21.6%
T: 19.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41355 38502.0 0 41355
4 8789 9625.5 0 8789
5 1801 2406.4 0 1801
6 276 601.6 0 276
7 35 150.4 0 35
8 38 150.4 0 38
9 35 150.4 0 35
10 27 150.4 0 27
11 44 150.4 0 44
12 27 150.4 0 27
13 39 150.4 0 39
14 57 150.4 0 57
15 43 150.4 0 43
16 27 150.4 0 27
17 36 150.4 0 36
18 23 150.4 0 23
19 34 150.4 0 34
20 39 150.4 0 39
21 46 150.4 0 46
22 44 150.4 0 44
23 37 150.4 0 37
24 39 150.4 0 39
25 43 150.4 0 43
26 50 150.4 0 50
27 37 150.4 0 37
28 48 150.4 0 48
29 31 150.4 0 31
30 46 150.4 0 46
31 37 150.4 0 37
32 43 150.4 0 43
33 31 150.4 0 31
34 35 150.4 0 35
35 40 150.4 0 40
36 53 150.4 0 53
37 29 150.4 0 29
38 26 150.4 0 26
39 27 150.4 0 27
40 25 150.4 0 25
41 34 150.4 0 34
42 34 150.4 0 34
43 23 150.4 0 23
44 38 150.4 0 38
45 22 150.4 0 22
46 18 150.4 0 18
47 22 150.4 0 22
48 41 150.4 0 41
49 26 150.4 0 26
50 31 150.4 0 31
51 43 150.4 0 43
52 40 150.4 0 40
53 26 150.4 0 26
54 26 150.4 0 26
55 31 150.4 0 31
56 21 150.4 0 21
57 26 150.4 0 26
58 34 150.4 0 34
59 33 150.4 0 33
60 29 150.4 0 29
61 40 150.4 0 40
62 39 150.4 0 39
63 21 150.4 0 21
64 33 150.4 0 33
65 26 150.4 0 26
66 19 150.4 0 19
67 30 150.4 0 30
68 32 150.4 0 32
69 23 150.4 0 23
70 40 150.4 0 40
71 41 150.4 0 41
72 21 150.4 0 21
73 42 150.4 0 42
74 42 150.4 0 42
75 33 150.4 0 33
76 19 150.4 0 19
77 82 150.4 0 82
78 49 150.4 0 49
79 32 150.4 0 32
80 34 150.4 0 34
81 25 150.4 0 25
82 42 150.4 0 42
83 60 150.4 0 60
84 35 150.4 0 35
85 46 150.4 0 46
86 50 150.4 0 50
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N49_S185_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N49_S185_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.24 s (9 µs/read; 6.47 M reads/minute).
=== Summary ===
Total reads processed: 2,506,865
Reads with adapters: 822,942 (32.8%)
== Read fate breakdown ==
Reads that were too short: 222,386 (8.9%)
Reads written (passing filters): 2,284,479 (91.1%)
Total basepairs processed: 253,193,365 bp
Total written (filtered): 180,480,937 bp (71.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 730773 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.3%
G: 27.5%
T: 28.8%
none/other: 13.3%
Overview of removed sequences
length count expect max.err error counts
3 59575 39169.8 0 59575
4 26340 9792.4 0 26340
5 13480 2448.1 0 13480
6 8806 612.0 0 8806
7 7325 153.0 0 7325
8 6513 38.3 0 6513
9 6480 38.3 0 6480
10 6710 38.3 0 6710
11 6448 38.3 0 6448
12 6420 38.3 0 6420
13 6627 38.3 0 6627
14 6731 38.3 0 6731
15 6774 38.3 0 6774
16 6899 38.3 0 6899
17 6809 38.3 0 6809
18 6774 38.3 0 6774
19 6944 38.3 0 6944
20 6702 38.3 0 6702
21 6750 38.3 0 6750
22 6858 38.3 0 6858
23 6409 38.3 0 6409
24 6548 38.3 0 6548
25 6392 38.3 0 6392
26 6299 38.3 0 6299
27 6449 38.3 0 6449
28 6602 38.3 0 6602
29 6682 38.3 0 6682
30 6712 38.3 0 6712
31 7175 38.3 0 7175
32 6771 38.3 0 6771
33 7328 38.3 0 7328
34 7251 38.3 0 7251
35 6744 38.3 0 6744
36 6552 38.3 0 6552
37 7018 38.3 0 7018
38 6408 38.3 0 6408
39 6645 38.3 0 6645
40 6364 38.3 0 6364
41 6447 38.3 0 6447
42 6683 38.3 0 6683
43 6442 38.3 0 6442
44 6067 38.3 0 6067
45 6608 38.3 0 6608
46 6410 38.3 0 6410
47 6455 38.3 0 6455
48 6352 38.3 0 6352
49 8693 38.3 0 8693
50 10416 38.3 0 10416
51 6776 38.3 0 6776
52 7088 38.3 0 7088
53 7060 38.3 0 7060
54 6232 38.3 0 6232
55 6625 38.3 0 6625
56 6531 38.3 0 6531
57 6194 38.3 0 6194
58 6789 38.3 0 6789
59 6581 38.3 0 6581
60 6443 38.3 0 6443
61 6585 38.3 0 6585
62 6450 38.3 0 6450
63 6365 38.3 0 6365
64 6316 38.3 0 6316
65 6345 38.3 0 6345
66 6141 38.3 0 6141
67 6223 38.3 0 6223
68 6183 38.3 0 6183
69 5818 38.3 0 5818
70 5506 38.3 0 5506
71 5963 38.3 0 5963
72 5741 38.3 0 5741
73 5460 38.3 0 5460
74 5128 38.3 0 5128
75 5242 38.3 0 5242
76 5227 38.3 0 5227
77 5043 38.3 0 5043
78 5346 38.3 0 5346
79 6102 38.3 0 6102
80 5741 38.3 0 5741
81 6455 38.3 0 6455
82 7895 38.3 0 7895
83 9026 38.3 0 9026
84 9693 38.3 0 9693
85 10153 38.3 0 10153
86 97420 38.3 0 97420
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 36384 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.1%
C: 33.0%
G: 0.0%
T: 37.2%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 12549 39169.8 0 12549
4 2825 9792.4 0 2825
5 972 2448.1 0 972
6 473 612.0 0 473
7 422 153.0 0 422
8 423 38.3 0 423
9 420 38.3 0 420
10 361 38.3 0 361
11 365 38.3 0 365
12 335 38.3 0 335
13 326 38.3 0 326
14 337 38.3 0 337
15 347 38.3 0 347
16 323 38.3 0 323
17 310 38.3 0 310
18 319 38.3 0 319
19 313 38.3 0 313
20 280 38.3 0 280
21 320 38.3 0 320
22 334 38.3 0 334
23 280 38.3 0 280
24 338 38.3 0 338
25 346 38.3 0 346
26 307 38.3 0 307
27 298 38.3 0 298
28 315 38.3 0 315
29 303 38.3 0 303
30 321 38.3 0 321
31 302 38.3 0 302
32 309 38.3 0 309
33 327 38.3 0 327
34 279 38.3 0 279
35 268 38.3 0 268
36 299 38.3 0 299
37 291 38.3 0 291
38 295 38.3 0 295
39 307 38.3 0 307
40 291 38.3 0 291
41 281 38.3 0 281
42 303 38.3 0 303
43 309 38.3 0 309
44 253 38.3 0 253
45 297 38.3 0 297
46 296 38.3 0 296
47 300 38.3 0 300
48 286 38.3 0 286
49 251 38.3 0 251
50 228 38.3 0 228
51 261 38.3 0 261
52 254 38.3 0 254
53 240 38.3 0 240
54 241 38.3 0 241
55 271 38.3 0 271
56 250 38.3 0 250
57 242 38.3 0 242
58 236 38.3 0 236
59 231 38.3 0 231
60 214 38.3 0 214
61 215 38.3 0 215
62 170 38.3 0 170
63 184 38.3 0 184
64 176 38.3 0 176
65 171 38.3 0 171
66 148 38.3 0 148
67 139 38.3 0 139
68 108 38.3 0 108
69 110 38.3 0 110
70 101 38.3 0 101
71 94 38.3 0 94
72 82 38.3 0 82
73 76 38.3 0 76
74 80 38.3 0 80
75 66 38.3 0 66
76 45 38.3 0 45
77 37 38.3 0 37
78 32 38.3 0 32
79 39 38.3 0 39
80 36 38.3 0 36
81 41 38.3 0 41
82 37 38.3 0 37
83 36 38.3 0 36
84 37 38.3 0 37
85 44 38.3 0 44
86 1006 38.3 0 1006
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 55785 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 22.8%
G: 21.9%
T: 19.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41732 39169.8 0 41732
4 9290 9792.4 0 9290
5 1737 2448.1 0 1737
6 287 612.0 0 287
7 41 153.0 0 41
8 42 153.0 0 42
9 27 153.0 0 27
10 26 153.0 0 26
11 33 153.0 0 33
12 41 153.0 0 41
13 41 153.0 0 41
14 33 153.0 0 33
15 40 153.0 0 40
16 32 153.0 0 32
17 30 153.0 0 30
18 31 153.0 0 31
19 44 153.0 0 44
20 38 153.0 0 38
21 35 153.0 0 35
22 37 153.0 0 37
23 34 153.0 0 34
24 29 153.0 0 29
25 29 153.0 0 29
26 37 153.0 0 37
27 23 153.0 0 23
28 30 153.0 0 30
29 35 153.0 0 35
30 30 153.0 0 30
31 24 153.0 0 24
32 53 153.0 0 53
33 43 153.0 0 43
34 33 153.0 0 33
35 35 153.0 0 35
36 50 153.0 0 50
37 24 153.0 0 24
38 36 153.0 0 36
39 18 153.0 0 18
40 23 153.0 0 23
41 30 153.0 0 30
42 32 153.0 0 32
43 38 153.0 0 38
44 26 153.0 0 26
45 28 153.0 0 28
46 23 153.0 0 23
47 32 153.0 0 32
48 35 153.0 0 35
49 37 153.0 0 37
50 31 153.0 0 31
51 36 153.0 0 36
52 33 153.0 0 33
53 26 153.0 0 26
54 27 153.0 0 27
55 40 153.0 0 40
56 20 153.0 0 20
57 22 153.0 0 22
58 29 153.0 0 29
59 21 153.0 0 21
60 36 153.0 0 36
61 20 153.0 0 20
62 40 153.0 0 40
63 26 153.0 0 26
64 36 153.0 0 36
65 47 153.0 0 47
66 36 153.0 0 36
67 31 153.0 0 31
68 29 153.0 0 29
69 39 153.0 0 39
70 43 153.0 0 43
71 38 153.0 0 38
72 36 153.0 0 36
73 32 153.0 0 32
74 40 153.0 0 40
75 36 153.0 0 36
76 27 153.0 0 27
77 84 153.0 0 84
78 47 153.0 0 47
79 21 153.0 0 21
80 36 153.0 0 36
81 37 153.0 0 37
82 36 153.0 0 36
83 48 153.0 0 48
84 27 153.0 0 27
85 31 153.0 0 31
86 57 153.0 0 57
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N50_S187_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N50_S187_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.83 s (9 µs/read; 6.84 M reads/minute).
=== Summary ===
Total reads processed: 3,058,705
Reads with adapters: 980,672 (32.1%)
== Read fate breakdown ==
Reads that were too short: 259,282 (8.5%)
Reads written (passing filters): 2,799,423 (91.5%)
Total basepairs processed: 308,929,205 bp
Total written (filtered): 221,378,653 bp (71.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 883074 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.8%
G: 28.2%
T: 29.8%
none/other: 11.2%
Overview of removed sequences
length count expect max.err error counts
3 71171 47792.3 0 71171
4 30471 11948.1 0 30471
5 15959 2987.0 0 15959
6 10603 746.8 0 10603
7 8703 186.7 0 8703
8 7703 46.7 0 7703
9 7546 46.7 0 7546
10 7917 46.7 0 7917
11 7790 46.7 0 7790
12 7877 46.7 0 7877
13 8109 46.7 0 8109
14 7842 46.7 0 7842
15 8408 46.7 0 8408
16 8907 46.7 0 8907
17 8038 46.7 0 8038
18 8728 46.7 0 8728
19 8771 46.7 0 8771
20 7738 46.7 0 7738
21 8338 46.7 0 8338
22 9217 46.7 0 9217
23 7684 46.7 0 7684
24 7618 46.7 0 7618
25 7403 46.7 0 7403
26 7250 46.7 0 7250
27 7257 46.7 0 7257
28 7975 46.7 0 7975
29 7928 46.7 0 7928
30 7687 46.7 0 7687
31 8961 46.7 0 8961
32 8109 46.7 0 8109
33 8472 46.7 0 8472
34 8539 46.7 0 8539
35 8396 46.7 0 8396
36 7887 46.7 0 7887
37 8513 46.7 0 8513
38 7935 46.7 0 7935
39 7887 46.7 0 7887
40 7979 46.7 0 7979
41 7793 46.7 0 7793
42 8391 46.7 0 8391
43 9068 46.7 0 9068
44 7908 46.7 0 7908
45 8239 46.7 0 8239
46 8977 46.7 0 8977
47 8444 46.7 0 8444
48 8111 46.7 0 8111
49 13059 46.7 0 13059
50 15336 46.7 0 15336
51 8458 46.7 0 8458
52 8842 46.7 0 8842
53 8569 46.7 0 8569
54 7432 46.7 0 7432
55 8193 46.7 0 8193
56 7999 46.7 0 7999
57 7556 46.7 0 7556
58 8261 46.7 0 8261
59 7836 46.7 0 7836
60 7730 46.7 0 7730
61 8281 46.7 0 8281
62 7915 46.7 0 7915
63 7239 46.7 0 7239
64 7779 46.7 0 7779
65 7786 46.7 0 7786
66 7485 46.7 0 7485
67 7720 46.7 0 7720
68 7620 46.7 0 7620
69 7195 46.7 0 7195
70 6801 46.7 0 6801
71 7946 46.7 0 7946
72 7803 46.7 0 7803
73 7018 46.7 0 7018
74 6987 46.7 0 6987
75 7110 46.7 0 7110
76 6878 46.7 0 6878
77 7245 46.7 0 7245
78 7308 46.7 0 7308
79 8256 46.7 0 8256
80 7717 46.7 0 7717
81 8799 46.7 0 8799
82 10110 46.7 0 10110
83 11177 46.7 0 11177
84 11980 46.7 0 11980
85 12698 46.7 0 12698
86 98703 46.7 0 98703
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30232 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.7%
C: 32.6%
G: 0.0%
T: 34.1%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 16663 47792.3 0 16663
4 3603 11948.1 0 3603
5 888 2987.0 0 888
6 295 746.8 0 295
7 209 186.7 0 209
8 210 46.7 0 210
9 191 46.7 0 191
10 149 46.7 0 149
11 184 46.7 0 184
12 147 46.7 0 147
13 137 46.7 0 137
14 155 46.7 0 155
15 129 46.7 0 129
16 136 46.7 0 136
17 137 46.7 0 137
18 123 46.7 0 123
19 135 46.7 0 135
20 149 46.7 0 149
21 118 46.7 0 118
22 135 46.7 0 135
23 124 46.7 0 124
24 117 46.7 0 117
25 126 46.7 0 126
26 134 46.7 0 134
27 158 46.7 0 158
28 123 46.7 0 123
29 126 46.7 0 126
30 113 46.7 0 113
31 105 46.7 0 105
32 110 46.7 0 110
33 127 46.7 0 127
34 136 46.7 0 136
35 126 46.7 0 126
36 123 46.7 0 123
37 100 46.7 0 100
38 110 46.7 0 110
39 114 46.7 0 114
40 127 46.7 0 127
41 111 46.7 0 111
42 108 46.7 0 108
43 119 46.7 0 119
44 108 46.7 0 108
45 113 46.7 0 113
46 111 46.7 0 111
47 111 46.7 0 111
48 111 46.7 0 111
49 99 46.7 0 99
50 110 46.7 0 110
51 129 46.7 0 129
52 108 46.7 0 108
53 120 46.7 0 120
54 94 46.7 0 94
55 110 46.7 0 110
56 100 46.7 0 100
57 106 46.7 0 106
58 94 46.7 0 94
59 102 46.7 0 102
60 93 46.7 0 93
61 94 46.7 0 94
62 89 46.7 0 89
63 83 46.7 0 83
64 84 46.7 0 84
65 73 46.7 0 73
66 61 46.7 0 61
67 73 46.7 0 73
68 64 46.7 0 64
69 56 46.7 0 56
70 49 46.7 0 49
71 50 46.7 0 50
72 43 46.7 0 43
73 41 46.7 0 41
74 29 46.7 0 29
75 30 46.7 0 30
76 31 46.7 0 31
77 21 46.7 0 21
78 24 46.7 0 24
79 24 46.7 0 24
80 23 46.7 0 23
81 29 46.7 0 29
82 22 46.7 0 22
83 24 46.7 0 24
84 41 46.7 0 41
85 30 46.7 0 30
86 795 46.7 0 795
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 67366 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 23.2%
G: 20.7%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 50556 47792.3 0 50556
4 10977 11948.1 0 10977
5 2376 2987.0 0 2376
6 321 746.8 0 321
7 28 186.7 0 28
8 53 186.7 0 53
9 30 186.7 0 30
10 44 186.7 0 44
11 52 186.7 0 52
12 24 186.7 0 24
13 54 186.7 0 54
14 66 186.7 0 66
15 45 186.7 0 45
16 31 186.7 0 31
17 61 186.7 0 61
18 38 186.7 0 38
19 61 186.7 0 61
20 44 186.7 0 44
21 40 186.7 0 40
22 53 186.7 0 53
23 31 186.7 0 31
24 40 186.7 0 40
25 54 186.7 0 54
26 38 186.7 0 38
27 50 186.7 0 50
28 50 186.7 0 50
29 37 186.7 0 37
30 41 186.7 0 41
31 38 186.7 0 38
32 49 186.7 0 49
33 29 186.7 0 29
34 30 186.7 0 30
35 45 186.7 0 45
36 32 186.7 0 32
37 36 186.7 0 36
38 49 186.7 0 49
39 33 186.7 0 33
40 27 186.7 0 27
41 42 186.7 0 42
42 44 186.7 0 44
43 35 186.7 0 35
44 28 186.7 0 28
45 37 186.7 0 37
46 32 186.7 0 32
47 37 186.7 0 37
48 44 186.7 0 44
49 30 186.7 0 30
50 47 186.7 0 47
51 29 186.7 0 29
52 39 186.7 0 39
53 27 186.7 0 27
54 43 186.7 0 43
55 45 186.7 0 45
56 39 186.7 0 39
57 40 186.7 0 40
58 44 186.7 0 44
59 42 186.7 0 42
60 46 186.7 0 46
61 37 186.7 0 37
62 31 186.7 0 31
63 33 186.7 0 33
64 36 186.7 0 36
65 47 186.7 0 47
66 37 186.7 0 37
67 46 186.7 0 46
68 30 186.7 0 30
69 28 186.7 0 28
70 26 186.7 0 26
71 44 186.7 0 44
72 33 186.7 0 33
73 31 186.7 0 31
74 46 186.7 0 46
75 39 186.7 0 39
76 26 186.7 0 26
77 68 186.7 0 68
78 40 186.7 0 40
79 14 186.7 0 14
80 29 186.7 0 29
81 36 186.7 0 36
82 32 186.7 0 32
83 43 186.7 0 43
84 27 186.7 0 27
85 31 186.7 0 31
86 43 186.7 0 43
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N50_S187_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N50_S187_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 29.41 s (9 µs/read; 6.38 M reads/minute).
=== Summary ===
Total reads processed: 3,129,180
Reads with adapters: 1,013,596 (32.4%)
== Read fate breakdown ==
Reads that were too short: 273,598 (8.7%)
Reads written (passing filters): 2,855,582 (91.3%)
Total basepairs processed: 316,047,180 bp
Total written (filtered): 225,599,931 bp (71.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 914234 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.9%
G: 28.1%
T: 29.5%
none/other: 11.5%
Overview of removed sequences
length count expect max.err error counts
3 72442 48893.4 0 72442
4 30921 12223.4 0 30921
5 16261 3055.8 0 16261
6 10702 764.0 0 10702
7 8908 191.0 0 8908
8 7855 47.7 0 7855
9 7829 47.7 0 7829
10 7882 47.7 0 7882
11 7938 47.7 0 7938
12 7816 47.7 0 7816
13 8020 47.7 0 8020
14 7840 47.7 0 7840
15 8615 47.7 0 8615
16 9283 47.7 0 9283
17 8257 47.7 0 8257
18 9022 47.7 0 9022
19 9098 47.7 0 9098
20 7913 47.7 0 7913
21 8813 47.7 0 8813
22 9530 47.7 0 9530
23 7804 47.7 0 7804
24 7675 47.7 0 7675
25 7800 47.7 0 7800
26 7743 47.7 0 7743
27 7560 47.7 0 7560
28 8134 47.7 0 8134
29 8250 47.7 0 8250
30 7850 47.7 0 7850
31 8981 47.7 0 8981
32 8471 47.7 0 8471
33 8682 47.7 0 8682
34 8752 47.7 0 8752
35 8620 47.7 0 8620
36 8140 47.7 0 8140
37 8706 47.7 0 8706
38 8075 47.7 0 8075
39 8170 47.7 0 8170
40 8377 47.7 0 8377
41 8055 47.7 0 8055
42 8639 47.7 0 8639
43 9398 47.7 0 9398
44 8222 47.7 0 8222
45 8490 47.7 0 8490
46 9269 47.7 0 9269
47 8931 47.7 0 8931
48 8126 47.7 0 8126
49 13582 47.7 0 13582
50 16086 47.7 0 16086
51 8808 47.7 0 8808
52 9056 47.7 0 9056
53 9031 47.7 0 9031
54 7518 47.7 0 7518
55 8252 47.7 0 8252
56 8172 47.7 0 8172
57 7780 47.7 0 7780
58 8623 47.7 0 8623
59 8253 47.7 0 8253
60 7949 47.7 0 7949
61 8572 47.7 0 8572
62 8322 47.7 0 8322
63 7703 47.7 0 7703
64 7898 47.7 0 7898
65 8005 47.7 0 8005
66 7405 47.7 0 7405
67 7829 47.7 0 7829
68 8029 47.7 0 8029
69 7547 47.7 0 7547
70 7061 47.7 0 7061
71 8302 47.7 0 8302
72 8176 47.7 0 8176
73 7650 47.7 0 7650
74 7399 47.7 0 7399
75 7591 47.7 0 7591
76 7298 47.7 0 7298
77 7647 47.7 0 7647
78 7650 47.7 0 7650
79 8686 47.7 0 8686
80 8060 47.7 0 8060
81 9343 47.7 0 9343
82 10778 47.7 0 10778
83 11680 47.7 0 11680
84 12841 47.7 0 12841
85 12991 47.7 0 12991
86 104796 47.7 0 104796
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 31021 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.7%
C: 32.5%
G: 0.0%
T: 34.0%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 16861 48893.4 0 16861
4 3557 12223.4 0 3557
5 892 3055.8 0 892
6 328 764.0 0 328
7 214 191.0 0 214
8 200 47.7 0 200
9 191 47.7 0 191
10 198 47.7 0 198
11 167 47.7 0 167
12 161 47.7 0 161
13 170 47.7 0 170
14 142 47.7 0 142
15 160 47.7 0 160
16 167 47.7 0 167
17 121 47.7 0 121
18 137 47.7 0 137
19 133 47.7 0 133
20 139 47.7 0 139
21 143 47.7 0 143
22 157 47.7 0 157
23 121 47.7 0 121
24 153 47.7 0 153
25 158 47.7 0 158
26 136 47.7 0 136
27 138 47.7 0 138
28 131 47.7 0 131
29 116 47.7 0 116
30 140 47.7 0 140
31 123 47.7 0 123
32 121 47.7 0 121
33 130 47.7 0 130
34 148 47.7 0 148
35 126 47.7 0 126
36 125 47.7 0 125
37 130 47.7 0 130
38 128 47.7 0 128
39 116 47.7 0 116
40 103 47.7 0 103
41 117 47.7 0 117
42 106 47.7 0 106
43 127 47.7 0 127
44 119 47.7 0 119
45 108 47.7 0 108
46 108 47.7 0 108
47 138 47.7 0 138
48 137 47.7 0 137
49 130 47.7 0 130
50 111 47.7 0 111
51 109 47.7 0 109
52 119 47.7 0 119
53 110 47.7 0 110
54 107 47.7 0 107
55 103 47.7 0 103
56 120 47.7 0 120
57 105 47.7 0 105
58 110 47.7 0 110
59 101 47.7 0 101
60 107 47.7 0 107
61 116 47.7 0 116
62 110 47.7 0 110
63 93 47.7 0 93
64 76 47.7 0 76
65 80 47.7 0 80
66 81 47.7 0 81
67 71 47.7 0 71
68 63 47.7 0 63
69 65 47.7 0 65
70 53 47.7 0 53
71 55 47.7 0 55
72 43 47.7 0 43
73 36 47.7 0 36
74 40 47.7 0 40
75 26 47.7 0 26
76 14 47.7 0 14
77 22 47.7 0 22
78 19 47.7 0 19
79 28 47.7 0 28
80 29 47.7 0 29
81 17 47.7 0 17
82 32 47.7 0 32
83 32 47.7 0 32
84 42 47.7 0 42
85 42 47.7 0 42
86 863 47.7 0 863
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 68341 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 23.3%
G: 20.6%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51199 48893.4 0 51199
4 11382 12223.4 0 11382
5 2364 3055.8 0 2364
6 302 764.0 0 302
7 26 191.0 0 26
8 42 191.0 0 42
9 33 191.0 0 33
10 31 191.0 0 31
11 52 191.0 0 52
12 33 191.0 0 33
13 61 191.0 0 61
14 55 191.0 0 55
15 41 191.0 0 41
16 44 191.0 0 44
17 69 191.0 0 69
18 42 191.0 0 42
19 56 191.0 0 56
20 52 191.0 0 52
21 40 191.0 0 40
22 65 191.0 0 65
23 27 191.0 0 27
24 35 191.0 0 35
25 50 191.0 0 50
26 49 191.0 0 49
27 34 191.0 0 34
28 37 191.0 0 37
29 39 191.0 0 39
30 46 191.0 0 46
31 30 191.0 0 30
32 41 191.0 0 41
33 33 191.0 0 33
34 39 191.0 0 39
35 35 191.0 0 35
36 43 191.0 0 43
37 35 191.0 0 35
38 37 191.0 0 37
39 37 191.0 0 37
40 27 191.0 0 27
41 60 191.0 0 60
42 25 191.0 0 25
43 31 191.0 0 31
44 42 191.0 0 42
45 42 191.0 0 42
46 40 191.0 0 40
47 44 191.0 0 44
48 41 191.0 0 41
49 32 191.0 0 32
50 36 191.0 0 36
51 65 191.0 0 65
52 52 191.0 0 52
53 34 191.0 0 34
54 40 191.0 0 40
55 44 191.0 0 44
56 30 191.0 0 30
57 24 191.0 0 24
58 45 191.0 0 45
59 34 191.0 0 34
60 45 191.0 0 45
61 31 191.0 0 31
62 38 191.0 0 38
63 36 191.0 0 36
64 35 191.0 0 35
65 44 191.0 0 44
66 36 191.0 0 36
67 36 191.0 0 36
68 30 191.0 0 30
69 23 191.0 0 23
70 31 191.0 0 31
71 39 191.0 0 39
72 30 191.0 0 30
73 32 191.0 0 32
74 24 191.0 0 24
75 30 191.0 0 30
76 26 191.0 0 26
77 45 191.0 0 45
78 26 191.0 0 26
79 27 191.0 0 27
80 26 191.0 0 26
81 35 191.0 0 35
82 34 191.0 0 34
83 33 191.0 0 33
84 34 191.0 0 34
85 43 191.0 0 43
86 48 191.0 0 48
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N51_S186_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N51_S186_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.43 s (10 µs/read; 6.19 M reads/minute).
=== Summary ===
Total reads processed: 2,625,585
Reads with adapters: 754,130 (28.7%)
== Read fate breakdown ==
Reads that were too short: 199,867 (7.6%)
Reads written (passing filters): 2,425,718 (92.4%)
Total basepairs processed: 265,184,085 bp
Total written (filtered): 194,519,276 bp (73.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 666570 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.4%
G: 28.6%
T: 29.0%
none/other: 12.0%
Overview of removed sequences
length count expect max.err error counts
3 61835 41024.8 0 61835
4 25464 10256.2 0 25464
5 12748 2564.0 0 12748
6 8086 641.0 0 8086
7 6555 160.3 0 6555
8 5633 40.1 0 5633
9 5666 40.1 0 5666
10 5812 40.1 0 5812
11 5673 40.1 0 5673
12 5749 40.1 0 5749
13 5808 40.1 0 5808
14 5801 40.1 0 5801
15 5986 40.1 0 5986
16 6179 40.1 0 6179
17 6022 40.1 0 6022
18 6264 40.1 0 6264
19 6127 40.1 0 6127
20 6018 40.1 0 6018
21 5980 40.1 0 5980
22 5943 40.1 0 5943
23 5456 40.1 0 5456
24 5477 40.1 0 5477
25 5485 40.1 0 5485
26 5530 40.1 0 5530
27 5468 40.1 0 5468
28 5801 40.1 0 5801
29 5745 40.1 0 5745
30 5647 40.1 0 5647
31 6531 40.1 0 6531
32 6105 40.1 0 6105
33 6577 40.1 0 6577
34 6561 40.1 0 6561
35 6092 40.1 0 6092
36 5860 40.1 0 5860
37 6308 40.1 0 6308
38 5670 40.1 0 5670
39 5843 40.1 0 5843
40 5750 40.1 0 5750
41 5626 40.1 0 5626
42 6004 40.1 0 6004
43 5971 40.1 0 5971
44 5477 40.1 0 5477
45 5651 40.1 0 5651
46 6047 40.1 0 6047
47 6014 40.1 0 6014
48 5698 40.1 0 5698
49 8944 40.1 0 8944
50 11526 40.1 0 11526
51 6163 40.1 0 6163
52 6677 40.1 0 6677
53 6454 40.1 0 6454
54 5538 40.1 0 5538
55 5749 40.1 0 5749
56 5956 40.1 0 5956
57 5496 40.1 0 5496
58 5973 40.1 0 5973
59 5615 40.1 0 5615
60 5777 40.1 0 5777
61 5763 40.1 0 5763
62 5697 40.1 0 5697
63 5377 40.1 0 5377
64 5573 40.1 0 5573
65 5543 40.1 0 5543
66 5248 40.1 0 5248
67 5620 40.1 0 5620
68 5411 40.1 0 5411
69 5274 40.1 0 5274
70 4979 40.1 0 4979
71 5671 40.1 0 5671
72 5632 40.1 0 5632
73 5301 40.1 0 5301
74 5084 40.1 0 5084
75 5197 40.1 0 5197
76 5051 40.1 0 5051
77 4911 40.1 0 4911
78 5189 40.1 0 5189
79 5980 40.1 0 5980
80 5667 40.1 0 5667
81 6627 40.1 0 6627
82 7829 40.1 0 7829
83 8886 40.1 0 8886
84 9507 40.1 0 9507
85 9888 40.1 0 9888
86 80054 40.1 0 80054
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 25140 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.4%
C: 32.8%
G: 0.0%
T: 32.3%
none/other: 3.5%
Overview of removed sequences
length count expect max.err error counts
3 15527 41024.8 0 15527
4 2981 10256.2 0 2981
5 781 2564.0 0 781
6 197 641.0 0 197
7 134 160.3 0 134
8 148 40.1 0 148
9 117 40.1 0 117
10 99 40.1 0 99
11 125 40.1 0 125
12 110 40.1 0 110
13 102 40.1 0 102
14 97 40.1 0 97
15 93 40.1 0 93
16 78 40.1 0 78
17 75 40.1 0 75
18 71 40.1 0 71
19 69 40.1 0 69
20 76 40.1 0 76
21 67 40.1 0 67
22 70 40.1 0 70
23 93 40.1 0 93
24 71 40.1 0 71
25 72 40.1 0 72
26 62 40.1 0 62
27 59 40.1 0 59
28 65 40.1 0 65
29 56 40.1 0 56
30 87 40.1 0 87
31 70 40.1 0 70
32 75 40.1 0 75
33 69 40.1 0 69
34 65 40.1 0 65
35 69 40.1 0 69
36 58 40.1 0 58
37 81 40.1 0 81
38 60 40.1 0 60
39 72 40.1 0 72
40 58 40.1 0 58
41 69 40.1 0 69
42 71 40.1 0 71
43 64 40.1 0 64
44 63 40.1 0 63
45 52 40.1 0 52
46 76 40.1 0 76
47 58 40.1 0 58
48 63 40.1 0 63
49 61 40.1 0 61
50 58 40.1 0 58
51 68 40.1 0 68
52 64 40.1 0 64
53 44 40.1 0 44
54 52 40.1 0 52
55 74 40.1 0 74
56 64 40.1 0 64
57 56 40.1 0 56
58 63 40.1 0 63
59 44 40.1 0 44
60 74 40.1 0 74
61 62 40.1 0 62
62 36 40.1 0 36
63 63 40.1 0 63
64 40 40.1 0 40
65 45 40.1 0 45
66 32 40.1 0 32
67 37 40.1 0 37
68 41 40.1 0 41
69 29 40.1 0 29
70 33 40.1 0 33
71 33 40.1 0 33
72 28 40.1 0 28
73 22 40.1 0 22
74 18 40.1 0 18
75 18 40.1 0 18
76 14 40.1 0 14
77 11 40.1 0 11
78 15 40.1 0 15
79 17 40.1 0 17
80 17 40.1 0 17
81 21 40.1 0 21
82 25 40.1 0 25
83 43 40.1 0 43
84 28 40.1 0 28
85 44 40.1 0 44
86 871 40.1 0 871
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 62420 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.8%
C: 23.4%
G: 21.9%
T: 19.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 46780 41024.8 0 46780
4 10169 10256.2 0 10169
5 2309 2564.0 0 2309
6 348 641.0 0 348
7 27 160.3 0 27
8 35 160.3 0 35
9 29 160.3 0 29
10 19 160.3 0 19
11 37 160.3 0 37
12 34 160.3 0 34
13 36 160.3 0 36
14 30 160.3 0 30
15 34 160.3 0 34
16 28 160.3 0 28
17 27 160.3 0 27
18 41 160.3 0 41
19 33 160.3 0 33
20 52 160.3 0 52
21 28 160.3 0 28
22 39 160.3 0 39
23 43 160.3 0 43
24 31 160.3 0 31
25 24 160.3 0 24
26 38 160.3 0 38
27 28 160.3 0 28
28 30 160.3 0 30
29 42 160.3 0 42
30 32 160.3 0 32
31 28 160.3 0 28
32 46 160.3 0 46
33 39 160.3 0 39
34 25 160.3 0 25
35 30 160.3 0 30
36 55 160.3 0 55
37 42 160.3 0 42
38 28 160.3 0 28
39 47 160.3 0 47
40 24 160.3 0 24
41 36 160.3 0 36
42 36 160.3 0 36
43 39 160.3 0 39
44 28 160.3 0 28
45 32 160.3 0 32
46 34 160.3 0 34
47 45 160.3 0 45
48 29 160.3 0 29
49 24 160.3 0 24
50 32 160.3 0 32
51 27 160.3 0 27
52 37 160.3 0 37
53 23 160.3 0 23
54 31 160.3 0 31
55 34 160.3 0 34
56 36 160.3 0 36
57 26 160.3 0 26
58 43 160.3 0 43
59 41 160.3 0 41
60 43 160.3 0 43
61 26 160.3 0 26
62 39 160.3 0 39
63 43 160.3 0 43
64 38 160.3 0 38
65 49 160.3 0 49
66 38 160.3 0 38
67 37 160.3 0 37
68 30 160.3 0 30
69 34 160.3 0 34
70 34 160.3 0 34
71 52 160.3 0 52
72 24 160.3 0 24
73 41 160.3 0 41
74 36 160.3 0 36
75 22 160.3 0 22
76 34 160.3 0 34
77 48 160.3 0 48
78 37 160.3 0 37
79 38 160.3 0 38
80 32 160.3 0 32
81 37 160.3 0 37
82 38 160.3 0 38
83 39 160.3 0 39
84 46 160.3 0 46
85 42 160.3 0 42
86 43 160.3 0 43
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N51_S186_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N51_S186_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.89 s (10 µs/read; 6.19 M reads/minute).
=== Summary ===
Total reads processed: 2,669,320
Reads with adapters: 772,348 (28.9%)
== Read fate breakdown ==
Reads that were too short: 208,333 (7.8%)
Reads written (passing filters): 2,460,987 (92.2%)
Total basepairs processed: 269,601,320 bp
Total written (filtered): 197,214,139 bp (73.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 683731 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.4%
G: 28.6%
T: 28.8%
none/other: 12.3%
Overview of removed sequences
length count expect max.err error counts
3 62263 41708.1 0 62263
4 25398 10427.0 0 25398
5 13030 2606.8 0 13030
6 8127 651.7 0 8127
7 6770 162.9 0 6770
8 5711 40.7 0 5711
9 5811 40.7 0 5811
10 5836 40.7 0 5836
11 5812 40.7 0 5812
12 5807 40.7 0 5807
13 5842 40.7 0 5842
14 6029 40.7 0 6029
15 5938 40.7 0 5938
16 6347 40.7 0 6347
17 6173 40.7 0 6173
18 6110 40.7 0 6110
19 5919 40.7 0 5919
20 5931 40.7 0 5931
21 5963 40.7 0 5963
22 6043 40.7 0 6043
23 5607 40.7 0 5607
24 5595 40.7 0 5595
25 5663 40.7 0 5663
26 5708 40.7 0 5708
27 5542 40.7 0 5542
28 5881 40.7 0 5881
29 5957 40.7 0 5957
30 5752 40.7 0 5752
31 6666 40.7 0 6666
32 6284 40.7 0 6284
33 6756 40.7 0 6756
34 6740 40.7 0 6740
35 6264 40.7 0 6264
36 5982 40.7 0 5982
37 6493 40.7 0 6493
38 5700 40.7 0 5700
39 5954 40.7 0 5954
40 6049 40.7 0 6049
41 5906 40.7 0 5906
42 6104 40.7 0 6104
43 6304 40.7 0 6304
44 5823 40.7 0 5823
45 5773 40.7 0 5773
46 6101 40.7 0 6101
47 6343 40.7 0 6343
48 5740 40.7 0 5740
49 9342 40.7 0 9342
50 11775 40.7 0 11775
51 6229 40.7 0 6229
52 6676 40.7 0 6676
53 6638 40.7 0 6638
54 5465 40.7 0 5465
55 5978 40.7 0 5978
56 5917 40.7 0 5917
57 5704 40.7 0 5704
58 5882 40.7 0 5882
59 5968 40.7 0 5968
60 5903 40.7 0 5903
61 5852 40.7 0 5852
62 5858 40.7 0 5858
63 5576 40.7 0 5576
64 5769 40.7 0 5769
65 5915 40.7 0 5915
66 5519 40.7 0 5519
67 5789 40.7 0 5789
68 5806 40.7 0 5806
69 5602 40.7 0 5602
70 5056 40.7 0 5056
71 5802 40.7 0 5802
72 5819 40.7 0 5819
73 5385 40.7 0 5385
74 5168 40.7 0 5168
75 5430 40.7 0 5430
76 5299 40.7 0 5299
77 5199 40.7 0 5199
78 5462 40.7 0 5462
79 6300 40.7 0 6300
80 6131 40.7 0 6131
81 6830 40.7 0 6830
82 8231 40.7 0 8231
83 9176 40.7 0 9176
84 9974 40.7 0 9974
85 10043 40.7 0 10043
86 83716 40.7 0 83716
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 25465 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 32.1%
C: 32.7%
G: 0.0%
T: 31.7%
none/other: 3.5%
Overview of removed sequences
length count expect max.err error counts
3 15917 41708.1 0 15917
4 2982 10427.0 0 2982
5 735 2606.8 0 735
6 221 651.7 0 221
7 157 162.9 0 157
8 155 40.7 0 155
9 120 40.7 0 120
10 107 40.7 0 107
11 101 40.7 0 101
12 94 40.7 0 94
13 101 40.7 0 101
14 69 40.7 0 69
15 73 40.7 0 73
16 85 40.7 0 85
17 58 40.7 0 58
18 62 40.7 0 62
19 78 40.7 0 78
20 85 40.7 0 85
21 59 40.7 0 59
22 82 40.7 0 82
23 66 40.7 0 66
24 75 40.7 0 75
25 71 40.7 0 71
26 61 40.7 0 61
27 81 40.7 0 81
28 78 40.7 0 78
29 75 40.7 0 75
30 66 40.7 0 66
31 77 40.7 0 77
32 76 40.7 0 76
33 82 40.7 0 82
34 90 40.7 0 90
35 67 40.7 0 67
36 74 40.7 0 74
37 75 40.7 0 75
38 65 40.7 0 65
39 75 40.7 0 75
40 63 40.7 0 63
41 63 40.7 0 63
42 54 40.7 0 54
43 68 40.7 0 68
44 61 40.7 0 61
45 51 40.7 0 51
46 64 40.7 0 64
47 66 40.7 0 66
48 60 40.7 0 60
49 51 40.7 0 51
50 65 40.7 0 65
51 57 40.7 0 57
52 68 40.7 0 68
53 48 40.7 0 48
54 61 40.7 0 61
55 57 40.7 0 57
56 52 40.7 0 52
57 46 40.7 0 46
58 52 40.7 0 52
59 44 40.7 0 44
60 61 40.7 0 61
61 46 40.7 0 46
62 63 40.7 0 63
63 51 40.7 0 51
64 43 40.7 0 43
65 50 40.7 0 50
66 39 40.7 0 39
67 51 40.7 0 51
68 36 40.7 0 36
69 22 40.7 0 22
70 36 40.7 0 36
71 34 40.7 0 34
72 28 40.7 0 28
73 31 40.7 0 31
74 20 40.7 0 20
75 21 40.7 0 21
76 22 40.7 0 22
77 14 40.7 0 14
78 22 40.7 0 22
79 10 40.7 0 10
80 16 40.7 0 16
81 15 40.7 0 15
82 15 40.7 0 15
83 30 40.7 0 30
84 21 40.7 0 21
85 37 40.7 0 37
86 885 40.7 0 885
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 63152 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.5%
C: 23.2%
G: 22.1%
T: 20.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47419 41708.1 0 47419
4 10170 10427.0 0 10170
5 2326 2606.8 0 2326
6 357 651.7 0 357
7 34 162.9 0 34
8 54 162.9 0 54
9 38 162.9 0 38
10 32 162.9 0 32
11 38 162.9 0 38
12 26 162.9 0 26
13 45 162.9 0 45
14 28 162.9 0 28
15 29 162.9 0 29
16 30 162.9 0 30
17 33 162.9 0 33
18 34 162.9 0 34
19 39 162.9 0 39
20 42 162.9 0 42
21 26 162.9 0 26
22 27 162.9 0 27
23 43 162.9 0 43
24 32 162.9 0 32
25 32 162.9 0 32
26 33 162.9 0 33
27 22 162.9 0 22
28 35 162.9 0 35
29 38 162.9 0 38
30 35 162.9 0 35
31 33 162.9 0 33
32 60 162.9 0 60
33 30 162.9 0 30
34 28 162.9 0 28
35 28 162.9 0 28
36 40 162.9 0 40
37 32 162.9 0 32
38 35 162.9 0 35
39 29 162.9 0 29
40 28 162.9 0 28
41 47 162.9 0 47
42 42 162.9 0 42
43 42 162.9 0 42
44 34 162.9 0 34
45 34 162.9 0 34
46 23 162.9 0 23
47 34 162.9 0 34
48 46 162.9 0 46
49 31 162.9 0 31
50 39 162.9 0 39
51 36 162.9 0 36
52 37 162.9 0 37
53 20 162.9 0 20
54 41 162.9 0 41
55 42 162.9 0 42
56 31 162.9 0 31
57 33 162.9 0 33
58 39 162.9 0 39
59 47 162.9 0 47
60 34 162.9 0 34
61 38 162.9 0 38
62 46 162.9 0 46
63 36 162.9 0 36
64 34 162.9 0 34
65 46 162.9 0 46
66 31 162.9 0 31
67 37 162.9 0 37
68 35 162.9 0 35
69 27 162.9 0 27
70 27 162.9 0 27
71 32 162.9 0 32
72 27 162.9 0 27
73 35 162.9 0 35
74 38 162.9 0 38
75 23 162.9 0 23
76 30 162.9 0 30
77 52 162.9 0 52
78 37 162.9 0 37
79 39 162.9 0 39
80 38 162.9 0 38
81 31 162.9 0 31
82 45 162.9 0 45
83 46 162.9 0 46
84 40 162.9 0 40
85 47 162.9 0 47
86 63 162.9 0 63
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N52_S184_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N52_S184_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 39.63 s (11 µs/read; 5.66 M reads/minute).
=== Summary ===
Total reads processed: 3,738,366
Reads with adapters: 1,444,268 (38.6%)
== Read fate breakdown ==
Reads that were too short: 349,665 (9.4%)
Reads written (passing filters): 3,388,701 (90.6%)
Total basepairs processed: 377,574,966 bp
Total written (filtered): 260,022,236 bp (68.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1291819 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 32.3%
G: 27.8%
T: 29.5%
none/other: 10.4%
Overview of removed sequences
length count expect max.err error counts
3 89588 58412.0 0 89588
4 41887 14603.0 0 41887
5 23002 3650.7 0 23002
6 16216 912.7 0 16216
7 13400 228.2 0 13400
8 12115 57.0 0 12115
9 12313 57.0 0 12313
10 12269 57.0 0 12269
11 12370 57.0 0 12370
12 12474 57.0 0 12474
13 12463 57.0 0 12463
14 12891 57.0 0 12891
15 12986 57.0 0 12986
16 13306 57.0 0 13306
17 12916 57.0 0 12916
18 13231 57.0 0 13231
19 13352 57.0 0 13352
20 12934 57.0 0 12934
21 13284 57.0 0 13284
22 13603 57.0 0 13603
23 12924 57.0 0 12924
24 12393 57.0 0 12393
25 12706 57.0 0 12706
26 12549 57.0 0 12549
27 12437 57.0 0 12437
28 12932 57.0 0 12932
29 13217 57.0 0 13217
30 12868 57.0 0 12868
31 13239 57.0 0 13239
32 12554 57.0 0 12554
33 13339 57.0 0 13339
34 12911 57.0 0 12911
35 12723 57.0 0 12723
36 12806 57.0 0 12806
37 12477 57.0 0 12477
38 12062 57.0 0 12062
39 12429 57.0 0 12429
40 12785 57.0 0 12785
41 12315 57.0 0 12315
42 12742 57.0 0 12742
43 12489 57.0 0 12489
44 12068 57.0 0 12068
45 12449 57.0 0 12449
46 12655 57.0 0 12655
47 12700 57.0 0 12700
48 12370 57.0 0 12370
49 16074 57.0 0 16074
50 18298 57.0 0 18298
51 13388 57.0 0 13388
52 13803 57.0 0 13803
53 13548 57.0 0 13548
54 12535 57.0 0 12535
55 13460 57.0 0 13460
56 13054 57.0 0 13054
57 12687 57.0 0 12687
58 13624 57.0 0 13624
59 13183 57.0 0 13183
60 12929 57.0 0 12929
61 13326 57.0 0 13326
62 13253 57.0 0 13253
63 12404 57.0 0 12404
64 12638 57.0 0 12638
65 12682 57.0 0 12682
66 12279 57.0 0 12279
67 11914 57.0 0 11914
68 11730 57.0 0 11730
69 11568 57.0 0 11568
70 11081 57.0 0 11081
71 11310 57.0 0 11310
72 10944 57.0 0 10944
73 10449 57.0 0 10449
74 9933 57.0 0 9933
75 9442 57.0 0 9442
76 9294 57.0 0 9294
77 9799 57.0 0 9799
78 8939 57.0 0 8939
79 10056 57.0 0 10056
80 9272 57.0 0 9272
81 9962 57.0 0 9962
82 11935 57.0 0 11935
83 13335 57.0 0 13335
84 13659 57.0 0 13659
85 14410 57.0 0 14410
86 133883 57.0 0 133883
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 82069 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 23.4%
C: 33.6%
G: 0.0%
T: 39.9%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 15322 58412.0 0 15322
4 4428 14603.0 0 4428
5 1890 3650.7 0 1890
6 1323 912.7 0 1323
7 1155 228.2 0 1155
8 1138 57.0 0 1138
9 1042 57.0 0 1042
10 1099 57.0 0 1099
11 1041 57.0 0 1041
12 1058 57.0 0 1058
13 999 57.0 0 999
14 1061 57.0 0 1061
15 937 57.0 0 937
16 1013 57.0 0 1013
17 948 57.0 0 948
18 984 57.0 0 984
19 960 57.0 0 960
20 905 57.0 0 905
21 905 57.0 0 905
22 926 57.0 0 926
23 966 57.0 0 966
24 990 57.0 0 990
25 977 57.0 0 977
26 931 57.0 0 931
27 947 57.0 0 947
28 956 57.0 0 956
29 927 57.0 0 927
30 986 57.0 0 986
31 874 57.0 0 874
32 941 57.0 0 941
33 943 57.0 0 943
34 965 57.0 0 965
35 941 57.0 0 941
36 879 57.0 0 879
37 927 57.0 0 927
38 861 57.0 0 861
39 858 57.0 0 858
40 978 57.0 0 978
41 795 57.0 0 795
42 954 57.0 0 954
43 850 57.0 0 850
44 894 57.0 0 894
45 915 57.0 0 915
46 941 57.0 0 941
47 907 57.0 0 907
48 933 57.0 0 933
49 934 57.0 0 934
50 895 57.0 0 895
51 765 57.0 0 765
52 873 57.0 0 873
53 811 57.0 0 811
54 741 57.0 0 741
55 815 57.0 0 815
56 795 57.0 0 795
57 734 57.0 0 734
58 749 57.0 0 749
59 756 57.0 0 756
60 708 57.0 0 708
61 643 57.0 0 643
62 615 57.0 0 615
63 582 57.0 0 582
64 518 57.0 0 518
65 548 57.0 0 548
66 445 57.0 0 445
67 446 57.0 0 446
68 379 57.0 0 379
69 372 57.0 0 372
70 293 57.0 0 293
71 273 57.0 0 273
72 241 57.0 0 241
73 223 57.0 0 223
74 229 57.0 0 229
75 150 57.0 0 150
76 135 57.0 0 135
77 116 57.0 0 116
78 95 57.0 0 95
79 99 57.0 0 99
80 87 57.0 0 87
81 60 57.0 0 60
82 51 57.0 0 51
83 68 57.0 0 68
84 84 57.0 0 84
85 73 57.0 0 73
86 2498 57.0 0 2498
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 70380 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.4%
C: 22.5%
G: 20.5%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 52521 58412.0 0 52521
4 12352 14603.0 0 12352
5 2094 3650.7 0 2094
6 289 912.7 0 289
7 31 228.2 0 31
8 43 228.2 0 43
9 42 228.2 0 42
10 29 228.2 0 29
11 43 228.2 0 43
12 34 228.2 0 34
13 55 228.2 0 55
14 39 228.2 0 39
15 40 228.2 0 40
16 48 228.2 0 48
17 61 228.2 0 61
18 47 228.2 0 47
19 55 228.2 0 55
20 56 228.2 0 56
21 36 228.2 0 36
22 34 228.2 0 34
23 48 228.2 0 48
24 34 228.2 0 34
25 44 228.2 0 44
26 58 228.2 0 58
27 33 228.2 0 33
28 46 228.2 0 46
29 60 228.2 0 60
30 36 228.2 0 36
31 22 228.2 0 22
32 46 228.2 0 46
33 43 228.2 0 43
34 38 228.2 0 38
35 38 228.2 0 38
36 43 228.2 0 43
37 43 228.2 0 43
38 42 228.2 0 42
39 35 228.2 0 35
40 29 228.2 0 29
41 51 228.2 0 51
42 37 228.2 0 37
43 33 228.2 0 33
44 39 228.2 0 39
45 42 228.2 0 42
46 40 228.2 0 40
47 29 228.2 0 29
48 31 228.2 0 31
49 34 228.2 0 34
50 27 228.2 0 27
51 45 228.2 0 45
52 34 228.2 0 34
53 27 228.2 0 27
54 35 228.2 0 35
55 40 228.2 0 40
56 34 228.2 0 34
57 31 228.2 0 31
58 37 228.2 0 37
59 36 228.2 0 36
60 30 228.2 0 30
61 27 228.2 0 27
62 33 228.2 0 33
63 32 228.2 0 32
64 29 228.2 0 29
65 45 228.2 0 45
66 37 228.2 0 37
67 37 228.2 0 37
68 49 228.2 0 49
69 35 228.2 0 35
70 38 228.2 0 38
71 42 228.2 0 42
72 33 228.2 0 33
73 39 228.2 0 39
74 37 228.2 0 37
75 32 228.2 0 32
76 34 228.2 0 34
77 73 228.2 0 73
78 53 228.2 0 53
79 32 228.2 0 32
80 17 228.2 0 17
81 43 228.2 0 43
82 33 228.2 0 33
83 44 228.2 0 44
84 38 228.2 0 38
85 34 228.2 0 34
86 35 228.2 0 35
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N52_S184_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N52_S184_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 29.07 s (8 µs/read; 7.83 M reads/minute).
=== Summary ===
Total reads processed: 3,795,401
Reads with adapters: 1,481,813 (39.0%)
== Read fate breakdown ==
Reads that were too short: 366,301 (9.7%)
Reads written (passing filters): 3,429,100 (90.3%)
Total basepairs processed: 383,335,501 bp
Total written (filtered): 262,670,736 bp (68.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1326660 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 32.3%
G: 27.7%
T: 29.3%
none/other: 10.7%
Overview of removed sequences
length count expect max.err error counts
3 89862 59303.1 0 89862
4 41783 14825.8 0 41783
5 22911 3706.4 0 22911
6 16227 926.6 0 16227
7 13637 231.7 0 13637
8 12500 57.9 0 12500
9 12481 57.9 0 12481
10 12684 57.9 0 12684
11 12574 57.9 0 12574
12 12530 57.9 0 12530
13 12522 57.9 0 12522
14 12850 57.9 0 12850
15 13217 57.9 0 13217
16 13763 57.9 0 13763
17 13318 57.9 0 13318
18 13607 57.9 0 13607
19 13720 57.9 0 13720
20 13132 57.9 0 13132
21 13444 57.9 0 13444
22 13879 57.9 0 13879
23 12956 57.9 0 12956
24 12717 57.9 0 12717
25 12884 57.9 0 12884
26 12811 57.9 0 12811
27 12777 57.9 0 12777
28 12903 57.9 0 12903
29 13398 57.9 0 13398
30 12924 57.9 0 12924
31 13498 57.9 0 13498
32 13097 57.9 0 13097
33 13508 57.9 0 13508
34 12866 57.9 0 12866
35 12847 57.9 0 12847
36 12951 57.9 0 12951
37 12747 57.9 0 12747
38 12165 57.9 0 12165
39 12884 57.9 0 12884
40 12976 57.9 0 12976
41 12515 57.9 0 12515
42 12928 57.9 0 12928
43 13049 57.9 0 13049
44 12349 57.9 0 12349
45 12870 57.9 0 12870
46 13002 57.9 0 13002
47 12803 57.9 0 12803
48 12919 57.9 0 12919
49 16732 57.9 0 16732
50 18931 57.9 0 18931
51 13952 57.9 0 13952
52 14257 57.9 0 14257
53 13888 57.9 0 13888
54 13008 57.9 0 13008
55 13896 57.9 0 13896
56 13615 57.9 0 13615
57 13172 57.9 0 13172
58 13964 57.9 0 13964
59 13690 57.9 0 13690
60 13517 57.9 0 13517
61 13915 57.9 0 13915
62 13499 57.9 0 13499
63 12802 57.9 0 12802
64 12987 57.9 0 12987
65 12879 57.9 0 12879
66 12630 57.9 0 12630
67 12574 57.9 0 12574
68 12170 57.9 0 12170
69 11664 57.9 0 11664
70 11410 57.9 0 11410
71 11837 57.9 0 11837
72 11372 57.9 0 11372
73 11041 57.9 0 11041
74 10231 57.9 0 10231
75 9979 57.9 0 9979
76 9626 57.9 0 9626
77 10247 57.9 0 10247
78 9351 57.9 0 9351
79 10258 57.9 0 10258
80 9820 57.9 0 9820
81 10463 57.9 0 10463
82 12494 57.9 0 12494
83 13975 57.9 0 13975
84 14446 57.9 0 14446
85 15022 57.9 0 15022
86 141361 57.9 0 141361
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 84220 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 23.5%
C: 33.5%
G: 0.0%
T: 39.7%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 15347 59303.1 0 15347
4 4488 14825.8 0 4488
5 1932 3706.4 0 1932
6 1339 926.6 0 1339
7 1164 231.7 0 1164
8 1192 57.9 0 1192
9 1172 57.9 0 1172
10 1124 57.9 0 1124
11 1082 57.9 0 1082
12 1109 57.9 0 1109
13 1009 57.9 0 1009
14 1003 57.9 0 1003
15 984 57.9 0 984
16 1048 57.9 0 1048
17 967 57.9 0 967
18 1003 57.9 0 1003
19 1033 57.9 0 1033
20 974 57.9 0 974
21 1000 57.9 0 1000
22 935 57.9 0 935
23 992 57.9 0 992
24 1051 57.9 0 1051
25 1015 57.9 0 1015
26 971 57.9 0 971
27 914 57.9 0 914
28 1029 57.9 0 1029
29 910 57.9 0 910
30 902 57.9 0 902
31 865 57.9 0 865
32 957 57.9 0 957
33 1000 57.9 0 1000
34 888 57.9 0 888
35 913 57.9 0 913
36 943 57.9 0 943
37 1007 57.9 0 1007
38 894 57.9 0 894
39 913 57.9 0 913
40 945 57.9 0 945
41 881 57.9 0 881
42 946 57.9 0 946
43 923 57.9 0 923
44 857 57.9 0 857
45 842 57.9 0 842
46 944 57.9 0 944
47 938 57.9 0 938
48 965 57.9 0 965
49 881 57.9 0 881
50 977 57.9 0 977
51 860 57.9 0 860
52 923 57.9 0 923
53 809 57.9 0 809
54 791 57.9 0 791
55 852 57.9 0 852
56 791 57.9 0 791
57 827 57.9 0 827
58 805 57.9 0 805
59 815 57.9 0 815
60 752 57.9 0 752
61 712 57.9 0 712
62 638 57.9 0 638
63 651 57.9 0 651
64 566 57.9 0 566
65 560 57.9 0 560
66 519 57.9 0 519
67 466 57.9 0 466
68 369 57.9 0 369
69 366 57.9 0 366
70 304 57.9 0 304
71 265 57.9 0 265
72 261 57.9 0 261
73 239 57.9 0 239
74 178 57.9 0 178
75 145 57.9 0 145
76 110 57.9 0 110
77 118 57.9 0 118
78 104 57.9 0 104
79 94 57.9 0 94
80 87 57.9 0 87
81 68 57.9 0 68
82 74 57.9 0 74
83 71 57.9 0 71
84 78 57.9 0 78
85 93 57.9 0 93
86 2691 57.9 0 2691
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 70933 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.1%
C: 22.5%
G: 20.8%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 52743 59303.1 0 52743
4 12544 14825.8 0 12544
5 2177 3706.4 0 2177
6 289 926.6 0 289
7 39 231.7 0 39
8 39 231.7 0 39
9 40 231.7 0 40
10 35 231.7 0 35
11 49 231.7 0 49
12 31 231.7 0 31
13 39 231.7 0 39
14 49 231.7 0 49
15 36 231.7 0 36
16 57 231.7 0 57
17 50 231.7 0 50
18 45 231.7 0 45
19 49 231.7 0 49
20 45 231.7 0 45
21 46 231.7 0 46
22 61 231.7 0 61
23 34 231.7 0 34
24 33 231.7 0 33
25 46 231.7 0 46
26 46 231.7 0 46
27 22 231.7 0 22
28 39 231.7 0 39
29 61 231.7 0 61
30 41 231.7 0 41
31 49 231.7 0 49
32 59 231.7 0 59
33 49 231.7 0 49
34 39 231.7 0 39
35 42 231.7 0 42
36 39 231.7 0 39
37 27 231.7 0 27
38 39 231.7 0 39
39 39 231.7 0 39
40 36 231.7 0 36
41 47 231.7 0 47
42 42 231.7 0 42
43 42 231.7 0 42
44 28 231.7 0 28
45 42 231.7 0 42
46 39 231.7 0 39
47 57 231.7 0 57
48 42 231.7 0 42
49 44 231.7 0 44
50 39 231.7 0 39
51 35 231.7 0 35
52 29 231.7 0 29
53 33 231.7 0 33
54 31 231.7 0 31
55 34 231.7 0 34
56 27 231.7 0 27
57 39 231.7 0 39
58 29 231.7 0 29
59 30 231.7 0 30
60 30 231.7 0 30
61 35 231.7 0 35
62 37 231.7 0 37
63 31 231.7 0 31
64 42 231.7 0 42
65 34 231.7 0 34
66 33 231.7 0 33
67 34 231.7 0 34
68 30 231.7 0 30
69 44 231.7 0 44
70 42 231.7 0 42
71 46 231.7 0 46
72 28 231.7 0 28
73 39 231.7 0 39
74 33 231.7 0 33
75 19 231.7 0 19
76 32 231.7 0 32
77 79 231.7 0 79
78 44 231.7 0 44
79 35 231.7 0 35
80 36 231.7 0 36
81 44 231.7 0 44
82 30 231.7 0 30
83 43 231.7 0 43
84 44 231.7 0 44
85 31 231.7 0 31
86 46 231.7 0 46
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N53_S188_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N53_S188_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.40 s (9 µs/read; 6.32 M reads/minute).
=== Summary ===
Total reads processed: 2,886,941
Reads with adapters: 925,991 (32.1%)
== Read fate breakdown ==
Reads that were too short: 277,858 (9.6%)
Reads written (passing filters): 2,609,083 (90.4%)
Total basepairs processed: 291,581,041 bp
Total written (filtered): 206,719,112 bp (70.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 829687 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.1%
G: 27.5%
T: 27.9%
none/other: 14.5%
Overview of removed sequences
length count expect max.err error counts
3 64879 45108.5 0 64879
4 27735 11277.1 0 27735
5 14393 2819.3 0 14393
6 9070 704.8 0 9070
7 7610 176.2 0 7610
8 6339 44.1 0 6339
9 6587 44.1 0 6587
10 6802 44.1 0 6802
11 6532 44.1 0 6532
12 6507 44.1 0 6507
13 6753 44.1 0 6753
14 6853 44.1 0 6853
15 7049 44.1 0 7049
16 7099 44.1 0 7099
17 7056 44.1 0 7056
18 7179 44.1 0 7179
19 6799 44.1 0 6799
20 6511 44.1 0 6511
21 6851 44.1 0 6851
22 7161 44.1 0 7161
23 6466 44.1 0 6466
24 6419 44.1 0 6419
25 6597 44.1 0 6597
26 6517 44.1 0 6517
27 6312 44.1 0 6312
28 6871 44.1 0 6871
29 6995 44.1 0 6995
30 6579 44.1 0 6579
31 7013 44.1 0 7013
32 6932 44.1 0 6932
33 7179 44.1 0 7179
34 6935 44.1 0 6935
35 7128 44.1 0 7128
36 6660 44.1 0 6660
37 6870 44.1 0 6870
38 6497 44.1 0 6497
39 6783 44.1 0 6783
40 7166 44.1 0 7166
41 7009 44.1 0 7009
42 7285 44.1 0 7285
43 7819 44.1 0 7819
44 6962 44.1 0 6962
45 7387 44.1 0 7387
46 8280 44.1 0 8280
47 7689 44.1 0 7689
48 7493 44.1 0 7493
49 11561 44.1 0 11561
50 14062 44.1 0 14062
51 8006 44.1 0 8006
52 8550 44.1 0 8550
53 8385 44.1 0 8385
54 7231 44.1 0 7231
55 7499 44.1 0 7499
56 7610 44.1 0 7610
57 7195 44.1 0 7195
58 7750 44.1 0 7750
59 7630 44.1 0 7630
60 7587 44.1 0 7587
61 7670 44.1 0 7670
62 7549 44.1 0 7549
63 7170 44.1 0 7170
64 7294 44.1 0 7294
65 7472 44.1 0 7472
66 7147 44.1 0 7147
67 7332 44.1 0 7332
68 7304 44.1 0 7304
69 6910 44.1 0 6910
70 6910 44.1 0 6910
71 7835 44.1 0 7835
72 7224 44.1 0 7224
73 6839 44.1 0 6839
74 6733 44.1 0 6733
75 6820 44.1 0 6820
76 6599 44.1 0 6599
77 7100 44.1 0 7100
78 6411 44.1 0 6411
79 7560 44.1 0 7560
80 7329 44.1 0 7329
81 8678 44.1 0 8678
82 10215 44.1 0 10215
83 11668 44.1 0 11668
84 12581 44.1 0 12581
85 12797 44.1 0 12797
86 119866 44.1 0 119866
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34124 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.5%
C: 31.7%
G: 0.0%
T: 34.6%
none/other: 4.1%
Overview of removed sequences
length count expect max.err error counts
3 15223 45108.5 0 15223
4 3126 11277.1 0 3126
5 876 2819.3 0 876
6 359 704.8 0 359
7 331 176.2 0 331
8 335 44.1 0 335
9 304 44.1 0 304
10 258 44.1 0 258
11 304 44.1 0 304
12 268 44.1 0 268
13 267 44.1 0 267
14 240 44.1 0 240
15 236 44.1 0 236
16 208 44.1 0 208
17 189 44.1 0 189
18 253 44.1 0 253
19 232 44.1 0 232
20 222 44.1 0 222
21 216 44.1 0 216
22 194 44.1 0 194
23 209 44.1 0 209
24 217 44.1 0 217
25 213 44.1 0 213
26 223 44.1 0 223
27 211 44.1 0 211
28 223 44.1 0 223
29 230 44.1 0 230
30 197 44.1 0 197
31 219 44.1 0 219
32 213 44.1 0 213
33 232 44.1 0 232
34 195 44.1 0 195
35 187 44.1 0 187
36 190 44.1 0 190
37 212 44.1 0 212
38 209 44.1 0 209
39 175 44.1 0 175
40 154 44.1 0 154
41 192 44.1 0 192
42 212 44.1 0 212
43 200 44.1 0 200
44 195 44.1 0 195
45 162 44.1 0 162
46 182 44.1 0 182
47 195 44.1 0 195
48 187 44.1 0 187
49 191 44.1 0 191
50 185 44.1 0 185
51 182 44.1 0 182
52 170 44.1 0 170
53 184 44.1 0 184
54 148 44.1 0 148
55 188 44.1 0 188
56 161 44.1 0 161
57 179 44.1 0 179
58 184 44.1 0 184
59 152 44.1 0 152
60 170 44.1 0 170
61 152 44.1 0 152
62 140 44.1 0 140
63 143 44.1 0 143
64 126 44.1 0 126
65 99 44.1 0 99
66 120 44.1 0 120
67 129 44.1 0 129
68 95 44.1 0 95
69 66 44.1 0 66
70 69 44.1 0 69
71 63 44.1 0 63
72 74 44.1 0 74
73 56 44.1 0 56
74 58 44.1 0 58
75 39 44.1 0 39
76 34 44.1 0 34
77 22 44.1 0 22
78 42 44.1 0 42
79 20 44.1 0 20
80 27 44.1 0 27
81 38 44.1 0 38
82 24 44.1 0 24
83 24 44.1 0 24
84 42 44.1 0 42
85 47 44.1 0 47
86 1406 44.1 0 1406
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 62180 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.6%
C: 23.6%
G: 21.6%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 46654 45108.5 0 46654
4 10225 11277.1 0 10225
5 2059 2819.3 0 2059
6 303 704.8 0 303
7 29 176.2 0 29
8 42 176.2 0 42
9 23 176.2 0 23
10 34 176.2 0 34
11 49 176.2 0 49
12 18 176.2 0 18
13 43 176.2 0 43
14 28 176.2 0 28
15 36 176.2 0 36
16 36 176.2 0 36
17 38 176.2 0 38
18 34 176.2 0 34
19 48 176.2 0 48
20 37 176.2 0 37
21 44 176.2 0 44
22 46 176.2 0 46
23 37 176.2 0 37
24 44 176.2 0 44
25 40 176.2 0 40
26 45 176.2 0 45
27 40 176.2 0 40
28 43 176.2 0 43
29 38 176.2 0 38
30 32 176.2 0 32
31 43 176.2 0 43
32 33 176.2 0 33
33 32 176.2 0 32
34 26 176.2 0 26
35 32 176.2 0 32
36 26 176.2 0 26
37 27 176.2 0 27
38 37 176.2 0 37
39 42 176.2 0 42
40 30 176.2 0 30
41 39 176.2 0 39
42 36 176.2 0 36
43 30 176.2 0 30
44 36 176.2 0 36
45 31 176.2 0 31
46 26 176.2 0 26
47 37 176.2 0 37
48 42 176.2 0 42
49 32 176.2 0 32
50 41 176.2 0 41
51 47 176.2 0 47
52 42 176.2 0 42
53 27 176.2 0 27
54 30 176.2 0 30
55 50 176.2 0 50
56 33 176.2 0 33
57 42 176.2 0 42
58 40 176.2 0 40
59 38 176.2 0 38
60 31 176.2 0 31
61 36 176.2 0 36
62 41 176.2 0 41
63 28 176.2 0 28
64 38 176.2 0 38
65 34 176.2 0 34
66 28 176.2 0 28
67 32 176.2 0 32
68 33 176.2 0 33
69 26 176.2 0 26
70 41 176.2 0 41
71 43 176.2 0 43
72 20 176.2 0 20
73 36 176.2 0 36
74 33 176.2 0 33
75 33 176.2 0 33
76 21 176.2 0 21
77 74 176.2 0 74
78 41 176.2 0 41
79 32 176.2 0 32
80 23 176.2 0 23
81 39 176.2 0 39
82 34 176.2 0 34
83 44 176.2 0 44
84 35 176.2 0 35
85 49 176.2 0 49
86 83 176.2 0 83
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N53_S188_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N53_S188_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.17 s (10 µs/read; 6.29 M reads/minute).
=== Summary ===
Total reads processed: 2,952,662
Reads with adapters: 954,815 (32.3%)
== Read fate breakdown ==
Reads that were too short: 291,971 (9.9%)
Reads written (passing filters): 2,660,691 (90.1%)
Total basepairs processed: 298,218,862 bp
Total written (filtered): 210,653,051 bp (70.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 856235 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.1%
G: 27.4%
T: 27.7%
none/other: 14.7%
Overview of removed sequences
length count expect max.err error counts
3 65812 46135.3 0 65812
4 28319 11533.8 0 28319
5 14554 2883.5 0 14554
6 9418 720.9 0 9418
7 7587 180.2 0 7587
8 6524 45.1 0 6524
9 6650 45.1 0 6650
10 6735 45.1 0 6735
11 6668 45.1 0 6668
12 6680 45.1 0 6680
13 6804 45.1 0 6804
14 6836 45.1 0 6836
15 6997 45.1 0 6997
16 7176 45.1 0 7176
17 7189 45.1 0 7189
18 7107 45.1 0 7107
19 6838 45.1 0 6838
20 6682 45.1 0 6682
21 6826 45.1 0 6826
22 7146 45.1 0 7146
23 6663 45.1 0 6663
24 6653 45.1 0 6653
25 6706 45.1 0 6706
26 6603 45.1 0 6603
27 6599 45.1 0 6599
28 7097 45.1 0 7097
29 7260 45.1 0 7260
30 6770 45.1 0 6770
31 7191 45.1 0 7191
32 7088 45.1 0 7088
33 7386 45.1 0 7386
34 7140 45.1 0 7140
35 7167 45.1 0 7167
36 6676 45.1 0 6676
37 7025 45.1 0 7025
38 6606 45.1 0 6606
39 7001 45.1 0 7001
40 7407 45.1 0 7407
41 7118 45.1 0 7118
42 7463 45.1 0 7463
43 8023 45.1 0 8023
44 7228 45.1 0 7228
45 7664 45.1 0 7664
46 8226 45.1 0 8226
47 7676 45.1 0 7676
48 7542 45.1 0 7542
49 12142 45.1 0 12142
50 14432 45.1 0 14432
51 8203 45.1 0 8203
52 8779 45.1 0 8779
53 8469 45.1 0 8469
54 7513 45.1 0 7513
55 7889 45.1 0 7889
56 7777 45.1 0 7777
57 7636 45.1 0 7636
58 8075 45.1 0 8075
59 7946 45.1 0 7946
60 7959 45.1 0 7959
61 7935 45.1 0 7935
62 7732 45.1 0 7732
63 7520 45.1 0 7520
64 7784 45.1 0 7784
65 7724 45.1 0 7724
66 7418 45.1 0 7418
67 7432 45.1 0 7432
68 7759 45.1 0 7759
69 7243 45.1 0 7243
70 7024 45.1 0 7024
71 8268 45.1 0 8268
72 7918 45.1 0 7918
73 7379 45.1 0 7379
74 7155 45.1 0 7155
75 7134 45.1 0 7134
76 6906 45.1 0 6906
77 7532 45.1 0 7532
78 7005 45.1 0 7005
79 8004 45.1 0 8004
80 7587 45.1 0 7587
81 9013 45.1 0 9013
82 10664 45.1 0 10664
83 12138 45.1 0 12138
84 12870 45.1 0 12870
85 13761 45.1 0 13761
86 125984 45.1 0 125984
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35256 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.6%
C: 31.8%
G: 0.0%
T: 34.5%
none/other: 4.2%
Overview of removed sequences
length count expect max.err error counts
3 15610 46135.3 0 15610
4 3192 11533.8 0 3192
5 877 2883.5 0 877
6 386 720.9 0 386
7 353 180.2 0 353
8 351 45.1 0 351
9 329 45.1 0 329
10 312 45.1 0 312
11 302 45.1 0 302
12 290 45.1 0 290
13 263 45.1 0 263
14 265 45.1 0 265
15 242 45.1 0 242
16 253 45.1 0 253
17 202 45.1 0 202
18 217 45.1 0 217
19 213 45.1 0 213
20 198 45.1 0 198
21 219 45.1 0 219
22 211 45.1 0 211
23 230 45.1 0 230
24 244 45.1 0 244
25 219 45.1 0 219
26 214 45.1 0 214
27 216 45.1 0 216
28 226 45.1 0 226
29 234 45.1 0 234
30 188 45.1 0 188
31 181 45.1 0 181
32 209 45.1 0 209
33 216 45.1 0 216
34 211 45.1 0 211
35 194 45.1 0 194
36 229 45.1 0 229
37 193 45.1 0 193
38 209 45.1 0 209
39 193 45.1 0 193
40 207 45.1 0 207
41 185 45.1 0 185
42 197 45.1 0 197
43 189 45.1 0 189
44 200 45.1 0 200
45 204 45.1 0 204
46 197 45.1 0 197
47 222 45.1 0 222
48 218 45.1 0 218
49 187 45.1 0 187
50 210 45.1 0 210
51 199 45.1 0 199
52 189 45.1 0 189
53 202 45.1 0 202
54 185 45.1 0 185
55 181 45.1 0 181
56 180 45.1 0 180
57 182 45.1 0 182
58 169 45.1 0 169
59 186 45.1 0 186
60 181 45.1 0 181
61 143 45.1 0 143
62 140 45.1 0 140
63 132 45.1 0 132
64 158 45.1 0 158
65 116 45.1 0 116
66 118 45.1 0 118
67 118 45.1 0 118
68 100 45.1 0 100
69 80 45.1 0 80
70 79 45.1 0 79
71 76 45.1 0 76
72 55 45.1 0 55
73 61 45.1 0 61
74 45 45.1 0 45
75 39 45.1 0 39
76 42 45.1 0 42
77 42 45.1 0 42
78 38 45.1 0 38
79 34 45.1 0 34
80 32 45.1 0 32
81 27 45.1 0 27
82 25 45.1 0 25
83 40 45.1 0 40
84 48 45.1 0 48
85 39 45.1 0 39
86 1468 45.1 0 1468
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 63324 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 33.9%
C: 23.9%
G: 21.6%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47372 46135.3 0 47372
4 10528 11533.8 0 10528
5 2217 2883.5 0 2217
6 373 720.9 0 373
7 32 180.2 0 32
8 33 180.2 0 33
9 26 180.2 0 26
10 30 180.2 0 30
11 27 180.2 0 27
12 26 180.2 0 26
13 44 180.2 0 44
14 24 180.2 0 24
15 34 180.2 0 34
16 22 180.2 0 22
17 51 180.2 0 51
18 34 180.2 0 34
19 46 180.2 0 46
20 43 180.2 0 43
21 31 180.2 0 31
22 47 180.2 0 47
23 20 180.2 0 20
24 26 180.2 0 26
25 49 180.2 0 49
26 45 180.2 0 45
27 38 180.2 0 38
28 41 180.2 0 41
29 43 180.2 0 43
30 32 180.2 0 32
31 19 180.2 0 19
32 48 180.2 0 48
33 45 180.2 0 45
34 32 180.2 0 32
35 28 180.2 0 28
36 32 180.2 0 32
37 34 180.2 0 34
38 36 180.2 0 36
39 47 180.2 0 47
40 26 180.2 0 26
41 35 180.2 0 35
42 32 180.2 0 32
43 46 180.2 0 46
44 34 180.2 0 34
45 30 180.2 0 30
46 26 180.2 0 26
47 33 180.2 0 33
48 36 180.2 0 36
49 36 180.2 0 36
50 39 180.2 0 39
51 42 180.2 0 42
52 45 180.2 0 45
53 28 180.2 0 28
54 38 180.2 0 38
55 35 180.2 0 35
56 33 180.2 0 33
57 22 180.2 0 22
58 28 180.2 0 28
59 41 180.2 0 41
60 39 180.2 0 39
61 31 180.2 0 31
62 47 180.2 0 47
63 43 180.2 0 43
64 28 180.2 0 28
65 46 180.2 0 46
66 43 180.2 0 43
67 32 180.2 0 32
68 45 180.2 0 45
69 26 180.2 0 26
70 29 180.2 0 29
71 34 180.2 0 34
72 26 180.2 0 26
73 24 180.2 0 24
74 22 180.2 0 22
75 31 180.2 0 31
76 20 180.2 0 20
77 57 180.2 0 57
78 42 180.2 0 42
79 32 180.2 0 32
80 17 180.2 0 17
81 32 180.2 0 32
82 47 180.2 0 47
83 60 180.2 0 60
84 31 180.2 0 31
85 44 180.2 0 44
86 56 180.2 0 56
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N54_S193_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N54_S193_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 30.40 s (9 µs/read; 6.44 M reads/minute).
=== Summary ===
Total reads processed: 3,262,859
Reads with adapters: 1,150,524 (35.3%)
== Read fate breakdown ==
Reads that were too short: 346,160 (10.6%)
Reads written (passing filters): 2,916,699 (89.4%)
Total basepairs processed: 329,548,759 bp
Total written (filtered): 228,219,762 bp (69.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1030009 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.5%
G: 27.6%
T: 27.4%
none/other: 15.5%
Overview of removed sequences
length count expect max.err error counts
3 69750 50982.2 0 69750
4 30152 12745.5 0 30152
5 16637 3186.4 0 16637
6 11647 796.6 0 11647
7 9985 199.1 0 9985
8 8905 49.8 0 8905
9 8527 49.8 0 8527
10 8839 49.8 0 8839
11 8752 49.8 0 8752
12 8520 49.8 0 8520
13 8761 49.8 0 8761
14 9043 49.8 0 9043
15 8813 49.8 0 8813
16 9265 49.8 0 9265
17 9166 49.8 0 9166
18 9080 49.8 0 9080
19 9178 49.8 0 9178
20 8848 49.8 0 8848
21 8902 49.8 0 8902
22 8914 49.8 0 8914
23 8538 49.8 0 8538
24 8598 49.8 0 8598
25 8709 49.8 0 8709
26 8563 49.8 0 8563
27 8436 49.8 0 8436
28 9050 49.8 0 9050
29 9052 49.8 0 9052
30 8572 49.8 0 8572
31 8855 49.8 0 8855
32 8805 49.8 0 8805
33 8718 49.8 0 8718
34 8881 49.8 0 8881
35 9195 49.8 0 9195
36 8690 49.8 0 8690
37 8678 49.8 0 8678
38 8582 49.8 0 8582
39 8846 49.8 0 8846
40 8944 49.8 0 8944
41 8783 49.8 0 8783
42 9080 49.8 0 9080
43 9351 49.8 0 9351
44 8583 49.8 0 8583
45 8998 49.8 0 8998
46 9182 49.8 0 9182
47 9478 49.8 0 9478
48 9188 49.8 0 9188
49 14152 49.8 0 14152
50 17563 49.8 0 17563
51 10108 49.8 0 10108
52 10512 49.8 0 10512
53 10373 49.8 0 10373
54 9219 49.8 0 9219
55 9755 49.8 0 9755
56 9629 49.8 0 9629
57 9144 49.8 0 9144
58 9689 49.8 0 9689
59 9453 49.8 0 9453
60 9338 49.8 0 9338
61 9746 49.8 0 9746
62 9808 49.8 0 9808
63 9292 49.8 0 9292
64 9108 49.8 0 9108
65 9240 49.8 0 9240
66 8956 49.8 0 8956
67 9108 49.8 0 9108
68 9116 49.8 0 9116
69 8770 49.8 0 8770
70 8312 49.8 0 8312
71 8861 49.8 0 8861
72 8665 49.8 0 8665
73 8106 49.8 0 8106
74 7890 49.8 0 7890
75 7794 49.8 0 7794
76 7369 49.8 0 7369
77 7447 49.8 0 7447
78 7884 49.8 0 7884
79 8694 49.8 0 8694
80 8615 49.8 0 8615
81 9809 49.8 0 9809
82 12077 49.8 0 12077
83 13229 49.8 0 13229
84 15475 49.8 0 15475
85 16414 49.8 0 16414
86 159250 49.8 0 159250
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 57318 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.5%
C: 38.6%
G: 0.0%
T: 34.6%
none/other: 1.3%
Overview of removed sequences
length count expect max.err error counts
3 19665 50982.2 0 19665
4 4285 12745.5 0 4285
5 1371 3186.4 0 1371
6 663 796.6 0 663
7 661 199.1 0 661
8 681 49.8 0 681
9 554 49.8 0 554
10 577 49.8 0 577
11 631 49.8 0 631
12 611 49.8 0 611
13 577 49.8 0 577
14 622 49.8 0 622
15 525 49.8 0 525
16 516 49.8 0 516
17 568 49.8 0 568
18 538 49.8 0 538
19 542 49.8 0 542
20 484 49.8 0 484
21 504 49.8 0 504
22 516 49.8 0 516
23 533 49.8 0 533
24 535 49.8 0 535
25 506 49.8 0 506
26 512 49.8 0 512
27 491 49.8 0 491
28 513 49.8 0 513
29 477 49.8 0 477
30 530 49.8 0 530
31 468 49.8 0 468
32 508 49.8 0 508
33 524 49.8 0 524
34 450 49.8 0 450
35 523 49.8 0 523
36 480 49.8 0 480
37 480 49.8 0 480
38 474 49.8 0 474
39 448 49.8 0 448
40 494 49.8 0 494
41 493 49.8 0 493
42 462 49.8 0 462
43 480 49.8 0 480
44 517 49.8 0 517
45 456 49.8 0 456
46 467 49.8 0 467
47 482 49.8 0 482
48 493 49.8 0 493
49 437 49.8 0 437
50 449 49.8 0 449
51 430 49.8 0 430
52 422 49.8 0 422
53 450 49.8 0 450
54 405 49.8 0 405
55 407 49.8 0 407
56 441 49.8 0 441
57 423 49.8 0 423
58 386 49.8 0 386
59 407 49.8 0 407
60 390 49.8 0 390
61 359 49.8 0 359
62 333 49.8 0 333
63 310 49.8 0 310
64 271 49.8 0 271
65 241 49.8 0 241
66 260 49.8 0 260
67 224 49.8 0 224
68 232 49.8 0 232
69 183 49.8 0 183
70 148 49.8 0 148
71 139 49.8 0 139
72 148 49.8 0 148
73 118 49.8 0 118
74 122 49.8 0 122
75 84 49.8 0 84
76 84 49.8 0 84
77 71 49.8 0 71
78 56 49.8 0 56
79 40 49.8 0 40
80 40 49.8 0 40
81 46 49.8 0 46
82 30 49.8 0 30
83 38 49.8 0 38
84 29 49.8 0 29
85 48 49.8 0 48
86 730 49.8 0 730
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 63197 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.8%
C: 23.8%
G: 19.3%
T: 22.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47660 50982.2 0 47660
4 10133 12745.5 0 10133
5 2421 3186.4 0 2421
6 394 796.6 0 394
7 48 199.1 0 48
8 24 199.1 0 24
9 28 199.1 0 28
10 29 199.1 0 29
11 31 199.1 0 31
12 38 199.1 0 38
13 38 199.1 0 38
14 43 199.1 0 43
15 31 199.1 0 31
16 33 199.1 0 33
17 37 199.1 0 37
18 32 199.1 0 32
19 26 199.1 0 26
20 31 199.1 0 31
21 41 199.1 0 41
22 35 199.1 0 35
23 36 199.1 0 36
24 18 199.1 0 18
25 27 199.1 0 27
26 31 199.1 0 31
27 17 199.1 0 17
28 22 199.1 0 22
29 32 199.1 0 32
30 36 199.1 0 36
31 25 199.1 0 25
32 19 199.1 0 19
33 28 199.1 0 28
34 25 199.1 0 25
35 31 199.1 0 31
36 43 199.1 0 43
37 20 199.1 0 20
38 26 199.1 0 26
39 24 199.1 0 24
40 26 199.1 0 26
41 26 199.1 0 26
42 33 199.1 0 33
43 33 199.1 0 33
44 23 199.1 0 23
45 35 199.1 0 35
46 37 199.1 0 37
47 26 199.1 0 26
48 24 199.1 0 24
49 36 199.1 0 36
50 36 199.1 0 36
51 31 199.1 0 31
52 31 199.1 0 31
53 32 199.1 0 32
54 43 199.1 0 43
55 27 199.1 0 27
56 39 199.1 0 39
57 30 199.1 0 30
58 39 199.1 0 39
59 31 199.1 0 31
60 44 199.1 0 44
61 30 199.1 0 30
62 47 199.1 0 47
63 34 199.1 0 34
64 25 199.1 0 25
65 58 199.1 0 58
66 43 199.1 0 43
67 33 199.1 0 33
68 29 199.1 0 29
69 18 199.1 0 18
70 33 199.1 0 33
71 35 199.1 0 35
72 40 199.1 0 40
73 38 199.1 0 38
74 35 199.1 0 35
75 26 199.1 0 26
76 20 199.1 0 20
77 64 199.1 0 64
78 35 199.1 0 35
79 31 199.1 0 31
80 20 199.1 0 20
81 35 199.1 0 35
82 34 199.1 0 34
83 35 199.1 0 35
84 27 199.1 0 27
85 32 199.1 0 32
86 45 199.1 0 45
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N54_S193_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N54_S193_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 30.90 s (9 µs/read; 6.45 M reads/minute).
=== Summary ===
Total reads processed: 3,321,081
Reads with adapters: 1,182,243 (35.6%)
== Read fate breakdown ==
Reads that were too short: 362,356 (10.9%)
Reads written (passing filters): 2,958,725 (89.1%)
Total basepairs processed: 335,429,181 bp
Total written (filtered): 231,231,246 bp (68.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1060545 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.4%
G: 27.5%
T: 27.3%
none/other: 15.8%
Overview of removed sequences
length count expect max.err error counts
3 70143 51891.9 0 70143
4 30466 12973.0 0 30466
5 16687 3243.2 0 16687
6 11658 810.8 0 11658
7 10231 202.7 0 10231
8 8940 50.7 0 8940
9 8702 50.7 0 8702
10 8940 50.7 0 8940
11 8842 50.7 0 8842
12 8903 50.7 0 8903
13 8875 50.7 0 8875
14 9269 50.7 0 9269
15 9102 50.7 0 9102
16 9458 50.7 0 9458
17 9214 50.7 0 9214
18 9252 50.7 0 9252
19 9092 50.7 0 9092
20 8994 50.7 0 8994
21 9237 50.7 0 9237
22 9105 50.7 0 9105
23 8723 50.7 0 8723
24 9031 50.7 0 9031
25 8837 50.7 0 8837
26 8531 50.7 0 8531
27 8621 50.7 0 8621
28 9193 50.7 0 9193
29 8884 50.7 0 8884
30 8744 50.7 0 8744
31 9216 50.7 0 9216
32 9058 50.7 0 9058
33 8750 50.7 0 8750
34 8843 50.7 0 8843
35 9399 50.7 0 9399
36 8856 50.7 0 8856
37 8973 50.7 0 8973
38 8969 50.7 0 8969
39 9036 50.7 0 9036
40 9276 50.7 0 9276
41 9037 50.7 0 9037
42 9249 50.7 0 9249
43 9498 50.7 0 9498
44 8977 50.7 0 8977
45 9128 50.7 0 9128
46 9799 50.7 0 9799
47 9451 50.7 0 9451
48 9312 50.7 0 9312
49 14559 50.7 0 14559
50 18418 50.7 0 18418
51 10354 50.7 0 10354
52 10980 50.7 0 10980
53 11111 50.7 0 11111
54 9273 50.7 0 9273
55 9829 50.7 0 9829
56 9939 50.7 0 9939
57 9354 50.7 0 9354
58 10060 50.7 0 10060
59 9577 50.7 0 9577
60 9725 50.7 0 9725
61 9976 50.7 0 9976
62 9877 50.7 0 9877
63 9409 50.7 0 9409
64 9482 50.7 0 9482
65 9800 50.7 0 9800
66 9434 50.7 0 9434
67 9424 50.7 0 9424
68 9555 50.7 0 9555
69 9062 50.7 0 9062
70 8620 50.7 0 8620
71 9074 50.7 0 9074
72 9199 50.7 0 9199
73 8346 50.7 0 8346
74 8123 50.7 0 8123
75 8094 50.7 0 8094
76 7810 50.7 0 7810
77 7691 50.7 0 7691
78 8366 50.7 0 8366
79 9104 50.7 0 9104
80 9062 50.7 0 9062
81 10456 50.7 0 10456
82 12577 50.7 0 12577
83 13890 50.7 0 13890
84 16002 50.7 0 16002
85 17261 50.7 0 17261
86 167171 50.7 0 167171
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 58550 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.5%
C: 38.3%
G: 0.0%
T: 34.9%
none/other: 1.3%
Overview of removed sequences
length count expect max.err error counts
3 19626 51891.9 0 19626
4 4471 12973.0 0 4471
5 1300 3243.2 0 1300
6 761 810.8 0 761
7 667 202.7 0 667
8 707 50.7 0 707
9 663 50.7 0 663
10 583 50.7 0 583
11 654 50.7 0 654
12 592 50.7 0 592
13 546 50.7 0 546
14 582 50.7 0 582
15 544 50.7 0 544
16 568 50.7 0 568
17 492 50.7 0 492
18 535 50.7 0 535
19 569 50.7 0 569
20 544 50.7 0 544
21 520 50.7 0 520
22 541 50.7 0 541
23 573 50.7 0 573
24 594 50.7 0 594
25 564 50.7 0 564
26 501 50.7 0 501
27 495 50.7 0 495
28 539 50.7 0 539
29 502 50.7 0 502
30 527 50.7 0 527
31 523 50.7 0 523
32 544 50.7 0 544
33 566 50.7 0 566
34 538 50.7 0 538
35 512 50.7 0 512
36 516 50.7 0 516
37 491 50.7 0 491
38 516 50.7 0 516
39 508 50.7 0 508
40 477 50.7 0 477
41 471 50.7 0 471
42 520 50.7 0 520
43 523 50.7 0 523
44 497 50.7 0 497
45 510 50.7 0 510
46 440 50.7 0 440
47 492 50.7 0 492
48 460 50.7 0 460
49 451 50.7 0 451
50 451 50.7 0 451
51 436 50.7 0 436
52 454 50.7 0 454
53 431 50.7 0 431
54 406 50.7 0 406
55 432 50.7 0 432
56 461 50.7 0 461
57 432 50.7 0 432
58 399 50.7 0 399
59 376 50.7 0 376
60 376 50.7 0 376
61 333 50.7 0 333
62 321 50.7 0 321
63 339 50.7 0 339
64 313 50.7 0 313
65 274 50.7 0 274
66 250 50.7 0 250
67 223 50.7 0 223
68 233 50.7 0 233
69 241 50.7 0 241
70 174 50.7 0 174
71 153 50.7 0 153
72 137 50.7 0 137
73 121 50.7 0 121
74 102 50.7 0 102
75 107 50.7 0 107
76 61 50.7 0 61
77 67 50.7 0 67
78 63 50.7 0 63
79 52 50.7 0 52
80 50 50.7 0 50
81 34 50.7 0 34
82 36 50.7 0 36
83 30 50.7 0 30
84 44 50.7 0 44
85 50 50.7 0 50
86 773 50.7 0 773
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 63148 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.5%
C: 24.0%
G: 19.5%
T: 21.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47074 51891.9 0 47074
4 10380 12973.0 0 10380
5 2537 3243.2 0 2537
6 422 810.8 0 422
7 46 202.7 0 46
8 34 202.7 0 34
9 26 202.7 0 26
10 37 202.7 0 37
11 27 202.7 0 27
12 41 202.7 0 41
13 31 202.7 0 31
14 42 202.7 0 42
15 40 202.7 0 40
16 38 202.7 0 38
17 25 202.7 0 25
18 62 202.7 0 62
19 34 202.7 0 34
20 40 202.7 0 40
21 39 202.7 0 39
22 33 202.7 0 33
23 39 202.7 0 39
24 32 202.7 0 32
25 34 202.7 0 34
26 33 202.7 0 33
27 26 202.7 0 26
28 28 202.7 0 28
29 30 202.7 0 30
30 23 202.7 0 23
31 19 202.7 0 19
32 33 202.7 0 33
33 27 202.7 0 27
34 30 202.7 0 30
35 20 202.7 0 20
36 35 202.7 0 35
37 29 202.7 0 29
38 21 202.7 0 21
39 27 202.7 0 27
40 24 202.7 0 24
41 33 202.7 0 33
42 31 202.7 0 31
43 32 202.7 0 32
44 32 202.7 0 32
45 23 202.7 0 23
46 43 202.7 0 43
47 29 202.7 0 29
48 18 202.7 0 18
49 31 202.7 0 31
50 40 202.7 0 40
51 37 202.7 0 37
52 53 202.7 0 53
53 31 202.7 0 31
54 21 202.7 0 21
55 39 202.7 0 39
56 23 202.7 0 23
57 25 202.7 0 25
58 27 202.7 0 27
59 44 202.7 0 44
60 46 202.7 0 46
61 33 202.7 0 33
62 48 202.7 0 48
63 44 202.7 0 44
64 36 202.7 0 36
65 47 202.7 0 47
66 46 202.7 0 46
67 43 202.7 0 43
68 29 202.7 0 29
69 33 202.7 0 33
70 33 202.7 0 33
71 42 202.7 0 42
72 30 202.7 0 30
73 30 202.7 0 30
74 37 202.7 0 37
75 36 202.7 0 36
76 24 202.7 0 24
77 73 202.7 0 73
78 25 202.7 0 25
79 32 202.7 0 32
80 35 202.7 0 35
81 28 202.7 0 28
82 27 202.7 0 27
83 48 202.7 0 48
84 38 202.7 0 38
85 25 202.7 0 25
86 50 202.7 0 50
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N55_S190_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N55_S190_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 22.01 s (10 µs/read; 5.71 M reads/minute).
=== Summary ===
Total reads processed: 2,095,872
Reads with adapters: 736,063 (35.1%)
== Read fate breakdown ==
Reads that were too short: 234,382 (11.2%)
Reads written (passing filters): 1,861,490 (88.8%)
Total basepairs processed: 211,683,072 bp
Total written (filtered): 146,116,977 bp (69.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 667486 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.2%
G: 26.3%
T: 28.4%
none/other: 16.1%
Overview of removed sequences
length count expect max.err error counts
3 47856 32748.0 0 47856
4 20566 8187.0 0 20566
5 10585 2046.8 0 10585
6 7022 511.7 0 7022
7 5816 127.9 0 5816
8 4993 32.0 0 4993
9 5025 32.0 0 5025
10 5232 32.0 0 5232
11 4993 32.0 0 4993
12 5097 32.0 0 5097
13 5210 32.0 0 5210
14 5199 32.0 0 5199
15 5474 32.0 0 5474
16 5659 32.0 0 5659
17 5383 32.0 0 5383
18 5703 32.0 0 5703
19 5408 32.0 0 5408
20 5169 32.0 0 5169
21 5517 32.0 0 5517
22 5740 32.0 0 5740
23 5082 32.0 0 5082
24 5145 32.0 0 5145
25 5059 32.0 0 5059
26 5195 32.0 0 5195
27 5151 32.0 0 5151
28 5386 32.0 0 5386
29 5493 32.0 0 5493
30 5608 32.0 0 5608
31 5892 32.0 0 5892
32 5590 32.0 0 5590
33 6048 32.0 0 6048
34 5753 32.0 0 5753
35 6034 32.0 0 6034
36 5622 32.0 0 5622
37 5609 32.0 0 5609
38 5534 32.0 0 5534
39 5554 32.0 0 5554
40 5517 32.0 0 5517
41 5826 32.0 0 5826
42 5739 32.0 0 5739
43 6012 32.0 0 6012
44 5691 32.0 0 5691
45 5727 32.0 0 5727
46 6818 32.0 0 6818
47 5919 32.0 0 5919
48 5794 32.0 0 5794
49 8682 32.0 0 8682
50 9631 32.0 0 9631
51 6232 32.0 0 6232
52 7097 32.0 0 7097
53 6581 32.0 0 6581
54 5695 32.0 0 5695
55 6026 32.0 0 6026
56 6287 32.0 0 6287
57 5883 32.0 0 5883
58 6353 32.0 0 6353
59 6120 32.0 0 6120
60 5956 32.0 0 5956
61 6235 32.0 0 6235
62 6014 32.0 0 6014
63 6001 32.0 0 6001
64 6087 32.0 0 6087
65 5931 32.0 0 5931
66 5825 32.0 0 5825
67 5846 32.0 0 5846
68 5856 32.0 0 5856
69 5454 32.0 0 5454
70 5179 32.0 0 5179
71 5998 32.0 0 5998
72 5731 32.0 0 5731
73 5347 32.0 0 5347
74 5234 32.0 0 5234
75 5077 32.0 0 5077
76 5123 32.0 0 5123
77 5440 32.0 0 5440
78 5547 32.0 0 5547
79 6336 32.0 0 6336
80 6014 32.0 0 6014
81 7175 32.0 0 7175
82 8549 32.0 0 8549
83 9745 32.0 0 9745
84 10483 32.0 0 10483
85 10976 32.0 0 10976
86 107295 32.0 0 107295
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 22304 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 32.0%
C: 30.6%
G: 0.0%
T: 34.0%
none/other: 3.4%
Overview of removed sequences
length count expect max.err error counts
3 10292 32748.0 0 10292
4 2238 8187.0 0 2238
5 599 2046.8 0 599
6 258 511.7 0 258
7 282 127.9 0 282
8 221 32.0 0 221
9 218 32.0 0 218
10 178 32.0 0 178
11 156 32.0 0 156
12 173 32.0 0 173
13 164 32.0 0 164
14 165 32.0 0 165
15 135 32.0 0 135
16 132 32.0 0 132
17 142 32.0 0 142
18 130 32.0 0 130
19 146 32.0 0 146
20 113 32.0 0 113
21 129 32.0 0 129
22 117 32.0 0 117
23 136 32.0 0 136
24 153 32.0 0 153
25 127 32.0 0 127
26 116 32.0 0 116
27 106 32.0 0 106
28 139 32.0 0 139
29 126 32.0 0 126
30 121 32.0 0 121
31 112 32.0 0 112
32 103 32.0 0 103
33 113 32.0 0 113
34 111 32.0 0 111
35 129 32.0 0 129
36 140 32.0 0 140
37 119 32.0 0 119
38 127 32.0 0 127
39 94 32.0 0 94
40 120 32.0 0 120
41 118 32.0 0 118
42 114 32.0 0 114
43 114 32.0 0 114
44 117 32.0 0 117
45 110 32.0 0 110
46 110 32.0 0 110
47 130 32.0 0 130
48 117 32.0 0 117
49 123 32.0 0 123
50 116 32.0 0 116
51 122 32.0 0 122
52 120 32.0 0 120
53 110 32.0 0 110
54 119 32.0 0 119
55 95 32.0 0 95
56 113 32.0 0 113
57 96 32.0 0 96
58 110 32.0 0 110
59 103 32.0 0 103
60 107 32.0 0 107
61 89 32.0 0 89
62 81 32.0 0 81
63 91 32.0 0 91
64 74 32.0 0 74
65 66 32.0 0 66
66 78 32.0 0 78
67 65 32.0 0 65
68 52 32.0 0 52
69 48 32.0 0 48
70 36 32.0 0 36
71 46 32.0 0 46
72 43 32.0 0 43
73 31 32.0 0 31
74 30 32.0 0 30
75 23 32.0 0 23
76 23 32.0 0 23
77 26 32.0 0 26
78 27 32.0 0 27
79 21 32.0 0 21
80 23 32.0 0 23
81 21 32.0 0 21
82 30 32.0 0 30
83 20 32.0 0 20
84 27 32.0 0 27
85 32 32.0 0 32
86 757 32.0 0 757
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 46273 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.8%
C: 23.0%
G: 21.1%
T: 20.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 34867 32748.0 0 34867
4 7489 8187.0 0 7489
5 1505 2046.8 0 1505
6 213 511.7 0 213
7 17 127.9 0 17
8 40 127.9 0 40
9 25 127.9 0 25
10 28 127.9 0 28
11 19 127.9 0 19
12 22 127.9 0 22
13 29 127.9 0 29
14 44 127.9 0 44
15 33 127.9 0 33
16 21 127.9 0 21
17 40 127.9 0 40
18 30 127.9 0 30
19 35 127.9 0 35
20 34 127.9 0 34
21 23 127.9 0 23
22 25 127.9 0 25
23 26 127.9 0 26
24 26 127.9 0 26
25 41 127.9 0 41
26 23 127.9 0 23
27 18 127.9 0 18
28 35 127.9 0 35
29 29 127.9 0 29
30 28 127.9 0 28
31 21 127.9 0 21
32 24 127.9 0 24
33 35 127.9 0 35
34 21 127.9 0 21
35 19 127.9 0 19
36 41 127.9 0 41
37 27 127.9 0 27
38 25 127.9 0 25
39 30 127.9 0 30
40 28 127.9 0 28
41 23 127.9 0 23
42 29 127.9 0 29
43 21 127.9 0 21
44 27 127.9 0 27
45 26 127.9 0 26
46 12 127.9 0 12
47 21 127.9 0 21
48 14 127.9 0 14
49 25 127.9 0 25
50 22 127.9 0 22
51 27 127.9 0 27
52 31 127.9 0 31
53 26 127.9 0 26
54 27 127.9 0 27
55 37 127.9 0 37
56 12 127.9 0 12
57 29 127.9 0 29
58 38 127.9 0 38
59 20 127.9 0 20
60 23 127.9 0 23
61 24 127.9 0 24
62 19 127.9 0 19
63 27 127.9 0 27
64 15 127.9 0 15
65 36 127.9 0 36
66 30 127.9 0 30
67 25 127.9 0 25
68 26 127.9 0 26
69 28 127.9 0 28
70 30 127.9 0 30
71 38 127.9 0 38
72 23 127.9 0 23
73 26 127.9 0 26
74 23 127.9 0 23
75 22 127.9 0 22
76 15 127.9 0 15
77 84 127.9 0 84
78 30 127.9 0 30
79 21 127.9 0 21
80 27 127.9 0 27
81 35 127.9 0 35
82 26 127.9 0 26
83 29 127.9 0 29
84 30 127.9 0 30
85 24 127.9 0 24
86 34 127.9 0 34
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N55_S190_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N55_S190_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 19.53 s (9 µs/read; 6.57 M reads/minute).
=== Summary ===
Total reads processed: 2,137,684
Reads with adapters: 758,809 (35.5%)
== Read fate breakdown ==
Reads that were too short: 245,182 (11.5%)
Reads written (passing filters): 1,892,502 (88.5%)
Total basepairs processed: 215,906,084 bp
Total written (filtered): 148,367,060 bp (68.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 688653 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.1%
G: 26.3%
T: 28.1%
none/other: 16.4%
Overview of removed sequences
length count expect max.err error counts
3 47879 33401.3 0 47879
4 20680 8350.3 0 20680
5 10926 2087.6 0 10926
6 7006 521.9 0 7006
7 5788 130.5 0 5788
8 5007 32.6 0 5007
9 5161 32.6 0 5161
10 5276 32.6 0 5276
11 5147 32.6 0 5147
12 5177 32.6 0 5177
13 5307 32.6 0 5307
14 5353 32.6 0 5353
15 5488 32.6 0 5488
16 5743 32.6 0 5743
17 5535 32.6 0 5535
18 5868 32.6 0 5868
19 5664 32.6 0 5664
20 5294 32.6 0 5294
21 5710 32.6 0 5710
22 5912 32.6 0 5912
23 5250 32.6 0 5250
24 5311 32.6 0 5311
25 5339 32.6 0 5339
26 5134 32.6 0 5134
27 5376 32.6 0 5376
28 5388 32.6 0 5388
29 5681 32.6 0 5681
30 5679 32.6 0 5679
31 6167 32.6 0 6167
32 5890 32.6 0 5890
33 6382 32.6 0 6382
34 5839 32.6 0 5839
35 6094 32.6 0 6094
36 5808 32.6 0 5808
37 5676 32.6 0 5676
38 5674 32.6 0 5674
39 5690 32.6 0 5690
40 5746 32.6 0 5746
41 5834 32.6 0 5834
42 5789 32.6 0 5789
43 6301 32.6 0 6301
44 5665 32.6 0 5665
45 5989 32.6 0 5989
46 6943 32.6 0 6943
47 6186 32.6 0 6186
48 6086 32.6 0 6086
49 9237 32.6 0 9237
50 9889 32.6 0 9889
51 6380 32.6 0 6380
52 7419 32.6 0 7419
53 6813 32.6 0 6813
54 6007 32.6 0 6007
55 6221 32.6 0 6221
56 6420 32.6 0 6420
57 6090 32.6 0 6090
58 6517 32.6 0 6517
59 6270 32.6 0 6270
60 6327 32.6 0 6327
61 6392 32.6 0 6392
62 6303 32.6 0 6303
63 6054 32.6 0 6054
64 6247 32.6 0 6247
65 6172 32.6 0 6172
66 5884 32.6 0 5884
67 6073 32.6 0 6073
68 5860 32.6 0 5860
69 5567 32.6 0 5567
70 5543 32.6 0 5543
71 6342 32.6 0 6342
72 5883 32.6 0 5883
73 5728 32.6 0 5728
74 5448 32.6 0 5448
75 5280 32.6 0 5280
76 5485 32.6 0 5485
77 5800 32.6 0 5800
78 5734 32.6 0 5734
79 6613 32.6 0 6613
80 6290 32.6 0 6290
81 7300 32.6 0 7300
82 8841 32.6 0 8841
83 10060 32.6 0 10060
84 10920 32.6 0 10920
85 11305 32.6 0 11305
86 113101 32.6 0 113101
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 23181 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.8%
C: 30.3%
G: 0.0%
T: 34.6%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 10863 33401.3 0 10863
4 2218 8350.3 0 2218
5 597 2087.6 0 597
6 260 521.9 0 260
7 244 130.5 0 244
8 265 32.6 0 265
9 214 32.6 0 214
10 181 32.6 0 181
11 189 32.6 0 189
12 194 32.6 0 194
13 158 32.6 0 158
14 157 32.6 0 157
15 137 32.6 0 137
16 137 32.6 0 137
17 158 32.6 0 158
18 149 32.6 0 149
19 148 32.6 0 148
20 122 32.6 0 122
21 117 32.6 0 117
22 126 32.6 0 126
23 129 32.6 0 129
24 122 32.6 0 122
25 142 32.6 0 142
26 150 32.6 0 150
27 124 32.6 0 124
28 125 32.6 0 125
29 127 32.6 0 127
30 124 32.6 0 124
31 117 32.6 0 117
32 125 32.6 0 125
33 145 32.6 0 145
34 115 32.6 0 115
35 123 32.6 0 123
36 133 32.6 0 133
37 142 32.6 0 142
38 130 32.6 0 130
39 112 32.6 0 112
40 123 32.6 0 123
41 116 32.6 0 116
42 132 32.6 0 132
43 123 32.6 0 123
44 102 32.6 0 102
45 123 32.6 0 123
46 114 32.6 0 114
47 119 32.6 0 119
48 122 32.6 0 122
49 128 32.6 0 128
50 110 32.6 0 110
51 118 32.6 0 118
52 107 32.6 0 107
53 117 32.6 0 117
54 101 32.6 0 101
55 110 32.6 0 110
56 105 32.6 0 105
57 121 32.6 0 121
58 114 32.6 0 114
59 95 32.6 0 95
60 94 32.6 0 94
61 95 32.6 0 95
62 98 32.6 0 98
63 79 32.6 0 79
64 91 32.6 0 91
65 86 32.6 0 86
66 72 32.6 0 72
67 76 32.6 0 76
68 80 32.6 0 80
69 50 32.6 0 50
70 41 32.6 0 41
71 46 32.6 0 46
72 48 32.6 0 48
73 27 32.6 0 27
74 39 32.6 0 39
75 26 32.6 0 26
76 35 32.6 0 35
77 26 32.6 0 26
78 22 32.6 0 22
79 23 32.6 0 23
80 28 32.6 0 28
81 21 32.6 0 21
82 25 32.6 0 25
83 23 32.6 0 23
84 35 32.6 0 35
85 26 32.6 0 26
86 750 32.6 0 750
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 46975 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 23.1%
G: 20.9%
T: 20.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 35515 33401.3 0 35515
4 7602 8350.3 0 7602
5 1473 2087.6 0 1473
6 224 521.9 0 224
7 16 130.5 0 16
8 32 130.5 0 32
9 28 130.5 0 28
10 31 130.5 0 31
11 28 130.5 0 28
12 41 130.5 0 41
13 52 130.5 0 52
14 24 130.5 0 24
15 35 130.5 0 35
16 28 130.5 0 28
17 23 130.5 0 23
18 26 130.5 0 26
19 41 130.5 0 41
20 24 130.5 0 24
21 34 130.5 0 34
22 33 130.5 0 33
23 17 130.5 0 17
24 29 130.5 0 29
25 46 130.5 0 46
26 20 130.5 0 20
27 19 130.5 0 19
28 22 130.5 0 22
29 25 130.5 0 25
30 32 130.5 0 32
31 26 130.5 0 26
32 23 130.5 0 23
33 27 130.5 0 27
34 18 130.5 0 18
35 14 130.5 0 14
36 27 130.5 0 27
37 21 130.5 0 21
38 17 130.5 0 17
39 30 130.5 0 30
40 16 130.5 0 16
41 15 130.5 0 15
42 22 130.5 0 22
43 18 130.5 0 18
44 26 130.5 0 26
45 27 130.5 0 27
46 25 130.5 0 25
47 27 130.5 0 27
48 27 130.5 0 27
49 16 130.5 0 16
50 26 130.5 0 26
51 32 130.5 0 32
52 36 130.5 0 36
53 18 130.5 0 18
54 30 130.5 0 30
55 23 130.5 0 23
56 20 130.5 0 20
57 25 130.5 0 25
58 27 130.5 0 27
59 34 130.5 0 34
60 30 130.5 0 30
61 20 130.5 0 20
62 34 130.5 0 34
63 27 130.5 0 27
64 27 130.5 0 27
65 27 130.5 0 27
66 35 130.5 0 35
67 19 130.5 0 19
68 27 130.5 0 27
69 21 130.5 0 21
70 28 130.5 0 28
71 33 130.5 0 33
72 21 130.5 0 21
73 28 130.5 0 28
74 21 130.5 0 21
75 26 130.5 0 26
76 14 130.5 0 14
77 64 130.5 0 64
78 46 130.5 0 46
79 22 130.5 0 22
80 24 130.5 0 24
81 27 130.5 0 27
82 21 130.5 0 21
83 31 130.5 0 31
84 38 130.5 0 38
85 25 130.5 0 25
86 26 130.5 0 26
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N56_S192_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N56_S192_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 3.40 s (8 µs/read; 7.97 M reads/minute).
=== Summary ===
Total reads processed: 451,236
Reads with adapters: 78,061 (17.3%)
== Read fate breakdown ==
Reads that were too short: 18,281 (4.1%)
Reads written (passing filters): 432,955 (95.9%)
Total basepairs processed: 45,574,836 bp
Total written (filtered): 35,930,477 bp (78.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 58647 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.9%
G: 22.5%
T: 29.8%
none/other: 16.7%
Overview of removed sequences
length count expect max.err error counts
3 9271 7050.6 0 9271
4 3859 1762.6 0 3859
5 1516 440.7 0 1516
6 693 110.2 0 693
7 405 27.5 0 405
8 376 6.9 0 376
9 302 6.9 0 302
10 371 6.9 0 371
11 374 6.9 0 374
12 392 6.9 0 392
13 376 6.9 0 376
14 681 6.9 0 681
15 449 6.9 0 449
16 418 6.9 0 418
17 398 6.9 0 398
18 396 6.9 0 396
19 337 6.9 0 337
20 406 6.9 0 406
21 393 6.9 0 393
22 521 6.9 0 521
23 458 6.9 0 458
24 417 6.9 0 417
25 425 6.9 0 425
26 455 6.9 0 455
27 407 6.9 0 407
28 383 6.9 0 383
29 405 6.9 0 405
30 434 6.9 0 434
31 529 6.9 0 529
32 369 6.9 0 369
33 392 6.9 0 392
34 439 6.9 0 439
35 603 6.9 0 603
36 371 6.9 0 371
37 480 6.9 0 480
38 487 6.9 0 487
39 391 6.9 0 391
40 393 6.9 0 393
41 432 6.9 0 432
42 412 6.9 0 412
43 385 6.9 0 385
44 419 6.9 0 419
45 405 6.9 0 405
46 358 6.9 0 358
47 381 6.9 0 381
48 404 6.9 0 404
49 420 6.9 0 420
50 415 6.9 0 415
51 425 6.9 0 425
52 431 6.9 0 431
53 465 6.9 0 465
54 440 6.9 0 440
55 436 6.9 0 436
56 454 6.9 0 454
57 479 6.9 0 479
58 419 6.9 0 419
59 458 6.9 0 458
60 525 6.9 0 525
61 493 6.9 0 493
62 474 6.9 0 474
63 617 6.9 0 617
64 505 6.9 0 505
65 437 6.9 0 437
66 494 6.9 0 494
67 489 6.9 0 489
68 578 6.9 0 578
69 521 6.9 0 521
70 435 6.9 0 435
71 469 6.9 0 469
72 492 6.9 0 492
73 427 6.9 0 427
74 423 6.9 0 423
75 438 6.9 0 438
76 388 6.9 0 388
77 408 6.9 0 408
78 364 6.9 0 364
79 349 6.9 0 349
80 330 6.9 0 330
81 315 6.9 0 315
82 233 6.9 0 233
83 257 6.9 0 257
84 302 6.9 0 302
85 287 6.9 0 287
86 9787 6.9 0 9787
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 10116 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.9%
C: 31.1%
G: 0.0%
T: 39.2%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 1930 7050.6 0 1930
4 551 1762.6 0 551
5 244 440.7 0 244
6 134 110.2 0 134
7 96 27.5 0 96
8 143 6.9 0 143
9 111 6.9 0 111
10 148 6.9 0 148
11 127 6.9 0 127
12 101 6.9 0 101
13 104 6.9 0 104
14 120 6.9 0 120
15 109 6.9 0 109
16 109 6.9 0 109
17 103 6.9 0 103
18 142 6.9 0 142
19 109 6.9 0 109
20 88 6.9 0 88
21 107 6.9 0 107
22 88 6.9 0 88
23 109 6.9 0 109
24 77 6.9 0 77
25 125 6.9 0 125
26 120 6.9 0 120
27 105 6.9 0 105
28 85 6.9 0 85
29 105 6.9 0 105
30 106 6.9 0 106
31 103 6.9 0 103
32 101 6.9 0 101
33 127 6.9 0 127
34 110 6.9 0 110
35 114 6.9 0 114
36 125 6.9 0 125
37 119 6.9 0 119
38 113 6.9 0 113
39 105 6.9 0 105
40 104 6.9 0 104
41 108 6.9 0 108
42 127 6.9 0 127
43 102 6.9 0 102
44 94 6.9 0 94
45 121 6.9 0 121
46 118 6.9 0 118
47 112 6.9 0 112
48 116 6.9 0 116
49 96 6.9 0 96
50 108 6.9 0 108
51 100 6.9 0 100
52 104 6.9 0 104
53 122 6.9 0 122
54 92 6.9 0 92
55 92 6.9 0 92
56 121 6.9 0 121
57 97 6.9 0 97
58 79 6.9 0 79
59 129 6.9 0 129
60 105 6.9 0 105
61 93 6.9 0 93
62 79 6.9 0 79
63 76 6.9 0 76
64 75 6.9 0 75
65 60 6.9 0 60
66 75 6.9 0 75
67 78 6.9 0 78
68 60 6.9 0 60
69 55 6.9 0 55
70 37 6.9 0 37
71 35 6.9 0 35
72 40 6.9 0 40
73 46 6.9 0 46
74 27 6.9 0 27
75 33 6.9 0 33
76 16 6.9 0 16
77 25 6.9 0 25
78 19 6.9 0 19
79 12 6.9 0 12
80 23 6.9 0 23
81 22 6.9 0 22
82 24 6.9 0 24
83 18 6.9 0 18
84 21 6.9 0 21
85 25 6.9 0 25
86 282 6.9 0 282
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 9298 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.8%
C: 21.6%
G: 19.9%
T: 21.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 6822 7050.6 0 6822
4 1698 1762.6 0 1698
5 310 440.7 0 310
6 26 110.2 0 26
7 4 27.5 0 4
8 5 27.5 0 5
10 6 27.5 0 6
11 4 27.5 0 4
12 2 27.5 0 2
13 4 27.5 0 4
14 3 27.5 0 3
15 1 27.5 0 1
16 2 27.5 0 2
17 4 27.5 0 4
18 1 27.5 0 1
19 3 27.5 0 3
20 2 27.5 0 2
21 3 27.5 0 3
22 4 27.5 0 4
23 4 27.5 0 4
24 2 27.5 0 2
25 6 27.5 0 6
26 9 27.5 0 9
27 9 27.5 0 9
28 7 27.5 0 7
29 19 27.5 0 19
30 5 27.5 0 5
31 4 27.5 0 4
32 19 27.5 0 19
33 5 27.5 0 5
34 2 27.5 0 2
35 2 27.5 0 2
36 6 27.5 0 6
37 10 27.5 0 10
38 7 27.5 0 7
39 6 27.5 0 6
40 12 27.5 0 12
41 8 27.5 0 8
42 2 27.5 0 2
43 8 27.5 0 8
44 8 27.5 0 8
45 3 27.5 0 3
46 8 27.5 0 8
47 3 27.5 0 3
48 8 27.5 0 8
49 8 27.5 0 8
51 4 27.5 0 4
52 23 27.5 0 23
53 19 27.5 0 19
54 4 27.5 0 4
55 3 27.5 0 3
56 2 27.5 0 2
57 1 27.5 0 1
58 1 27.5 0 1
59 8 27.5 0 8
60 4 27.5 0 4
61 11 27.5 0 11
62 3 27.5 0 3
63 4 27.5 0 4
64 8 27.5 0 8
65 11 27.5 0 11
66 7 27.5 0 7
67 3 27.5 0 3
68 5 27.5 0 5
70 5 27.5 0 5
71 6 27.5 0 6
72 3 27.5 0 3
73 3 27.5 0 3
74 15 27.5 0 15
76 8 27.5 0 8
77 8 27.5 0 8
78 3 27.5 0 3
79 5 27.5 0 5
80 3 27.5 0 3
81 2 27.5 0 2
82 4 27.5 0 4
83 2 27.5 0 2
84 2 27.5 0 2
85 2 27.5 0 2
86 12 27.5 0 12
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N56_S192_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N56_S192_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 3.52 s (8 µs/read; 7.91 M reads/minute).
=== Summary ===
Total reads processed: 463,902
Reads with adapters: 81,217 (17.5%)
== Read fate breakdown ==
Reads that were too short: 19,308 (4.2%)
Reads written (passing filters): 444,594 (95.8%)
Total basepairs processed: 46,854,102 bp
Total written (filtered): 36,870,691 bp (78.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 61030 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.5%
G: 22.3%
T: 29.1%
none/other: 17.2%
Overview of removed sequences
length count expect max.err error counts
3 9576 7248.5 0 9576
4 3965 1812.1 0 3965
5 1469 453.0 0 1469
6 693 113.3 0 693
7 466 28.3 0 466
8 426 7.1 0 426
9 370 7.1 0 370
10 420 7.1 0 420
11 373 7.1 0 373
12 394 7.1 0 394
13 396 7.1 0 396
14 663 7.1 0 663
15 423 7.1 0 423
16 430 7.1 0 430
17 336 7.1 0 336
18 413 7.1 0 413
19 372 7.1 0 372
20 383 7.1 0 383
21 423 7.1 0 423
22 510 7.1 0 510
23 459 7.1 0 459
24 372 7.1 0 372
25 432 7.1 0 432
26 401 7.1 0 401
27 452 7.1 0 452
28 397 7.1 0 397
29 439 7.1 0 439
30 416 7.1 0 416
31 451 7.1 0 451
32 410 7.1 0 410
33 487 7.1 0 487
34 450 7.1 0 450
35 580 7.1 0 580
36 425 7.1 0 425
37 480 7.1 0 480
38 513 7.1 0 513
39 437 7.1 0 437
40 404 7.1 0 404
41 446 7.1 0 446
42 394 7.1 0 394
43 428 7.1 0 428
44 415 7.1 0 415
45 417 7.1 0 417
46 399 7.1 0 399
47 451 7.1 0 451
48 469 7.1 0 469
49 476 7.1 0 476
50 460 7.1 0 460
51 443 7.1 0 443
52 454 7.1 0 454
53 438 7.1 0 438
54 487 7.1 0 487
55 452 7.1 0 452
56 459 7.1 0 459
57 441 7.1 0 441
58 475 7.1 0 475
59 477 7.1 0 477
60 504 7.1 0 504
61 455 7.1 0 455
62 530 7.1 0 530
63 702 7.1 0 702
64 519 7.1 0 519
65 528 7.1 0 528
66 502 7.1 0 502
67 523 7.1 0 523
68 527 7.1 0 527
69 553 7.1 0 553
70 491 7.1 0 491
71 506 7.1 0 506
72 481 7.1 0 481
73 488 7.1 0 488
74 472 7.1 0 472
75 426 7.1 0 426
76 407 7.1 0 407
77 423 7.1 0 423
78 405 7.1 0 405
79 334 7.1 0 334
80 308 7.1 0 308
81 301 7.1 0 301
82 296 7.1 0 296
83 287 7.1 0 287
84 310 7.1 0 310
85 299 7.1 0 299
86 10466 7.1 0 10466
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 10609 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.5%
C: 32.1%
G: 0.0%
T: 38.9%
none/other: 2.4%
Overview of removed sequences
length count expect max.err error counts
3 2001 7248.5 0 2001
4 590 1812.1 0 590
5 214 453.0 0 214
6 130 113.3 0 130
7 119 28.3 0 119
8 149 7.1 0 149
9 120 7.1 0 120
10 129 7.1 0 129
11 116 7.1 0 116
12 133 7.1 0 133
13 110 7.1 0 110
14 122 7.1 0 122
15 116 7.1 0 116
16 105 7.1 0 105
17 96 7.1 0 96
18 119 7.1 0 119
19 137 7.1 0 137
20 118 7.1 0 118
21 103 7.1 0 103
22 92 7.1 0 92
23 107 7.1 0 107
24 97 7.1 0 97
25 116 7.1 0 116
26 91 7.1 0 91
27 115 7.1 0 115
28 111 7.1 0 111
29 117 7.1 0 117
30 104 7.1 0 104
31 109 7.1 0 109
32 106 7.1 0 106
33 120 7.1 0 120
34 124 7.1 0 124
35 129 7.1 0 129
36 134 7.1 0 134
37 108 7.1 0 108
38 101 7.1 0 101
39 105 7.1 0 105
40 109 7.1 0 109
41 117 7.1 0 117
42 137 7.1 0 137
43 119 7.1 0 119
44 117 7.1 0 117
45 132 7.1 0 132
46 112 7.1 0 112
47 123 7.1 0 123
48 137 7.1 0 137
49 134 7.1 0 134
50 94 7.1 0 94
51 114 7.1 0 114
52 100 7.1 0 100
53 148 7.1 0 148
54 114 7.1 0 114
55 126 7.1 0 126
56 121 7.1 0 121
57 98 7.1 0 98
58 109 7.1 0 109
59 132 7.1 0 132
60 92 7.1 0 92
61 110 7.1 0 110
62 86 7.1 0 86
63 80 7.1 0 80
64 73 7.1 0 73
65 82 7.1 0 82
66 58 7.1 0 58
67 66 7.1 0 66
68 72 7.1 0 72
69 49 7.1 0 49
70 39 7.1 0 39
71 49 7.1 0 49
72 51 7.1 0 51
73 51 7.1 0 51
74 24 7.1 0 24
75 28 7.1 0 28
76 30 7.1 0 30
77 18 7.1 0 18
78 20 7.1 0 20
79 13 7.1 0 13
80 26 7.1 0 26
81 26 7.1 0 26
82 28 7.1 0 28
83 7 7.1 0 7
84 37 7.1 0 37
85 29 7.1 0 29
86 259 7.1 0 259
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 9578 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 22.1%
G: 20.1%
T: 21.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 7010 7248.5 0 7010
4 1746 1812.1 0 1746
5 342 453.0 0 342
6 34 113.3 0 34
7 3 28.3 0 3
8 3 28.3 0 3
9 3 28.3 0 3
10 10 28.3 0 10
11 2 28.3 0 2
13 6 28.3 0 6
14 2 28.3 0 2
15 3 28.3 0 3
16 1 28.3 0 1
17 2 28.3 0 2
18 3 28.3 0 3
20 6 28.3 0 6
21 4 28.3 0 4
22 3 28.3 0 3
23 2 28.3 0 2
24 5 28.3 0 5
25 3 28.3 0 3
26 15 28.3 0 15
27 18 28.3 0 18
28 7 28.3 0 7
29 22 28.3 0 22
30 3 28.3 0 3
31 7 28.3 0 7
32 24 28.3 0 24
33 1 28.3 0 1
34 5 28.3 0 5
35 1 28.3 0 1
36 4 28.3 0 4
37 10 28.3 0 10
38 14 28.3 0 14
39 8 28.3 0 8
40 14 28.3 0 14
41 9 28.3 0 9
42 2 28.3 0 2
43 12 28.3 0 12
44 9 28.3 0 9
45 7 28.3 0 7
46 7 28.3 0 7
47 5 28.3 0 5
48 5 28.3 0 5
49 4 28.3 0 4
50 1 28.3 0 1
51 5 28.3 0 5
52 13 28.3 0 13
53 13 28.3 0 13
54 6 28.3 0 6
56 1 28.3 0 1
59 8 28.3 0 8
60 4 28.3 0 4
61 16 28.3 0 16
62 3 28.3 0 3
63 1 28.3 0 1
65 12 28.3 0 12
66 6 28.3 0 6
67 1 28.3 0 1
68 2 28.3 0 2
69 1 28.3 0 1
70 10 28.3 0 10
71 5 28.3 0 5
72 2 28.3 0 2
73 2 28.3 0 2
74 10 28.3 0 10
75 1 28.3 0 1
76 4 28.3 0 4
77 5 28.3 0 5
78 6 28.3 0 6
79 8 28.3 0 8
80 6 28.3 0 6
81 3 28.3 0 3
82 4 28.3 0 4
83 2 28.3 0 2
84 1 28.3 0 1
85 4 28.3 0 4
86 6 28.3 0 6
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N57_S191_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N57_S191_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.79 s (9 µs/read; 6.94 M reads/minute).
=== Summary ===
Total reads processed: 2,984,542
Reads with adapters: 1,068,323 (35.8%)
== Read fate breakdown ==
Reads that were too short: 275,727 (9.2%)
Reads written (passing filters): 2,708,815 (90.8%)
Total basepairs processed: 301,438,742 bp
Total written (filtered): 210,555,281 bp (69.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 935020 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 32.0%
G: 26.3%
T: 29.4%
none/other: 12.3%
Overview of removed sequences
length count expect max.err error counts
3 71900 46633.5 0 71900
4 32124 11658.4 0 32124
5 16898 2914.6 0 16898
6 11139 728.6 0 11139
7 9254 182.2 0 9254
8 8367 45.5 0 8367
9 8486 45.5 0 8486
10 8418 45.5 0 8418
11 8310 45.5 0 8310
12 8290 45.5 0 8290
13 8478 45.5 0 8478
14 8631 45.5 0 8631
15 8658 45.5 0 8658
16 8955 45.5 0 8955
17 8697 45.5 0 8697
18 8861 45.5 0 8861
19 8648 45.5 0 8648
20 8641 45.5 0 8641
21 8539 45.5 0 8539
22 8912 45.5 0 8912
23 8641 45.5 0 8641
24 8499 45.5 0 8499
25 8387 45.5 0 8387
26 8416 45.5 0 8416
27 8258 45.5 0 8258
28 8506 45.5 0 8506
29 8556 45.5 0 8556
30 8587 45.5 0 8587
31 8612 45.5 0 8612
32 8411 45.5 0 8411
33 8631 45.5 0 8631
34 8497 45.5 0 8497
35 8651 45.5 0 8651
36 8385 45.5 0 8385
37 8455 45.5 0 8455
38 8288 45.5 0 8288
39 8713 45.5 0 8713
40 8725 45.5 0 8725
41 8612 45.5 0 8612
42 8625 45.5 0 8625
43 8661 45.5 0 8661
44 8338 45.5 0 8338
45 8811 45.5 0 8811
46 8731 45.5 0 8731
47 8920 45.5 0 8920
48 8835 45.5 0 8835
49 10063 45.5 0 10063
50 11276 45.5 0 11276
51 9348 45.5 0 9348
52 9472 45.5 0 9472
53 9054 45.5 0 9054
54 8962 45.5 0 8962
55 9509 45.5 0 9509
56 9091 45.5 0 9091
57 8986 45.5 0 8986
58 9198 45.5 0 9198
59 9217 45.5 0 9217
60 9621 45.5 0 9621
61 9706 45.5 0 9706
62 9694 45.5 0 9694
63 9642 45.5 0 9642
64 9722 45.5 0 9722
65 9856 45.5 0 9856
66 9378 45.5 0 9378
67 9432 45.5 0 9432
68 9014 45.5 0 9014
69 8953 45.5 0 8953
70 8705 45.5 0 8705
71 9117 45.5 0 9117
72 8265 45.5 0 8265
73 8309 45.5 0 8309
74 7477 45.5 0 7477
75 7345 45.5 0 7345
76 7133 45.5 0 7133
77 7184 45.5 0 7184
78 6694 45.5 0 6694
79 7182 45.5 0 7182
80 6757 45.5 0 6757
81 7375 45.5 0 7375
82 8307 45.5 0 8307
83 9036 45.5 0 9036
84 9711 45.5 0 9711
85 9494 45.5 0 9494
86 114778 45.5 0 114778
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 77501 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 23.0%
C: 35.6%
G: 0.0%
T: 39.3%
none/other: 2.1%
Overview of removed sequences
length count expect max.err error counts
3 11819 46633.5 0 11819
4 3721 11658.4 0 3721
5 1840 2914.6 0 1840
6 1307 728.6 0 1307
7 1255 182.2 0 1255
8 1195 45.5 0 1195
9 1143 45.5 0 1143
10 1144 45.5 0 1144
11 1174 45.5 0 1174
12 1094 45.5 0 1094
13 1153 45.5 0 1153
14 1057 45.5 0 1057
15 1074 45.5 0 1074
16 1048 45.5 0 1048
17 1056 45.5 0 1056
18 985 45.5 0 985
19 1076 45.5 0 1076
20 954 45.5 0 954
21 1029 45.5 0 1029
22 943 45.5 0 943
23 1044 45.5 0 1044
24 977 45.5 0 977
25 1017 45.5 0 1017
26 1028 45.5 0 1028
27 965 45.5 0 965
28 941 45.5 0 941
29 872 45.5 0 872
30 890 45.5 0 890
31 931 45.5 0 931
32 943 45.5 0 943
33 1003 45.5 0 1003
34 1050 45.5 0 1050
35 1100 45.5 0 1100
36 1001 45.5 0 1001
37 989 45.5 0 989
38 895 45.5 0 895
39 894 45.5 0 894
40 849 45.5 0 849
41 846 45.5 0 846
42 990 45.5 0 990
43 917 45.5 0 917
44 833 45.5 0 833
45 865 45.5 0 865
46 893 45.5 0 893
47 893 45.5 0 893
48 889 45.5 0 889
49 819 45.5 0 819
50 769 45.5 0 769
51 761 45.5 0 761
52 836 45.5 0 836
53 797 45.5 0 797
54 712 45.5 0 712
55 752 45.5 0 752
56 727 45.5 0 727
57 721 45.5 0 721
58 734 45.5 0 734
59 710 45.5 0 710
60 663 45.5 0 663
61 614 45.5 0 614
62 584 45.5 0 584
63 517 45.5 0 517
64 516 45.5 0 516
65 439 45.5 0 439
66 423 45.5 0 423
67 374 45.5 0 374
68 377 45.5 0 377
69 318 45.5 0 318
70 263 45.5 0 263
71 239 45.5 0 239
72 225 45.5 0 225
73 227 45.5 0 227
74 186 45.5 0 186
75 150 45.5 0 150
76 132 45.5 0 132
77 114 45.5 0 114
78 117 45.5 0 117
79 94 45.5 0 94
80 77 45.5 0 77
81 60 45.5 0 60
82 66 45.5 0 66
83 54 45.5 0 54
84 65 45.5 0 65
85 57 45.5 0 57
86 1630 45.5 0 1630
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 55802 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 22.0%
G: 19.8%
T: 22.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 40815 46633.5 0 40815
4 10441 11658.4 0 10441
5 1814 2914.6 0 1814
6 218 728.6 0 218
7 34 182.2 0 34
8 37 182.2 0 37
9 37 182.2 0 37
10 31 182.2 0 31
11 28 182.2 0 28
12 24 182.2 0 24
13 11 182.2 0 11
14 27 182.2 0 27
15 32 182.2 0 32
16 25 182.2 0 25
17 17 182.2 0 17
18 26 182.2 0 26
19 36 182.2 0 36
20 31 182.2 0 31
21 26 182.2 0 26
22 33 182.2 0 33
23 22 182.2 0 22
24 38 182.2 0 38
25 50 182.2 0 50
26 37 182.2 0 37
27 27 182.2 0 27
28 35 182.2 0 35
29 39 182.2 0 39
30 39 182.2 0 39
31 31 182.2 0 31
32 37 182.2 0 37
33 34 182.2 0 34
34 42 182.2 0 42
35 39 182.2 0 39
36 46 182.2 0 46
37 26 182.2 0 26
38 33 182.2 0 33
39 47 182.2 0 47
40 26 182.2 0 26
41 33 182.2 0 33
42 39 182.2 0 39
43 25 182.2 0 25
44 22 182.2 0 22
45 41 182.2 0 41
46 35 182.2 0 35
47 27 182.2 0 27
48 38 182.2 0 38
49 39 182.2 0 39
50 31 182.2 0 31
51 38 182.2 0 38
52 45 182.2 0 45
53 32 182.2 0 32
54 26 182.2 0 26
55 14 182.2 0 14
56 28 182.2 0 28
57 23 182.2 0 23
58 34 182.2 0 34
59 31 182.2 0 31
60 22 182.2 0 22
61 26 182.2 0 26
62 39 182.2 0 39
63 19 182.2 0 19
64 24 182.2 0 24
65 26 182.2 0 26
66 20 182.2 0 20
67 29 182.2 0 29
68 29 182.2 0 29
69 28 182.2 0 28
70 25 182.2 0 25
71 23 182.2 0 23
72 19 182.2 0 19
73 37 182.2 0 37
74 36 182.2 0 36
75 16 182.2 0 16
76 27 182.2 0 27
77 77 182.2 0 77
78 46 182.2 0 46
79 37 182.2 0 37
80 20 182.2 0 20
81 25 182.2 0 25
82 38 182.2 0 38
83 35 182.2 0 35
84 28 182.2 0 28
85 32 182.2 0 32
86 27 182.2 0 27
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N57_S191_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N57_S191_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 30.17 s (10 µs/read; 6.06 M reads/minute).
=== Summary ===
Total reads processed: 3,045,905
Reads with adapters: 1,100,363 (36.1%)
== Read fate breakdown ==
Reads that were too short: 289,624 (9.5%)
Reads written (passing filters): 2,756,281 (90.5%)
Total basepairs processed: 307,636,405 bp
Total written (filtered): 213,968,796 bp (69.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 964003 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 32.1%
G: 26.2%
T: 29.0%
none/other: 12.7%
Overview of removed sequences
length count expect max.err error counts
3 72641 47592.3 0 72641
4 32408 11898.1 0 32408
5 16849 2974.5 0 16849
6 11173 743.6 0 11173
7 9448 185.9 0 9448
8 8548 46.5 0 8548
9 8621 46.5 0 8621
10 8663 46.5 0 8663
11 8365 46.5 0 8365
12 8572 46.5 0 8572
13 8549 46.5 0 8549
14 8870 46.5 0 8870
15 8787 46.5 0 8787
16 9005 46.5 0 9005
17 8841 46.5 0 8841
18 8758 46.5 0 8758
19 8777 46.5 0 8777
20 8781 46.5 0 8781
21 9011 46.5 0 9011
22 9368 46.5 0 9368
23 8749 46.5 0 8749
24 8744 46.5 0 8744
25 8644 46.5 0 8644
26 8614 46.5 0 8614
27 8706 46.5 0 8706
28 8714 46.5 0 8714
29 8815 46.5 0 8815
30 8747 46.5 0 8747
31 8756 46.5 0 8756
32 8563 46.5 0 8563
33 8771 46.5 0 8771
34 8818 46.5 0 8818
35 8619 46.5 0 8619
36 8743 46.5 0 8743
37 8709 46.5 0 8709
38 8634 46.5 0 8634
39 8546 46.5 0 8546
40 8882 46.5 0 8882
41 8696 46.5 0 8696
42 8833 46.5 0 8833
43 9082 46.5 0 9082
44 8618 46.5 0 8618
45 9127 46.5 0 9127
46 8963 46.5 0 8963
47 8966 46.5 0 8966
48 9079 46.5 0 9079
49 10349 46.5 0 10349
50 11427 46.5 0 11427
51 9855 46.5 0 9855
52 9717 46.5 0 9717
53 9492 46.5 0 9492
54 9289 46.5 0 9289
55 9679 46.5 0 9679
56 9234 46.5 0 9234
57 9385 46.5 0 9385
58 9763 46.5 0 9763
59 9545 46.5 0 9545
60 10000 46.5 0 10000
61 9869 46.5 0 9869
62 9980 46.5 0 9980
63 9793 46.5 0 9793
64 10006 46.5 0 10006
65 10296 46.5 0 10296
66 10199 46.5 0 10199
67 9833 46.5 0 9833
68 9435 46.5 0 9435
69 9231 46.5 0 9231
70 9002 46.5 0 9002
71 9446 46.5 0 9446
72 8615 46.5 0 8615
73 8612 46.5 0 8612
74 7895 46.5 0 7895
75 7770 46.5 0 7770
76 7234 46.5 0 7234
77 7592 46.5 0 7592
78 6911 46.5 0 6911
79 7303 46.5 0 7303
80 7048 46.5 0 7048
81 7913 46.5 0 7913
82 8677 46.5 0 8677
83 9365 46.5 0 9365
84 10097 46.5 0 10097
85 9998 46.5 0 9998
86 121975 46.5 0 121975
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 79964 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 23.0%
C: 35.2%
G: 0.0%
T: 39.7%
none/other: 2.1%
Overview of removed sequences
length count expect max.err error counts
3 12042 47592.3 0 12042
4 3828 11898.1 0 3828
5 1835 2974.5 0 1835
6 1289 743.6 0 1289
7 1277 185.9 0 1277
8 1307 46.5 0 1307
9 1146 46.5 0 1146
10 1157 46.5 0 1157
11 1134 46.5 0 1134
12 1092 46.5 0 1092
13 1185 46.5 0 1185
14 1078 46.5 0 1078
15 1083 46.5 0 1083
16 1032 46.5 0 1032
17 1026 46.5 0 1026
18 1042 46.5 0 1042
19 1081 46.5 0 1081
20 967 46.5 0 967
21 1058 46.5 0 1058
22 1032 46.5 0 1032
23 1057 46.5 0 1057
24 1085 46.5 0 1085
25 1069 46.5 0 1069
26 1006 46.5 0 1006
27 1030 46.5 0 1030
28 977 46.5 0 977
29 1007 46.5 0 1007
30 1017 46.5 0 1017
31 1007 46.5 0 1007
32 1071 46.5 0 1071
33 1051 46.5 0 1051
34 1000 46.5 0 1000
35 1037 46.5 0 1037
36 976 46.5 0 976
37 980 46.5 0 980
38 961 46.5 0 961
39 959 46.5 0 959
40 916 46.5 0 916
41 927 46.5 0 927
42 988 46.5 0 988
43 955 46.5 0 955
44 962 46.5 0 962
45 883 46.5 0 883
46 914 46.5 0 914
47 978 46.5 0 978
48 851 46.5 0 851
49 883 46.5 0 883
50 825 46.5 0 825
51 820 46.5 0 820
52 797 46.5 0 797
53 786 46.5 0 786
54 787 46.5 0 787
55 796 46.5 0 796
56 794 46.5 0 794
57 792 46.5 0 792
58 685 46.5 0 685
59 666 46.5 0 666
60 689 46.5 0 689
61 641 46.5 0 641
62 565 46.5 0 565
63 561 46.5 0 561
64 578 46.5 0 578
65 499 46.5 0 499
66 444 46.5 0 444
67 397 46.5 0 397
68 396 46.5 0 396
69 345 46.5 0 345
70 334 46.5 0 334
71 264 46.5 0 264
72 232 46.5 0 232
73 218 46.5 0 218
74 205 46.5 0 205
75 158 46.5 0 158
76 104 46.5 0 104
77 105 46.5 0 105
78 99 46.5 0 99
79 87 46.5 0 87
80 94 46.5 0 94
81 70 46.5 0 70
82 67 46.5 0 67
83 62 46.5 0 62
84 52 46.5 0 52
85 50 46.5 0 50
86 1662 46.5 0 1662
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 56396 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 22.3%
G: 20.3%
T: 22.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41111 47592.3 0 41111
4 10568 11898.1 0 10568
5 1889 2974.5 0 1889
6 254 743.6 0 254
7 35 185.9 0 35
8 33 185.9 0 33
9 20 185.9 0 20
10 41 185.9 0 41
11 33 185.9 0 33
12 15 185.9 0 15
13 37 185.9 0 37
14 39 185.9 0 39
15 17 185.9 0 17
16 19 185.9 0 19
17 20 185.9 0 20
18 37 185.9 0 37
19 42 185.9 0 42
20 30 185.9 0 30
21 31 185.9 0 31
22 32 185.9 0 32
23 29 185.9 0 29
24 38 185.9 0 38
25 36 185.9 0 36
26 37 185.9 0 37
27 32 185.9 0 32
28 35 185.9 0 35
29 28 185.9 0 28
30 47 185.9 0 47
31 19 185.9 0 19
32 26 185.9 0 26
33 41 185.9 0 41
34 28 185.9 0 28
35 29 185.9 0 29
36 45 185.9 0 45
37 31 185.9 0 31
38 33 185.9 0 33
39 42 185.9 0 42
40 37 185.9 0 37
41 32 185.9 0 32
42 38 185.9 0 38
43 35 185.9 0 35
44 22 185.9 0 22
45 50 185.9 0 50
46 43 185.9 0 43
47 29 185.9 0 29
48 27 185.9 0 27
49 32 185.9 0 32
50 33 185.9 0 33
51 45 185.9 0 45
52 47 185.9 0 47
53 32 185.9 0 32
54 22 185.9 0 22
55 31 185.9 0 31
56 15 185.9 0 15
57 25 185.9 0 25
58 21 185.9 0 21
59 29 185.9 0 29
60 18 185.9 0 18
61 28 185.9 0 28
62 32 185.9 0 32
63 24 185.9 0 24
64 38 185.9 0 38
65 33 185.9 0 33
66 28 185.9 0 28
67 17 185.9 0 17
68 30 185.9 0 30
69 21 185.9 0 21
70 22 185.9 0 22
71 27 185.9 0 27
72 14 185.9 0 14
73 35 185.9 0 35
74 43 185.9 0 43
75 18 185.9 0 18
76 25 185.9 0 25
77 99 185.9 0 99
78 53 185.9 0 53
79 39 185.9 0 39
80 33 185.9 0 33
81 25 185.9 0 25
82 37 185.9 0 37
83 32 185.9 0 32
84 32 185.9 0 32
85 39 185.9 0 39
86 30 185.9 0 30
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N58_S195_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N58_S195_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.62 s (9 µs/read; 6.32 M reads/minute).
=== Summary ===
Total reads processed: 2,804,987
Reads with adapters: 786,965 (28.1%)
== Read fate breakdown ==
Reads that were too short: 220,413 (7.9%)
Reads written (passing filters): 2,584,574 (92.1%)
Total basepairs processed: 283,303,687 bp
Total written (filtered): 208,151,929 bp (73.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 692327 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.3%
G: 28.2%
T: 28.6%
none/other: 13.8%
Overview of removed sequences
length count expect max.err error counts
3 65301 43827.9 0 65301
4 27061 10957.0 0 27061
5 13077 2739.2 0 13077
6 8285 684.8 0 8285
7 6678 171.2 0 6678
8 5757 42.8 0 5757
9 5676 42.8 0 5676
10 5890 42.8 0 5890
11 5728 42.8 0 5728
12 6030 42.8 0 6030
13 5954 42.8 0 5954
14 6126 42.8 0 6126
15 6053 42.8 0 6053
16 6501 42.8 0 6501
17 6149 42.8 0 6149
18 6098 42.8 0 6098
19 6034 42.8 0 6034
20 5776 42.8 0 5776
21 5828 42.8 0 5828
22 5981 42.8 0 5981
23 5597 42.8 0 5597
24 5622 42.8 0 5622
25 5522 42.8 0 5522
26 5477 42.8 0 5477
27 5561 42.8 0 5561
28 5880 42.8 0 5880
29 5860 42.8 0 5860
30 5716 42.8 0 5716
31 6372 42.8 0 6372
32 6049 42.8 0 6049
33 5958 42.8 0 5958
34 6014 42.8 0 6014
35 5832 42.8 0 5832
36 5596 42.8 0 5596
37 5780 42.8 0 5780
38 5377 42.8 0 5377
39 5726 42.8 0 5726
40 5808 42.8 0 5808
41 5569 42.8 0 5569
42 5762 42.8 0 5762
43 5889 42.8 0 5889
44 5273 42.8 0 5273
45 5723 42.8 0 5723
46 5992 42.8 0 5992
47 5813 42.8 0 5813
48 5686 42.8 0 5686
49 9430 42.8 0 9430
50 12483 42.8 0 12483
51 6299 42.8 0 6299
52 6534 42.8 0 6534
53 6675 42.8 0 6675
54 5432 42.8 0 5432
55 5681 42.8 0 5681
56 5778 42.8 0 5778
57 5623 42.8 0 5623
58 6132 42.8 0 6132
59 6009 42.8 0 6009
60 5789 42.8 0 5789
61 5852 42.8 0 5852
62 5681 42.8 0 5681
63 5309 42.8 0 5309
64 5439 42.8 0 5439
65 5429 42.8 0 5429
66 5226 42.8 0 5226
67 5386 42.8 0 5386
68 5257 42.8 0 5257
69 5244 42.8 0 5244
70 4835 42.8 0 4835
71 5662 42.8 0 5662
72 5794 42.8 0 5794
73 5243 42.8 0 5243
74 5140 42.8 0 5140
75 5285 42.8 0 5285
76 5125 42.8 0 5125
77 5191 42.8 0 5191
78 5306 42.8 0 5306
79 6202 42.8 0 6202
80 6075 42.8 0 6075
81 7253 42.8 0 7253
82 8337 42.8 0 8337
83 9453 42.8 0 9453
84 10470 42.8 0 10470
85 11035 42.8 0 11035
86 95796 42.8 0 95796
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27625 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 32.9%
C: 30.7%
G: 0.0%
T: 32.4%
none/other: 4.0%
Overview of removed sequences
length count expect max.err error counts
3 17145 43827.9 0 17145
4 3594 10957.0 0 3594
5 743 2739.2 0 743
6 203 684.8 0 203
7 156 171.2 0 156
8 134 42.8 0 134
9 137 42.8 0 137
10 106 42.8 0 106
11 102 42.8 0 102
12 102 42.8 0 102
13 77 42.8 0 77
14 101 42.8 0 101
15 83 42.8 0 83
16 87 42.8 0 87
17 72 42.8 0 72
18 66 42.8 0 66
19 86 42.8 0 86
20 60 42.8 0 60
21 67 42.8 0 67
22 69 42.8 0 69
23 67 42.8 0 67
24 68 42.8 0 68
25 74 42.8 0 74
26 83 42.8 0 83
27 69 42.8 0 69
28 68 42.8 0 68
29 75 42.8 0 75
30 63 42.8 0 63
31 70 42.8 0 70
32 58 42.8 0 58
33 68 42.8 0 68
34 70 42.8 0 70
35 79 42.8 0 79
36 67 42.8 0 67
37 78 42.8 0 78
38 84 42.8 0 84
39 68 42.8 0 68
40 55 42.8 0 55
41 80 42.8 0 80
42 87 42.8 0 87
43 73 42.8 0 73
44 67 42.8 0 67
45 79 42.8 0 79
46 65 42.8 0 65
47 56 42.8 0 56
48 56 42.8 0 56
49 78 42.8 0 78
50 73 42.8 0 73
51 61 42.8 0 61
52 54 42.8 0 54
53 72 42.8 0 72
54 55 42.8 0 55
55 60 42.8 0 60
56 75 42.8 0 75
57 61 42.8 0 61
58 58 42.8 0 58
59 54 42.8 0 54
60 57 42.8 0 57
61 47 42.8 0 47
62 41 42.8 0 41
63 64 42.8 0 64
64 47 42.8 0 47
65 31 42.8 0 31
66 45 42.8 0 45
67 35 42.8 0 35
68 34 42.8 0 34
69 44 42.8 0 44
70 43 42.8 0 43
71 27 42.8 0 27
72 11 42.8 0 11
73 19 42.8 0 19
74 27 42.8 0 27
75 14 42.8 0 14
76 19 42.8 0 19
77 14 42.8 0 14
78 23 42.8 0 23
79 19 42.8 0 19
80 14 42.8 0 14
81 20 42.8 0 20
82 26 42.8 0 26
83 18 42.8 0 18
84 31 42.8 0 31
85 35 42.8 0 35
86 1102 42.8 0 1102
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 67013 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 24.1%
G: 20.7%
T: 19.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 50224 43827.9 0 50224
4 10956 10957.0 0 10956
5 2529 2739.2 0 2529
6 397 684.8 0 397
7 24 171.2 0 24
8 46 171.2 0 46
9 37 171.2 0 37
10 35 171.2 0 35
11 26 171.2 0 26
12 29 171.2 0 29
13 27 171.2 0 27
14 41 171.2 0 41
15 42 171.2 0 42
16 38 171.2 0 38
17 43 171.2 0 43
18 35 171.2 0 35
19 43 171.2 0 43
20 27 171.2 0 27
21 43 171.2 0 43
22 28 171.2 0 28
23 28 171.2 0 28
24 33 171.2 0 33
25 42 171.2 0 42
26 39 171.2 0 39
27 21 171.2 0 21
28 34 171.2 0 34
29 46 171.2 0 46
30 37 171.2 0 37
31 31 171.2 0 31
32 54 171.2 0 54
33 43 171.2 0 43
34 34 171.2 0 34
35 42 171.2 0 42
36 40 171.2 0 40
37 35 171.2 0 35
38 35 171.2 0 35
39 45 171.2 0 45
40 22 171.2 0 22
41 35 171.2 0 35
42 45 171.2 0 45
43 41 171.2 0 41
44 39 171.2 0 39
45 28 171.2 0 28
46 37 171.2 0 37
47 27 171.2 0 27
48 19 171.2 0 19
49 31 171.2 0 31
50 31 171.2 0 31
51 45 171.2 0 45
52 39 171.2 0 39
53 23 171.2 0 23
54 43 171.2 0 43
55 40 171.2 0 40
56 27 171.2 0 27
57 28 171.2 0 28
58 36 171.2 0 36
59 38 171.2 0 38
60 43 171.2 0 43
61 35 171.2 0 35
62 37 171.2 0 37
63 40 171.2 0 40
64 39 171.2 0 39
65 54 171.2 0 54
66 33 171.2 0 33
67 29 171.2 0 29
68 28 171.2 0 28
69 39 171.2 0 39
70 35 171.2 0 35
71 48 171.2 0 48
72 31 171.2 0 31
73 32 171.2 0 32
74 36 171.2 0 36
75 39 171.2 0 39
76 25 171.2 0 25
77 51 171.2 0 51
78 36 171.2 0 36
79 27 171.2 0 27
80 36 171.2 0 36
81 29 171.2 0 29
82 38 171.2 0 38
83 51 171.2 0 51
84 46 171.2 0 46
85 38 171.2 0 38
86 55 171.2 0 55
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N58_S195_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N58_S195_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.15 s (9 µs/read; 6.33 M reads/minute).
=== Summary ===
Total reads processed: 2,866,478
Reads with adapters: 812,930 (28.4%)
== Read fate breakdown ==
Reads that were too short: 232,454 (8.1%)
Reads written (passing filters): 2,634,024 (91.9%)
Total basepairs processed: 289,514,278 bp
Total written (filtered): 211,913,633 bp (73.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 717297 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.2%
G: 28.2%
T: 28.5%
none/other: 14.2%
Overview of removed sequences
length count expect max.err error counts
3 66648 44788.7 0 66648
4 26896 11197.2 0 26896
5 13653 2799.3 0 13653
6 8455 699.8 0 8455
7 6666 175.0 0 6666
8 5825 43.7 0 5825
9 5857 43.7 0 5857
10 6043 43.7 0 6043
11 5963 43.7 0 5963
12 5978 43.7 0 5978
13 6026 43.7 0 6026
14 6214 43.7 0 6214
15 6037 43.7 0 6037
16 6437 43.7 0 6437
17 6196 43.7 0 6196
18 6269 43.7 0 6269
19 6103 43.7 0 6103
20 5857 43.7 0 5857
21 6084 43.7 0 6084
22 6098 43.7 0 6098
23 5650 43.7 0 5650
24 5798 43.7 0 5798
25 5737 43.7 0 5737
26 5656 43.7 0 5656
27 5476 43.7 0 5476
28 5961 43.7 0 5961
29 6013 43.7 0 6013
30 5840 43.7 0 5840
31 6458 43.7 0 6458
32 6021 43.7 0 6021
33 6224 43.7 0 6224
34 6370 43.7 0 6370
35 6045 43.7 0 6045
36 5867 43.7 0 5867
37 5916 43.7 0 5916
38 5540 43.7 0 5540
39 5967 43.7 0 5967
40 5981 43.7 0 5981
41 5732 43.7 0 5732
42 5960 43.7 0 5960
43 6120 43.7 0 6120
44 5516 43.7 0 5516
45 5913 43.7 0 5913
46 6061 43.7 0 6061
47 5984 43.7 0 5984
48 5824 43.7 0 5824
49 9926 43.7 0 9926
50 13151 43.7 0 13151
51 6475 43.7 0 6475
52 7093 43.7 0 7093
53 6779 43.7 0 6779
54 5643 43.7 0 5643
55 6016 43.7 0 6016
56 5961 43.7 0 5961
57 5713 43.7 0 5713
58 6352 43.7 0 6352
59 6123 43.7 0 6123
60 6240 43.7 0 6240
61 6255 43.7 0 6255
62 5790 43.7 0 5790
63 5545 43.7 0 5545
64 5799 43.7 0 5799
65 5815 43.7 0 5815
66 5536 43.7 0 5536
67 5519 43.7 0 5519
68 5607 43.7 0 5607
69 5458 43.7 0 5458
70 5135 43.7 0 5135
71 5797 43.7 0 5797
72 5978 43.7 0 5978
73 5480 43.7 0 5480
74 5366 43.7 0 5366
75 5574 43.7 0 5574
76 5489 43.7 0 5489
77 5571 43.7 0 5571
78 5439 43.7 0 5439
79 6428 43.7 0 6428
80 6331 43.7 0 6331
81 7638 43.7 0 7638
82 8940 43.7 0 8940
83 9927 43.7 0 9927
84 11150 43.7 0 11150
85 11536 43.7 0 11536
86 101787 43.7 0 101787
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27835 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 32.8%
C: 31.3%
G: 0.0%
T: 32.2%
none/other: 3.8%
Overview of removed sequences
length count expect max.err error counts
3 17629 44788.7 0 17629
4 3451 11197.2 0 3451
5 745 2799.3 0 745
6 215 699.8 0 215
7 183 175.0 0 183
8 151 43.7 0 151
9 117 43.7 0 117
10 123 43.7 0 123
11 98 43.7 0 98
12 112 43.7 0 112
13 98 43.7 0 98
14 92 43.7 0 92
15 81 43.7 0 81
16 81 43.7 0 81
17 69 43.7 0 69
18 58 43.7 0 58
19 79 43.7 0 79
20 66 43.7 0 66
21 68 43.7 0 68
22 59 43.7 0 59
23 65 43.7 0 65
24 83 43.7 0 83
25 68 43.7 0 68
26 71 43.7 0 71
27 58 43.7 0 58
28 55 43.7 0 55
29 57 43.7 0 57
30 64 43.7 0 64
31 63 43.7 0 63
32 66 43.7 0 66
33 56 43.7 0 56
34 79 43.7 0 79
35 73 43.7 0 73
36 77 43.7 0 77
37 70 43.7 0 70
38 53 43.7 0 53
39 54 43.7 0 54
40 68 43.7 0 68
41 56 43.7 0 56
42 61 43.7 0 61
43 74 43.7 0 74
44 53 43.7 0 53
45 70 43.7 0 70
46 57 43.7 0 57
47 63 43.7 0 63
48 72 43.7 0 72
49 64 43.7 0 64
50 58 43.7 0 58
51 51 43.7 0 51
52 73 43.7 0 73
53 70 43.7 0 70
54 79 43.7 0 79
55 75 43.7 0 75
56 60 43.7 0 60
57 55 43.7 0 55
58 61 43.7 0 61
59 50 43.7 0 50
60 45 43.7 0 45
61 52 43.7 0 52
62 42 43.7 0 42
63 53 43.7 0 53
64 55 43.7 0 55
65 34 43.7 0 34
66 44 43.7 0 44
67 47 43.7 0 47
68 34 43.7 0 34
69 59 43.7 0 59
70 37 43.7 0 37
71 29 43.7 0 29
72 32 43.7 0 32
73 22 43.7 0 22
74 13 43.7 0 13
75 10 43.7 0 10
76 12 43.7 0 12
77 9 43.7 0 9
78 19 43.7 0 19
79 19 43.7 0 19
80 22 43.7 0 22
81 28 43.7 0 28
82 27 43.7 0 27
83 33 43.7 0 33
84 29 43.7 0 29
85 27 43.7 0 27
86 1045 43.7 0 1045
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 67798 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 24.1%
G: 20.7%
T: 19.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 50785 44788.7 0 50785
4 11088 11197.2 0 11088
5 2537 2799.3 0 2537
6 409 699.8 0 409
7 32 175.0 0 32
8 34 175.0 0 34
9 41 175.0 0 41
10 18 175.0 0 18
11 35 175.0 0 35
12 33 175.0 0 33
13 26 175.0 0 26
14 35 175.0 0 35
15 35 175.0 0 35
16 30 175.0 0 30
17 32 175.0 0 32
18 48 175.0 0 48
19 26 175.0 0 26
20 45 175.0 0 45
21 39 175.0 0 39
22 31 175.0 0 31
23 40 175.0 0 40
24 32 175.0 0 32
25 28 175.0 0 28
26 32 175.0 0 32
27 37 175.0 0 37
28 23 175.0 0 23
29 35 175.0 0 35
30 39 175.0 0 39
31 34 175.0 0 34
32 54 175.0 0 54
33 46 175.0 0 46
34 33 175.0 0 33
35 30 175.0 0 30
36 56 175.0 0 56
37 39 175.0 0 39
38 52 175.0 0 52
39 38 175.0 0 38
40 39 175.0 0 39
41 45 175.0 0 45
42 54 175.0 0 54
43 51 175.0 0 51
44 38 175.0 0 38
45 27 175.0 0 27
46 32 175.0 0 32
47 39 175.0 0 39
48 35 175.0 0 35
49 35 175.0 0 35
50 27 175.0 0 27
51 43 175.0 0 43
52 50 175.0 0 50
53 28 175.0 0 28
54 45 175.0 0 45
55 35 175.0 0 35
56 24 175.0 0 24
57 34 175.0 0 34
58 42 175.0 0 42
59 46 175.0 0 46
60 35 175.0 0 35
61 35 175.0 0 35
62 47 175.0 0 47
63 36 175.0 0 36
64 31 175.0 0 31
65 47 175.0 0 47
66 40 175.0 0 40
67 40 175.0 0 40
68 30 175.0 0 30
69 34 175.0 0 34
70 33 175.0 0 33
71 45 175.0 0 45
72 42 175.0 0 42
73 28 175.0 0 28
74 28 175.0 0 28
75 35 175.0 0 35
76 22 175.0 0 22
77 66 175.0 0 66
78 37 175.0 0 37
79 28 175.0 0 28
80 36 175.0 0 36
81 39 175.0 0 39
82 45 175.0 0 45
83 36 175.0 0 36
84 46 175.0 0 46
85 33 175.0 0 33
86 48 175.0 0 48
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N59_S189_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N59_S189_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.38 s (9 µs/read; 6.41 M reads/minute).
=== Summary ===
Total reads processed: 2,922,817
Reads with adapters: 992,448 (34.0%)
== Read fate breakdown ==
Reads that were too short: 373,778 (12.8%)
Reads written (passing filters): 2,549,039 (87.2%)
Total basepairs processed: 295,204,517 bp
Total written (filtered): 202,184,075 bp (68.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 894119 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.6%
G: 23.9%
T: 24.7%
none/other: 21.7%
Overview of removed sequences
length count expect max.err error counts
3 64553 45669.0 0 64553
4 27538 11417.3 0 27538
5 13068 2854.3 0 13068
6 8220 713.6 0 8220
7 6427 178.4 0 6427
8 5632 44.6 0 5632
9 5715 44.6 0 5715
10 5769 44.6 0 5769
11 5725 44.6 0 5725
12 5558 44.6 0 5558
13 5694 44.6 0 5694
14 5939 44.6 0 5939
15 6143 44.6 0 6143
16 6212 44.6 0 6212
17 6257 44.6 0 6257
18 6404 44.6 0 6404
19 5912 44.6 0 5912
20 5874 44.6 0 5874
21 6232 44.6 0 6232
22 6340 44.6 0 6340
23 6691 44.6 0 6691
24 6098 44.6 0 6098
25 6463 44.6 0 6463
26 6631 44.6 0 6631
27 6184 44.6 0 6184
28 7051 44.6 0 7051
29 7848 44.6 0 7848
30 6779 44.6 0 6779
31 8193 44.6 0 8193
32 6434 44.6 0 6434
33 7256 44.6 0 7256
34 6491 44.6 0 6491
35 6206 44.6 0 6206
36 6389 44.6 0 6389
37 6412 44.6 0 6412
38 6032 44.6 0 6032
39 6296 44.6 0 6296
40 6880 44.6 0 6880
41 6636 44.6 0 6636
42 6622 44.6 0 6622
43 6724 44.6 0 6724
44 6013 44.6 0 6013
45 6830 44.6 0 6830
46 6754 44.6 0 6754
47 6132 44.6 0 6132
48 7006 44.6 0 7006
49 7986 44.6 0 7986
50 9219 44.6 0 9219
51 7684 44.6 0 7684
52 7408 44.6 0 7408
53 7068 44.6 0 7068
54 7028 44.6 0 7028
55 7822 44.6 0 7822
56 7361 44.6 0 7361
57 7643 44.6 0 7643
58 8383 44.6 0 8383
59 8664 44.6 0 8664
60 8074 44.6 0 8074
61 8553 44.6 0 8553
62 8213 44.6 0 8213
63 7423 44.6 0 7423
64 8193 44.6 0 8193
65 7887 44.6 0 7887
66 7781 44.6 0 7781
67 7983 44.6 0 7983
68 7854 44.6 0 7854
69 7546 44.6 0 7546
70 8248 44.6 0 8248
71 10747 44.6 0 10747
72 8955 44.6 0 8955
73 9879 44.6 0 9879
74 9308 44.6 0 9308
75 7701 44.6 0 7701
76 8725 44.6 0 8725
77 10864 44.6 0 10864
78 7726 44.6 0 7726
79 9037 44.6 0 9037
80 7478 44.6 0 7478
81 8542 44.6 0 8542
82 9995 44.6 0 9995
83 10753 44.6 0 10753
84 11401 44.6 0 11401
85 12480 44.6 0 12480
86 194244 44.6 0 194244
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38817 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.3%
C: 26.1%
G: 0.0%
T: 37.9%
none/other: 5.7%
Overview of removed sequences
length count expect max.err error counts
3 12020 45669.0 0 12020
4 2958 11417.3 0 2958
5 1001 2854.3 0 1001
6 557 713.6 0 557
7 693 178.4 0 693
8 730 44.6 0 730
9 584 44.6 0 584
10 516 44.6 0 516
11 523 44.6 0 523
12 470 44.6 0 470
13 410 44.6 0 410
14 435 44.6 0 435
15 413 44.6 0 413
16 351 44.6 0 351
17 362 44.6 0 362
18 393 44.6 0 393
19 359 44.6 0 359
20 284 44.6 0 284
21 332 44.6 0 332
22 298 44.6 0 298
23 324 44.6 0 324
24 297 44.6 0 297
25 355 44.6 0 355
26 267 44.6 0 267
27 305 44.6 0 305
28 333 44.6 0 333
29 295 44.6 0 295
30 314 44.6 0 314
31 291 44.6 0 291
32 302 44.6 0 302
33 332 44.6 0 332
34 303 44.6 0 303
35 311 44.6 0 311
36 317 44.6 0 317
37 313 44.6 0 313
38 297 44.6 0 297
39 261 44.6 0 261
40 302 44.6 0 302
41 284 44.6 0 284
42 253 44.6 0 253
43 266 44.6 0 266
44 251 44.6 0 251
45 263 44.6 0 263
46 265 44.6 0 265
47 267 44.6 0 267
48 243 44.6 0 243
49 266 44.6 0 266
50 276 44.6 0 276
51 226 44.6 0 226
52 273 44.6 0 273
53 283 44.6 0 283
54 249 44.6 0 249
55 226 44.6 0 226
56 221 44.6 0 221
57 242 44.6 0 242
58 217 44.6 0 217
59 197 44.6 0 197
60 224 44.6 0 224
61 197 44.6 0 197
62 180 44.6 0 180
63 177 44.6 0 177
64 154 44.6 0 154
65 188 44.6 0 188
66 171 44.6 0 171
67 140 44.6 0 140
68 140 44.6 0 140
69 115 44.6 0 115
70 96 44.6 0 96
71 119 44.6 0 119
72 85 44.6 0 85
73 74 44.6 0 74
74 68 44.6 0 68
75 52 44.6 0 52
76 43 44.6 0 43
77 57 44.6 0 57
78 48 44.6 0 48
79 27 44.6 0 27
80 41 44.6 0 41
81 38 44.6 0 38
82 51 44.6 0 51
83 42 44.6 0 42
84 38 44.6 0 38
85 76 44.6 0 76
86 2200 44.6 0 2200
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 59512 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.5%
C: 24.2%
G: 18.5%
T: 20.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44668 45669.0 0 44668
4 10260 11417.3 0 10260
5 1742 2854.3 0 1742
6 188 713.6 0 188
7 32 178.4 0 32
8 39 178.4 0 39
9 19 178.4 0 19
10 34 178.4 0 34
11 30 178.4 0 30
12 20 178.4 0 20
13 41 178.4 0 41
14 51 178.4 0 51
15 27 178.4 0 27
16 33 178.4 0 33
17 30 178.4 0 30
18 19 178.4 0 19
19 57 178.4 0 57
20 31 178.4 0 31
21 23 178.4 0 23
22 60 178.4 0 60
23 33 178.4 0 33
24 25 178.4 0 25
25 80 178.4 0 80
26 40 178.4 0 40
27 30 178.4 0 30
28 43 178.4 0 43
29 39 178.4 0 39
30 35 178.4 0 35
31 23 178.4 0 23
32 46 178.4 0 46
33 29 178.4 0 29
34 18 178.4 0 18
35 19 178.4 0 19
36 30 178.4 0 30
37 36 178.4 0 36
38 32 178.4 0 32
39 32 178.4 0 32
40 38 178.4 0 38
41 32 178.4 0 32
42 38 178.4 0 38
43 40 178.4 0 40
44 32 178.4 0 32
45 41 178.4 0 41
46 23 178.4 0 23
47 17 178.4 0 17
48 38 178.4 0 38
49 32 178.4 0 32
50 31 178.4 0 31
51 45 178.4 0 45
52 23 178.4 0 23
53 25 178.4 0 25
54 29 178.4 0 29
55 27 178.4 0 27
56 15 178.4 0 15
57 24 178.4 0 24
58 10 178.4 0 10
59 27 178.4 0 27
60 27 178.4 0 27
61 21 178.4 0 21
62 24 178.4 0 24
63 14 178.4 0 14
64 30 178.4 0 30
65 29 178.4 0 29
66 24 178.4 0 24
67 30 178.4 0 30
68 19 178.4 0 19
69 29 178.4 0 29
70 37 178.4 0 37
71 17 178.4 0 17
72 34 178.4 0 34
73 24 178.4 0 24
74 23 178.4 0 23
75 28 178.4 0 28
76 24 178.4 0 24
77 155 178.4 0 155
78 60 178.4 0 60
79 39 178.4 0 39
80 33 178.4 0 33
81 32 178.4 0 32
82 35 178.4 0 35
83 39 178.4 0 39
84 35 178.4 0 35
85 37 178.4 0 37
86 32 178.4 0 32
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: N59_S189_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/N59_S189_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.12 s (9 µs/read; 6.59 M reads/minute).
=== Summary ===
Total reads processed: 2,979,708
Reads with adapters: 1,023,679 (34.4%)
== Read fate breakdown ==
Reads that were too short: 391,849 (13.2%)
Reads written (passing filters): 2,587,859 (86.8%)
Total basepairs processed: 300,950,508 bp
Total written (filtered): 205,028,807 bp (68.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 923647 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.5%
G: 23.7%
T: 24.4%
none/other: 22.3%
Overview of removed sequences
length count expect max.err error counts
3 65037 46557.9 0 65037
4 28427 11639.5 0 28427
5 13403 2909.9 0 13403
6 8232 727.5 0 8232
7 6246 181.9 0 6246
8 5537 45.5 0 5537
9 5688 45.5 0 5688
10 5837 45.5 0 5837
11 5925 45.5 0 5925
12 5675 45.5 0 5675
13 5623 45.5 0 5623
14 6046 45.5 0 6046
15 6248 45.5 0 6248
16 6266 45.5 0 6266
17 6314 45.5 0 6314
18 6611 45.5 0 6611
19 6318 45.5 0 6318
20 5889 45.5 0 5889
21 6451 45.5 0 6451
22 6432 45.5 0 6432
23 6617 45.5 0 6617
24 6260 45.5 0 6260
25 6744 45.5 0 6744
26 6801 45.5 0 6801
27 6202 45.5 0 6202
28 7265 45.5 0 7265
29 7836 45.5 0 7836
30 6846 45.5 0 6846
31 8281 45.5 0 8281
32 6677 45.5 0 6677
33 7335 45.5 0 7335
34 6620 45.5 0 6620
35 6462 45.5 0 6462
36 6426 45.5 0 6426
37 6319 45.5 0 6319
38 6278 45.5 0 6278
39 6392 45.5 0 6392
40 7052 45.5 0 7052
41 6864 45.5 0 6864
42 6907 45.5 0 6907
43 6712 45.5 0 6712
44 6136 45.5 0 6136
45 6984 45.5 0 6984
46 6804 45.5 0 6804
47 6343 45.5 0 6343
48 6951 45.5 0 6951
49 8133 45.5 0 8133
50 9465 45.5 0 9465
51 7725 45.5 0 7725
52 7680 45.5 0 7680
53 7394 45.5 0 7394
54 7391 45.5 0 7391
55 8175 45.5 0 8175
56 7691 45.5 0 7691
57 7931 45.5 0 7931
58 8712 45.5 0 8712
59 8909 45.5 0 8909
60 8385 45.5 0 8385
61 9033 45.5 0 9033
62 8698 45.5 0 8698
63 7702 45.5 0 7702
64 8358 45.5 0 8358
65 8415 45.5 0 8415
66 8143 45.5 0 8143
67 8312 45.5 0 8312
68 7945 45.5 0 7945
69 7880 45.5 0 7880
70 8217 45.5 0 8217
71 11071 45.5 0 11071
72 9062 45.5 0 9062
73 10151 45.5 0 10151
74 9755 45.5 0 9755
75 8057 45.5 0 8057
76 8829 45.5 0 8829
77 11411 45.5 0 11411
78 8191 45.5 0 8191
79 9500 45.5 0 9500
80 7707 45.5 0 7707
81 9174 45.5 0 9174
82 10323 45.5 0 10323
83 11002 45.5 0 11002
84 11868 45.5 0 11868
85 12894 45.5 0 12894
86 206039 45.5 0 206039
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39901 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.7%
C: 26.4%
G: 0.0%
T: 37.2%
none/other: 5.7%
Overview of removed sequences
length count expect max.err error counts
3 12065 46557.9 0 12065
4 3131 11639.5 0 3131
5 1058 2909.9 0 1058
6 507 727.5 0 507
7 735 181.9 0 735
8 735 45.5 0 735
9 670 45.5 0 670
10 572 45.5 0 572
11 511 45.5 0 511
12 488 45.5 0 488
13 467 45.5 0 467
14 452 45.5 0 452
15 404 45.5 0 404
16 339 45.5 0 339
17 357 45.5 0 357
18 355 45.5 0 355
19 368 45.5 0 368
20 321 45.5 0 321
21 287 45.5 0 287
22 340 45.5 0 340
23 288 45.5 0 288
24 333 45.5 0 333
25 367 45.5 0 367
26 315 45.5 0 315
27 314 45.5 0 314
28 351 45.5 0 351
29 289 45.5 0 289
30 293 45.5 0 293
31 308 45.5 0 308
32 313 45.5 0 313
33 326 45.5 0 326
34 355 45.5 0 355
35 308 45.5 0 308
36 336 45.5 0 336
37 287 45.5 0 287
38 300 45.5 0 300
39 284 45.5 0 284
40 324 45.5 0 324
41 288 45.5 0 288
42 269 45.5 0 269
43 283 45.5 0 283
44 269 45.5 0 269
45 266 45.5 0 266
46 269 45.5 0 269
47 286 45.5 0 286
48 279 45.5 0 279
49 245 45.5 0 245
50 275 45.5 0 275
51 248 45.5 0 248
52 234 45.5 0 234
53 245 45.5 0 245
54 248 45.5 0 248
55 271 45.5 0 271
56 260 45.5 0 260
57 249 45.5 0 249
58 237 45.5 0 237
59 243 45.5 0 243
60 230 45.5 0 230
61 231 45.5 0 231
62 231 45.5 0 231
63 179 45.5 0 179
64 168 45.5 0 168
65 192 45.5 0 192
66 161 45.5 0 161
67 167 45.5 0 167
68 139 45.5 0 139
69 121 45.5 0 121
70 119 45.5 0 119
71 113 45.5 0 113
72 97 45.5 0 97
73 87 45.5 0 87
74 75 45.5 0 75
75 63 45.5 0 63
76 43 45.5 0 43
77 42 45.5 0 42
78 35 45.5 0 35
79 39 45.5 0 39
80 34 45.5 0 34
81 32 45.5 0 32
82 53 45.5 0 53
83 42 45.5 0 42
84 46 45.5 0 46
85 56 45.5 0 56
86 2289 45.5 0 2289
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60131 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.3%
C: 24.4%
G: 18.3%
T: 20.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45110 46557.9 0 45110
4 10373 11639.5 0 10373
5 1760 2909.9 0 1760
6 219 727.5 0 219
7 17 181.9 0 17
8 24 181.9 0 24
9 28 181.9 0 28
10 21 181.9 0 21
11 34 181.9 0 34
12 26 181.9 0 26
13 37 181.9 0 37
14 35 181.9 0 35
15 28 181.9 0 28
16 29 181.9 0 29
17 34 181.9 0 34
18 19 181.9 0 19
19 58 181.9 0 58
20 34 181.9 0 34
21 30 181.9 0 30
22 51 181.9 0 51
23 34 181.9 0 34
24 28 181.9 0 28
25 68 181.9 0 68
26 49 181.9 0 49
27 32 181.9 0 32
28 46 181.9 0 46
29 41 181.9 0 41
30 34 181.9 0 34
31 31 181.9 0 31
32 36 181.9 0 36
33 29 181.9 0 29
34 18 181.9 0 18
35 32 181.9 0 32
36 29 181.9 0 29
37 30 181.9 0 30
38 40 181.9 0 40
39 37 181.9 0 37
40 35 181.9 0 35
41 47 181.9 0 47
42 24 181.9 0 24
43 42 181.9 0 42
44 31 181.9 0 31
45 38 181.9 0 38
46 29 181.9 0 29
47 29 181.9 0 29
48 33 181.9 0 33
49 31 181.9 0 31
50 35 181.9 0 35
51 44 181.9 0 44
52 26 181.9 0 26
53 22 181.9 0 22
54 31 181.9 0 31
55 20 181.9 0 20
56 23 181.9 0 23
57 24 181.9 0 24
58 20 181.9 0 20
59 26 181.9 0 26
60 23 181.9 0 23
61 26 181.9 0 26
62 21 181.9 0 21
63 25 181.9 0 25
64 13 181.9 0 13
65 43 181.9 0 43
66 20 181.9 0 20
67 27 181.9 0 27
68 19 181.9 0 19
69 27 181.9 0 27
70 53 181.9 0 53
71 31 181.9 0 31
72 32 181.9 0 32
73 27 181.9 0 27
74 28 181.9 0 28
75 20 181.9 0 20
76 24 181.9 0 24
77 157 181.9 0 157
78 49 181.9 0 49
79 38 181.9 0 38
80 21 181.9 0 21
81 18 181.9 0 18
82 38 181.9 0 38
83 43 181.9 0 43
84 41 181.9 0 41
85 48 181.9 0 48
86 28 181.9 0 28
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R41_S181_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R41_S181_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 29.69 s (9 µs/read; 6.77 M reads/minute).
=== Summary ===
Total reads processed: 3,348,976
Reads with adapters: 1,239,592 (37.0%)
== Read fate breakdown ==
Reads that were too short: 380,967 (11.4%)
Reads written (passing filters): 2,968,009 (88.6%)
Total basepairs processed: 338,246,576 bp
Total written (filtered): 230,707,616 bp (68.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1121016 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.0%
G: 26.2%
T: 28.4%
none/other: 15.4%
Overview of removed sequences
length count expect max.err error counts
3 75817 52327.8 0 75817
4 33952 13081.9 0 33952
5 17920 3270.5 0 17920
6 12223 817.6 0 12223
7 9996 204.4 0 9996
8 9018 51.1 0 9018
9 8921 51.1 0 8921
10 9002 51.1 0 9002
11 8974 51.1 0 8974
12 9036 51.1 0 9036
13 9073 51.1 0 9073
14 9260 51.1 0 9260
15 9343 51.1 0 9343
16 9642 51.1 0 9642
17 9468 51.1 0 9468
18 9684 51.1 0 9684
19 9309 51.1 0 9309
20 9317 51.1 0 9317
21 9598 51.1 0 9598
22 9322 51.1 0 9322
23 9405 51.1 0 9405
24 9179 51.1 0 9179
25 9316 51.1 0 9316
26 9313 51.1 0 9313
27 9077 51.1 0 9077
28 9650 51.1 0 9650
29 9886 51.1 0 9886
30 9375 51.1 0 9375
31 9866 51.1 0 9866
32 9254 51.1 0 9254
33 9789 51.1 0 9789
34 9960 51.1 0 9960
35 9531 51.1 0 9531
36 9474 51.1 0 9474
37 9390 51.1 0 9390
38 9197 51.1 0 9197
39 9551 51.1 0 9551
40 9717 51.1 0 9717
41 10004 51.1 0 10004
42 9882 51.1 0 9882
43 10626 51.1 0 10626
44 9893 51.1 0 9893
45 10344 51.1 0 10344
46 10623 51.1 0 10623
47 10355 51.1 0 10355
48 10250 51.1 0 10250
49 13026 51.1 0 13026
50 14682 51.1 0 14682
51 10931 51.1 0 10931
52 11313 51.1 0 11313
53 10874 51.1 0 10874
54 10447 51.1 0 10447
55 11172 51.1 0 11172
56 10934 51.1 0 10934
57 10715 51.1 0 10715
58 11450 51.1 0 11450
59 11082 51.1 0 11082
60 11214 51.1 0 11214
61 11133 51.1 0 11133
62 11033 51.1 0 11033
63 10604 51.1 0 10604
64 10856 51.1 0 10856
65 10923 51.1 0 10923
66 10311 51.1 0 10311
67 10337 51.1 0 10337
68 10006 51.1 0 10006
69 9400 51.1 0 9400
70 9308 51.1 0 9308
71 10035 51.1 0 10035
72 9370 51.1 0 9370
73 9302 51.1 0 9302
74 8661 51.1 0 8661
75 8075 51.1 0 8075
76 8544 51.1 0 8544
77 9130 51.1 0 9130
78 8489 51.1 0 8489
79 9882 51.1 0 9882
80 9529 51.1 0 9529
81 10894 51.1 0 10894
82 13466 51.1 0 13466
83 15344 51.1 0 15344
84 16503 51.1 0 16503
85 17570 51.1 0 17570
86 172689 51.1 0 172689
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 49575 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.4%
C: 30.5%
G: 0.0%
T: 38.6%
none/other: 3.5%
Overview of removed sequences
length count expect max.err error counts
3 14722 52327.8 0 14722
4 3696 13081.9 0 3696
5 1226 3270.5 0 1226
6 728 817.6 0 728
7 758 204.4 0 758
8 738 51.1 0 738
9 649 51.1 0 649
10 589 51.1 0 589
11 601 51.1 0 601
12 571 51.1 0 571
13 542 51.1 0 542
14 489 51.1 0 489
15 521 51.1 0 521
16 454 51.1 0 454
17 469 51.1 0 469
18 510 51.1 0 510
19 485 51.1 0 485
20 477 51.1 0 477
21 478 51.1 0 478
22 457 51.1 0 457
23 437 51.1 0 437
24 532 51.1 0 532
25 511 51.1 0 511
26 469 51.1 0 469
27 422 51.1 0 422
28 445 51.1 0 445
29 444 51.1 0 444
30 440 51.1 0 440
31 431 51.1 0 431
32 425 51.1 0 425
33 449 51.1 0 449
34 422 51.1 0 422
35 436 51.1 0 436
36 439 51.1 0 439
37 428 51.1 0 428
38 426 51.1 0 426
39 399 51.1 0 399
40 448 51.1 0 448
41 388 51.1 0 388
42 382 51.1 0 382
43 426 51.1 0 426
44 384 51.1 0 384
45 414 51.1 0 414
46 368 51.1 0 368
47 375 51.1 0 375
48 371 51.1 0 371
49 366 51.1 0 366
50 366 51.1 0 366
51 372 51.1 0 372
52 387 51.1 0 387
53 353 51.1 0 353
54 336 51.1 0 336
55 353 51.1 0 353
56 349 51.1 0 349
57 374 51.1 0 374
58 322 51.1 0 322
59 335 51.1 0 335
60 315 51.1 0 315
61 298 51.1 0 298
62 292 51.1 0 292
63 263 51.1 0 263
64 243 51.1 0 243
65 229 51.1 0 229
66 205 51.1 0 205
67 220 51.1 0 220
68 167 51.1 0 167
69 145 51.1 0 145
70 157 51.1 0 157
71 152 51.1 0 152
72 116 51.1 0 116
73 120 51.1 0 120
74 91 51.1 0 91
75 84 51.1 0 84
76 63 51.1 0 63
77 55 51.1 0 55
78 65 51.1 0 65
79 70 51.1 0 70
80 43 51.1 0 43
81 33 51.1 0 33
82 60 51.1 0 60
83 59 51.1 0 59
84 46 51.1 0 46
85 68 51.1 0 68
86 1732 51.1 0 1732
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69001 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 22.5%
G: 20.8%
T: 20.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51572 52327.8 0 51572
4 11869 13081.9 0 11869
5 2128 3270.5 0 2128
6 257 817.6 0 257
7 39 204.4 0 39
8 35 204.4 0 35
9 19 204.4 0 19
10 33 204.4 0 33
11 40 204.4 0 40
12 28 204.4 0 28
13 50 204.4 0 50
14 53 204.4 0 53
15 31 204.4 0 31
16 31 204.4 0 31
17 42 204.4 0 42
18 39 204.4 0 39
19 48 204.4 0 48
20 44 204.4 0 44
21 34 204.4 0 34
22 51 204.4 0 51
23 38 204.4 0 38
24 37 204.4 0 37
25 44 204.4 0 44
26 41 204.4 0 41
27 31 204.4 0 31
28 45 204.4 0 45
29 39 204.4 0 39
30 50 204.4 0 50
31 31 204.4 0 31
32 51 204.4 0 51
33 47 204.4 0 47
34 34 204.4 0 34
35 19 204.4 0 19
36 44 204.4 0 44
37 48 204.4 0 48
38 31 204.4 0 31
39 25 204.4 0 25
40 43 204.4 0 43
41 34 204.4 0 34
42 55 204.4 0 55
43 40 204.4 0 40
44 27 204.4 0 27
45 39 204.4 0 39
46 29 204.4 0 29
47 36 204.4 0 36
48 36 204.4 0 36
49 48 204.4 0 48
50 26 204.4 0 26
51 49 204.4 0 49
52 51 204.4 0 51
53 28 204.4 0 28
54 40 204.4 0 40
55 50 204.4 0 50
56 24 204.4 0 24
57 38 204.4 0 38
58 31 204.4 0 31
59 42 204.4 0 42
60 25 204.4 0 25
61 35 204.4 0 35
62 43 204.4 0 43
63 37 204.4 0 37
64 31 204.4 0 31
65 40 204.4 0 40
66 39 204.4 0 39
67 28 204.4 0 28
68 41 204.4 0 41
69 30 204.4 0 30
70 53 204.4 0 53
71 42 204.4 0 42
72 29 204.4 0 29
73 53 204.4 0 53
74 43 204.4 0 43
75 43 204.4 0 43
76 41 204.4 0 41
77 76 204.4 0 76
78 57 204.4 0 57
79 43 204.4 0 43
80 37 204.4 0 37
81 30 204.4 0 30
82 49 204.4 0 49
83 49 204.4 0 49
84 48 204.4 0 48
85 39 204.4 0 39
86 56 204.4 0 56
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R41_S181_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R41_S181_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 31.54 s (9 µs/read; 6.49 M reads/minute).
=== Summary ===
Total reads processed: 3,413,375
Reads with adapters: 1,278,034 (37.4%)
== Read fate breakdown ==
Reads that were too short: 399,184 (11.7%)
Reads written (passing filters): 3,014,191 (88.3%)
Total basepairs processed: 344,750,875 bp
Total written (filtered): 233,893,215 bp (67.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1157333 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.1%
G: 26.2%
T: 28.1%
none/other: 15.7%
Overview of removed sequences
length count expect max.err error counts
3 76041 53334.0 0 76041
4 34531 13333.5 0 34531
5 18101 3333.4 0 18101
6 12580 833.3 0 12580
7 10149 208.3 0 10149
8 9131 52.1 0 9131
9 9189 52.1 0 9189
10 9113 52.1 0 9113
11 9119 52.1 0 9119
12 9112 52.1 0 9112
13 9187 52.1 0 9187
14 9304 52.1 0 9304
15 9443 52.1 0 9443
16 9589 52.1 0 9589
17 9652 52.1 0 9652
18 10108 52.1 0 10108
19 9594 52.1 0 9594
20 9352 52.1 0 9352
21 9881 52.1 0 9881
22 9651 52.1 0 9651
23 9509 52.1 0 9509
24 9393 52.1 0 9393
25 9274 52.1 0 9274
26 9244 52.1 0 9244
27 9307 52.1 0 9307
28 9811 52.1 0 9811
29 10102 52.1 0 10102
30 9450 52.1 0 9450
31 10360 52.1 0 10360
32 9522 52.1 0 9522
33 9861 52.1 0 9861
34 9919 52.1 0 9919
35 9760 52.1 0 9760
36 9612 52.1 0 9612
37 9573 52.1 0 9573
38 9407 52.1 0 9407
39 9895 52.1 0 9895
40 9984 52.1 0 9984
41 10227 52.1 0 10227
42 10365 52.1 0 10365
43 11066 52.1 0 11066
44 10229 52.1 0 10229
45 10694 52.1 0 10694
46 10968 52.1 0 10968
47 10839 52.1 0 10839
48 10475 52.1 0 10475
49 13819 52.1 0 13819
50 15086 52.1 0 15086
51 11411 52.1 0 11411
52 11641 52.1 0 11641
53 11184 52.1 0 11184
54 10811 52.1 0 10811
55 11459 52.1 0 11459
56 11515 52.1 0 11515
57 11344 52.1 0 11344
58 11947 52.1 0 11947
59 11683 52.1 0 11683
60 11661 52.1 0 11661
61 11683 52.1 0 11683
62 11568 52.1 0 11568
63 10803 52.1 0 10803
64 11128 52.1 0 11128
65 11297 52.1 0 11297
66 10914 52.1 0 10914
67 10787 52.1 0 10787
68 10384 52.1 0 10384
69 9940 52.1 0 9940
70 9586 52.1 0 9586
71 10450 52.1 0 10450
72 9560 52.1 0 9560
73 9643 52.1 0 9643
74 9117 52.1 0 9117
75 8829 52.1 0 8829
76 9081 52.1 0 9081
77 9611 52.1 0 9611
78 9071 52.1 0 9071
79 10499 52.1 0 10499
80 9997 52.1 0 9997
81 11739 52.1 0 11739
82 13990 52.1 0 13990
83 16420 52.1 0 16420
84 16820 52.1 0 16820
85 17898 52.1 0 17898
86 181284 52.1 0 181284
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 50581 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.7%
C: 30.4%
G: 0.0%
T: 38.4%
none/other: 3.5%
Overview of removed sequences
length count expect max.err error counts
3 14977 53334.0 0 14977
4 3742 13333.5 0 3742
5 1203 3333.4 0 1203
6 709 833.3 0 709
7 720 208.3 0 720
8 714 52.1 0 714
9 704 52.1 0 704
10 640 52.1 0 640
11 604 52.1 0 604
12 586 52.1 0 586
13 521 52.1 0 521
14 499 52.1 0 499
15 532 52.1 0 532
16 501 52.1 0 501
17 493 52.1 0 493
18 493 52.1 0 493
19 536 52.1 0 536
20 467 52.1 0 467
21 475 52.1 0 475
22 467 52.1 0 467
23 480 52.1 0 480
24 480 52.1 0 480
25 501 52.1 0 501
26 478 52.1 0 478
27 440 52.1 0 440
28 434 52.1 0 434
29 446 52.1 0 446
30 494 52.1 0 494
31 466 52.1 0 466
32 470 52.1 0 470
33 457 52.1 0 457
34 399 52.1 0 399
35 460 52.1 0 460
36 443 52.1 0 443
37 453 52.1 0 453
38 429 52.1 0 429
39 391 52.1 0 391
40 412 52.1 0 412
41 424 52.1 0 424
42 420 52.1 0 420
43 412 52.1 0 412
44 415 52.1 0 415
45 433 52.1 0 433
46 411 52.1 0 411
47 415 52.1 0 415
48 407 52.1 0 407
49 376 52.1 0 376
50 398 52.1 0 398
51 382 52.1 0 382
52 389 52.1 0 389
53 394 52.1 0 394
54 352 52.1 0 352
55 346 52.1 0 346
56 321 52.1 0 321
57 364 52.1 0 364
58 340 52.1 0 340
59 339 52.1 0 339
60 361 52.1 0 361
61 313 52.1 0 313
62 303 52.1 0 303
63 273 52.1 0 273
64 241 52.1 0 241
65 256 52.1 0 256
66 222 52.1 0 222
67 208 52.1 0 208
68 187 52.1 0 187
69 173 52.1 0 173
70 135 52.1 0 135
71 127 52.1 0 127
72 115 52.1 0 115
73 77 52.1 0 77
74 89 52.1 0 89
75 94 52.1 0 94
76 76 52.1 0 76
77 47 52.1 0 47
78 62 52.1 0 62
79 43 52.1 0 43
80 62 52.1 0 62
81 64 52.1 0 64
82 56 52.1 0 56
83 44 52.1 0 44
84 60 52.1 0 60
85 71 52.1 0 71
86 1768 52.1 0 1768
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 70120 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 22.2%
G: 21.1%
T: 20.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 52242 53334.0 0 52242
4 12130 13333.5 0 12130
5 2208 3333.4 0 2208
6 248 833.3 0 248
7 34 208.3 0 34
8 41 208.3 0 41
9 28 208.3 0 28
10 30 208.3 0 30
11 44 208.3 0 44
12 24 208.3 0 24
13 56 208.3 0 56
14 27 208.3 0 27
15 51 208.3 0 51
16 34 208.3 0 34
17 27 208.3 0 27
18 35 208.3 0 35
19 50 208.3 0 50
20 41 208.3 0 41
21 40 208.3 0 40
22 35 208.3 0 35
23 41 208.3 0 41
24 35 208.3 0 35
25 37 208.3 0 37
26 50 208.3 0 50
27 37 208.3 0 37
28 45 208.3 0 45
29 45 208.3 0 45
30 44 208.3 0 44
31 26 208.3 0 26
32 36 208.3 0 36
33 36 208.3 0 36
34 25 208.3 0 25
35 40 208.3 0 40
36 46 208.3 0 46
37 40 208.3 0 40
38 30 208.3 0 30
39 56 208.3 0 56
40 53 208.3 0 53
41 32 208.3 0 32
42 41 208.3 0 41
43 48 208.3 0 48
44 34 208.3 0 34
45 40 208.3 0 40
46 35 208.3 0 35
47 47 208.3 0 47
48 42 208.3 0 42
49 52 208.3 0 52
50 46 208.3 0 46
51 64 208.3 0 64
52 57 208.3 0 57
53 46 208.3 0 46
54 36 208.3 0 36
55 43 208.3 0 43
56 35 208.3 0 35
57 33 208.3 0 33
58 37 208.3 0 37
59 32 208.3 0 32
60 45 208.3 0 45
61 47 208.3 0 47
62 22 208.3 0 22
63 30 208.3 0 30
64 33 208.3 0 33
65 45 208.3 0 45
66 31 208.3 0 31
67 35 208.3 0 35
68 30 208.3 0 30
69 35 208.3 0 35
70 57 208.3 0 57
71 46 208.3 0 46
72 27 208.3 0 27
73 35 208.3 0 35
74 34 208.3 0 34
75 54 208.3 0 54
76 40 208.3 0 40
77 104 208.3 0 104
78 62 208.3 0 62
79 29 208.3 0 29
80 44 208.3 0 44
81 40 208.3 0 40
82 36 208.3 0 36
83 65 208.3 0 65
84 39 208.3 0 39
85 47 208.3 0 47
86 61 208.3 0 61
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R42_S175_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R42_S175_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.38 s (10 µs/read; 6.13 M reads/minute).
=== Summary ===
Total reads processed: 2,593,121
Reads with adapters: 856,692 (33.0%)
== Read fate breakdown ==
Reads that were too short: 234,275 (9.0%)
Reads written (passing filters): 2,358,846 (91.0%)
Total basepairs processed: 261,905,221 bp
Total written (filtered): 186,341,410 bp (71.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 764076 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.9%
G: 27.5%
T: 29.0%
none/other: 13.6%
Overview of removed sequences
length count expect max.err error counts
3 61031 40517.5 0 61031
4 26330 10129.4 0 26330
5 13999 2532.3 0 13999
6 9713 633.1 0 9713
7 7884 158.3 0 7884
8 6988 39.6 0 6988
9 7107 39.6 0 7107
10 7081 39.6 0 7081
11 6635 39.6 0 6635
12 7052 39.6 0 7052
13 6951 39.6 0 6951
14 7001 39.6 0 7001
15 7038 39.6 0 7038
16 7137 39.6 0 7137
17 6975 39.6 0 6975
18 7177 39.6 0 7177
19 7030 39.6 0 7030
20 6936 39.6 0 6936
21 7166 39.6 0 7166
22 6833 39.6 0 6833
23 6777 39.6 0 6777
24 6589 39.6 0 6589
25 6707 39.6 0 6707
26 6697 39.6 0 6697
27 6802 39.6 0 6802
28 7055 39.6 0 7055
29 7070 39.6 0 7070
30 6853 39.6 0 6853
31 7380 39.6 0 7380
32 6930 39.6 0 6930
33 7460 39.6 0 7460
34 7254 39.6 0 7254
35 7054 39.6 0 7054
36 6875 39.6 0 6875
37 7136 39.6 0 7136
38 6640 39.6 0 6640
39 6927 39.6 0 6927
40 6950 39.6 0 6950
41 6661 39.6 0 6661
42 7128 39.6 0 7128
43 7283 39.6 0 7283
44 6549 39.6 0 6549
45 6969 39.6 0 6969
46 7175 39.6 0 7175
47 7000 39.6 0 7000
48 6788 39.6 0 6788
49 9492 39.6 0 9492
50 11139 39.6 0 11139
51 6966 39.6 0 6966
52 7805 39.6 0 7805
53 7174 39.6 0 7174
54 6241 39.6 0 6241
55 6676 39.6 0 6676
56 6733 39.6 0 6733
57 6401 39.6 0 6401
58 7241 39.6 0 7241
59 6625 39.6 0 6625
60 6545 39.6 0 6545
61 6832 39.6 0 6832
62 6732 39.6 0 6732
63 6105 39.6 0 6105
64 6473 39.6 0 6473
65 6374 39.6 0 6374
66 6129 39.6 0 6129
67 6232 39.6 0 6232
68 6194 39.6 0 6194
69 5865 39.6 0 5865
70 5855 39.6 0 5855
71 6106 39.6 0 6106
72 5943 39.6 0 5943
73 5700 39.6 0 5700
74 5419 39.6 0 5419
75 5574 39.6 0 5574
76 5276 39.6 0 5276
77 5580 39.6 0 5580
78 5701 39.6 0 5701
79 6849 39.6 0 6849
80 6221 39.6 0 6221
81 6964 39.6 0 6964
82 8428 39.6 0 8428
83 9207 39.6 0 9207
84 10094 39.6 0 10094
85 10587 39.6 0 10587
86 103825 39.6 0 103825
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34803 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.7%
C: 33.2%
G: 0.0%
T: 35.8%
none/other: 2.3%
Overview of removed sequences
length count expect max.err error counts
3 14017 40517.5 0 14017
4 3260 10129.4 0 3260
5 930 2532.3 0 930
6 432 633.1 0 432
7 414 158.3 0 414
8 353 39.6 0 353
9 364 39.6 0 364
10 338 39.6 0 338
11 328 39.6 0 328
12 331 39.6 0 331
13 271 39.6 0 271
14 264 39.6 0 264
15 288 39.6 0 288
16 285 39.6 0 285
17 250 39.6 0 250
18 261 39.6 0 261
19 270 39.6 0 270
20 230 39.6 0 230
21 268 39.6 0 268
22 252 39.6 0 252
23 256 39.6 0 256
24 273 39.6 0 273
25 233 39.6 0 233
26 253 39.6 0 253
27 234 39.6 0 234
28 227 39.6 0 227
29 245 39.6 0 245
30 247 39.6 0 247
31 269 39.6 0 269
32 217 39.6 0 217
33 260 39.6 0 260
34 229 39.6 0 229
35 237 39.6 0 237
36 250 39.6 0 250
37 237 39.6 0 237
38 229 39.6 0 229
39 286 39.6 0 286
40 199 39.6 0 199
41 240 39.6 0 240
42 221 39.6 0 221
43 213 39.6 0 213
44 214 39.6 0 214
45 224 39.6 0 224
46 219 39.6 0 219
47 221 39.6 0 221
48 223 39.6 0 223
49 188 39.6 0 188
50 214 39.6 0 214
51 208 39.6 0 208
52 203 39.6 0 203
53 203 39.6 0 203
54 197 39.6 0 197
55 218 39.6 0 218
56 202 39.6 0 202
57 211 39.6 0 211
58 179 39.6 0 179
59 187 39.6 0 187
60 170 39.6 0 170
61 171 39.6 0 171
62 191 39.6 0 191
63 161 39.6 0 161
64 155 39.6 0 155
65 126 39.6 0 126
66 133 39.6 0 133
67 111 39.6 0 111
68 111 39.6 0 111
69 104 39.6 0 104
70 103 39.6 0 103
71 80 39.6 0 80
72 76 39.6 0 76
73 60 39.6 0 60
74 57 39.6 0 57
75 52 39.6 0 52
76 44 39.6 0 44
77 33 39.6 0 33
78 39 39.6 0 39
79 37 39.6 0 37
80 25 39.6 0 25
81 27 39.6 0 27
82 34 39.6 0 34
83 32 39.6 0 32
84 45 39.6 0 45
85 54 39.6 0 54
86 800 39.6 0 800
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 57813 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.9%
C: 23.0%
G: 20.7%
T: 21.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 43599 40517.5 0 43599
4 9393 10129.4 0 9393
5 1950 2532.3 0 1950
6 246 633.1 0 246
7 25 158.3 0 25
8 26 158.3 0 26
9 26 158.3 0 26
10 23 158.3 0 23
11 26 158.3 0 26
12 21 158.3 0 21
13 31 158.3 0 31
14 35 158.3 0 35
15 40 158.3 0 40
16 38 158.3 0 38
17 29 158.3 0 29
18 31 158.3 0 31
19 52 158.3 0 52
20 33 158.3 0 33
21 45 158.3 0 45
22 27 158.3 0 27
23 30 158.3 0 30
24 22 158.3 0 22
25 34 158.3 0 34
26 43 158.3 0 43
27 43 158.3 0 43
28 30 158.3 0 30
29 34 158.3 0 34
30 35 158.3 0 35
31 33 158.3 0 33
32 38 158.3 0 38
33 17 158.3 0 17
34 24 158.3 0 24
35 25 158.3 0 25
36 29 158.3 0 29
37 20 158.3 0 20
38 23 158.3 0 23
39 33 158.3 0 33
40 25 158.3 0 25
41 31 158.3 0 31
42 23 158.3 0 23
43 24 158.3 0 24
44 37 158.3 0 37
45 31 158.3 0 31
46 19 158.3 0 19
47 42 158.3 0 42
48 26 158.3 0 26
49 37 158.3 0 37
50 33 158.3 0 33
51 41 158.3 0 41
52 41 158.3 0 41
53 25 158.3 0 25
54 31 158.3 0 31
55 36 158.3 0 36
56 26 158.3 0 26
57 34 158.3 0 34
58 39 158.3 0 39
59 45 158.3 0 45
60 35 158.3 0 35
61 28 158.3 0 28
62 33 158.3 0 33
63 23 158.3 0 23
64 34 158.3 0 34
65 40 158.3 0 40
66 34 158.3 0 34
67 39 158.3 0 39
68 28 158.3 0 28
69 48 158.3 0 48
70 33 158.3 0 33
71 34 158.3 0 34
72 21 158.3 0 21
73 34 158.3 0 34
74 36 158.3 0 36
75 27 158.3 0 27
76 29 158.3 0 29
77 65 158.3 0 65
78 36 158.3 0 36
79 29 158.3 0 29
80 30 158.3 0 30
81 35 158.3 0 35
82 36 158.3 0 36
83 42 158.3 0 42
84 35 158.3 0 35
85 42 158.3 0 42
86 52 158.3 0 52
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R42_S175_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R42_S175_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.73 s (9 µs/read; 6.43 M reads/minute).
=== Summary ===
Total reads processed: 2,648,440
Reads with adapters: 881,167 (33.3%)
== Read fate breakdown ==
Reads that were too short: 244,544 (9.2%)
Reads written (passing filters): 2,403,896 (90.8%)
Total basepairs processed: 267,492,440 bp
Total written (filtered): 189,724,538 bp (70.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 786677 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.8%
G: 27.4%
T: 28.9%
none/other: 13.9%
Overview of removed sequences
length count expect max.err error counts
3 61784 41381.9 0 61784
4 26803 10345.5 0 26803
5 14148 2586.4 0 14148
6 9688 646.6 0 9688
7 7882 161.6 0 7882
8 7064 40.4 0 7064
9 7181 40.4 0 7181
10 7167 40.4 0 7167
11 6975 40.4 0 6975
12 7028 40.4 0 7028
13 7124 40.4 0 7124
14 7051 40.4 0 7051
15 7242 40.4 0 7242
16 7240 40.4 0 7240
17 7229 40.4 0 7229
18 7238 40.4 0 7238
19 7222 40.4 0 7222
20 7165 40.4 0 7165
21 7222 40.4 0 7222
22 7051 40.4 0 7051
23 6789 40.4 0 6789
24 6996 40.4 0 6996
25 6819 40.4 0 6819
26 6842 40.4 0 6842
27 6982 40.4 0 6982
28 7147 40.4 0 7147
29 7168 40.4 0 7168
30 6979 40.4 0 6979
31 7594 40.4 0 7594
32 7207 40.4 0 7207
33 7385 40.4 0 7385
34 7508 40.4 0 7508
35 6990 40.4 0 6990
36 7169 40.4 0 7169
37 7383 40.4 0 7383
38 6404 40.4 0 6404
39 7149 40.4 0 7149
40 7146 40.4 0 7146
41 6994 40.4 0 6994
42 7116 40.4 0 7116
43 7205 40.4 0 7205
44 7056 40.4 0 7056
45 7130 40.4 0 7130
46 7295 40.4 0 7295
47 7127 40.4 0 7127
48 7021 40.4 0 7021
49 9946 40.4 0 9946
50 11737 40.4 0 11737
51 6962 40.4 0 6962
52 8084 40.4 0 8084
53 7566 40.4 0 7566
54 6469 40.4 0 6469
55 6979 40.4 0 6979
56 6935 40.4 0 6935
57 6804 40.4 0 6804
58 7297 40.4 0 7297
59 6972 40.4 0 6972
60 6857 40.4 0 6857
61 7222 40.4 0 7222
62 6769 40.4 0 6769
63 6456 40.4 0 6456
64 6646 40.4 0 6646
65 6588 40.4 0 6588
66 6476 40.4 0 6476
67 6300 40.4 0 6300
68 6527 40.4 0 6527
69 6160 40.4 0 6160
70 6114 40.4 0 6114
71 6421 40.4 0 6421
72 6219 40.4 0 6219
73 5834 40.4 0 5834
74 5626 40.4 0 5626
75 5817 40.4 0 5817
76 5632 40.4 0 5632
77 5819 40.4 0 5819
78 5856 40.4 0 5856
79 6812 40.4 0 6812
80 6461 40.4 0 6461
81 7403 40.4 0 7403
82 8621 40.4 0 8621
83 9502 40.4 0 9502
84 10207 40.4 0 10207
85 10835 40.4 0 10835
86 109641 40.4 0 109641
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35697 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.9%
C: 33.6%
G: 0.0%
T: 35.2%
none/other: 2.4%
Overview of removed sequences
length count expect max.err error counts
3 14180 41381.9 0 14180
4 3328 10345.5 0 3328
5 880 2586.4 0 880
6 415 646.6 0 415
7 396 161.6 0 396
8 413 40.4 0 413
9 386 40.4 0 386
10 368 40.4 0 368
11 363 40.4 0 363
12 353 40.4 0 353
13 314 40.4 0 314
14 302 40.4 0 302
15 310 40.4 0 310
16 250 40.4 0 250
17 265 40.4 0 265
18 273 40.4 0 273
19 299 40.4 0 299
20 255 40.4 0 255
21 275 40.4 0 275
22 250 40.4 0 250
23 277 40.4 0 277
24 274 40.4 0 274
25 262 40.4 0 262
26 238 40.4 0 238
27 224 40.4 0 224
28 229 40.4 0 229
29 267 40.4 0 267
30 257 40.4 0 257
31 219 40.4 0 219
32 240 40.4 0 240
33 262 40.4 0 262
34 269 40.4 0 269
35 232 40.4 0 232
36 262 40.4 0 262
37 272 40.4 0 272
38 232 40.4 0 232
39 249 40.4 0 249
40 235 40.4 0 235
41 252 40.4 0 252
42 274 40.4 0 274
43 248 40.4 0 248
44 230 40.4 0 230
45 235 40.4 0 235
46 248 40.4 0 248
47 214 40.4 0 214
48 222 40.4 0 222
49 232 40.4 0 232
50 209 40.4 0 209
51 217 40.4 0 217
52 194 40.4 0 194
53 215 40.4 0 215
54 230 40.4 0 230
55 202 40.4 0 202
56 212 40.4 0 212
57 187 40.4 0 187
58 190 40.4 0 190
59 191 40.4 0 191
60 206 40.4 0 206
61 165 40.4 0 165
62 166 40.4 0 166
63 157 40.4 0 157
64 168 40.4 0 168
65 138 40.4 0 138
66 136 40.4 0 136
67 128 40.4 0 128
68 96 40.4 0 96
69 104 40.4 0 104
70 74 40.4 0 74
71 86 40.4 0 86
72 81 40.4 0 81
73 77 40.4 0 77
74 65 40.4 0 65
75 52 40.4 0 52
76 39 40.4 0 39
77 44 40.4 0 44
78 38 40.4 0 38
79 33 40.4 0 33
80 26 40.4 0 26
81 19 40.4 0 19
82 30 40.4 0 30
83 44 40.4 0 44
84 49 40.4 0 49
85 45 40.4 0 45
86 854 40.4 0 854
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 58793 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 22.5%
G: 20.7%
T: 21.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44076 41381.9 0 44076
4 9728 10345.5 0 9728
5 1978 2586.4 0 1978
6 300 646.6 0 300
7 22 161.6 0 22
8 36 161.6 0 36
9 22 161.6 0 22
10 32 161.6 0 32
11 26 161.6 0 26
12 19 161.6 0 19
13 37 161.6 0 37
14 23 161.6 0 23
15 23 161.6 0 23
16 41 161.6 0 41
17 45 161.6 0 45
18 28 161.6 0 28
19 47 161.6 0 47
20 42 161.6 0 42
21 25 161.6 0 25
22 29 161.6 0 29
23 35 161.6 0 35
24 28 161.6 0 28
25 40 161.6 0 40
26 54 161.6 0 54
27 31 161.6 0 31
28 29 161.6 0 29
29 41 161.6 0 41
30 30 161.6 0 30
31 26 161.6 0 26
32 53 161.6 0 53
33 28 161.6 0 28
34 31 161.6 0 31
35 23 161.6 0 23
36 44 161.6 0 44
37 22 161.6 0 22
38 29 161.6 0 29
39 25 161.6 0 25
40 26 161.6 0 26
41 39 161.6 0 39
42 36 161.6 0 36
43 31 161.6 0 31
44 26 161.6 0 26
45 27 161.6 0 27
46 22 161.6 0 22
47 24 161.6 0 24
48 31 161.6 0 31
49 41 161.6 0 41
50 37 161.6 0 37
51 45 161.6 0 45
52 52 161.6 0 52
53 39 161.6 0 39
54 36 161.6 0 36
55 42 161.6 0 42
56 32 161.6 0 32
57 30 161.6 0 30
58 27 161.6 0 27
59 35 161.6 0 35
60 24 161.6 0 24
61 28 161.6 0 28
62 40 161.6 0 40
63 15 161.6 0 15
64 39 161.6 0 39
65 38 161.6 0 38
66 30 161.6 0 30
67 29 161.6 0 29
68 41 161.6 0 41
69 30 161.6 0 30
70 38 161.6 0 38
71 48 161.6 0 48
72 25 161.6 0 25
73 28 161.6 0 28
74 37 161.6 0 37
75 22 161.6 0 22
76 23 161.6 0 23
77 92 161.6 0 92
78 48 161.6 0 48
79 29 161.6 0 29
80 30 161.6 0 30
81 31 161.6 0 31
82 30 161.6 0 30
83 46 161.6 0 46
84 36 161.6 0 36
85 35 161.6 0 35
86 55 161.6 0 55
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R43_S177_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R43_S177_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.92 s (9 µs/read; 6.49 M reads/minute).
=== Summary ===
Total reads processed: 3,022,184
Reads with adapters: 1,073,363 (35.5%)
== Read fate breakdown ==
Reads that were too short: 283,526 (9.4%)
Reads written (passing filters): 2,738,658 (90.6%)
Total basepairs processed: 305,240,584 bp
Total written (filtered): 213,926,786 bp (70.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 980766 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.2%
G: 28.2%
T: 29.9%
none/other: 11.7%
Overview of removed sequences
length count expect max.err error counts
3 71764 47221.6 0 71764
4 32890 11805.4 0 32890
5 17780 2951.4 0 17780
6 12637 737.8 0 12637
7 10305 184.5 0 10305
8 9583 46.1 0 9583
9 9666 46.1 0 9666
10 9265 46.1 0 9265
11 9283 46.1 0 9283
12 9309 46.1 0 9309
13 9361 46.1 0 9361
14 9503 46.1 0 9503
15 9569 46.1 0 9569
16 9757 46.1 0 9757
17 9265 46.1 0 9265
18 9308 46.1 0 9308
19 9412 46.1 0 9412
20 9277 46.1 0 9277
21 9461 46.1 0 9461
22 9265 46.1 0 9265
23 8950 46.1 0 8950
24 9174 46.1 0 9174
25 9024 46.1 0 9024
26 9064 46.1 0 9064
27 9283 46.1 0 9283
28 9382 46.1 0 9382
29 9278 46.1 0 9278
30 9768 46.1 0 9768
31 10830 46.1 0 10830
32 9731 46.1 0 9731
33 10488 46.1 0 10488
34 10386 46.1 0 10386
35 9297 46.1 0 9297
36 9491 46.1 0 9491
37 10280 46.1 0 10280
38 9178 46.1 0 9178
39 9281 46.1 0 9281
40 9397 46.1 0 9397
41 9396 46.1 0 9396
42 9462 46.1 0 9462
43 10138 46.1 0 10138
44 9227 46.1 0 9227
45 9260 46.1 0 9260
46 9786 46.1 0 9786
47 9399 46.1 0 9399
48 8991 46.1 0 8991
49 11906 46.1 0 11906
50 13287 46.1 0 13287
51 8859 46.1 0 8859
52 9283 46.1 0 9283
53 9342 46.1 0 9342
54 8357 46.1 0 8357
55 8896 46.1 0 8896
56 8950 46.1 0 8950
57 8670 46.1 0 8670
58 9139 46.1 0 9139
59 8663 46.1 0 8663
60 8821 46.1 0 8821
61 9323 46.1 0 9323
62 8510 46.1 0 8510
63 8254 46.1 0 8254
64 8426 46.1 0 8426
65 8588 46.1 0 8588
66 8033 46.1 0 8033
67 7810 46.1 0 7810
68 7825 46.1 0 7825
69 7411 46.1 0 7411
70 6926 46.1 0 6926
71 7425 46.1 0 7425
72 7216 46.1 0 7216
73 7042 46.1 0 7042
74 6503 46.1 0 6503
75 6701 46.1 0 6701
76 6744 46.1 0 6744
77 6665 46.1 0 6665
78 7306 46.1 0 7306
79 8789 46.1 0 8789
80 8332 46.1 0 8332
81 9661 46.1 0 9661
82 12122 46.1 0 12122
83 12870 46.1 0 12870
84 14362 46.1 0 14362
85 14639 46.1 0 14639
86 114509 46.1 0 114509
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29567 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.9%
C: 30.0%
G: 0.0%
T: 36.7%
none/other: 3.5%
Overview of removed sequences
length count expect max.err error counts
3 13571 47221.6 0 13571
4 3189 11805.4 0 3189
5 815 2951.4 0 815
6 353 737.8 0 353
7 264 184.5 0 264
8 224 46.1 0 224
9 248 46.1 0 248
10 202 46.1 0 202
11 195 46.1 0 195
12 172 46.1 0 172
13 170 46.1 0 170
14 199 46.1 0 199
15 158 46.1 0 158
16 175 46.1 0 175
17 178 46.1 0 178
18 199 46.1 0 199
19 163 46.1 0 163
20 161 46.1 0 161
21 169 46.1 0 169
22 177 46.1 0 177
23 162 46.1 0 162
24 190 46.1 0 190
25 185 46.1 0 185
26 177 46.1 0 177
27 162 46.1 0 162
28 200 46.1 0 200
29 152 46.1 0 152
30 165 46.1 0 165
31 180 46.1 0 180
32 145 46.1 0 145
33 170 46.1 0 170
34 166 46.1 0 166
35 160 46.1 0 160
36 145 46.1 0 145
37 161 46.1 0 161
38 168 46.1 0 168
39 151 46.1 0 151
40 178 46.1 0 178
41 167 46.1 0 167
42 171 46.1 0 171
43 191 46.1 0 191
44 150 46.1 0 150
45 151 46.1 0 151
46 175 46.1 0 175
47 149 46.1 0 149
48 140 46.1 0 140
49 144 46.1 0 144
50 154 46.1 0 154
51 155 46.1 0 155
52 140 46.1 0 140
53 162 46.1 0 162
54 116 46.1 0 116
55 116 46.1 0 116
56 123 46.1 0 123
57 124 46.1 0 124
58 149 46.1 0 149
59 132 46.1 0 132
60 129 46.1 0 129
61 136 46.1 0 136
62 123 46.1 0 123
63 114 46.1 0 114
64 102 46.1 0 102
65 99 46.1 0 99
66 101 46.1 0 101
67 96 46.1 0 96
68 81 46.1 0 81
69 65 46.1 0 65
70 61 46.1 0 61
71 60 46.1 0 60
72 51 46.1 0 51
73 71 46.1 0 71
74 41 46.1 0 41
75 51 46.1 0 51
76 43 46.1 0 43
77 23 46.1 0 23
78 35 46.1 0 35
79 43 46.1 0 43
80 35 46.1 0 35
81 41 46.1 0 41
82 37 46.1 0 37
83 27 46.1 0 27
84 41 46.1 0 41
85 36 46.1 0 36
86 1017 46.1 0 1017
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 63030 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.4%
C: 23.2%
G: 20.5%
T: 19.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47280 47221.6 0 47280
4 10476 11805.4 0 10476
5 1999 2951.4 0 1999
6 227 737.8 0 227
7 44 184.5 0 44
8 37 184.5 0 37
9 48 184.5 0 48
10 32 184.5 0 32
11 38 184.5 0 38
12 44 184.5 0 44
13 47 184.5 0 47
14 39 184.5 0 39
15 33 184.5 0 33
16 55 184.5 0 55
17 45 184.5 0 45
18 43 184.5 0 43
19 60 184.5 0 60
20 53 184.5 0 53
21 32 184.5 0 32
22 54 184.5 0 54
23 44 184.5 0 44
24 35 184.5 0 35
25 69 184.5 0 69
26 47 184.5 0 47
27 48 184.5 0 48
28 38 184.5 0 38
29 32 184.5 0 32
30 45 184.5 0 45
31 38 184.5 0 38
32 40 184.5 0 40
33 45 184.5 0 45
34 32 184.5 0 32
35 31 184.5 0 31
36 36 184.5 0 36
37 33 184.5 0 33
38 44 184.5 0 44
39 39 184.5 0 39
40 35 184.5 0 35
41 39 184.5 0 39
42 50 184.5 0 50
43 31 184.5 0 31
44 37 184.5 0 37
45 35 184.5 0 35
46 34 184.5 0 34
47 25 184.5 0 25
48 40 184.5 0 40
49 37 184.5 0 37
50 35 184.5 0 35
51 40 184.5 0 40
52 37 184.5 0 37
53 36 184.5 0 36
54 45 184.5 0 45
55 35 184.5 0 35
56 27 184.5 0 27
57 42 184.5 0 42
58 33 184.5 0 33
59 41 184.5 0 41
60 22 184.5 0 22
61 31 184.5 0 31
62 33 184.5 0 33
63 29 184.5 0 29
64 19 184.5 0 19
65 35 184.5 0 35
66 32 184.5 0 32
67 39 184.5 0 39
68 40 184.5 0 40
69 33 184.5 0 33
70 29 184.5 0 29
71 37 184.5 0 37
72 27 184.5 0 27
73 27 184.5 0 27
74 33 184.5 0 33
75 35 184.5 0 35
76 24 184.5 0 24
77 65 184.5 0 65
78 36 184.5 0 36
79 24 184.5 0 24
80 26 184.5 0 26
81 41 184.5 0 41
82 32 184.5 0 32
83 36 184.5 0 36
84 41 184.5 0 41
85 48 184.5 0 48
86 40 184.5 0 40
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R43_S177_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R43_S177_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.01 s (9 µs/read; 6.55 M reads/minute).
=== Summary ===
Total reads processed: 3,059,986
Reads with adapters: 1,100,563 (36.0%)
== Read fate breakdown ==
Reads that were too short: 296,301 (9.7%)
Reads written (passing filters): 2,763,685 (90.3%)
Total basepairs processed: 309,058,586 bp
Total written (filtered): 215,581,843 bp (69.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1006139 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.2%
G: 28.1%
T: 29.7%
none/other: 12.0%
Overview of removed sequences
length count expect max.err error counts
3 72310 47812.3 0 72310
4 32999 11953.1 0 32999
5 17772 2988.3 0 17772
6 12778 747.1 0 12778
7 10477 186.8 0 10477
8 9608 46.7 0 9608
9 9809 46.7 0 9809
10 9541 46.7 0 9541
11 9689 46.7 0 9689
12 9428 46.7 0 9428
13 9347 46.7 0 9347
14 9358 46.7 0 9358
15 9611 46.7 0 9611
16 9811 46.7 0 9811
17 9588 46.7 0 9588
18 9574 46.7 0 9574
19 9710 46.7 0 9710
20 9428 46.7 0 9428
21 9595 46.7 0 9595
22 9651 46.7 0 9651
23 9036 46.7 0 9036
24 9207 46.7 0 9207
25 9071 46.7 0 9071
26 9127 46.7 0 9127
27 9413 46.7 0 9413
28 9514 46.7 0 9514
29 9315 46.7 0 9315
30 9840 46.7 0 9840
31 11338 46.7 0 11338
32 9948 46.7 0 9948
33 10675 46.7 0 10675
34 10757 46.7 0 10757
35 9565 46.7 0 9565
36 9848 46.7 0 9848
37 10709 46.7 0 10709
38 9319 46.7 0 9319
39 9374 46.7 0 9374
40 9538 46.7 0 9538
41 9493 46.7 0 9493
42 9942 46.7 0 9942
43 10026 46.7 0 10026
44 9358 46.7 0 9358
45 9361 46.7 0 9361
46 9925 46.7 0 9925
47 9797 46.7 0 9797
48 9119 46.7 0 9119
49 12154 46.7 0 12154
50 13671 46.7 0 13671
51 9033 46.7 0 9033
52 9557 46.7 0 9557
53 9596 46.7 0 9596
54 8625 46.7 0 8625
55 9123 46.7 0 9123
56 9196 46.7 0 9196
57 8757 46.7 0 8757
58 9480 46.7 0 9480
59 9097 46.7 0 9097
60 8808 46.7 0 8808
61 9444 46.7 0 9444
62 8976 46.7 0 8976
63 8704 46.7 0 8704
64 8737 46.7 0 8737
65 8544 46.7 0 8544
66 8326 46.7 0 8326
67 7964 46.7 0 7964
68 8089 46.7 0 8089
69 7719 46.7 0 7719
70 7351 46.7 0 7351
71 7735 46.7 0 7735
72 7547 46.7 0 7547
73 7310 46.7 0 7310
74 6872 46.7 0 6872
75 7060 46.7 0 7060
76 7110 46.7 0 7110
77 6837 46.7 0 6837
78 7786 46.7 0 7786
79 8981 46.7 0 8981
80 8661 46.7 0 8661
81 10277 46.7 0 10277
82 12434 46.7 0 12434
83 13143 46.7 0 13143
84 14660 46.7 0 14660
85 15311 46.7 0 15311
86 120765 46.7 0 120765
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30481 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.3%
C: 30.9%
G: 0.0%
T: 36.5%
none/other: 3.3%
Overview of removed sequences
length count expect max.err error counts
3 13622 47812.3 0 13622
4 3264 11953.1 0 3264
5 899 2988.3 0 899
6 322 747.1 0 322
7 277 186.8 0 277
8 258 46.7 0 258
9 240 46.7 0 240
10 236 46.7 0 236
11 228 46.7 0 228
12 204 46.7 0 204
13 193 46.7 0 193
14 208 46.7 0 208
15 171 46.7 0 171
16 172 46.7 0 172
17 207 46.7 0 207
18 186 46.7 0 186
19 201 46.7 0 201
20 192 46.7 0 192
21 218 46.7 0 218
22 185 46.7 0 185
23 185 46.7 0 185
24 209 46.7 0 209
25 191 46.7 0 191
26 183 46.7 0 183
27 168 46.7 0 168
28 197 46.7 0 197
29 154 46.7 0 154
30 187 46.7 0 187
31 218 46.7 0 218
32 167 46.7 0 167
33 177 46.7 0 177
34 195 46.7 0 195
35 190 46.7 0 190
36 164 46.7 0 164
37 157 46.7 0 157
38 192 46.7 0 192
39 176 46.7 0 176
40 180 46.7 0 180
41 160 46.7 0 160
42 197 46.7 0 197
43 170 46.7 0 170
44 173 46.7 0 173
45 163 46.7 0 163
46 193 46.7 0 193
47 167 46.7 0 167
48 185 46.7 0 185
49 151 46.7 0 151
50 164 46.7 0 164
51 142 46.7 0 142
52 135 46.7 0 135
53 154 46.7 0 154
54 149 46.7 0 149
55 124 46.7 0 124
56 156 46.7 0 156
57 139 46.7 0 139
58 144 46.7 0 144
59 138 46.7 0 138
60 143 46.7 0 143
61 122 46.7 0 122
62 129 46.7 0 129
63 94 46.7 0 94
64 90 46.7 0 90
65 94 46.7 0 94
66 93 46.7 0 93
67 91 46.7 0 91
68 94 46.7 0 94
69 83 46.7 0 83
70 79 46.7 0 79
71 62 46.7 0 62
72 61 46.7 0 61
73 58 46.7 0 58
74 52 46.7 0 52
75 35 46.7 0 35
76 26 46.7 0 26
77 38 46.7 0 38
78 31 46.7 0 31
79 31 46.7 0 31
80 32 46.7 0 32
81 34 46.7 0 34
82 27 46.7 0 27
83 32 46.7 0 32
84 37 46.7 0 37
85 38 46.7 0 38
86 998 46.7 0 998
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 63943 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.1%
C: 23.2%
G: 20.9%
T: 19.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47813 47812.3 0 47813
4 10795 11953.1 0 10795
5 2064 2988.3 0 2064
6 235 747.1 0 235
7 30 186.8 0 30
8 39 186.8 0 39
9 41 186.8 0 41
10 47 186.8 0 47
11 42 186.8 0 42
12 38 186.8 0 38
13 58 186.8 0 58
14 56 186.8 0 56
15 36 186.8 0 36
16 45 186.8 0 45
17 41 186.8 0 41
18 34 186.8 0 34
19 56 186.8 0 56
20 45 186.8 0 45
21 54 186.8 0 54
22 49 186.8 0 49
23 39 186.8 0 39
24 34 186.8 0 34
25 56 186.8 0 56
26 33 186.8 0 33
27 41 186.8 0 41
28 52 186.8 0 52
29 29 186.8 0 29
30 47 186.8 0 47
31 31 186.8 0 31
32 33 186.8 0 33
33 33 186.8 0 33
34 34 186.8 0 34
35 37 186.8 0 37
36 39 186.8 0 39
37 39 186.8 0 39
38 35 186.8 0 35
39 35 186.8 0 35
40 31 186.8 0 31
41 41 186.8 0 41
42 36 186.8 0 36
43 26 186.8 0 26
44 39 186.8 0 39
45 34 186.8 0 34
46 39 186.8 0 39
47 33 186.8 0 33
48 31 186.8 0 31
49 43 186.8 0 43
50 22 186.8 0 22
51 54 186.8 0 54
52 45 186.8 0 45
53 45 186.8 0 45
54 44 186.8 0 44
55 33 186.8 0 33
56 19 186.8 0 19
57 41 186.8 0 41
58 36 186.8 0 36
59 31 186.8 0 31
60 24 186.8 0 24
61 33 186.8 0 33
62 37 186.8 0 37
63 28 186.8 0 28
64 27 186.8 0 27
65 29 186.8 0 29
66 27 186.8 0 27
67 18 186.8 0 18
68 35 186.8 0 35
69 33 186.8 0 33
70 42 186.8 0 42
71 30 186.8 0 30
72 34 186.8 0 34
73 29 186.8 0 29
74 33 186.8 0 33
75 25 186.8 0 25
76 25 186.8 0 25
77 61 186.8 0 61
78 47 186.8 0 47
79 23 186.8 0 23
80 31 186.8 0 31
81 49 186.8 0 49
82 45 186.8 0 45
83 47 186.8 0 47
84 40 186.8 0 40
85 47 186.8 0 47
86 56 186.8 0 56
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R46_S178_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R46_S178_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 36.72 s (10 µs/read; 5.86 M reads/minute).
=== Summary ===
Total reads processed: 3,583,970
Reads with adapters: 1,344,263 (37.5%)
== Read fate breakdown ==
Reads that were too short: 429,910 (12.0%)
Reads written (passing filters): 3,154,060 (88.0%)
Total basepairs processed: 361,980,970 bp
Total written (filtered): 245,685,078 bp (67.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1215010 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.5%
G: 26.2%
T: 28.3%
none/other: 17.0%
Overview of removed sequences
length count expect max.err error counts
3 85433 55999.5 0 85433
4 37366 13999.9 0 37366
5 19968 3500.0 0 19968
6 13779 875.0 0 13779
7 11186 218.7 0 11186
8 9989 54.7 0 9989
9 10053 54.7 0 10053
10 10003 54.7 0 10003
11 9798 54.7 0 9798
12 9949 54.7 0 9949
13 9835 54.7 0 9835
14 9970 54.7 0 9970
15 10126 54.7 0 10126
16 10258 54.7 0 10258
17 10489 54.7 0 10489
18 10460 54.7 0 10460
19 10375 54.7 0 10375
20 9852 54.7 0 9852
21 10485 54.7 0 10485
22 10141 54.7 0 10141
23 9872 54.7 0 9872
24 9990 54.7 0 9990
25 9979 54.7 0 9979
26 9641 54.7 0 9641
27 9751 54.7 0 9751
28 10032 54.7 0 10032
29 10052 54.7 0 10052
30 10027 54.7 0 10027
31 10279 54.7 0 10279
32 10122 54.7 0 10122
33 10203 54.7 0 10203
34 10178 54.7 0 10178
35 10134 54.7 0 10134
36 9967 54.7 0 9967
37 10120 54.7 0 10120
38 9928 54.7 0 9928
39 10334 54.7 0 10334
40 10371 54.7 0 10371
41 10349 54.7 0 10349
42 10642 54.7 0 10642
43 11429 54.7 0 11429
44 10822 54.7 0 10822
45 10930 54.7 0 10930
46 11479 54.7 0 11479
47 11453 54.7 0 11453
48 10879 54.7 0 10879
49 13219 54.7 0 13219
50 13920 54.7 0 13920
51 11332 54.7 0 11332
52 11501 54.7 0 11501
53 11102 54.7 0 11102
54 10476 54.7 0 10476
55 11268 54.7 0 11268
56 10951 54.7 0 10951
57 11003 54.7 0 11003
58 11141 54.7 0 11141
59 10986 54.7 0 10986
60 11134 54.7 0 11134
61 11052 54.7 0 11052
62 10877 54.7 0 10877
63 10507 54.7 0 10507
64 10595 54.7 0 10595
65 10412 54.7 0 10412
66 10193 54.7 0 10193
67 9854 54.7 0 9854
68 9696 54.7 0 9696
69 9378 54.7 0 9378
70 8880 54.7 0 8880
71 8766 54.7 0 8766
72 8803 54.7 0 8803
73 8182 54.7 0 8182
74 7626 54.7 0 7626
75 8090 54.7 0 8090
76 7711 54.7 0 7711
77 7902 54.7 0 7902
78 8732 54.7 0 8732
79 9845 54.7 0 9845
80 10842 54.7 0 10842
81 12585 54.7 0 12585
82 16219 54.7 0 16219
83 19301 54.7 0 19301
84 22223 54.7 0 22223
85 24111 54.7 0 24111
86 206117 54.7 0 206117
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 58927 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.6%
C: 33.4%
G: 0.0%
T: 37.9%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 16557 55999.5 0 16557
4 4103 13999.9 0 4103
5 1445 3500.0 0 1445
6 893 875.0 0 893
7 807 218.7 0 807
8 772 54.7 0 772
9 717 54.7 0 717
10 652 54.7 0 652
11 713 54.7 0 713
12 675 54.7 0 675
13 647 54.7 0 647
14 662 54.7 0 662
15 607 54.7 0 607
16 583 54.7 0 583
17 590 54.7 0 590
18 639 54.7 0 639
19 584 54.7 0 584
20 585 54.7 0 585
21 565 54.7 0 565
22 561 54.7 0 561
23 521 54.7 0 521
24 567 54.7 0 567
25 607 54.7 0 607
26 561 54.7 0 561
27 576 54.7 0 576
28 553 54.7 0 553
29 555 54.7 0 555
30 588 54.7 0 588
31 525 54.7 0 525
32 572 54.7 0 572
33 544 54.7 0 544
34 557 54.7 0 557
35 568 54.7 0 568
36 542 54.7 0 542
37 535 54.7 0 535
38 542 54.7 0 542
39 472 54.7 0 472
40 474 54.7 0 474
41 497 54.7 0 497
42 488 54.7 0 488
43 505 54.7 0 505
44 518 54.7 0 518
45 502 54.7 0 502
46 502 54.7 0 502
47 519 54.7 0 519
48 530 54.7 0 530
49 461 54.7 0 461
50 429 54.7 0 429
51 498 54.7 0 498
52 446 54.7 0 446
53 485 54.7 0 485
54 472 54.7 0 472
55 464 54.7 0 464
56 453 54.7 0 453
57 476 54.7 0 476
58 428 54.7 0 428
59 413 54.7 0 413
60 394 54.7 0 394
61 392 54.7 0 392
62 332 54.7 0 332
63 337 54.7 0 337
64 295 54.7 0 295
65 302 54.7 0 302
66 291 54.7 0 291
67 273 54.7 0 273
68 251 54.7 0 251
69 190 54.7 0 190
70 194 54.7 0 194
71 176 54.7 0 176
72 165 54.7 0 165
73 167 54.7 0 167
74 141 54.7 0 141
75 132 54.7 0 132
76 82 54.7 0 82
77 108 54.7 0 108
78 91 54.7 0 91
79 80 54.7 0 80
80 72 54.7 0 72
81 58 54.7 0 58
82 46 54.7 0 46
83 61 54.7 0 61
84 59 54.7 0 59
85 69 54.7 0 69
86 1867 54.7 0 1867
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 70326 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.5%
C: 22.9%
G: 20.4%
T: 21.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51999 55999.5 0 51999
4 11978 13999.9 0 11978
5 2325 3500.0 0 2325
6 320 875.0 0 320
7 40 218.7 0 40
8 44 218.7 0 44
9 31 218.7 0 31
10 52 218.7 0 52
11 65 218.7 0 65
12 49 218.7 0 49
13 45 218.7 0 45
14 91 218.7 0 91
15 51 218.7 0 51
16 77 218.7 0 77
17 67 218.7 0 67
18 45 218.7 0 45
19 93 218.7 0 93
20 83 218.7 0 83
21 68 218.7 0 68
22 85 218.7 0 85
23 66 218.7 0 66
24 70 218.7 0 70
25 123 218.7 0 123
26 55 218.7 0 55
27 54 218.7 0 54
28 61 218.7 0 61
29 38 218.7 0 38
30 43 218.7 0 43
31 48 218.7 0 48
32 54 218.7 0 54
33 40 218.7 0 40
34 54 218.7 0 54
35 34 218.7 0 34
36 44 218.7 0 44
37 39 218.7 0 39
38 40 218.7 0 40
39 39 218.7 0 39
40 38 218.7 0 38
41 40 218.7 0 40
42 34 218.7 0 34
43 44 218.7 0 44
44 42 218.7 0 42
45 38 218.7 0 38
46 28 218.7 0 28
47 32 218.7 0 32
48 43 218.7 0 43
49 78 218.7 0 78
50 26 218.7 0 26
51 41 218.7 0 41
52 48 218.7 0 48
53 40 218.7 0 40
54 38 218.7 0 38
55 47 218.7 0 47
56 30 218.7 0 30
57 27 218.7 0 27
58 29 218.7 0 29
59 46 218.7 0 46
60 45 218.7 0 45
61 41 218.7 0 41
62 33 218.7 0 33
63 39 218.7 0 39
64 29 218.7 0 29
65 30 218.7 0 30
66 45 218.7 0 45
67 21 218.7 0 21
68 34 218.7 0 34
69 38 218.7 0 38
70 35 218.7 0 35
71 30 218.7 0 30
72 43 218.7 0 43
73 44 218.7 0 44
74 44 218.7 0 44
75 35 218.7 0 35
76 29 218.7 0 29
77 71 218.7 0 71
78 49 218.7 0 49
79 29 218.7 0 29
80 31 218.7 0 31
81 43 218.7 0 43
82 44 218.7 0 44
83 35 218.7 0 35
84 33 218.7 0 33
85 33 218.7 0 33
86 44 218.7 0 44
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R46_S178_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R46_S178_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.51 s (8 µs/read; 7.68 M reads/minute).
=== Summary ===
Total reads processed: 3,647,225
Reads with adapters: 1,379,931 (37.8%)
== Read fate breakdown ==
Reads that were too short: 449,499 (12.3%)
Reads written (passing filters): 3,197,726 (87.7%)
Total basepairs processed: 368,369,725 bp
Total written (filtered): 248,858,888 bp (67.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1248475 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.5%
G: 26.1%
T: 28.1%
none/other: 17.3%
Overview of removed sequences
length count expect max.err error counts
3 85924 56987.9 0 85924
4 38125 14247.0 0 38125
5 20336 3561.7 0 20336
6 13700 890.4 0 13700
7 11190 222.6 0 11190
8 10030 55.7 0 10030
9 10216 55.7 0 10216
10 10178 55.7 0 10178
11 10002 55.7 0 10002
12 9972 55.7 0 9972
13 9950 55.7 0 9950
14 10191 55.7 0 10191
15 10220 55.7 0 10220
16 10357 55.7 0 10357
17 10337 55.7 0 10337
18 10559 55.7 0 10559
19 10533 55.7 0 10533
20 10131 55.7 0 10131
21 10731 55.7 0 10731
22 10542 55.7 0 10542
23 10100 55.7 0 10100
24 9865 55.7 0 9865
25 10009 55.7 0 10009
26 9873 55.7 0 9873
27 9893 55.7 0 9893
28 10223 55.7 0 10223
29 10341 55.7 0 10341
30 10218 55.7 0 10218
31 10475 55.7 0 10475
32 10151 55.7 0 10151
33 10290 55.7 0 10290
34 10583 55.7 0 10583
35 10294 55.7 0 10294
36 10196 55.7 0 10196
37 10394 55.7 0 10394
38 10128 55.7 0 10128
39 10285 55.7 0 10285
40 10636 55.7 0 10636
41 10789 55.7 0 10789
42 10690 55.7 0 10690
43 11842 55.7 0 11842
44 11196 55.7 0 11196
45 11395 55.7 0 11395
46 11436 55.7 0 11436
47 11852 55.7 0 11852
48 10867 55.7 0 10867
49 13585 55.7 0 13585
50 14133 55.7 0 14133
51 11473 55.7 0 11473
52 11710 55.7 0 11710
53 11198 55.7 0 11198
54 10910 55.7 0 10910
55 11573 55.7 0 11573
56 11202 55.7 0 11202
57 11070 55.7 0 11070
58 11441 55.7 0 11441
59 11233 55.7 0 11233
60 11505 55.7 0 11505
61 11394 55.7 0 11394
62 11341 55.7 0 11341
63 11068 55.7 0 11068
64 10857 55.7 0 10857
65 10735 55.7 0 10735
66 10487 55.7 0 10487
67 10332 55.7 0 10332
68 9933 55.7 0 9933
69 9580 55.7 0 9580
70 9320 55.7 0 9320
71 9249 55.7 0 9249
72 9415 55.7 0 9415
73 8350 55.7 0 8350
74 8186 55.7 0 8186
75 8229 55.7 0 8229
76 7996 55.7 0 7996
77 8165 55.7 0 8165
78 9195 55.7 0 9195
79 10539 55.7 0 10539
80 11243 55.7 0 11243
81 13371 55.7 0 13371
82 16671 55.7 0 16671
83 20027 55.7 0 20027
84 23261 55.7 0 23261
85 25091 55.7 0 25091
86 216162 55.7 0 216162
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 60369 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.8%
C: 33.7%
G: 0.0%
T: 37.3%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 16645 56987.9 0 16645
4 4286 14247.0 0 4286
5 1398 3561.7 0 1398
6 875 890.4 0 875
7 740 222.6 0 740
8 822 55.7 0 822
9 757 55.7 0 757
10 752 55.7 0 752
11 710 55.7 0 710
12 694 55.7 0 694
13 652 55.7 0 652
14 630 55.7 0 630
15 655 55.7 0 655
16 648 55.7 0 648
17 570 55.7 0 570
18 641 55.7 0 641
19 584 55.7 0 584
20 601 55.7 0 601
21 591 55.7 0 591
22 620 55.7 0 620
23 582 55.7 0 582
24 581 55.7 0 581
25 611 55.7 0 611
26 604 55.7 0 604
27 581 55.7 0 581
28 633 55.7 0 633
29 582 55.7 0 582
30 565 55.7 0 565
31 593 55.7 0 593
32 540 55.7 0 540
33 597 55.7 0 597
34 629 55.7 0 629
35 565 55.7 0 565
36 517 55.7 0 517
37 573 55.7 0 573
38 517 55.7 0 517
39 540 55.7 0 540
40 540 55.7 0 540
41 510 55.7 0 510
42 553 55.7 0 553
43 525 55.7 0 525
44 533 55.7 0 533
45 553 55.7 0 553
46 524 55.7 0 524
47 509 55.7 0 509
48 509 55.7 0 509
49 510 55.7 0 510
50 502 55.7 0 502
51 493 55.7 0 493
52 474 55.7 0 474
53 463 55.7 0 463
54 490 55.7 0 490
55 478 55.7 0 478
56 438 55.7 0 438
57 448 55.7 0 448
58 412 55.7 0 412
59 438 55.7 0 438
60 406 55.7 0 406
61 396 55.7 0 396
62 357 55.7 0 357
63 325 55.7 0 325
64 321 55.7 0 321
65 303 55.7 0 303
66 290 55.7 0 290
67 248 55.7 0 248
68 229 55.7 0 229
69 243 55.7 0 243
70 210 55.7 0 210
71 176 55.7 0 176
72 217 55.7 0 217
73 161 55.7 0 161
74 142 55.7 0 142
75 118 55.7 0 118
76 96 55.7 0 96
77 67 55.7 0 67
78 79 55.7 0 79
79 87 55.7 0 87
80 56 55.7 0 56
81 78 55.7 0 78
82 52 55.7 0 52
83 63 55.7 0 63
84 62 55.7 0 62
85 68 55.7 0 68
86 1936 55.7 0 1936
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 71087 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 22.8%
G: 20.8%
T: 21.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 52425 56987.9 0 52425
4 12186 14247.0 0 12186
5 2283 3561.7 0 2283
6 338 890.4 0 338
7 52 222.6 0 52
8 55 222.6 0 55
9 43 222.6 0 43
10 58 222.6 0 58
11 73 222.6 0 73
12 44 222.6 0 44
13 69 222.6 0 69
14 61 222.6 0 61
15 45 222.6 0 45
16 72 222.6 0 72
17 70 222.6 0 70
18 36 222.6 0 36
19 85 222.6 0 85
20 64 222.6 0 64
21 67 222.6 0 67
22 86 222.6 0 86
23 53 222.6 0 53
24 72 222.6 0 72
25 95 222.6 0 95
26 66 222.6 0 66
27 40 222.6 0 40
28 66 222.6 0 66
29 39 222.6 0 39
30 56 222.6 0 56
31 49 222.6 0 49
32 42 222.6 0 42
33 45 222.6 0 45
34 35 222.6 0 35
35 36 222.6 0 36
36 54 222.6 0 54
37 43 222.6 0 43
38 37 222.6 0 37
39 37 222.6 0 37
40 43 222.6 0 43
41 41 222.6 0 41
42 33 222.6 0 33
43 41 222.6 0 41
44 46 222.6 0 46
45 60 222.6 0 60
46 53 222.6 0 53
47 32 222.6 0 32
48 32 222.6 0 32
49 68 222.6 0 68
50 44 222.6 0 44
51 51 222.6 0 51
52 44 222.6 0 44
53 36 222.6 0 36
54 42 222.6 0 42
55 59 222.6 0 59
56 41 222.6 0 41
57 45 222.6 0 45
58 39 222.6 0 39
59 44 222.6 0 44
60 48 222.6 0 48
61 54 222.6 0 54
62 43 222.6 0 43
63 43 222.6 0 43
64 30 222.6 0 30
65 53 222.6 0 53
66 49 222.6 0 49
67 33 222.6 0 33
68 38 222.6 0 38
69 34 222.6 0 34
70 32 222.6 0 32
71 37 222.6 0 37
72 32 222.6 0 32
73 40 222.6 0 40
74 20 222.6 0 20
75 34 222.6 0 34
76 42 222.6 0 42
77 64 222.6 0 64
78 54 222.6 0 54
79 24 222.6 0 24
80 47 222.6 0 47
81 58 222.6 0 58
82 22 222.6 0 22
83 39 222.6 0 39
84 47 222.6 0 47
85 38 222.6 0 38
86 61 222.6 0 61
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R47_S179_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R47_S179_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.30 s (10 µs/read; 5.88 M reads/minute).
=== Summary ===
Total reads processed: 2,481,966
Reads with adapters: 858,654 (34.6%)
== Read fate breakdown ==
Reads that were too short: 216,210 (8.7%)
Reads written (passing filters): 2,265,756 (91.3%)
Total basepairs processed: 250,678,566 bp
Total written (filtered): 177,280,941 bp (70.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 776031 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.7%
G: 28.1%
T: 30.4%
none/other: 10.7%
Overview of removed sequences
length count expect max.err error counts
3 57503 38780.7 0 57503
4 25822 9695.2 0 25822
5 14104 2423.8 0 14104
6 10117 605.9 0 10117
7 8561 151.5 0 8561
8 7471 37.9 0 7471
9 7653 37.9 0 7653
10 7818 37.9 0 7818
11 7511 37.9 0 7511
12 7675 37.9 0 7675
13 7652 37.9 0 7652
14 7693 37.9 0 7693
15 7748 37.9 0 7748
16 7796 37.9 0 7796
17 7586 37.9 0 7586
18 7771 37.9 0 7771
19 7578 37.9 0 7578
20 7508 37.9 0 7508
21 7636 37.9 0 7636
22 7598 37.9 0 7598
23 7276 37.9 0 7276
24 7272 37.9 0 7272
25 7149 37.9 0 7149
26 7217 37.9 0 7217
27 7200 37.9 0 7200
28 7551 37.9 0 7551
29 7599 37.9 0 7599
30 7326 37.9 0 7326
31 7623 37.9 0 7623
32 7638 37.9 0 7638
33 8032 37.9 0 8032
34 7662 37.9 0 7662
35 7447 37.9 0 7447
36 7476 37.9 0 7476
37 7719 37.9 0 7719
38 7104 37.9 0 7104
39 7484 37.9 0 7484
40 7510 37.9 0 7510
41 7407 37.9 0 7407
42 7658 37.9 0 7658
43 8076 37.9 0 8076
44 7582 37.9 0 7582
45 7825 37.9 0 7825
46 8249 37.9 0 8249
47 8123 37.9 0 8123
48 7410 37.9 0 7410
49 9875 37.9 0 9875
50 10898 37.9 0 10898
51 7379 37.9 0 7379
52 7563 37.9 0 7563
53 7517 37.9 0 7517
54 6694 37.9 0 6694
55 7229 37.9 0 7229
56 7036 37.9 0 7036
57 6906 37.9 0 6906
58 7569 37.9 0 7569
59 7172 37.9 0 7172
60 7118 37.9 0 7118
61 7429 37.9 0 7429
62 7085 37.9 0 7085
63 6707 37.9 0 6707
64 6941 37.9 0 6941
65 6965 37.9 0 6965
66 6504 37.9 0 6504
67 6612 37.9 0 6612
68 6544 37.9 0 6544
69 6132 37.9 0 6132
70 6014 37.9 0 6014
71 6221 37.9 0 6221
72 6009 37.9 0 6009
73 5785 37.9 0 5785
74 5577 37.9 0 5577
75 5516 37.9 0 5516
76 5469 37.9 0 5469
77 5437 37.9 0 5437
78 5744 37.9 0 5744
79 6698 37.9 0 6698
80 6397 37.9 0 6397
81 7278 37.9 0 7278
82 8849 37.9 0 8849
83 9334 37.9 0 9334
84 10351 37.9 0 10351
85 10768 37.9 0 10768
86 83293 37.9 0 83293
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 31544 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.5%
C: 34.5%
G: 0.0%
T: 35.9%
none/other: 2.1%
Overview of removed sequences
length count expect max.err error counts
3 12987 38780.7 0 12987
4 3198 9695.2 0 3198
5 832 2423.8 0 832
6 372 605.9 0 372
7 306 151.5 0 306
8 266 37.9 0 266
9 258 37.9 0 258
10 271 37.9 0 271
11 303 37.9 0 303
12 253 37.9 0 253
13 265 37.9 0 265
14 268 37.9 0 268
15 244 37.9 0 244
16 242 37.9 0 242
17 231 37.9 0 231
18 219 37.9 0 219
19 255 37.9 0 255
20 213 37.9 0 213
21 230 37.9 0 230
22 247 37.9 0 247
23 243 37.9 0 243
24 219 37.9 0 219
25 250 37.9 0 250
26 228 37.9 0 228
27 223 37.9 0 223
28 229 37.9 0 229
29 215 37.9 0 215
30 224 37.9 0 224
31 217 37.9 0 217
32 199 37.9 0 199
33 240 37.9 0 240
34 224 37.9 0 224
35 198 37.9 0 198
36 223 37.9 0 223
37 207 37.9 0 207
38 225 37.9 0 225
39 200 37.9 0 200
40 255 37.9 0 255
41 240 37.9 0 240
42 207 37.9 0 207
43 225 37.9 0 225
44 236 37.9 0 236
45 211 37.9 0 211
46 241 37.9 0 241
47 218 37.9 0 218
48 173 37.9 0 173
49 200 37.9 0 200
50 199 37.9 0 199
51 161 37.9 0 161
52 199 37.9 0 199
53 177 37.9 0 177
54 148 37.9 0 148
55 157 37.9 0 157
56 175 37.9 0 175
57 144 37.9 0 144
58 165 37.9 0 165
59 144 37.9 0 144
60 147 37.9 0 147
61 144 37.9 0 144
62 127 37.9 0 127
63 141 37.9 0 141
64 120 37.9 0 120
65 100 37.9 0 100
66 102 37.9 0 102
67 102 37.9 0 102
68 81 37.9 0 81
69 74 37.9 0 74
70 70 37.9 0 70
71 72 37.9 0 72
72 59 37.9 0 59
73 49 37.9 0 49
74 50 37.9 0 50
75 47 37.9 0 47
76 31 37.9 0 31
77 32 37.9 0 32
78 28 37.9 0 28
79 32 37.9 0 32
80 29 37.9 0 29
81 20 37.9 0 20
82 31 37.9 0 31
83 23 37.9 0 23
84 23 37.9 0 23
85 45 37.9 0 45
86 666 37.9 0 666
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 51079 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.1%
C: 23.0%
G: 20.3%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 38052 38780.7 0 38052
4 8537 9695.2 0 8537
5 1826 2423.8 0 1826
6 232 605.9 0 232
7 30 151.5 0 30
8 29 151.5 0 29
9 22 151.5 0 22
10 29 151.5 0 29
11 27 151.5 0 27
12 37 151.5 0 37
13 44 151.5 0 44
14 30 151.5 0 30
15 28 151.5 0 28
16 36 151.5 0 36
17 24 151.5 0 24
18 31 151.5 0 31
19 44 151.5 0 44
20 33 151.5 0 33
21 51 151.5 0 51
22 32 151.5 0 32
23 25 151.5 0 25
24 25 151.5 0 25
25 46 151.5 0 46
26 36 151.5 0 36
27 22 151.5 0 22
28 31 151.5 0 31
29 20 151.5 0 20
30 35 151.5 0 35
31 22 151.5 0 22
32 58 151.5 0 58
33 39 151.5 0 39
34 20 151.5 0 20
35 14 151.5 0 14
36 24 151.5 0 24
37 23 151.5 0 23
38 26 151.5 0 26
39 26 151.5 0 26
40 36 151.5 0 36
41 24 151.5 0 24
42 27 151.5 0 27
43 20 151.5 0 20
44 28 151.5 0 28
45 23 151.5 0 23
46 28 151.5 0 28
47 34 151.5 0 34
48 27 151.5 0 27
49 20 151.5 0 20
50 21 151.5 0 21
51 25 151.5 0 25
52 44 151.5 0 44
53 26 151.5 0 26
54 42 151.5 0 42
55 40 151.5 0 40
56 27 151.5 0 27
57 25 151.5 0 25
58 32 151.5 0 32
59 30 151.5 0 30
60 27 151.5 0 27
61 28 151.5 0 28
62 43 151.5 0 43
63 29 151.5 0 29
64 22 151.5 0 22
65 31 151.5 0 31
66 36 151.5 0 36
67 28 151.5 0 28
68 29 151.5 0 29
69 24 151.5 0 24
70 43 151.5 0 43
71 32 151.5 0 32
72 16 151.5 0 16
73 27 151.5 0 27
74 35 151.5 0 35
75 27 151.5 0 27
76 25 151.5 0 25
77 59 151.5 0 59
78 30 151.5 0 30
79 22 151.5 0 22
80 18 151.5 0 18
81 35 151.5 0 35
82 33 151.5 0 33
83 30 151.5 0 30
84 38 151.5 0 38
85 35 151.5 0 35
86 32 151.5 0 32
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R47_S179_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R47_S179_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.86 s (9 µs/read; 6.40 M reads/minute).
=== Summary ===
Total reads processed: 2,544,850
Reads with adapters: 888,009 (34.9%)
== Read fate breakdown ==
Reads that were too short: 226,677 (8.9%)
Reads written (passing filters): 2,318,173 (91.1%)
Total basepairs processed: 257,029,850 bp
Total written (filtered): 181,176,300 bp (70.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 803075 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.8%
G: 28.2%
T: 30.0%
none/other: 11.0%
Overview of removed sequences
length count expect max.err error counts
3 58617 39763.3 0 58617
4 25958 9940.8 0 25958
5 14326 2485.2 0 14326
6 10560 621.3 0 10560
7 8831 155.3 0 8831
8 7567 38.8 0 7567
9 7831 38.8 0 7831
10 7735 38.8 0 7735
11 7762 38.8 0 7762
12 7893 38.8 0 7893
13 7675 38.8 0 7675
14 7980 38.8 0 7980
15 7840 38.8 0 7840
16 8114 38.8 0 8114
17 7778 38.8 0 7778
18 8139 38.8 0 8139
19 7613 38.8 0 7613
20 7612 38.8 0 7612
21 8167 38.8 0 8167
22 7776 38.8 0 7776
23 7445 38.8 0 7445
24 7622 38.8 0 7622
25 7315 38.8 0 7315
26 7462 38.8 0 7462
27 7509 38.8 0 7509
28 7829 38.8 0 7829
29 7933 38.8 0 7933
30 7625 38.8 0 7625
31 8128 38.8 0 8128
32 7842 38.8 0 7842
33 8148 38.8 0 8148
34 8009 38.8 0 8009
35 7815 38.8 0 7815
36 7455 38.8 0 7455
37 7754 38.8 0 7754
38 7243 38.8 0 7243
39 7478 38.8 0 7478
40 7772 38.8 0 7772
41 7548 38.8 0 7548
42 7874 38.8 0 7874
43 8471 38.8 0 8471
44 7955 38.8 0 7955
45 7869 38.8 0 7869
46 8438 38.8 0 8438
47 8197 38.8 0 8197
48 7507 38.8 0 7507
49 10575 38.8 0 10575
50 11687 38.8 0 11687
51 7745 38.8 0 7745
52 8017 38.8 0 8017
53 7628 38.8 0 7628
54 7017 38.8 0 7017
55 7523 38.8 0 7523
56 7475 38.8 0 7475
57 7212 38.8 0 7212
58 7909 38.8 0 7909
59 7332 38.8 0 7332
60 7348 38.8 0 7348
61 7559 38.8 0 7559
62 7413 38.8 0 7413
63 7154 38.8 0 7154
64 7044 38.8 0 7044
65 7084 38.8 0 7084
66 6839 38.8 0 6839
67 6876 38.8 0 6876
68 6803 38.8 0 6803
69 6462 38.8 0 6462
70 6211 38.8 0 6211
71 6440 38.8 0 6440
72 6312 38.8 0 6312
73 6097 38.8 0 6097
74 5695 38.8 0 5695
75 5736 38.8 0 5736
76 6038 38.8 0 6038
77 5826 38.8 0 5826
78 6169 38.8 0 6169
79 7010 38.8 0 7010
80 6682 38.8 0 6682
81 7716 38.8 0 7716
82 8990 38.8 0 8990
83 9614 38.8 0 9614
84 10696 38.8 0 10696
85 11031 38.8 0 11031
86 88093 38.8 0 88093
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 32686 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.4%
C: 35.4%
G: 0.0%
T: 35.3%
none/other: 1.9%
Overview of removed sequences
length count expect max.err error counts
3 13312 39763.3 0 13312
4 3308 9940.8 0 3308
5 823 2485.2 0 823
6 390 621.3 0 390
7 304 155.3 0 304
8 334 38.8 0 334
9 292 38.8 0 292
10 275 38.8 0 275
11 286 38.8 0 286
12 258 38.8 0 258
13 256 38.8 0 256
14 231 38.8 0 231
15 284 38.8 0 284
16 261 38.8 0 261
17 301 38.8 0 301
18 259 38.8 0 259
19 245 38.8 0 245
20 246 38.8 0 246
21 225 38.8 0 225
22 235 38.8 0 235
23 243 38.8 0 243
24 254 38.8 0 254
25 260 38.8 0 260
26 276 38.8 0 276
27 222 38.8 0 222
28 216 38.8 0 216
29 224 38.8 0 224
30 243 38.8 0 243
31 225 38.8 0 225
32 228 38.8 0 228
33 246 38.8 0 246
34 229 38.8 0 229
35 232 38.8 0 232
36 245 38.8 0 245
37 214 38.8 0 214
38 238 38.8 0 238
39 244 38.8 0 244
40 236 38.8 0 236
41 241 38.8 0 241
42 232 38.8 0 232
43 217 38.8 0 217
44 219 38.8 0 219
45 202 38.8 0 202
46 190 38.8 0 190
47 203 38.8 0 203
48 175 38.8 0 175
49 205 38.8 0 205
50 213 38.8 0 213
51 188 38.8 0 188
52 198 38.8 0 198
53 222 38.8 0 222
54 175 38.8 0 175
55 173 38.8 0 173
56 190 38.8 0 190
57 166 38.8 0 166
58 173 38.8 0 173
59 176 38.8 0 176
60 167 38.8 0 167
61 158 38.8 0 158
62 137 38.8 0 137
63 135 38.8 0 135
64 143 38.8 0 143
65 118 38.8 0 118
66 128 38.8 0 128
67 118 38.8 0 118
68 94 38.8 0 94
69 83 38.8 0 83
70 70 38.8 0 70
71 62 38.8 0 62
72 59 38.8 0 59
73 48 38.8 0 48
74 36 38.8 0 36
75 52 38.8 0 52
76 32 38.8 0 32
77 42 38.8 0 42
78 30 38.8 0 30
79 32 38.8 0 32
80 19 38.8 0 19
81 26 38.8 0 26
82 22 38.8 0 22
83 32 38.8 0 32
84 27 38.8 0 27
85 38 38.8 0 38
86 620 38.8 0 620
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 52248 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.1%
C: 22.8%
G: 20.4%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 38855 39763.3 0 38855
4 8834 9940.8 0 8834
5 1825 2485.2 0 1825
6 250 621.3 0 250
7 28 155.3 0 28
8 21 155.3 0 21
9 30 155.3 0 30
10 37 155.3 0 37
11 36 155.3 0 36
12 28 155.3 0 28
13 33 155.3 0 33
14 32 155.3 0 32
15 24 155.3 0 24
16 33 155.3 0 33
17 41 155.3 0 41
18 34 155.3 0 34
19 43 155.3 0 43
20 30 155.3 0 30
21 35 155.3 0 35
22 26 155.3 0 26
23 33 155.3 0 33
24 22 155.3 0 22
25 45 155.3 0 45
26 32 155.3 0 32
27 28 155.3 0 28
28 26 155.3 0 26
29 22 155.3 0 22
30 31 155.3 0 31
31 26 155.3 0 26
32 52 155.3 0 52
33 30 155.3 0 30
34 20 155.3 0 20
35 26 155.3 0 26
36 35 155.3 0 35
37 26 155.3 0 26
38 32 155.3 0 32
39 35 155.3 0 35
40 22 155.3 0 22
41 28 155.3 0 28
42 26 155.3 0 26
43 24 155.3 0 24
44 22 155.3 0 22
45 30 155.3 0 30
46 27 155.3 0 27
47 38 155.3 0 38
48 28 155.3 0 28
49 30 155.3 0 30
50 19 155.3 0 19
51 41 155.3 0 41
52 38 155.3 0 38
53 22 155.3 0 22
54 43 155.3 0 43
55 32 155.3 0 32
56 27 155.3 0 27
57 29 155.3 0 29
58 32 155.3 0 32
59 28 155.3 0 28
60 35 155.3 0 35
61 27 155.3 0 27
62 50 155.3 0 50
63 27 155.3 0 27
64 21 155.3 0 21
65 31 155.3 0 31
66 37 155.3 0 37
67 24 155.3 0 24
68 29 155.3 0 29
69 36 155.3 0 36
70 33 155.3 0 33
71 34 155.3 0 34
72 24 155.3 0 24
73 22 155.3 0 22
74 40 155.3 0 40
75 23 155.3 0 23
76 21 155.3 0 21
77 48 155.3 0 48
78 36 155.3 0 36
79 23 155.3 0 23
80 30 155.3 0 30
81 32 155.3 0 32
82 37 155.3 0 37
83 34 155.3 0 34
84 33 155.3 0 33
85 35 155.3 0 35
86 44 155.3 0 44
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R48_S176_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R48_S176_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.86 s (10 µs/read; 6.21 M reads/minute).
=== Summary ===
Total reads processed: 2,573,427
Reads with adapters: 932,080 (36.2%)
== Read fate breakdown ==
Reads that were too short: 228,566 (8.9%)
Reads written (passing filters): 2,344,861 (91.1%)
Total basepairs processed: 259,916,127 bp
Total written (filtered): 181,793,850 bp (69.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 824781 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.6%
G: 27.8%
T: 29.5%
none/other: 11.0%
Overview of removed sequences
length count expect max.err error counts
3 61692 40209.8 0 61692
4 28680 10052.4 0 28680
5 15263 2513.1 0 15263
6 10489 628.3 0 10489
7 8461 157.1 0 8461
8 7869 39.3 0 7869
9 7717 39.3 0 7717
10 7811 39.3 0 7811
11 7509 39.3 0 7509
12 7647 39.3 0 7647
13 7581 39.3 0 7581
14 7913 39.3 0 7913
15 7808 39.3 0 7808
16 7844 39.3 0 7844
17 7774 39.3 0 7774
18 8308 39.3 0 8308
19 7954 39.3 0 7954
20 7785 39.3 0 7785
21 8238 39.3 0 8238
22 8256 39.3 0 8256
23 7918 39.3 0 7918
24 7915 39.3 0 7915
25 7821 39.3 0 7821
26 7738 39.3 0 7738
27 7636 39.3 0 7636
28 8024 39.3 0 8024
29 8132 39.3 0 8132
30 7986 39.3 0 7986
31 8034 39.3 0 8034
32 7733 39.3 0 7733
33 8104 39.3 0 8104
34 7904 39.3 0 7904
35 7833 39.3 0 7833
36 7949 39.3 0 7949
37 7833 39.3 0 7833
38 7559 39.3 0 7559
39 7713 39.3 0 7713
40 7808 39.3 0 7808
41 7879 39.3 0 7879
42 7776 39.3 0 7776
43 7921 39.3 0 7921
44 7842 39.3 0 7842
45 8050 39.3 0 8050
46 7945 39.3 0 7945
47 7963 39.3 0 7963
48 8229 39.3 0 8229
49 9031 39.3 0 9031
50 9704 39.3 0 9704
51 8479 39.3 0 8479
52 8535 39.3 0 8535
53 8229 39.3 0 8229
54 8200 39.3 0 8200
55 8443 39.3 0 8443
56 8186 39.3 0 8186
57 8299 39.3 0 8299
58 8645 39.3 0 8645
59 8350 39.3 0 8350
60 8517 39.3 0 8517
61 8471 39.3 0 8471
62 8597 39.3 0 8597
63 8271 39.3 0 8271
64 8111 39.3 0 8111
65 8498 39.3 0 8498
66 8246 39.3 0 8246
67 7887 39.3 0 7887
68 7681 39.3 0 7681
69 7594 39.3 0 7594
70 7312 39.3 0 7312
71 7924 39.3 0 7924
72 7113 39.3 0 7113
73 7323 39.3 0 7323
74 6577 39.3 0 6577
75 6298 39.3 0 6298
76 6226 39.3 0 6226
77 6494 39.3 0 6494
78 5743 39.3 0 5743
79 6365 39.3 0 6365
80 5632 39.3 0 5632
81 6183 39.3 0 6183
82 7054 39.3 0 7054
83 7423 39.3 0 7423
84 7918 39.3 0 7918
85 8400 39.3 0 8400
86 90978 39.3 0 90978
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 57243 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 23.9%
C: 33.7%
G: 0.0%
T: 40.0%
none/other: 2.4%
Overview of removed sequences
length count expect max.err error counts
3 10531 40209.8 0 10531
4 3246 10052.4 0 3246
5 1352 2513.1 0 1352
6 908 628.3 0 908
7 855 157.1 0 855
8 928 39.3 0 928
9 804 39.3 0 804
10 791 39.3 0 791
11 811 39.3 0 811
12 719 39.3 0 719
13 709 39.3 0 709
14 784 39.3 0 784
15 785 39.3 0 785
16 751 39.3 0 751
17 742 39.3 0 742
18 774 39.3 0 774
19 746 39.3 0 746
20 629 39.3 0 629
21 694 39.3 0 694
22 636 39.3 0 636
23 701 39.3 0 701
24 695 39.3 0 695
25 704 39.3 0 704
26 698 39.3 0 698
27 629 39.3 0 629
28 672 39.3 0 672
29 647 39.3 0 647
30 713 39.3 0 713
31 594 39.3 0 594
32 653 39.3 0 653
33 605 39.3 0 605
34 653 39.3 0 653
35 639 39.3 0 639
36 592 39.3 0 592
37 602 39.3 0 602
38 639 39.3 0 639
39 637 39.3 0 637
40 607 39.3 0 607
41 577 39.3 0 577
42 635 39.3 0 635
43 655 39.3 0 655
44 582 39.3 0 582
45 583 39.3 0 583
46 584 39.3 0 584
47 641 39.3 0 641
48 625 39.3 0 625
49 603 39.3 0 603
50 559 39.3 0 559
51 553 39.3 0 553
52 578 39.3 0 578
53 549 39.3 0 549
54 557 39.3 0 557
55 533 39.3 0 533
56 542 39.3 0 542
57 502 39.3 0 502
58 523 39.3 0 523
59 503 39.3 0 503
60 445 39.3 0 445
61 439 39.3 0 439
62 423 39.3 0 423
63 414 39.3 0 414
64 353 39.3 0 353
65 333 39.3 0 333
66 284 39.3 0 284
67 327 39.3 0 327
68 264 39.3 0 264
69 218 39.3 0 218
70 193 39.3 0 193
71 196 39.3 0 196
72 162 39.3 0 162
73 167 39.3 0 167
74 128 39.3 0 128
75 129 39.3 0 129
76 103 39.3 0 103
77 74 39.3 0 74
78 68 39.3 0 68
79 86 39.3 0 86
80 54 39.3 0 54
81 52 39.3 0 52
82 50 39.3 0 50
83 50 39.3 0 50
84 57 39.3 0 57
85 62 39.3 0 62
86 1353 39.3 0 1353
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 50056 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 23.0%
G: 19.7%
T: 21.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 36739 40209.8 0 36739
4 9091 10052.4 0 9091
5 1546 2513.1 0 1546
6 202 628.3 0 202
7 27 157.1 0 27
8 28 157.1 0 28
9 27 157.1 0 27
10 27 157.1 0 27
11 27 157.1 0 27
12 23 157.1 0 23
13 30 157.1 0 30
14 31 157.1 0 31
15 32 157.1 0 32
16 25 157.1 0 25
17 27 157.1 0 27
18 29 157.1 0 29
19 28 157.1 0 28
20 30 157.1 0 30
21 35 157.1 0 35
22 39 157.1 0 39
23 27 157.1 0 27
24 32 157.1 0 32
25 34 157.1 0 34
26 40 157.1 0 40
27 15 157.1 0 15
28 34 157.1 0 34
29 42 157.1 0 42
30 19 157.1 0 19
31 29 157.1 0 29
32 42 157.1 0 42
33 38 157.1 0 38
34 41 157.1 0 41
35 34 157.1 0 34
36 42 157.1 0 42
37 34 157.1 0 34
38 39 157.1 0 39
39 46 157.1 0 46
40 23 157.1 0 23
41 35 157.1 0 35
42 45 157.1 0 45
43 26 157.1 0 26
44 18 157.1 0 18
45 38 157.1 0 38
46 29 157.1 0 29
47 39 157.1 0 39
48 23 157.1 0 23
49 26 157.1 0 26
50 35 157.1 0 35
51 29 157.1 0 29
52 33 157.1 0 33
53 35 157.1 0 35
54 28 157.1 0 28
55 26 157.1 0 26
56 22 157.1 0 22
57 30 157.1 0 30
58 31 157.1 0 31
59 20 157.1 0 20
60 26 157.1 0 26
61 35 157.1 0 35
62 39 157.1 0 39
63 18 157.1 0 18
64 24 157.1 0 24
65 23 157.1 0 23
66 21 157.1 0 21
67 20 157.1 0 20
68 38 157.1 0 38
69 18 157.1 0 18
70 29 157.1 0 29
71 41 157.1 0 41
72 17 157.1 0 17
73 30 157.1 0 30
74 35 157.1 0 35
75 31 157.1 0 31
76 21 157.1 0 21
77 73 157.1 0 73
78 42 157.1 0 42
79 28 157.1 0 28
80 23 157.1 0 23
81 40 157.1 0 40
82 23 157.1 0 23
83 35 157.1 0 35
84 36 157.1 0 36
85 28 157.1 0 28
86 40 157.1 0 40
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R48_S176_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R48_S176_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.58 s (9 µs/read; 6.41 M reads/minute).
=== Summary ===
Total reads processed: 2,623,429
Reads with adapters: 960,011 (36.6%)
== Read fate breakdown ==
Reads that were too short: 239,863 (9.1%)
Reads written (passing filters): 2,383,566 (90.9%)
Total basepairs processed: 264,966,329 bp
Total written (filtered): 184,450,044 bp (69.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 850792 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.6%
G: 27.8%
T: 29.3%
none/other: 11.3%
Overview of removed sequences
length count expect max.err error counts
3 61796 40991.1 0 61796
4 28970 10247.8 0 28970
5 15493 2561.9 0 15493
6 10635 640.5 0 10635
7 8606 160.1 0 8606
8 7912 40.0 0 7912
9 7890 40.0 0 7890
10 7813 40.0 0 7813
11 7821 40.0 0 7821
12 7776 40.0 0 7776
13 7523 40.0 0 7523
14 7957 40.0 0 7957
15 7936 40.0 0 7936
16 8036 40.0 0 8036
17 8008 40.0 0 8008
18 8533 40.0 0 8533
19 8040 40.0 0 8040
20 7982 40.0 0 7982
21 8151 40.0 0 8151
22 8324 40.0 0 8324
23 8051 40.0 0 8051
24 7883 40.0 0 7883
25 7798 40.0 0 7798
26 7825 40.0 0 7825
27 8040 40.0 0 8040
28 8240 40.0 0 8240
29 8375 40.0 0 8375
30 8050 40.0 0 8050
31 8287 40.0 0 8287
32 7689 40.0 0 7689
33 8372 40.0 0 8372
34 8150 40.0 0 8150
35 8023 40.0 0 8023
36 8141 40.0 0 8141
37 8066 40.0 0 8066
38 7814 40.0 0 7814
39 8092 40.0 0 8092
40 8063 40.0 0 8063
41 7841 40.0 0 7841
42 8066 40.0 0 8066
43 8362 40.0 0 8362
44 7866 40.0 0 7866
45 8261 40.0 0 8261
46 8341 40.0 0 8341
47 8384 40.0 0 8384
48 8210 40.0 0 8210
49 9326 40.0 0 9326
50 10061 40.0 0 10061
51 8864 40.0 0 8864
52 8940 40.0 0 8940
53 8802 40.0 0 8802
54 8517 40.0 0 8517
55 8714 40.0 0 8714
56 8617 40.0 0 8617
57 8695 40.0 0 8695
58 8856 40.0 0 8856
59 8886 40.0 0 8886
60 9065 40.0 0 9065
61 9097 40.0 0 9097
62 9108 40.0 0 9108
63 8429 40.0 0 8429
64 8506 40.0 0 8506
65 8833 40.0 0 8833
66 8669 40.0 0 8669
67 8159 40.0 0 8159
68 7974 40.0 0 7974
69 7817 40.0 0 7817
70 7742 40.0 0 7742
71 8484 40.0 0 8484
72 7473 40.0 0 7473
73 7711 40.0 0 7711
74 6925 40.0 0 6925
75 6402 40.0 0 6402
76 6540 40.0 0 6540
77 6926 40.0 0 6926
78 6103 40.0 0 6103
79 6477 40.0 0 6477
80 5856 40.0 0 5856
81 6469 40.0 0 6469
82 7238 40.0 0 7238
83 7818 40.0 0 7818
84 8301 40.0 0 8301
85 8705 40.0 0 8705
86 96195 40.0 0 96195
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 58751 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 24.1%
C: 33.8%
G: 0.0%
T: 39.8%
none/other: 2.4%
Overview of removed sequences
length count expect max.err error counts
3 10811 40991.1 0 10811
4 3363 10247.8 0 3363
5 1404 2561.9 0 1404
6 913 640.5 0 913
7 928 160.1 0 928
8 920 40.0 0 920
9 900 40.0 0 900
10 773 40.0 0 773
11 827 40.0 0 827
12 838 40.0 0 838
13 743 40.0 0 743
14 784 40.0 0 784
15 787 40.0 0 787
16 745 40.0 0 745
17 713 40.0 0 713
18 729 40.0 0 729
19 717 40.0 0 717
20 695 40.0 0 695
21 710 40.0 0 710
22 663 40.0 0 663
23 661 40.0 0 661
24 746 40.0 0 746
25 709 40.0 0 709
26 694 40.0 0 694
27 648 40.0 0 648
28 650 40.0 0 650
29 664 40.0 0 664
30 667 40.0 0 667
31 627 40.0 0 627
32 627 40.0 0 627
33 697 40.0 0 697
34 652 40.0 0 652
35 652 40.0 0 652
36 679 40.0 0 679
37 640 40.0 0 640
38 702 40.0 0 702
39 671 40.0 0 671
40 591 40.0 0 591
41 664 40.0 0 664
42 683 40.0 0 683
43 600 40.0 0 600
44 610 40.0 0 610
45 594 40.0 0 594
46 584 40.0 0 584
47 630 40.0 0 630
48 628 40.0 0 628
49 564 40.0 0 564
50 596 40.0 0 596
51 580 40.0 0 580
52 576 40.0 0 576
53 572 40.0 0 572
54 540 40.0 0 540
55 589 40.0 0 589
56 532 40.0 0 532
57 537 40.0 0 537
58 529 40.0 0 529
59 492 40.0 0 492
60 514 40.0 0 514
61 447 40.0 0 447
62 432 40.0 0 432
63 362 40.0 0 362
64 397 40.0 0 397
65 343 40.0 0 343
66 387 40.0 0 387
67 305 40.0 0 305
68 228 40.0 0 228
69 252 40.0 0 252
70 197 40.0 0 197
71 198 40.0 0 198
72 182 40.0 0 182
73 168 40.0 0 168
74 175 40.0 0 175
75 118 40.0 0 118
76 93 40.0 0 93
77 107 40.0 0 107
78 77 40.0 0 77
79 66 40.0 0 66
80 47 40.0 0 47
81 49 40.0 0 49
82 43 40.0 0 43
83 45 40.0 0 45
84 51 40.0 0 51
85 50 40.0 0 50
86 1378 40.0 0 1378
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 50468 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 22.7%
G: 19.8%
T: 21.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 36956 40991.1 0 36956
4 9157 10247.8 0 9157
5 1555 2561.9 0 1555
6 174 640.5 0 174
7 26 160.1 0 26
8 28 160.1 0 28
9 36 160.1 0 36
10 27 160.1 0 27
11 33 160.1 0 33
12 42 160.1 0 42
13 28 160.1 0 28
14 36 160.1 0 36
15 28 160.1 0 28
16 28 160.1 0 28
17 22 160.1 0 22
18 39 160.1 0 39
19 31 160.1 0 31
20 32 160.1 0 32
21 34 160.1 0 34
22 43 160.1 0 43
23 28 160.1 0 28
24 36 160.1 0 36
25 35 160.1 0 35
26 39 160.1 0 39
27 26 160.1 0 26
28 37 160.1 0 37
29 44 160.1 0 44
30 39 160.1 0 39
31 19 160.1 0 19
32 34 160.1 0 34
33 33 160.1 0 33
34 27 160.1 0 27
35 18 160.1 0 18
36 39 160.1 0 39
37 25 160.1 0 25
38 44 160.1 0 44
39 41 160.1 0 41
40 27 160.1 0 27
41 44 160.1 0 44
42 33 160.1 0 33
43 38 160.1 0 38
44 32 160.1 0 32
45 31 160.1 0 31
46 27 160.1 0 27
47 31 160.1 0 31
48 27 160.1 0 27
49 30 160.1 0 30
50 27 160.1 0 27
51 31 160.1 0 31
52 27 160.1 0 27
53 23 160.1 0 23
54 33 160.1 0 33
55 38 160.1 0 38
56 19 160.1 0 19
57 38 160.1 0 38
58 27 160.1 0 27
59 35 160.1 0 35
60 30 160.1 0 30
61 38 160.1 0 38
62 32 160.1 0 32
63 26 160.1 0 26
64 20 160.1 0 20
65 38 160.1 0 38
66 28 160.1 0 28
67 36 160.1 0 36
68 42 160.1 0 42
69 44 160.1 0 44
70 39 160.1 0 39
71 40 160.1 0 40
72 20 160.1 0 20
73 39 160.1 0 39
74 37 160.1 0 37
75 22 160.1 0 22
76 24 160.1 0 24
77 70 160.1 0 70
78 38 160.1 0 38
79 42 160.1 0 42
80 32 160.1 0 32
81 43 160.1 0 43
82 33 160.1 0 33
83 28 160.1 0 28
84 29 160.1 0 29
85 33 160.1 0 33
86 28 160.1 0 28
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R50_S174_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R50_S174_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.97 s (9 µs/read; 6.54 M reads/minute).
=== Summary ===
Total reads processed: 2,611,492
Reads with adapters: 982,431 (37.6%)
== Read fate breakdown ==
Reads that were too short: 342,682 (13.1%)
Reads written (passing filters): 2,268,810 (86.9%)
Total basepairs processed: 263,760,692 bp
Total written (filtered): 176,718,114 bp (67.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 897768 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.7%
G: 25.2%
T: 27.3%
none/other: 17.8%
Overview of removed sequences
length count expect max.err error counts
3 57916 40804.6 0 57916
4 26412 10201.1 0 26412
5 13079 2550.3 0 13079
6 8848 637.6 0 8848
7 6736 159.4 0 6736
8 6227 39.8 0 6227
9 6332 39.8 0 6332
10 6430 39.8 0 6430
11 6353 39.8 0 6353
12 6485 39.8 0 6485
13 6539 39.8 0 6539
14 6348 39.8 0 6348
15 6712 39.8 0 6712
16 6853 39.8 0 6853
17 6643 39.8 0 6643
18 6489 39.8 0 6489
19 6829 39.8 0 6829
20 6736 39.8 0 6736
21 6583 39.8 0 6583
22 6890 39.8 0 6890
23 6481 39.8 0 6481
24 6911 39.8 0 6911
25 6651 39.8 0 6651
26 6864 39.8 0 6864
27 7105 39.8 0 7105
28 6786 39.8 0 6786
29 7299 39.8 0 7299
30 7720 39.8 0 7720
31 8359 39.8 0 8359
32 7077 39.8 0 7077
33 7438 39.8 0 7438
34 7568 39.8 0 7568
35 6736 39.8 0 6736
36 7056 39.8 0 7056
37 7199 39.8 0 7199
38 6557 39.8 0 6557
39 6954 39.8 0 6954
40 7566 39.8 0 7566
41 7533 39.8 0 7533
42 7544 39.8 0 7544
43 7581 39.8 0 7581
44 7148 39.8 0 7148
45 7350 39.8 0 7350
46 7999 39.8 0 7999
47 7810 39.8 0 7810
48 7297 39.8 0 7297
49 9871 39.8 0 9871
50 11404 39.8 0 11404
51 8106 39.8 0 8106
52 8624 39.8 0 8624
53 8392 39.8 0 8392
54 7860 39.8 0 7860
55 8706 39.8 0 8706
56 8556 39.8 0 8556
57 8532 39.8 0 8532
58 9226 39.8 0 9226
59 8578 39.8 0 8578
60 8794 39.8 0 8794
61 8842 39.8 0 8842
62 8827 39.8 0 8827
63 8252 39.8 0 8252
64 8565 39.8 0 8565
65 8668 39.8 0 8668
66 8370 39.8 0 8370
67 8250 39.8 0 8250
68 8239 39.8 0 8239
69 7991 39.8 0 7991
70 7743 39.8 0 7743
71 9387 39.8 0 9387
72 8452 39.8 0 8452
73 8608 39.8 0 8608
74 8222 39.8 0 8222
75 7572 39.8 0 7572
76 8177 39.8 0 8177
77 9373 39.8 0 9373
78 8025 39.8 0 8025
79 8986 39.8 0 8986
80 8170 39.8 0 8170
81 9441 39.8 0 9441
82 11338 39.8 0 11338
83 13051 39.8 0 13051
84 14281 39.8 0 14281
85 14419 39.8 0 14419
86 159841 39.8 0 159841
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28582 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.5%
C: 26.9%
G: 0.0%
T: 37.1%
none/other: 5.4%
Overview of removed sequences
length count expect max.err error counts
3 11095 40804.6 0 11095
4 2601 10201.1 0 2601
5 753 2550.3 0 753
6 361 637.6 0 361
7 377 159.4 0 377
8 395 39.8 0 395
9 319 39.8 0 319
10 295 39.8 0 295
11 275 39.8 0 275
12 287 39.8 0 287
13 254 39.8 0 254
14 207 39.8 0 207
15 205 39.8 0 205
16 212 39.8 0 212
17 198 39.8 0 198
18 202 39.8 0 202
19 191 39.8 0 191
20 179 39.8 0 179
21 200 39.8 0 200
22 187 39.8 0 187
23 199 39.8 0 199
24 197 39.8 0 197
25 223 39.8 0 223
26 208 39.8 0 208
27 165 39.8 0 165
28 189 39.8 0 189
29 185 39.8 0 185
30 174 39.8 0 174
31 177 39.8 0 177
32 163 39.8 0 163
33 170 39.8 0 170
34 209 39.8 0 209
35 176 39.8 0 176
36 182 39.8 0 182
37 184 39.8 0 184
38 187 39.8 0 187
39 173 39.8 0 173
40 161 39.8 0 161
41 158 39.8 0 158
42 202 39.8 0 202
43 176 39.8 0 176
44 173 39.8 0 173
45 175 39.8 0 175
46 190 39.8 0 190
47 173 39.8 0 173
48 178 39.8 0 178
49 170 39.8 0 170
50 169 39.8 0 169
51 173 39.8 0 173
52 192 39.8 0 192
53 148 39.8 0 148
54 157 39.8 0 157
55 177 39.8 0 177
56 150 39.8 0 150
57 161 39.8 0 161
58 143 39.8 0 143
59 160 39.8 0 160
60 147 39.8 0 147
61 117 39.8 0 117
62 128 39.8 0 128
63 127 39.8 0 127
64 99 39.8 0 99
65 108 39.8 0 108
66 91 39.8 0 91
67 76 39.8 0 76
68 94 39.8 0 94
69 82 39.8 0 82
70 68 39.8 0 68
71 57 39.8 0 57
72 54 39.8 0 54
73 41 39.8 0 41
74 47 39.8 0 47
75 40 39.8 0 40
76 36 39.8 0 36
77 23 39.8 0 23
78 28 39.8 0 28
79 33 39.8 0 33
80 28 39.8 0 28
81 19 39.8 0 19
82 34 39.8 0 34
83 42 39.8 0 42
84 32 39.8 0 32
85 42 39.8 0 42
86 1549 39.8 0 1549
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 56081 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.3%
C: 23.5%
G: 20.3%
T: 19.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 42213 40804.6 0 42213
4 9223 10201.1 0 9223
5 1783 2550.3 0 1783
6 184 637.6 0 184
7 30 159.4 0 30
8 30 159.4 0 30
9 32 159.4 0 32
10 24 159.4 0 24
11 33 159.4 0 33
12 16 159.4 0 16
13 41 159.4 0 41
14 28 159.4 0 28
15 29 159.4 0 29
16 31 159.4 0 31
17 37 159.4 0 37
18 37 159.4 0 37
19 62 159.4 0 62
20 37 159.4 0 37
21 22 159.4 0 22
22 36 159.4 0 36
23 36 159.4 0 36
24 29 159.4 0 29
25 50 159.4 0 50
26 44 159.4 0 44
27 20 159.4 0 20
28 31 159.4 0 31
29 25 159.4 0 25
30 28 159.4 0 28
31 31 159.4 0 31
32 49 159.4 0 49
33 50 159.4 0 50
34 27 159.4 0 27
35 39 159.4 0 39
36 32 159.4 0 32
37 40 159.4 0 40
38 23 159.4 0 23
39 35 159.4 0 35
40 41 159.4 0 41
41 44 159.4 0 44
42 25 159.4 0 25
43 36 159.4 0 36
44 27 159.4 0 27
45 15 159.4 0 15
46 27 159.4 0 27
47 33 159.4 0 33
48 27 159.4 0 27
49 31 159.4 0 31
50 45 159.4 0 45
51 41 159.4 0 41
52 30 159.4 0 30
53 25 159.4 0 25
54 35 159.4 0 35
55 39 159.4 0 39
56 16 159.4 0 16
57 35 159.4 0 35
58 26 159.4 0 26
59 33 159.4 0 33
60 33 159.4 0 33
61 35 159.4 0 35
62 41 159.4 0 41
63 48 159.4 0 48
64 27 159.4 0 27
65 26 159.4 0 26
66 32 159.4 0 32
67 19 159.4 0 19
68 32 159.4 0 32
69 36 159.4 0 36
70 37 159.4 0 37
71 36 159.4 0 36
72 23 159.4 0 23
73 39 159.4 0 39
74 32 159.4 0 32
75 26 159.4 0 26
76 23 159.4 0 23
77 86 159.4 0 86
78 48 159.4 0 48
79 20 159.4 0 20
80 32 159.4 0 32
81 29 159.4 0 29
82 18 159.4 0 18
83 35 159.4 0 35
84 34 159.4 0 34
85 43 159.4 0 43
86 43 159.4 0 43
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R50_S174_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R50_S174_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.29 s (9 µs/read; 6.60 M reads/minute).
=== Summary ===
Total reads processed: 2,671,218
Reads with adapters: 1,013,032 (37.9%)
== Read fate breakdown ==
Reads that were too short: 359,130 (13.4%)
Reads written (passing filters): 2,312,088 (86.6%)
Total basepairs processed: 269,793,018 bp
Total written (filtered): 179,911,807 bp (66.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 927163 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.8%
G: 25.2%
T: 26.9%
none/other: 18.1%
Overview of removed sequences
length count expect max.err error counts
3 58459 41737.8 0 58459
4 26385 10434.4 0 26385
5 13301 2608.6 0 13301
6 8862 652.2 0 8862
7 7179 163.0 0 7179
8 6263 40.8 0 6263
9 6314 40.8 0 6314
10 6495 40.8 0 6495
11 6431 40.8 0 6431
12 6443 40.8 0 6443
13 6439 40.8 0 6439
14 6661 40.8 0 6661
15 6689 40.8 0 6689
16 7072 40.8 0 7072
17 6672 40.8 0 6672
18 6798 40.8 0 6798
19 7068 40.8 0 7068
20 6821 40.8 0 6821
21 6807 40.8 0 6807
22 7215 40.8 0 7215
23 6570 40.8 0 6570
24 7290 40.8 0 7290
25 6619 40.8 0 6619
26 6842 40.8 0 6842
27 7217 40.8 0 7217
28 7054 40.8 0 7054
29 7302 40.8 0 7302
30 8166 40.8 0 8166
31 8644 40.8 0 8644
32 7231 40.8 0 7231
33 7807 40.8 0 7807
34 7511 40.8 0 7511
35 6973 40.8 0 6973
36 7338 40.8 0 7338
37 7456 40.8 0 7456
38 6690 40.8 0 6690
39 7374 40.8 0 7374
40 7564 40.8 0 7564
41 7854 40.8 0 7854
42 7641 40.8 0 7641
43 7930 40.8 0 7930
44 7539 40.8 0 7539
45 7444 40.8 0 7444
46 7951 40.8 0 7951
47 8113 40.8 0 8113
48 7627 40.8 0 7627
49 10234 40.8 0 10234
50 11509 40.8 0 11509
51 8416 40.8 0 8416
52 8972 40.8 0 8972
53 8645 40.8 0 8645
54 8073 40.8 0 8073
55 8813 40.8 0 8813
56 8871 40.8 0 8871
57 8614 40.8 0 8614
58 9417 40.8 0 9417
59 9009 40.8 0 9009
60 9112 40.8 0 9112
61 9308 40.8 0 9308
62 9169 40.8 0 9169
63 8517 40.8 0 8517
64 8897 40.8 0 8897
65 8979 40.8 0 8979
66 8521 40.8 0 8521
67 8809 40.8 0 8809
68 8485 40.8 0 8485
69 8268 40.8 0 8268
70 8063 40.8 0 8063
71 9980 40.8 0 9980
72 8547 40.8 0 8547
73 9233 40.8 0 9233
74 8632 40.8 0 8632
75 8018 40.8 0 8018
76 8549 40.8 0 8549
77 9715 40.8 0 9715
78 8255 40.8 0 8255
79 9464 40.8 0 9464
80 8392 40.8 0 8392
81 10111 40.8 0 10111
82 11865 40.8 0 11865
83 13568 40.8 0 13568
84 14511 40.8 0 14511
85 15306 40.8 0 15306
86 168195 40.8 0 168195
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29255 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.7%
C: 26.9%
G: 0.0%
T: 37.2%
none/other: 5.2%
Overview of removed sequences
length count expect max.err error counts
3 11186 41737.8 0 11186
4 2747 10434.4 0 2747
5 743 2608.6 0 743
6 332 652.2 0 332
7 400 163.0 0 400
8 343 40.8 0 343
9 340 40.8 0 340
10 328 40.8 0 328
11 298 40.8 0 298
12 296 40.8 0 296
13 233 40.8 0 233
14 225 40.8 0 225
15 227 40.8 0 227
16 240 40.8 0 240
17 208 40.8 0 208
18 205 40.8 0 205
19 222 40.8 0 222
20 160 40.8 0 160
21 206 40.8 0 206
22 156 40.8 0 156
23 218 40.8 0 218
24 204 40.8 0 204
25 249 40.8 0 249
26 208 40.8 0 208
27 210 40.8 0 210
28 212 40.8 0 212
29 186 40.8 0 186
30 193 40.8 0 193
31 201 40.8 0 201
32 183 40.8 0 183
33 195 40.8 0 195
34 218 40.8 0 218
35 195 40.8 0 195
36 177 40.8 0 177
37 188 40.8 0 188
38 178 40.8 0 178
39 157 40.8 0 157
40 175 40.8 0 175
41 182 40.8 0 182
42 174 40.8 0 174
43 170 40.8 0 170
44 188 40.8 0 188
45 186 40.8 0 186
46 190 40.8 0 190
47 181 40.8 0 181
48 177 40.8 0 177
49 188 40.8 0 188
50 185 40.8 0 185
51 163 40.8 0 163
52 198 40.8 0 198
53 181 40.8 0 181
54 155 40.8 0 155
55 185 40.8 0 185
56 148 40.8 0 148
57 148 40.8 0 148
58 153 40.8 0 153
59 140 40.8 0 140
60 159 40.8 0 159
61 129 40.8 0 129
62 156 40.8 0 156
63 123 40.8 0 123
64 135 40.8 0 135
65 93 40.8 0 93
66 95 40.8 0 95
67 79 40.8 0 79
68 92 40.8 0 92
69 89 40.8 0 89
70 60 40.8 0 60
71 68 40.8 0 68
72 44 40.8 0 44
73 54 40.8 0 54
74 56 40.8 0 56
75 35 40.8 0 35
76 37 40.8 0 37
77 27 40.8 0 27
78 31 40.8 0 31
79 33 40.8 0 33
80 19 40.8 0 19
81 23 40.8 0 23
82 33 40.8 0 33
83 38 40.8 0 38
84 46 40.8 0 46
85 34 40.8 0 34
86 1533 40.8 0 1533
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 56614 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 23.8%
G: 20.3%
T: 19.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 42385 41737.8 0 42385
4 9514 10434.4 0 9514
5 1777 2608.6 0 1777
6 191 652.2 0 191
7 24 163.0 0 24
8 17 163.0 0 17
9 21 163.0 0 21
10 38 163.0 0 38
11 42 163.0 0 42
12 19 163.0 0 19
13 39 163.0 0 39
14 33 163.0 0 33
15 27 163.0 0 27
16 39 163.0 0 39
17 35 163.0 0 35
18 25 163.0 0 25
19 39 163.0 0 39
20 33 163.0 0 33
21 34 163.0 0 34
22 43 163.0 0 43
23 28 163.0 0 28
24 35 163.0 0 35
25 49 163.0 0 49
26 37 163.0 0 37
27 39 163.0 0 39
28 35 163.0 0 35
29 34 163.0 0 34
30 29 163.0 0 29
31 32 163.0 0 32
32 37 163.0 0 37
33 42 163.0 0 42
34 33 163.0 0 33
35 33 163.0 0 33
36 49 163.0 0 49
37 33 163.0 0 33
38 39 163.0 0 39
39 30 163.0 0 30
40 25 163.0 0 25
41 38 163.0 0 38
42 46 163.0 0 46
43 39 163.0 0 39
44 38 163.0 0 38
45 26 163.0 0 26
46 32 163.0 0 32
47 33 163.0 0 33
48 33 163.0 0 33
49 41 163.0 0 41
50 40 163.0 0 40
51 47 163.0 0 47
52 34 163.0 0 34
53 26 163.0 0 26
54 33 163.0 0 33
55 30 163.0 0 30
56 19 163.0 0 19
57 35 163.0 0 35
58 38 163.0 0 38
59 20 163.0 0 20
60 38 163.0 0 38
61 22 163.0 0 22
62 25 163.0 0 25
63 39 163.0 0 39
64 25 163.0 0 25
65 40 163.0 0 40
66 30 163.0 0 30
67 41 163.0 0 41
68 27 163.0 0 27
69 42 163.0 0 42
70 32 163.0 0 32
71 33 163.0 0 33
72 24 163.0 0 24
73 35 163.0 0 35
74 32 163.0 0 32
75 22 163.0 0 22
76 34 163.0 0 34
77 103 163.0 0 103
78 35 163.0 0 35
79 29 163.0 0 29
80 27 163.0 0 27
81 34 163.0 0 34
82 36 163.0 0 36
83 33 163.0 0 33
84 45 163.0 0 45
85 31 163.0 0 31
86 38 163.0 0 38
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R51_S205_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R51_S205_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.47 s (9 µs/read; 6.43 M reads/minute).
=== Summary ===
Total reads processed: 2,837,780
Reads with adapters: 922,471 (32.5%)
== Read fate breakdown ==
Reads that were too short: 210,906 (7.4%)
Reads written (passing filters): 2,626,874 (92.6%)
Total basepairs processed: 286,615,780 bp
Total written (filtered): 206,553,186 bp (72.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 807603 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 32.0%
G: 28.0%
T: 29.8%
none/other: 10.2%
Overview of removed sequences
length count expect max.err error counts
3 67230 44340.3 0 67230
4 29874 11085.1 0 29874
5 15469 2771.3 0 15469
6 10312 692.8 0 10312
7 8616 173.2 0 8616
8 7805 43.3 0 7805
9 7796 43.3 0 7796
10 7879 43.3 0 7879
11 7791 43.3 0 7791
12 7700 43.3 0 7700
13 7788 43.3 0 7788
14 7999 43.3 0 7999
15 7939 43.3 0 7939
16 7926 43.3 0 7926
17 8026 43.3 0 8026
18 8185 43.3 0 8185
19 8012 43.3 0 8012
20 7928 43.3 0 7928
21 8168 43.3 0 8168
22 7949 43.3 0 7949
23 7789 43.3 0 7789
24 7875 43.3 0 7875
25 7801 43.3 0 7801
26 7754 43.3 0 7754
27 7904 43.3 0 7904
28 7914 43.3 0 7914
29 8034 43.3 0 8034
30 7875 43.3 0 7875
31 8083 43.3 0 8083
32 7853 43.3 0 7853
33 7760 43.3 0 7760
34 7803 43.3 0 7803
35 7810 43.3 0 7810
36 7976 43.3 0 7976
37 7853 43.3 0 7853
38 7466 43.3 0 7466
39 7687 43.3 0 7687
40 7811 43.3 0 7811
41 7553 43.3 0 7553
42 7868 43.3 0 7868
43 7965 43.3 0 7965
44 7397 43.3 0 7397
45 7837 43.3 0 7837
46 8018 43.3 0 8018
47 7903 43.3 0 7903
48 7846 43.3 0 7846
49 10071 43.3 0 10071
50 11535 43.3 0 11535
51 8301 43.3 0 8301
52 8366 43.3 0 8366
53 8187 43.3 0 8187
54 7815 43.3 0 7815
55 7898 43.3 0 7898
56 7921 43.3 0 7921
57 7623 43.3 0 7623
58 7948 43.3 0 7948
59 7766 43.3 0 7766
60 7898 43.3 0 7898
61 7793 43.3 0 7793
62 7764 43.3 0 7764
63 7580 43.3 0 7580
64 7503 43.3 0 7503
65 7587 43.3 0 7587
66 7555 43.3 0 7555
67 7270 43.3 0 7270
68 7150 43.3 0 7150
69 7264 43.3 0 7264
70 6596 43.3 0 6596
71 6946 43.3 0 6946
72 6720 43.3 0 6720
73 6120 43.3 0 6120
74 5808 43.3 0 5808
75 5891 43.3 0 5891
76 5418 43.3 0 5418
77 5789 43.3 0 5789
78 5176 43.3 0 5176
79 5629 43.3 0 5629
80 5472 43.3 0 5472
81 5903 43.3 0 5903
82 6849 43.3 0 6849
83 7727 43.3 0 7727
84 7973 43.3 0 7973
85 8263 43.3 0 8263
86 82701 43.3 0 82701
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 55069 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.3%
C: 33.4%
G: 0.0%
T: 38.7%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 13926 44340.3 0 13926
4 3607 11085.1 0 3607
5 1260 2771.3 0 1260
6 695 692.8 0 695
7 693 173.2 0 693
8 673 43.3 0 673
9 660 43.3 0 660
10 669 43.3 0 669
11 627 43.3 0 627
12 546 43.3 0 546
13 589 43.3 0 589
14 614 43.3 0 614
15 592 43.3 0 592
16 582 43.3 0 582
17 588 43.3 0 588
18 557 43.3 0 557
19 527 43.3 0 527
20 546 43.3 0 546
21 564 43.3 0 564
22 553 43.3 0 553
23 487 43.3 0 487
24 533 43.3 0 533
25 569 43.3 0 569
26 558 43.3 0 558
27 548 43.3 0 548
28 523 43.3 0 523
29 542 43.3 0 542
30 552 43.3 0 552
31 600 43.3 0 600
32 511 43.3 0 511
33 580 43.3 0 580
34 531 43.3 0 531
35 534 43.3 0 534
36 532 43.3 0 532
37 586 43.3 0 586
38 563 43.3 0 563
39 555 43.3 0 555
40 501 43.3 0 501
41 560 43.3 0 560
42 585 43.3 0 585
43 508 43.3 0 508
44 539 43.3 0 539
45 574 43.3 0 574
46 553 43.3 0 553
47 520 43.3 0 520
48 559 43.3 0 559
49 542 43.3 0 542
50 505 43.3 0 505
51 493 43.3 0 493
52 532 43.3 0 532
53 540 43.3 0 540
54 489 43.3 0 489
55 518 43.3 0 518
56 533 43.3 0 533
57 485 43.3 0 485
58 506 43.3 0 506
59 485 43.3 0 485
60 440 43.3 0 440
61 415 43.3 0 415
62 404 43.3 0 404
63 379 43.3 0 379
64 354 43.3 0 354
65 307 43.3 0 307
66 302 43.3 0 302
67 277 43.3 0 277
68 228 43.3 0 228
69 245 43.3 0 245
70 193 43.3 0 193
71 149 43.3 0 149
72 149 43.3 0 149
73 128 43.3 0 128
74 122 43.3 0 122
75 92 43.3 0 92
76 80 43.3 0 80
77 75 43.3 0 75
78 74 43.3 0 74
79 44 43.3 0 44
80 61 43.3 0 61
81 34 43.3 0 34
82 39 43.3 0 39
83 39 43.3 0 39
84 69 43.3 0 69
85 58 43.3 0 58
86 1413 43.3 0 1413
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 59799 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 22.1%
G: 21.1%
T: 21.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44105 44340.3 0 44105
4 10626 11085.1 0 10626
5 2146 2771.3 0 2146
6 243 692.8 0 243
7 29 173.2 0 29
8 28 173.2 0 28
9 36 173.2 0 36
10 27 173.2 0 27
11 34 173.2 0 34
12 20 173.2 0 20
13 25 173.2 0 25
14 48 173.2 0 48
15 36 173.2 0 36
16 28 173.2 0 28
17 41 173.2 0 41
18 31 173.2 0 31
19 37 173.2 0 37
20 33 173.2 0 33
21 41 173.2 0 41
22 26 173.2 0 26
23 26 173.2 0 26
24 31 173.2 0 31
25 31 173.2 0 31
26 42 173.2 0 42
27 41 173.2 0 41
28 26 173.2 0 26
29 48 173.2 0 48
30 36 173.2 0 36
31 31 173.2 0 31
32 47 173.2 0 47
33 29 173.2 0 29
34 18 173.2 0 18
35 32 173.2 0 32
36 45 173.2 0 45
37 41 173.2 0 41
38 35 173.2 0 35
39 35 173.2 0 35
40 37 173.2 0 37
41 24 173.2 0 24
42 22 173.2 0 22
43 33 173.2 0 33
44 36 173.2 0 36
45 41 173.2 0 41
46 28 173.2 0 28
47 37 173.2 0 37
48 36 173.2 0 36
49 43 173.2 0 43
50 31 173.2 0 31
51 30 173.2 0 30
52 35 173.2 0 35
53 30 173.2 0 30
54 36 173.2 0 36
55 42 173.2 0 42
56 39 173.2 0 39
57 21 173.2 0 21
58 39 173.2 0 39
59 41 173.2 0 41
60 24 173.2 0 24
61 33 173.2 0 33
62 28 173.2 0 28
63 30 173.2 0 30
64 33 173.2 0 33
65 32 173.2 0 32
66 32 173.2 0 32
67 26 173.2 0 26
68 34 173.2 0 34
69 25 173.2 0 25
70 42 173.2 0 42
71 36 173.2 0 36
72 19 173.2 0 19
73 40 173.2 0 40
74 31 173.2 0 31
75 22 173.2 0 22
76 16 173.2 0 16
77 41 173.2 0 41
78 37 173.2 0 37
79 28 173.2 0 28
80 36 173.2 0 36
81 27 173.2 0 27
82 48 173.2 0 48
83 45 173.2 0 45
84 29 173.2 0 29
85 35 173.2 0 35
86 55 173.2 0 55
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R51_S205_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R51_S205_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.30 s (9 µs/read; 6.34 M reads/minute).
=== Summary ===
Total reads processed: 2,885,722
Reads with adapters: 946,977 (32.8%)
== Read fate breakdown ==
Reads that were too short: 219,717 (7.6%)
Reads written (passing filters): 2,666,005 (92.4%)
Total basepairs processed: 291,457,922 bp
Total written (filtered): 209,375,295 bp (71.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 828362 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 32.0%
G: 28.0%
T: 29.5%
none/other: 10.5%
Overview of removed sequences
length count expect max.err error counts
3 67691 45089.4 0 67691
4 30315 11272.4 0 30315
5 15669 2818.1 0 15669
6 10610 704.5 0 10610
7 8600 176.1 0 8600
8 7968 44.0 0 7968
9 8051 44.0 0 8051
10 7944 44.0 0 7944
11 7942 44.0 0 7942
12 7821 44.0 0 7821
13 7882 44.0 0 7882
14 8236 44.0 0 8236
15 7870 44.0 0 7870
16 8331 44.0 0 8331
17 8149 44.0 0 8149
18 8135 44.0 0 8135
19 8074 44.0 0 8074
20 8001 44.0 0 8001
21 8235 44.0 0 8235
22 8057 44.0 0 8057
23 7871 44.0 0 7871
24 7928 44.0 0 7928
25 7762 44.0 0 7762
26 7886 44.0 0 7886
27 8007 44.0 0 8007
28 8252 44.0 0 8252
29 8178 44.0 0 8178
30 7928 44.0 0 7928
31 8406 44.0 0 8406
32 7946 44.0 0 7946
33 7904 44.0 0 7904
34 8044 44.0 0 8044
35 7870 44.0 0 7870
36 8048 44.0 0 8048
37 8019 44.0 0 8019
38 7733 44.0 0 7733
39 7951 44.0 0 7951
40 7983 44.0 0 7983
41 7739 44.0 0 7739
42 8000 44.0 0 8000
43 8193 44.0 0 8193
44 7776 44.0 0 7776
45 7994 44.0 0 7994
46 8112 44.0 0 8112
47 7961 44.0 0 7961
48 8084 44.0 0 8084
49 10421 44.0 0 10421
50 11902 44.0 0 11902
51 8648 44.0 0 8648
52 8700 44.0 0 8700
53 8513 44.0 0 8513
54 7805 44.0 0 7805
55 7944 44.0 0 7944
56 8123 44.0 0 8123
57 8085 44.0 0 8085
58 8346 44.0 0 8346
59 7916 44.0 0 7916
60 7949 44.0 0 7949
61 8216 44.0 0 8216
62 7973 44.0 0 7973
63 7799 44.0 0 7799
64 7796 44.0 0 7796
65 7963 44.0 0 7963
66 7817 44.0 0 7817
67 7630 44.0 0 7630
68 7403 44.0 0 7403
69 7322 44.0 0 7322
70 6938 44.0 0 6938
71 7094 44.0 0 7094
72 6895 44.0 0 6895
73 6343 44.0 0 6343
74 6102 44.0 0 6102
75 6065 44.0 0 6065
76 5616 44.0 0 5616
77 5950 44.0 0 5950
78 5598 44.0 0 5598
79 5984 44.0 0 5984
80 5698 44.0 0 5698
81 6122 44.0 0 6122
82 7077 44.0 0 7077
83 7865 44.0 0 7865
84 8303 44.0 0 8303
85 8537 44.0 0 8537
86 86748 44.0 0 86748
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 57836 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.2%
C: 33.7%
G: 0.0%
T: 38.8%
none/other: 2.4%
Overview of removed sequences
length count expect max.err error counts
3 14482 45089.4 0 14482
4 3557 11272.4 0 3557
5 1183 2818.1 0 1183
6 793 704.5 0 793
7 722 176.1 0 722
8 703 44.0 0 703
9 652 44.0 0 652
10 669 44.0 0 669
11 630 44.0 0 630
12 634 44.0 0 634
13 579 44.0 0 579
14 627 44.0 0 627
15 622 44.0 0 622
16 609 44.0 0 609
17 564 44.0 0 564
18 640 44.0 0 640
19 584 44.0 0 584
20 569 44.0 0 569
21 546 44.0 0 546
22 550 44.0 0 550
23 572 44.0 0 572
24 617 44.0 0 617
25 643 44.0 0 643
26 565 44.0 0 565
27 561 44.0 0 561
28 619 44.0 0 619
29 603 44.0 0 603
30 576 44.0 0 576
31 581 44.0 0 581
32 588 44.0 0 588
33 628 44.0 0 628
34 572 44.0 0 572
35 591 44.0 0 591
36 598 44.0 0 598
37 635 44.0 0 635
38 636 44.0 0 636
39 569 44.0 0 569
40 571 44.0 0 571
41 591 44.0 0 591
42 579 44.0 0 579
43 588 44.0 0 588
44 611 44.0 0 611
45 564 44.0 0 564
46 568 44.0 0 568
47 631 44.0 0 631
48 611 44.0 0 611
49 519 44.0 0 519
50 537 44.0 0 537
51 485 44.0 0 485
52 514 44.0 0 514
53 484 44.0 0 484
54 528 44.0 0 528
55 557 44.0 0 557
56 541 44.0 0 541
57 534 44.0 0 534
58 534 44.0 0 534
59 537 44.0 0 537
60 511 44.0 0 511
61 467 44.0 0 467
62 418 44.0 0 418
63 439 44.0 0 439
64 418 44.0 0 418
65 349 44.0 0 349
66 326 44.0 0 326
67 305 44.0 0 305
68 275 44.0 0 275
69 258 44.0 0 258
70 180 44.0 0 180
71 187 44.0 0 187
72 175 44.0 0 175
73 154 44.0 0 154
74 126 44.0 0 126
75 117 44.0 0 117
76 91 44.0 0 91
77 89 44.0 0 89
78 71 44.0 0 71
79 60 44.0 0 60
80 53 44.0 0 53
81 38 44.0 0 38
82 37 44.0 0 37
83 40 44.0 0 40
84 46 44.0 0 46
85 55 44.0 0 55
86 1398 44.0 0 1398
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60779 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 22.6%
G: 20.8%
T: 21.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44843 45089.4 0 44843
4 10768 11272.4 0 10768
5 2132 2818.1 0 2132
6 287 704.5 0 287
7 46 176.1 0 46
8 27 176.1 0 27
9 27 176.1 0 27
10 32 176.1 0 32
11 44 176.1 0 44
12 37 176.1 0 37
13 25 176.1 0 25
14 35 176.1 0 35
15 37 176.1 0 37
16 31 176.1 0 31
17 33 176.1 0 33
18 31 176.1 0 31
19 31 176.1 0 31
20 36 176.1 0 36
21 33 176.1 0 33
22 34 176.1 0 34
23 31 176.1 0 31
24 38 176.1 0 38
25 46 176.1 0 46
26 50 176.1 0 50
27 30 176.1 0 30
28 27 176.1 0 27
29 46 176.1 0 46
30 35 176.1 0 35
31 26 176.1 0 26
32 49 176.1 0 49
33 41 176.1 0 41
34 22 176.1 0 22
35 38 176.1 0 38
36 42 176.1 0 42
37 30 176.1 0 30
38 37 176.1 0 37
39 33 176.1 0 33
40 41 176.1 0 41
41 45 176.1 0 45
42 26 176.1 0 26
43 30 176.1 0 30
44 48 176.1 0 48
45 25 176.1 0 25
46 29 176.1 0 29
47 51 176.1 0 51
48 36 176.1 0 36
49 39 176.1 0 39
50 20 176.1 0 20
51 41 176.1 0 41
52 32 176.1 0 32
53 31 176.1 0 31
54 33 176.1 0 33
55 37 176.1 0 37
56 27 176.1 0 27
57 36 176.1 0 36
58 34 176.1 0 34
59 33 176.1 0 33
60 33 176.1 0 33
61 32 176.1 0 32
62 40 176.1 0 40
63 37 176.1 0 37
64 25 176.1 0 25
65 35 176.1 0 35
66 21 176.1 0 21
67 23 176.1 0 23
68 30 176.1 0 30
69 24 176.1 0 24
70 35 176.1 0 35
71 37 176.1 0 37
72 24 176.1 0 24
73 31 176.1 0 31
74 25 176.1 0 25
75 27 176.1 0 27
76 22 176.1 0 22
77 53 176.1 0 53
78 46 176.1 0 46
79 33 176.1 0 33
80 31 176.1 0 31
81 25 176.1 0 25
82 36 176.1 0 36
83 37 176.1 0 37
84 37 176.1 0 37
85 44 176.1 0 44
86 52 176.1 0 52
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R52_S204_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R52_S204_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.05 s (10 µs/read; 6.22 M reads/minute).
=== Summary ===
Total reads processed: 2,388,638
Reads with adapters: 600,106 (25.1%)
== Read fate breakdown ==
Reads that were too short: 141,456 (5.9%)
Reads written (passing filters): 2,247,182 (94.1%)
Total basepairs processed: 241,252,438 bp
Total written (filtered): 182,341,495 bp (75.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 508095 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.4%
G: 27.7%
T: 30.9%
none/other: 12.0%
Overview of removed sequences
length count expect max.err error counts
3 59750 37322.5 0 59750
4 24479 9330.6 0 24479
5 12056 2332.7 0 12056
6 6665 583.2 0 6665
7 5179 145.8 0 5179
8 4472 36.4 0 4472
9 4422 36.4 0 4422
10 4456 36.4 0 4456
11 4424 36.4 0 4424
12 4423 36.4 0 4423
13 4478 36.4 0 4478
14 4442 36.4 0 4442
15 4426 36.4 0 4426
16 4630 36.4 0 4630
17 4454 36.4 0 4454
18 4707 36.4 0 4707
19 4475 36.4 0 4475
20 4389 36.4 0 4389
21 4317 36.4 0 4317
22 4526 36.4 0 4526
23 4412 36.4 0 4412
24 4322 36.4 0 4322
25 4291 36.4 0 4291
26 4245 36.4 0 4245
27 4271 36.4 0 4271
28 4226 36.4 0 4226
29 4289 36.4 0 4289
30 4223 36.4 0 4223
31 4401 36.4 0 4401
32 4298 36.4 0 4298
33 4460 36.4 0 4460
34 4433 36.4 0 4433
35 4280 36.4 0 4280
36 4208 36.4 0 4208
37 4246 36.4 0 4246
38 3996 36.4 0 3996
39 4239 36.4 0 4239
40 4287 36.4 0 4287
41 4195 36.4 0 4195
42 4450 36.4 0 4450
43 4442 36.4 0 4442
44 4310 36.4 0 4310
45 4388 36.4 0 4388
46 4499 36.4 0 4499
47 4538 36.4 0 4538
48 4218 36.4 0 4218
49 5875 36.4 0 5875
50 6753 36.4 0 6753
51 4498 36.4 0 4498
52 4829 36.4 0 4829
53 4663 36.4 0 4663
54 4287 36.4 0 4287
55 4302 36.4 0 4302
56 4330 36.4 0 4330
57 4165 36.4 0 4165
58 4414 36.4 0 4414
59 4402 36.4 0 4402
60 4362 36.4 0 4362
61 4425 36.4 0 4425
62 4327 36.4 0 4327
63 4197 36.4 0 4197
64 4183 36.4 0 4183
65 4323 36.4 0 4323
66 3988 36.4 0 3988
67 4094 36.4 0 4094
68 3865 36.4 0 3865
69 3867 36.4 0 3867
70 3629 36.4 0 3629
71 3738 36.4 0 3738
72 3726 36.4 0 3726
73 3564 36.4 0 3564
74 3358 36.4 0 3358
75 3434 36.4 0 3434
76 3268 36.4 0 3268
77 3242 36.4 0 3242
78 3302 36.4 0 3302
79 3714 36.4 0 3714
80 3712 36.4 0 3712
81 4166 36.4 0 4166
82 5015 36.4 0 5015
83 5509 36.4 0 5509
84 6131 36.4 0 6131
85 6276 36.4 0 6276
86 60825 36.4 0 60825
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35797 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.3%
C: 32.8%
G: 0.0%
T: 35.8%
none/other: 3.1%
Overview of removed sequences
length count expect max.err error counts
3 13673 37322.5 0 13673
4 3283 9330.6 0 3283
5 895 2332.7 0 895
6 420 583.2 0 420
7 335 145.8 0 335
8 329 36.4 0 329
9 335 36.4 0 335
10 320 36.4 0 320
11 327 36.4 0 327
12 277 36.4 0 277
13 285 36.4 0 285
14 261 36.4 0 261
15 306 36.4 0 306
16 304 36.4 0 304
17 283 36.4 0 283
18 299 36.4 0 299
19 287 36.4 0 287
20 288 36.4 0 288
21 276 36.4 0 276
22 278 36.4 0 278
23 298 36.4 0 298
24 289 36.4 0 289
25 292 36.4 0 292
26 319 36.4 0 319
27 238 36.4 0 238
28 281 36.4 0 281
29 273 36.4 0 273
30 254 36.4 0 254
31 274 36.4 0 274
32 251 36.4 0 251
33 264 36.4 0 264
34 265 36.4 0 265
35 273 36.4 0 273
36 239 36.4 0 239
37 267 36.4 0 267
38 229 36.4 0 229
39 260 36.4 0 260
40 251 36.4 0 251
41 244 36.4 0 244
42 268 36.4 0 268
43 211 36.4 0 211
44 255 36.4 0 255
45 263 36.4 0 263
46 256 36.4 0 256
47 263 36.4 0 263
48 230 36.4 0 230
49 252 36.4 0 252
50 221 36.4 0 221
51 232 36.4 0 232
52 250 36.4 0 250
53 213 36.4 0 213
54 222 36.4 0 222
55 208 36.4 0 208
56 175 36.4 0 175
57 198 36.4 0 198
58 216 36.4 0 216
59 204 36.4 0 204
60 225 36.4 0 225
61 189 36.4 0 189
62 171 36.4 0 171
63 157 36.4 0 157
64 169 36.4 0 169
65 129 36.4 0 129
66 147 36.4 0 147
67 129 36.4 0 129
68 118 36.4 0 118
69 112 36.4 0 112
70 95 36.4 0 95
71 83 36.4 0 83
72 94 36.4 0 94
73 87 36.4 0 87
74 77 36.4 0 77
75 48 36.4 0 48
76 42 36.4 0 42
77 49 36.4 0 49
78 39 36.4 0 39
79 42 36.4 0 42
80 47 36.4 0 47
81 27 36.4 0 27
82 29 36.4 0 29
83 41 36.4 0 41
84 50 36.4 0 50
85 52 36.4 0 52
86 1090 36.4 0 1090
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 56214 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.0%
C: 22.9%
G: 21.6%
T: 21.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41571 37322.5 0 41571
4 9732 9330.6 0 9732
5 2010 2332.7 0 2010
6 312 583.2 0 312
7 33 145.8 0 33
8 42 145.8 0 42
9 22 145.8 0 22
10 32 145.8 0 32
11 29 145.8 0 29
12 26 145.8 0 26
13 39 145.8 0 39
14 39 145.8 0 39
15 42 145.8 0 42
16 30 145.8 0 30
17 35 145.8 0 35
18 37 145.8 0 37
19 30 145.8 0 30
20 37 145.8 0 37
21 40 145.8 0 40
22 26 145.8 0 26
23 21 145.8 0 21
24 24 145.8 0 24
25 38 145.8 0 38
26 32 145.8 0 32
27 30 145.8 0 30
28 36 145.8 0 36
29 39 145.8 0 39
30 31 145.8 0 31
31 30 145.8 0 30
32 30 145.8 0 30
33 21 145.8 0 21
34 31 145.8 0 31
35 28 145.8 0 28
36 27 145.8 0 27
37 39 145.8 0 39
38 24 145.8 0 24
39 27 145.8 0 27
40 37 145.8 0 37
41 31 145.8 0 31
42 22 145.8 0 22
43 35 145.8 0 35
44 33 145.8 0 33
45 26 145.8 0 26
46 23 145.8 0 23
47 37 145.8 0 37
48 32 145.8 0 32
49 32 145.8 0 32
50 36 145.8 0 36
51 37 145.8 0 37
52 31 145.8 0 31
53 28 145.8 0 28
54 29 145.8 0 29
55 38 145.8 0 38
56 21 145.8 0 21
57 37 145.8 0 37
58 31 145.8 0 31
59 42 145.8 0 42
60 43 145.8 0 43
61 29 145.8 0 29
62 36 145.8 0 36
63 30 145.8 0 30
64 20 145.8 0 20
65 44 145.8 0 44
66 32 145.8 0 32
67 29 145.8 0 29
68 30 145.8 0 30
69 30 145.8 0 30
70 43 145.8 0 43
71 33 145.8 0 33
72 18 145.8 0 18
73 31 145.8 0 31
74 30 145.8 0 30
75 20 145.8 0 20
76 22 145.8 0 22
77 64 145.8 0 64
78 37 145.8 0 37
79 31 145.8 0 31
80 37 145.8 0 37
81 30 145.8 0 30
82 35 145.8 0 35
83 38 145.8 0 38
84 25 145.8 0 25
85 51 145.8 0 51
86 36 145.8 0 36
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R52_S204_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R52_S204_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.11 s (9 µs/read; 6.34 M reads/minute).
=== Summary ===
Total reads processed: 2,441,192
Reads with adapters: 616,442 (25.3%)
== Read fate breakdown ==
Reads that were too short: 148,061 (6.1%)
Reads written (passing filters): 2,293,131 (93.9%)
Total basepairs processed: 246,560,392 bp
Total written (filtered): 186,007,928 bp (75.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 522731 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.5%
G: 27.7%
T: 30.5%
none/other: 12.2%
Overview of removed sequences
length count expect max.err error counts
3 60619 38143.6 0 60619
4 25209 9535.9 0 25209
5 12007 2384.0 0 12007
6 6685 596.0 0 6685
7 5480 149.0 0 5480
8 4594 37.2 0 4594
9 4343 37.2 0 4343
10 4386 37.2 0 4386
11 4494 37.2 0 4494
12 4421 37.2 0 4421
13 4486 37.2 0 4486
14 4548 37.2 0 4548
15 4555 37.2 0 4555
16 4614 37.2 0 4614
17 4609 37.2 0 4609
18 4632 37.2 0 4632
19 4585 37.2 0 4585
20 4527 37.2 0 4527
21 4624 37.2 0 4624
22 4612 37.2 0 4612
23 4305 37.2 0 4305
24 4440 37.2 0 4440
25 4356 37.2 0 4356
26 4339 37.2 0 4339
27 4439 37.2 0 4439
28 4378 37.2 0 4378
29 4475 37.2 0 4475
30 4433 37.2 0 4433
31 4494 37.2 0 4494
32 4512 37.2 0 4512
33 4357 37.2 0 4357
34 4293 37.2 0 4293
35 4321 37.2 0 4321
36 4511 37.2 0 4511
37 4336 37.2 0 4336
38 4389 37.2 0 4389
39 4449 37.2 0 4449
40 4473 37.2 0 4473
41 4395 37.2 0 4395
42 4557 37.2 0 4557
43 4540 37.2 0 4540
44 4304 37.2 0 4304
45 4427 37.2 0 4427
46 4613 37.2 0 4613
47 4559 37.2 0 4559
48 4410 37.2 0 4410
49 5877 37.2 0 5877
50 6904 37.2 0 6904
51 4720 37.2 0 4720
52 4955 37.2 0 4955
53 4721 37.2 0 4721
54 4346 37.2 0 4346
55 4504 37.2 0 4504
56 4525 37.2 0 4525
57 4351 37.2 0 4351
58 4501 37.2 0 4501
59 4536 37.2 0 4536
60 4549 37.2 0 4549
61 4343 37.2 0 4343
62 4439 37.2 0 4439
63 4247 37.2 0 4247
64 4396 37.2 0 4396
65 4310 37.2 0 4310
66 4218 37.2 0 4218
67 4315 37.2 0 4315
68 4063 37.2 0 4063
69 3963 37.2 0 3963
70 3821 37.2 0 3821
71 4063 37.2 0 4063
72 3903 37.2 0 3903
73 3746 37.2 0 3746
74 3532 37.2 0 3532
75 3715 37.2 0 3715
76 3395 37.2 0 3395
77 3406 37.2 0 3406
78 3382 37.2 0 3382
79 3934 37.2 0 3934
80 3817 37.2 0 3817
81 4431 37.2 0 4431
82 5181 37.2 0 5181
83 5859 37.2 0 5859
84 6263 37.2 0 6263
85 6524 37.2 0 6524
86 63841 37.2 0 63841
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 36275 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.3%
C: 32.7%
G: 0.0%
T: 36.3%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 13754 38143.6 0 13754
4 3215 9535.9 0 3215
5 906 2384.0 0 906
6 432 596.0 0 432
7 358 149.0 0 358
8 350 37.2 0 350
9 320 37.2 0 320
10 331 37.2 0 331
11 323 37.2 0 323
12 335 37.2 0 335
13 296 37.2 0 296
14 317 37.2 0 317
15 309 37.2 0 309
16 290 37.2 0 290
17 284 37.2 0 284
18 296 37.2 0 296
19 286 37.2 0 286
20 277 37.2 0 277
21 301 37.2 0 301
22 276 37.2 0 276
23 313 37.2 0 313
24 289 37.2 0 289
25 260 37.2 0 260
26 308 37.2 0 308
27 287 37.2 0 287
28 277 37.2 0 277
29 270 37.2 0 270
30 290 37.2 0 290
31 251 37.2 0 251
32 272 37.2 0 272
33 294 37.2 0 294
34 270 37.2 0 270
35 259 37.2 0 259
36 261 37.2 0 261
37 241 37.2 0 241
38 270 37.2 0 270
39 251 37.2 0 251
40 271 37.2 0 271
41 227 37.2 0 227
42 242 37.2 0 242
43 270 37.2 0 270
44 245 37.2 0 245
45 266 37.2 0 266
46 253 37.2 0 253
47 239 37.2 0 239
48 238 37.2 0 238
49 218 37.2 0 218
50 247 37.2 0 247
51 242 37.2 0 242
52 243 37.2 0 243
53 253 37.2 0 253
54 253 37.2 0 253
55 222 37.2 0 222
56 207 37.2 0 207
57 267 37.2 0 267
58 227 37.2 0 227
59 220 37.2 0 220
60 211 37.2 0 211
61 224 37.2 0 224
62 194 37.2 0 194
63 178 37.2 0 178
64 163 37.2 0 163
65 136 37.2 0 136
66 164 37.2 0 164
67 127 37.2 0 127
68 136 37.2 0 136
69 105 37.2 0 105
70 105 37.2 0 105
71 89 37.2 0 89
72 79 37.2 0 79
73 80 37.2 0 80
74 64 37.2 0 64
75 65 37.2 0 65
76 51 37.2 0 51
77 44 37.2 0 44
78 42 37.2 0 42
79 36 37.2 0 36
80 33 37.2 0 33
81 25 37.2 0 25
82 28 37.2 0 28
83 32 37.2 0 32
84 45 37.2 0 45
85 44 37.2 0 44
86 1006 37.2 0 1006
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 57436 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.2%
C: 22.8%
G: 21.1%
T: 21.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 42134 38143.6 0 42134
4 10225 9535.9 0 10225
5 2082 2384.0 0 2082
6 302 596.0 0 302
7 37 149.0 0 37
8 39 149.0 0 39
9 28 149.0 0 28
10 29 149.0 0 29
11 34 149.0 0 34
12 30 149.0 0 30
13 36 149.0 0 36
14 27 149.0 0 27
15 25 149.0 0 25
16 36 149.0 0 36
17 32 149.0 0 32
18 38 149.0 0 38
19 32 149.0 0 32
20 41 149.0 0 41
21 16 149.0 0 16
22 30 149.0 0 30
23 41 149.0 0 41
24 22 149.0 0 22
25 39 149.0 0 39
26 41 149.0 0 41
27 36 149.0 0 36
28 30 149.0 0 30
29 43 149.0 0 43
30 33 149.0 0 33
31 38 149.0 0 38
32 53 149.0 0 53
33 35 149.0 0 35
34 22 149.0 0 22
35 23 149.0 0 23
36 28 149.0 0 28
37 34 149.0 0 34
38 25 149.0 0 25
39 36 149.0 0 36
40 36 149.0 0 36
41 39 149.0 0 39
42 37 149.0 0 37
43 20 149.0 0 20
44 32 149.0 0 32
45 31 149.0 0 31
46 26 149.0 0 26
47 34 149.0 0 34
48 24 149.0 0 24
49 32 149.0 0 32
50 30 149.0 0 30
51 41 149.0 0 41
52 45 149.0 0 45
53 22 149.0 0 22
54 27 149.0 0 27
55 44 149.0 0 44
56 33 149.0 0 33
57 31 149.0 0 31
58 50 149.0 0 50
59 33 149.0 0 33
60 40 149.0 0 40
61 32 149.0 0 32
62 36 149.0 0 36
63 32 149.0 0 32
64 40 149.0 0 40
65 49 149.0 0 49
66 37 149.0 0 37
67 31 149.0 0 31
68 28 149.0 0 28
69 16 149.0 0 16
70 35 149.0 0 35
71 44 149.0 0 44
72 29 149.0 0 29
73 25 149.0 0 25
74 36 149.0 0 36
75 26 149.0 0 26
76 24 149.0 0 24
77 60 149.0 0 60
78 29 149.0 0 29
79 28 149.0 0 28
80 35 149.0 0 35
81 42 149.0 0 42
82 38 149.0 0 38
83 52 149.0 0 52
84 29 149.0 0 29
85 29 149.0 0 29
86 35 149.0 0 35
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R53_S199_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R53_S199_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.16 s (9 µs/read; 6.67 M reads/minute).
=== Summary ===
Total reads processed: 2,795,462
Reads with adapters: 1,036,638 (37.1%)
== Read fate breakdown ==
Reads that were too short: 368,817 (13.2%)
Reads written (passing filters): 2,426,645 (86.8%)
Total basepairs processed: 282,341,662 bp
Total written (filtered): 189,898,774 bp (67.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 935560 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 27.1%
G: 26.1%
T: 27.7%
none/other: 19.1%
Overview of removed sequences
length count expect max.err error counts
3 60802 43679.1 0 60802
4 26050 10919.8 0 26050
5 14306 2729.9 0 14306
6 9833 682.5 0 9833
7 8128 170.6 0 8128
8 7067 42.7 0 7067
9 6986 42.7 0 6986
10 7064 42.7 0 7064
11 6970 42.7 0 6970
12 6938 42.7 0 6938
13 7026 42.7 0 7026
14 7256 42.7 0 7256
15 7234 42.7 0 7234
16 7494 42.7 0 7494
17 7325 42.7 0 7325
18 7433 42.7 0 7433
19 7483 42.7 0 7483
20 7041 42.7 0 7041
21 7385 42.7 0 7385
22 7450 42.7 0 7450
23 6885 42.7 0 6885
24 7025 42.7 0 7025
25 7394 42.7 0 7394
26 7178 42.7 0 7178
27 6952 42.7 0 6952
28 7257 42.7 0 7257
29 7449 42.7 0 7449
30 7051 42.7 0 7051
31 7799 42.7 0 7799
32 7273 42.7 0 7273
33 7107 42.7 0 7107
34 7370 42.7 0 7370
35 7237 42.7 0 7237
36 7112 42.7 0 7112
37 7322 42.7 0 7322
38 6799 42.7 0 6799
39 7121 42.7 0 7121
40 7182 42.7 0 7182
41 7488 42.7 0 7488
42 7217 42.7 0 7217
43 7374 42.7 0 7374
44 7226 42.7 0 7226
45 7500 42.7 0 7500
46 7736 42.7 0 7736
47 7949 42.7 0 7949
48 7582 42.7 0 7582
49 10339 42.7 0 10339
50 12277 42.7 0 12277
51 8110 42.7 0 8110
52 8541 42.7 0 8541
53 8528 42.7 0 8528
54 7639 42.7 0 7639
55 8493 42.7 0 8493
56 8168 42.7 0 8168
57 7654 42.7 0 7654
58 8484 42.7 0 8484
59 8057 42.7 0 8057
60 8256 42.7 0 8256
61 8671 42.7 0 8671
62 8191 42.7 0 8191
63 7984 42.7 0 7984
64 8057 42.7 0 8057
65 8017 42.7 0 8017
66 7945 42.7 0 7945
67 7935 42.7 0 7935
68 7584 42.7 0 7584
69 7337 42.7 0 7337
70 6735 42.7 0 6735
71 7075 42.7 0 7075
72 6756 42.7 0 6756
73 6479 42.7 0 6479
74 6174 42.7 0 6174
75 5905 42.7 0 5905
76 6200 42.7 0 6200
77 6226 42.7 0 6226
78 7310 42.7 0 7310
79 8821 42.7 0 8821
80 9338 42.7 0 9338
81 10658 42.7 0 10658
82 14553 42.7 0 14553
83 17681 42.7 0 17681
84 21287 42.7 0 21287
85 22680 42.7 0 22680
86 178559 42.7 0 178559
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 49730 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 24.7%
C: 35.4%
G: 0.0%
T: 37.6%
none/other: 2.2%
Overview of removed sequences
length count expect max.err error counts
3 15221 43679.1 0 15221
4 3540 10919.8 0 3540
5 1208 2729.9 0 1208
6 686 682.5 0 686
7 605 170.6 0 605
8 605 42.7 0 605
9 566 42.7 0 566
10 607 42.7 0 607
11 568 42.7 0 568
12 537 42.7 0 537
13 532 42.7 0 532
14 459 42.7 0 459
15 518 42.7 0 518
16 511 42.7 0 511
17 479 42.7 0 479
18 548 42.7 0 548
19 521 42.7 0 521
20 475 42.7 0 475
21 459 42.7 0 459
22 460 42.7 0 460
23 462 42.7 0 462
24 493 42.7 0 493
25 479 42.7 0 479
26 466 42.7 0 466
27 470 42.7 0 470
28 470 42.7 0 470
29 467 42.7 0 467
30 485 42.7 0 485
31 453 42.7 0 453
32 433 42.7 0 433
33 448 42.7 0 448
34 464 42.7 0 464
35 457 42.7 0 457
36 436 42.7 0 436
37 446 42.7 0 446
38 403 42.7 0 403
39 383 42.7 0 383
40 428 42.7 0 428
41 427 42.7 0 427
42 387 42.7 0 387
43 431 42.7 0 431
44 420 42.7 0 420
45 387 42.7 0 387
46 404 42.7 0 404
47 395 42.7 0 395
48 402 42.7 0 402
49 412 42.7 0 412
50 388 42.7 0 388
51 433 42.7 0 433
52 394 42.7 0 394
53 393 42.7 0 393
54 371 42.7 0 371
55 361 42.7 0 361
56 375 42.7 0 375
57 347 42.7 0 347
58 366 42.7 0 366
59 359 42.7 0 359
60 332 42.7 0 332
61 332 42.7 0 332
62 342 42.7 0 342
63 301 42.7 0 301
64 286 42.7 0 286
65 207 42.7 0 207
66 226 42.7 0 226
67 206 42.7 0 206
68 159 42.7 0 159
69 186 42.7 0 186
70 181 42.7 0 181
71 142 42.7 0 142
72 133 42.7 0 133
73 137 42.7 0 137
74 118 42.7 0 118
75 101 42.7 0 101
76 82 42.7 0 82
77 75 42.7 0 75
78 52 42.7 0 52
79 50 42.7 0 50
80 54 42.7 0 54
81 36 42.7 0 36
82 40 42.7 0 40
83 46 42.7 0 46
84 41 42.7 0 41
85 57 42.7 0 57
86 1108 42.7 0 1108
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 51348 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 23.0%
G: 19.3%
T: 22.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 38433 43679.1 0 38433
4 8642 10919.8 0 8642
5 1730 2729.9 0 1730
6 316 682.5 0 316
7 27 170.6 0 27
8 28 170.6 0 28
9 26 170.6 0 26
10 27 170.6 0 27
11 28 170.6 0 28
12 32 170.6 0 32
13 33 170.6 0 33
14 22 170.6 0 22
15 47 170.6 0 47
16 23 170.6 0 23
17 42 170.6 0 42
18 36 170.6 0 36
19 31 170.6 0 31
20 40 170.6 0 40
21 31 170.6 0 31
22 23 170.6 0 23
23 33 170.6 0 33
24 24 170.6 0 24
25 34 170.6 0 34
26 26 170.6 0 26
27 18 170.6 0 18
28 35 170.6 0 35
29 33 170.6 0 33
30 34 170.6 0 34
31 27 170.6 0 27
32 23 170.6 0 23
33 21 170.6 0 21
34 21 170.6 0 21
35 24 170.6 0 24
36 25 170.6 0 25
37 30 170.6 0 30
38 22 170.6 0 22
39 17 170.6 0 17
40 17 170.6 0 17
41 16 170.6 0 16
42 36 170.6 0 36
43 31 170.6 0 31
44 26 170.6 0 26
45 23 170.6 0 23
46 33 170.6 0 33
47 27 170.6 0 27
48 44 170.6 0 44
49 35 170.6 0 35
50 27 170.6 0 27
51 37 170.6 0 37
52 27 170.6 0 27
53 18 170.6 0 18
54 21 170.6 0 21
55 35 170.6 0 35
56 24 170.6 0 24
57 15 170.6 0 15
58 26 170.6 0 26
59 27 170.6 0 27
60 33 170.6 0 33
61 22 170.6 0 22
62 30 170.6 0 30
63 32 170.6 0 32
64 25 170.6 0 25
65 41 170.6 0 41
66 36 170.6 0 36
67 25 170.6 0 25
68 22 170.6 0 22
69 22 170.6 0 22
70 26 170.6 0 26
71 27 170.6 0 27
72 28 170.6 0 28
73 22 170.6 0 22
74 29 170.6 0 29
75 27 170.6 0 27
76 18 170.6 0 18
77 32 170.6 0 32
78 35 170.6 0 35
79 23 170.6 0 23
80 25 170.6 0 25
81 27 170.6 0 27
82 18 170.6 0 18
83 25 170.6 0 25
84 32 170.6 0 32
85 34 170.6 0 34
86 23 170.6 0 23
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R53_S199_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R53_S199_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.77 s (9 µs/read; 6.66 M reads/minute).
=== Summary ===
Total reads processed: 2,859,267
Reads with adapters: 1,071,338 (37.5%)
== Read fate breakdown ==
Reads that were too short: 385,090 (13.5%)
Reads written (passing filters): 2,474,177 (86.5%)
Total basepairs processed: 288,785,967 bp
Total written (filtered): 193,381,487 bp (67.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 967764 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 27.1%
G: 26.2%
T: 27.4%
none/other: 19.4%
Overview of removed sequences
length count expect max.err error counts
3 61547 44676.0 0 61547
4 26690 11169.0 0 26690
5 14303 2792.3 0 14303
6 10107 698.1 0 10107
7 8475 174.5 0 8475
8 7258 43.6 0 7258
9 7152 43.6 0 7152
10 7427 43.6 0 7427
11 7190 43.6 0 7190
12 7102 43.6 0 7102
13 7232 43.6 0 7232
14 7607 43.6 0 7607
15 7385 43.6 0 7385
16 7458 43.6 0 7458
17 7328 43.6 0 7328
18 7642 43.6 0 7642
19 7871 43.6 0 7871
20 7304 43.6 0 7304
21 7539 43.6 0 7539
22 7698 43.6 0 7698
23 7265 43.6 0 7265
24 7428 43.6 0 7428
25 7474 43.6 0 7474
26 7175 43.6 0 7175
27 7052 43.6 0 7052
28 7515 43.6 0 7515
29 7601 43.6 0 7601
30 7214 43.6 0 7214
31 7876 43.6 0 7876
32 7509 43.6 0 7509
33 7300 43.6 0 7300
34 7701 43.6 0 7701
35 7530 43.6 0 7530
36 7139 43.6 0 7139
37 7539 43.6 0 7539
38 6900 43.6 0 6900
39 7240 43.6 0 7240
40 7589 43.6 0 7589
41 7814 43.6 0 7814
42 7453 43.6 0 7453
43 7729 43.6 0 7729
44 7563 43.6 0 7563
45 7709 43.6 0 7709
46 8151 43.6 0 8151
47 8077 43.6 0 8077
48 7852 43.6 0 7852
49 10885 43.6 0 10885
50 12468 43.6 0 12468
51 8487 43.6 0 8487
52 9026 43.6 0 9026
53 8817 43.6 0 8817
54 7698 43.6 0 7698
55 8838 43.6 0 8838
56 8460 43.6 0 8460
57 8036 43.6 0 8036
58 8726 43.6 0 8726
59 8340 43.6 0 8340
60 8471 43.6 0 8471
61 8909 43.6 0 8909
62 8435 43.6 0 8435
63 8375 43.6 0 8375
64 8168 43.6 0 8168
65 8181 43.6 0 8181
66 8286 43.6 0 8286
67 8178 43.6 0 8178
68 7759 43.6 0 7759
69 7414 43.6 0 7414
70 7169 43.6 0 7169
71 7246 43.6 0 7246
72 7115 43.6 0 7115
73 6576 43.6 0 6576
74 6282 43.6 0 6282
75 6079 43.6 0 6079
76 6445 43.6 0 6445
77 6517 43.6 0 6517
78 7525 43.6 0 7525
79 9303 43.6 0 9303
80 9713 43.6 0 9713
81 11136 43.6 0 11136
82 15205 43.6 0 15205
83 18294 43.6 0 18294
84 22232 43.6 0 22232
85 23545 43.6 0 23545
86 187715 43.6 0 187715
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 51563 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.2%
C: 35.0%
G: 0.0%
T: 37.5%
none/other: 2.2%
Overview of removed sequences
length count expect max.err error counts
3 15574 44676.0 0 15574
4 3659 11169.0 0 3659
5 1209 2792.3 0 1209
6 674 698.1 0 674
7 632 174.5 0 632
8 631 43.6 0 631
9 603 43.6 0 603
10 592 43.6 0 592
11 563 43.6 0 563
12 572 43.6 0 572
13 540 43.6 0 540
14 490 43.6 0 490
15 535 43.6 0 535
16 530 43.6 0 530
17 522 43.6 0 522
18 507 43.6 0 507
19 521 43.6 0 521
20 520 43.6 0 520
21 462 43.6 0 462
22 482 43.6 0 482
23 479 43.6 0 479
24 487 43.6 0 487
25 506 43.6 0 506
26 463 43.6 0 463
27 511 43.6 0 511
28 506 43.6 0 506
29 469 43.6 0 469
30 502 43.6 0 502
31 463 43.6 0 463
32 513 43.6 0 513
33 549 43.6 0 549
34 474 43.6 0 474
35 513 43.6 0 513
36 465 43.6 0 465
37 477 43.6 0 477
38 497 43.6 0 497
39 412 43.6 0 412
40 469 43.6 0 469
41 437 43.6 0 437
42 446 43.6 0 446
43 405 43.6 0 405
44 407 43.6 0 407
45 425 43.6 0 425
46 408 43.6 0 408
47 436 43.6 0 436
48 433 43.6 0 433
49 448 43.6 0 448
50 434 43.6 0 434
51 391 43.6 0 391
52 419 43.6 0 419
53 446 43.6 0 446
54 378 43.6 0 378
55 389 43.6 0 389
56 380 43.6 0 380
57 392 43.6 0 392
58 363 43.6 0 363
59 373 43.6 0 373
60 343 43.6 0 343
61 342 43.6 0 342
62 287 43.6 0 287
63 306 43.6 0 306
64 265 43.6 0 265
65 262 43.6 0 262
66 236 43.6 0 236
67 195 43.6 0 195
68 199 43.6 0 199
69 183 43.6 0 183
70 185 43.6 0 185
71 147 43.6 0 147
72 126 43.6 0 126
73 133 43.6 0 133
74 125 43.6 0 125
75 118 43.6 0 118
76 97 43.6 0 97
77 87 43.6 0 87
78 64 43.6 0 64
79 47 43.6 0 47
80 64 43.6 0 64
81 56 43.6 0 56
82 41 43.6 0 41
83 38 43.6 0 38
84 48 43.6 0 48
85 45 43.6 0 45
86 1141 43.6 0 1141
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 52011 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 22.9%
G: 19.4%
T: 22.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 39076 44676.0 0 39076
4 8702 11169.0 0 8702
5 1770 2792.3 0 1770
6 322 698.1 0 322
7 38 174.5 0 38
8 27 174.5 0 27
9 27 174.5 0 27
10 36 174.5 0 36
11 32 174.5 0 32
12 29 174.5 0 29
13 32 174.5 0 32
14 41 174.5 0 41
15 34 174.5 0 34
16 30 174.5 0 30
17 38 174.5 0 38
18 38 174.5 0 38
19 14 174.5 0 14
20 27 174.5 0 27
21 30 174.5 0 30
22 21 174.5 0 21
23 25 174.5 0 25
24 21 174.5 0 21
25 35 174.5 0 35
26 29 174.5 0 29
27 26 174.5 0 26
28 26 174.5 0 26
29 23 174.5 0 23
30 28 174.5 0 28
31 21 174.5 0 21
32 22 174.5 0 22
33 15 174.5 0 15
34 19 174.5 0 19
35 19 174.5 0 19
36 27 174.5 0 27
37 27 174.5 0 27
38 13 174.5 0 13
39 20 174.5 0 20
40 18 174.5 0 18
41 15 174.5 0 15
42 22 174.5 0 22
43 29 174.5 0 29
44 19 174.5 0 19
45 32 174.5 0 32
46 27 174.5 0 27
47 32 174.5 0 32
48 34 174.5 0 34
49 26 174.5 0 26
50 35 174.5 0 35
51 36 174.5 0 36
52 37 174.5 0 37
53 32 174.5 0 32
54 23 174.5 0 23
55 32 174.5 0 32
56 29 174.5 0 29
57 22 174.5 0 22
58 20 174.5 0 20
59 19 174.5 0 19
60 35 174.5 0 35
61 30 174.5 0 30
62 32 174.5 0 32
63 23 174.5 0 23
64 23 174.5 0 23
65 29 174.5 0 29
66 37 174.5 0 37
67 36 174.5 0 36
68 27 174.5 0 27
69 15 174.5 0 15
70 15 174.5 0 15
71 24 174.5 0 24
72 27 174.5 0 27
73 20 174.5 0 20
74 24 174.5 0 24
75 28 174.5 0 28
76 19 174.5 0 19
77 37 174.5 0 37
78 40 174.5 0 40
79 21 174.5 0 21
80 19 174.5 0 19
81 26 174.5 0 26
82 20 174.5 0 20
83 23 174.5 0 23
84 30 174.5 0 30
85 20 174.5 0 20
86 32 174.5 0 32
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R54_S206_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R54_S206_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.76 s (9 µs/read; 6.40 M reads/minute).
=== Summary ===
Total reads processed: 3,067,312
Reads with adapters: 1,049,446 (34.2%)
== Read fate breakdown ==
Reads that were too short: 273,726 (8.9%)
Reads written (passing filters): 2,793,586 (91.1%)
Total basepairs processed: 309,798,512 bp
Total written (filtered): 219,169,604 bp (70.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 939711 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.3%
G: 28.8%
T: 27.5%
none/other: 12.4%
Overview of removed sequences
length count expect max.err error counts
3 70793 47926.8 0 70793
4 32532 11981.7 0 32532
5 17134 2995.4 0 17134
6 11787 748.9 0 11787
7 9873 187.2 0 9873
8 8736 46.8 0 8736
9 8856 46.8 0 8856
10 8935 46.8 0 8935
11 8883 46.8 0 8883
12 8860 46.8 0 8860
13 8848 46.8 0 8848
14 8967 46.8 0 8967
15 8981 46.8 0 8981
16 9471 46.8 0 9471
17 9317 46.8 0 9317
18 9350 46.8 0 9350
19 8964 46.8 0 8964
20 8771 46.8 0 8771
21 9191 46.8 0 9191
22 9139 46.8 0 9139
23 8527 46.8 0 8527
24 8681 46.8 0 8681
25 8594 46.8 0 8594
26 8550 46.8 0 8550
27 8438 46.8 0 8438
28 9063 46.8 0 9063
29 8842 46.8 0 8842
30 8469 46.8 0 8469
31 9348 46.8 0 9348
32 8772 46.8 0 8772
33 8721 46.8 0 8721
34 8691 46.8 0 8691
35 8806 46.8 0 8806
36 8621 46.8 0 8621
37 8450 46.8 0 8450
38 8186 46.8 0 8186
39 8661 46.8 0 8661
40 8927 46.8 0 8927
41 8588 46.8 0 8588
42 8928 46.8 0 8928
43 9159 46.8 0 9159
44 8215 46.8 0 8215
45 8508 46.8 0 8508
46 9038 46.8 0 9038
47 8459 46.8 0 8459
48 8529 46.8 0 8529
49 12699 46.8 0 12699
50 15115 46.8 0 15115
51 9422 46.8 0 9422
52 9909 46.8 0 9909
53 9458 46.8 0 9458
54 8320 46.8 0 8320
55 8675 46.8 0 8675
56 8556 46.8 0 8556
57 8594 46.8 0 8594
58 9039 46.8 0 9039
59 8558 46.8 0 8558
60 8722 46.8 0 8722
61 8471 46.8 0 8471
62 8380 46.8 0 8380
63 8261 46.8 0 8261
64 8194 46.8 0 8194
65 8058 46.8 0 8058
66 7821 46.8 0 7821
67 7691 46.8 0 7691
68 7894 46.8 0 7894
69 7502 46.8 0 7502
70 6993 46.8 0 6993
71 7895 46.8 0 7895
72 7350 46.8 0 7350
73 7053 46.8 0 7053
74 6714 46.8 0 6714
75 6616 46.8 0 6616
76 6451 46.8 0 6451
77 6681 46.8 0 6681
78 6399 46.8 0 6399
79 7464 46.8 0 7464
80 7176 46.8 0 7176
81 8665 46.8 0 8665
82 10301 46.8 0 10301
83 11159 46.8 0 11159
84 11873 46.8 0 11873
85 12260 46.8 0 12260
86 116163 46.8 0 116163
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 42426 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.8%
C: 32.0%
G: 0.0%
T: 37.3%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 15272 47926.8 0 15272
4 3494 11981.7 0 3494
5 1088 2995.4 0 1088
6 570 748.9 0 570
7 531 187.2 0 531
8 472 46.8 0 472
9 489 46.8 0 489
10 422 46.8 0 422
11 405 46.8 0 405
12 405 46.8 0 405
13 380 46.8 0 380
14 406 46.8 0 406
15 415 46.8 0 415
16 353 46.8 0 353
17 395 46.8 0 395
18 381 46.8 0 381
19 387 46.8 0 387
20 338 46.8 0 338
21 340 46.8 0 340
22 349 46.8 0 349
23 363 46.8 0 363
24 363 46.8 0 363
25 376 46.8 0 376
26 363 46.8 0 363
27 328 46.8 0 328
28 358 46.8 0 358
29 332 46.8 0 332
30 309 46.8 0 309
31 341 46.8 0 341
32 326 46.8 0 326
33 297 46.8 0 297
34 328 46.8 0 328
35 329 46.8 0 329
36 315 46.8 0 315
37 315 46.8 0 315
38 330 46.8 0 330
39 319 46.8 0 319
40 328 46.8 0 328
41 301 46.8 0 301
42 343 46.8 0 343
43 339 46.8 0 339
44 283 46.8 0 283
45 341 46.8 0 341
46 290 46.8 0 290
47 296 46.8 0 296
48 328 46.8 0 328
49 296 46.8 0 296
50 294 46.8 0 294
51 296 46.8 0 296
52 309 46.8 0 309
53 276 46.8 0 276
54 263 46.8 0 263
55 270 46.8 0 270
56 267 46.8 0 267
57 281 46.8 0 281
58 266 46.8 0 266
59 254 46.8 0 254
60 237 46.8 0 237
61 225 46.8 0 225
62 244 46.8 0 244
63 181 46.8 0 181
64 201 46.8 0 201
65 168 46.8 0 168
66 165 46.8 0 165
67 154 46.8 0 154
68 129 46.8 0 129
69 105 46.8 0 105
70 113 46.8 0 113
71 84 46.8 0 84
72 74 46.8 0 74
73 100 46.8 0 100
74 67 46.8 0 67
75 62 46.8 0 62
76 60 46.8 0 60
77 41 46.8 0 41
78 32 46.8 0 32
79 43 46.8 0 43
80 36 46.8 0 36
81 33 46.8 0 33
82 47 46.8 0 47
83 32 46.8 0 32
84 41 46.8 0 41
85 50 46.8 0 50
86 1197 46.8 0 1197
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 67309 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 23.4%
G: 21.9%
T: 18.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 50110 47926.8 0 50110
4 11038 11981.7 0 11038
5 2294 2995.4 0 2294
6 356 748.9 0 356
7 36 187.2 0 36
8 56 187.2 0 56
9 29 187.2 0 29
10 40 187.2 0 40
11 41 187.2 0 41
12 28 187.2 0 28
13 45 187.2 0 45
14 32 187.2 0 32
15 26 187.2 0 26
16 36 187.2 0 36
17 36 187.2 0 36
18 39 187.2 0 39
19 32 187.2 0 32
20 57 187.2 0 57
21 52 187.2 0 52
22 46 187.2 0 46
23 39 187.2 0 39
24 38 187.2 0 38
25 52 187.2 0 52
26 67 187.2 0 67
27 37 187.2 0 37
28 45 187.2 0 45
29 54 187.2 0 54
30 47 187.2 0 47
31 33 187.2 0 33
32 59 187.2 0 59
33 45 187.2 0 45
34 50 187.2 0 50
35 53 187.2 0 53
36 50 187.2 0 50
37 42 187.2 0 42
38 49 187.2 0 49
39 45 187.2 0 45
40 44 187.2 0 44
41 45 187.2 0 45
42 35 187.2 0 35
43 39 187.2 0 39
44 36 187.2 0 36
45 39 187.2 0 39
46 45 187.2 0 45
47 42 187.2 0 42
48 36 187.2 0 36
49 43 187.2 0 43
50 40 187.2 0 40
51 51 187.2 0 51
52 40 187.2 0 40
53 36 187.2 0 36
54 41 187.2 0 41
55 46 187.2 0 46
56 29 187.2 0 29
57 33 187.2 0 33
58 40 187.2 0 40
59 53 187.2 0 53
60 31 187.2 0 31
61 70 187.2 0 70
62 54 187.2 0 54
63 44 187.2 0 44
64 31 187.2 0 31
65 61 187.2 0 61
66 45 187.2 0 45
67 32 187.2 0 32
68 40 187.2 0 40
69 36 187.2 0 36
70 45 187.2 0 45
71 36 187.2 0 36
72 37 187.2 0 37
73 32 187.2 0 32
74 45 187.2 0 45
75 25 187.2 0 25
76 30 187.2 0 30
77 97 187.2 0 97
78 51 187.2 0 51
79 37 187.2 0 37
80 49 187.2 0 49
81 37 187.2 0 37
82 48 187.2 0 48
83 70 187.2 0 70
84 40 187.2 0 40
85 65 187.2 0 65
86 74 187.2 0 74
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R54_S206_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R54_S206_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 29.71 s (9 µs/read; 6.33 M reads/minute).
=== Summary ===
Total reads processed: 3,133,880
Reads with adapters: 1,084,697 (34.6%)
== Read fate breakdown ==
Reads that were too short: 288,955 (9.2%)
Reads written (passing filters): 2,844,925 (90.8%)
Total basepairs processed: 316,521,880 bp
Total written (filtered): 222,883,282 bp (70.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 972572 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.3%
G: 28.7%
T: 27.3%
none/other: 12.8%
Overview of removed sequences
length count expect max.err error counts
3 72224 48966.9 0 72224
4 32433 12241.7 0 32433
5 17248 3060.4 0 17248
6 12107 765.1 0 12107
7 10019 191.3 0 10019
8 8979 47.8 0 8979
9 8824 47.8 0 8824
10 9202 47.8 0 9202
11 9023 47.8 0 9023
12 8974 47.8 0 8974
13 9121 47.8 0 9121
14 9351 47.8 0 9351
15 9081 47.8 0 9081
16 9643 47.8 0 9643
17 9171 47.8 0 9171
18 9413 47.8 0 9413
19 9407 47.8 0 9407
20 8927 47.8 0 8927
21 9333 47.8 0 9333
22 9366 47.8 0 9366
23 8777 47.8 0 8777
24 8931 47.8 0 8931
25 8958 47.8 0 8958
26 8789 47.8 0 8789
27 8785 47.8 0 8785
28 9481 47.8 0 9481
29 9376 47.8 0 9376
30 8846 47.8 0 8846
31 9616 47.8 0 9616
32 8942 47.8 0 8942
33 8966 47.8 0 8966
34 9036 47.8 0 9036
35 8801 47.8 0 8801
36 8879 47.8 0 8879
37 8807 47.8 0 8807
38 8219 47.8 0 8219
39 8750 47.8 0 8750
40 9167 47.8 0 9167
41 8756 47.8 0 8756
42 8898 47.8 0 8898
43 9165 47.8 0 9165
44 8439 47.8 0 8439
45 8987 47.8 0 8987
46 9160 47.8 0 9160
47 8977 47.8 0 8977
48 8862 47.8 0 8862
49 13099 47.8 0 13099
50 16159 47.8 0 16159
51 9510 47.8 0 9510
52 10150 47.8 0 10150
53 9599 47.8 0 9599
54 8681 47.8 0 8681
55 8928 47.8 0 8928
56 8933 47.8 0 8933
57 8851 47.8 0 8851
58 9386 47.8 0 9386
59 8956 47.8 0 8956
60 8996 47.8 0 8996
61 9008 47.8 0 9008
62 8752 47.8 0 8752
63 8718 47.8 0 8718
64 8516 47.8 0 8516
65 8616 47.8 0 8616
66 8202 47.8 0 8202
67 8062 47.8 0 8062
68 8181 47.8 0 8181
69 7903 47.8 0 7903
70 7353 47.8 0 7353
71 8078 47.8 0 8078
72 8053 47.8 0 8053
73 7274 47.8 0 7274
74 7030 47.8 0 7030
75 6875 47.8 0 6875
76 6592 47.8 0 6592
77 7029 47.8 0 7029
78 6677 47.8 0 6677
79 7541 47.8 0 7541
80 7425 47.8 0 7425
81 9024 47.8 0 9024
82 10755 47.8 0 10755
83 11803 47.8 0 11803
84 12537 47.8 0 12537
85 12744 47.8 0 12744
86 124360 47.8 0 124360
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 43685 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.2%
C: 31.7%
G: 0.0%
T: 37.2%
none/other: 2.9%
Overview of removed sequences
length count expect max.err error counts
3 15625 48966.9 0 15625
4 3629 12241.7 0 3629
5 1014 3060.4 0 1014
6 524 765.1 0 524
7 501 191.3 0 501
8 446 47.8 0 446
9 535 47.8 0 535
10 459 47.8 0 459
11 419 47.8 0 419
12 405 47.8 0 405
13 395 47.8 0 395
14 398 47.8 0 398
15 414 47.8 0 414
16 383 47.8 0 383
17 388 47.8 0 388
18 360 47.8 0 360
19 385 47.8 0 385
20 323 47.8 0 323
21 338 47.8 0 338
22 389 47.8 0 389
23 316 47.8 0 316
24 391 47.8 0 391
25 395 47.8 0 395
26 321 47.8 0 321
27 342 47.8 0 342
28 339 47.8 0 339
29 351 47.8 0 351
30 359 47.8 0 359
31 337 47.8 0 337
32 323 47.8 0 323
33 376 47.8 0 376
34 341 47.8 0 341
35 332 47.8 0 332
36 350 47.8 0 350
37 346 47.8 0 346
38 326 47.8 0 326
39 372 47.8 0 372
40 355 47.8 0 355
41 307 47.8 0 307
42 321 47.8 0 321
43 341 47.8 0 341
44 309 47.8 0 309
45 327 47.8 0 327
46 328 47.8 0 328
47 355 47.8 0 355
48 342 47.8 0 342
49 303 47.8 0 303
50 326 47.8 0 326
51 261 47.8 0 261
52 317 47.8 0 317
53 299 47.8 0 299
54 284 47.8 0 284
55 278 47.8 0 278
56 294 47.8 0 294
57 274 47.8 0 274
58 277 47.8 0 277
59 283 47.8 0 283
60 268 47.8 0 268
61 237 47.8 0 237
62 239 47.8 0 239
63 234 47.8 0 234
64 200 47.8 0 200
65 198 47.8 0 198
66 181 47.8 0 181
67 117 47.8 0 117
68 163 47.8 0 163
69 116 47.8 0 116
70 122 47.8 0 122
71 121 47.8 0 121
72 98 47.8 0 98
73 107 47.8 0 107
74 81 47.8 0 81
75 63 47.8 0 63
76 61 47.8 0 61
77 48 47.8 0 48
78 37 47.8 0 37
79 36 47.8 0 36
80 37 47.8 0 37
81 32 47.8 0 32
82 41 47.8 0 41
83 38 47.8 0 38
84 44 47.8 0 44
85 59 47.8 0 59
86 1279 47.8 0 1279
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 68440 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 23.0%
G: 21.9%
T: 19.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 50950 48966.9 0 50950
4 11176 12241.7 0 11176
5 2357 3060.4 0 2357
6 360 765.1 0 360
7 27 191.3 0 27
8 59 191.3 0 59
9 41 191.3 0 41
10 32 191.3 0 32
11 48 191.3 0 48
12 41 191.3 0 41
13 38 191.3 0 38
14 36 191.3 0 36
15 48 191.3 0 48
16 31 191.3 0 31
17 31 191.3 0 31
18 46 191.3 0 46
19 48 191.3 0 48
20 36 191.3 0 36
21 61 191.3 0 61
22 46 191.3 0 46
23 44 191.3 0 44
24 44 191.3 0 44
25 54 191.3 0 54
26 68 191.3 0 68
27 46 191.3 0 46
28 56 191.3 0 56
29 57 191.3 0 57
30 50 191.3 0 50
31 29 191.3 0 29
32 44 191.3 0 44
33 49 191.3 0 49
34 46 191.3 0 46
35 48 191.3 0 48
36 73 191.3 0 73
37 48 191.3 0 48
38 49 191.3 0 49
39 59 191.3 0 59
40 25 191.3 0 25
41 53 191.3 0 53
42 50 191.3 0 50
43 27 191.3 0 27
44 47 191.3 0 47
45 47 191.3 0 47
46 29 191.3 0 29
47 45 191.3 0 45
48 35 191.3 0 35
49 32 191.3 0 32
50 43 191.3 0 43
51 47 191.3 0 47
52 48 191.3 0 48
53 36 191.3 0 36
54 41 191.3 0 41
55 47 191.3 0 47
56 35 191.3 0 35
57 43 191.3 0 43
58 36 191.3 0 36
59 38 191.3 0 38
60 32 191.3 0 32
61 39 191.3 0 39
62 54 191.3 0 54
63 43 191.3 0 43
64 38 191.3 0 38
65 53 191.3 0 53
66 42 191.3 0 42
67 51 191.3 0 51
68 44 191.3 0 44
69 42 191.3 0 42
70 37 191.3 0 37
71 31 191.3 0 31
72 31 191.3 0 31
73 38 191.3 0 38
74 29 191.3 0 29
75 44 191.3 0 44
76 33 191.3 0 33
77 109 191.3 0 109
78 66 191.3 0 66
79 34 191.3 0 34
80 45 191.3 0 45
81 32 191.3 0 32
82 40 191.3 0 40
83 70 191.3 0 70
84 47 191.3 0 47
85 59 191.3 0 59
86 77 191.3 0 77
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R55_S196_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R55_S196_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.28 s (10 µs/read; 6.31 M reads/minute).
=== Summary ===
Total reads processed: 2,763,503
Reads with adapters: 894,120 (32.4%)
== Read fate breakdown ==
Reads that were too short: 293,601 (10.6%)
Reads written (passing filters): 2,469,902 (89.4%)
Total basepairs processed: 279,113,803 bp
Total written (filtered): 196,151,026 bp (70.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 795780 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.1%
G: 26.0%
T: 26.6%
none/other: 17.3%
Overview of removed sequences
length count expect max.err error counts
3 63433 43179.7 0 63433
4 27514 10794.9 0 27514
5 13004 2698.7 0 13004
6 7817 674.7 0 7817
7 6353 168.7 0 6353
8 5640 42.2 0 5640
9 5749 42.2 0 5749
10 5615 42.2 0 5615
11 5695 42.2 0 5695
12 5649 42.2 0 5649
13 5642 42.2 0 5642
14 5999 42.2 0 5999
15 6020 42.2 0 6020
16 6313 42.2 0 6313
17 5915 42.2 0 5915
18 6306 42.2 0 6306
19 6004 42.2 0 6004
20 6023 42.2 0 6023
21 5918 42.2 0 5918
22 6626 42.2 0 6626
23 6470 42.2 0 6470
24 6072 42.2 0 6072
25 6114 42.2 0 6114
26 6574 42.2 0 6574
27 6157 42.2 0 6157
28 6760 42.2 0 6760
29 7129 42.2 0 7129
30 6548 42.2 0 6548
31 7266 42.2 0 7266
32 6012 42.2 0 6012
33 6459 42.2 0 6459
34 6304 42.2 0 6304
35 6154 42.2 0 6154
36 5975 42.2 0 5975
37 6084 42.2 0 6084
38 5955 42.2 0 5955
39 6543 42.2 0 6543
40 6575 42.2 0 6575
41 6457 42.2 0 6457
42 6436 42.2 0 6436
43 6529 42.2 0 6529
44 5929 42.2 0 5929
45 6580 42.2 0 6580
46 6494 42.2 0 6494
47 6288 42.2 0 6288
48 6482 42.2 0 6482
49 8190 42.2 0 8190
50 9472 42.2 0 9472
51 7287 42.2 0 7287
52 7334 42.2 0 7334
53 6934 42.2 0 6934
54 6772 42.2 0 6772
55 7166 42.2 0 7166
56 6947 42.2 0 6947
57 6800 42.2 0 6800
58 7691 42.2 0 7691
59 7268 42.2 0 7268
60 7268 42.2 0 7268
61 7485 42.2 0 7485
62 7435 42.2 0 7435
63 6849 42.2 0 6849
64 7310 42.2 0 7310
65 7233 42.2 0 7233
66 6987 42.2 0 6987
67 7046 42.2 0 7046
68 7566 42.2 0 7566
69 7113 42.2 0 7113
70 7258 42.2 0 7258
71 8932 42.2 0 8932
72 7496 42.2 0 7496
73 8322 42.2 0 8322
74 7946 42.2 0 7946
75 6827 42.2 0 6827
76 7704 42.2 0 7704
77 9196 42.2 0 9196
78 6621 42.2 0 6621
79 7805 42.2 0 7805
80 6281 42.2 0 6281
81 7248 42.2 0 7248
82 8841 42.2 0 8841
83 9808 42.2 0 9808
84 10164 42.2 0 10164
85 10231 42.2 0 10231
86 137366 42.2 0 137366
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39203 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.0%
C: 28.8%
G: 0.0%
T: 37.9%
none/other: 4.3%
Overview of removed sequences
length count expect max.err error counts
3 12156 43179.7 0 12156
4 2887 10794.9 0 2887
5 926 2698.7 0 926
6 512 674.7 0 512
7 532 168.7 0 532
8 498 42.2 0 498
9 472 42.2 0 472
10 417 42.2 0 417
11 463 42.2 0 463
12 394 42.2 0 394
13 423 42.2 0 423
14 430 42.2 0 430
15 427 42.2 0 427
16 358 42.2 0 358
17 347 42.2 0 347
18 377 42.2 0 377
19 349 42.2 0 349
20 335 42.2 0 335
21 340 42.2 0 340
22 353 42.2 0 353
23 356 42.2 0 356
24 337 42.2 0 337
25 389 42.2 0 389
26 326 42.2 0 326
27 299 42.2 0 299
28 299 42.2 0 299
29 346 42.2 0 346
30 367 42.2 0 367
31 309 42.2 0 309
32 322 42.2 0 322
33 343 42.2 0 343
34 323 42.2 0 323
35 322 42.2 0 322
36 286 42.2 0 286
37 355 42.2 0 355
38 329 42.2 0 329
39 307 42.2 0 307
40 335 42.2 0 335
41 305 42.2 0 305
42 312 42.2 0 312
43 333 42.2 0 333
44 311 42.2 0 311
45 310 42.2 0 310
46 275 42.2 0 275
47 336 42.2 0 336
48 286 42.2 0 286
49 318 42.2 0 318
50 309 42.2 0 309
51 285 42.2 0 285
52 274 42.2 0 274
53 324 42.2 0 324
54 245 42.2 0 245
55 299 42.2 0 299
56 268 42.2 0 268
57 309 42.2 0 309
58 300 42.2 0 300
59 261 42.2 0 261
60 248 42.2 0 248
61 221 42.2 0 221
62 232 42.2 0 232
63 213 42.2 0 213
64 196 42.2 0 196
65 183 42.2 0 183
66 161 42.2 0 161
67 166 42.2 0 166
68 153 42.2 0 153
69 145 42.2 0 145
70 137 42.2 0 137
71 110 42.2 0 110
72 101 42.2 0 101
73 87 42.2 0 87
74 73 42.2 0 73
75 64 42.2 0 64
76 62 42.2 0 62
77 46 42.2 0 46
78 46 42.2 0 46
79 40 42.2 0 40
80 28 42.2 0 28
81 31 42.2 0 31
82 43 42.2 0 43
83 49 42.2 0 49
84 47 42.2 0 47
85 43 42.2 0 43
86 1672 42.2 0 1672
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 59137 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 23.3%
G: 21.0%
T: 20.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44175 43179.7 0 44175
4 10240 10794.9 0 10240
5 1870 2698.7 0 1870
6 223 674.7 0 223
7 23 168.7 0 23
8 35 168.7 0 35
9 25 168.7 0 25
10 30 168.7 0 30
11 32 168.7 0 32
12 15 168.7 0 15
13 42 168.7 0 42
14 37 168.7 0 37
15 35 168.7 0 35
16 35 168.7 0 35
17 29 168.7 0 29
18 19 168.7 0 19
19 40 168.7 0 40
20 27 168.7 0 27
21 28 168.7 0 28
22 38 168.7 0 38
23 25 168.7 0 25
24 23 168.7 0 23
25 41 168.7 0 41
26 35 168.7 0 35
27 35 168.7 0 35
28 30 168.7 0 30
29 40 168.7 0 40
30 25 168.7 0 25
31 28 168.7 0 28
32 45 168.7 0 45
33 39 168.7 0 39
34 23 168.7 0 23
35 30 168.7 0 30
36 32 168.7 0 32
37 38 168.7 0 38
38 49 168.7 0 49
39 31 168.7 0 31
40 42 168.7 0 42
41 31 168.7 0 31
42 30 168.7 0 30
43 40 168.7 0 40
44 39 168.7 0 39
45 30 168.7 0 30
46 28 168.7 0 28
47 46 168.7 0 46
48 40 168.7 0 40
49 36 168.7 0 36
50 30 168.7 0 30
51 40 168.7 0 40
52 27 168.7 0 27
53 25 168.7 0 25
54 32 168.7 0 32
55 28 168.7 0 28
56 19 168.7 0 19
57 29 168.7 0 29
58 29 168.7 0 29
59 20 168.7 0 20
60 46 168.7 0 46
61 23 168.7 0 23
62 32 168.7 0 32
63 35 168.7 0 35
64 30 168.7 0 30
65 34 168.7 0 34
66 42 168.7 0 42
67 28 168.7 0 28
68 22 168.7 0 22
69 37 168.7 0 37
70 36 168.7 0 36
71 26 168.7 0 26
72 34 168.7 0 34
73 40 168.7 0 40
74 30 168.7 0 30
75 20 168.7 0 20
76 32 168.7 0 32
77 94 168.7 0 94
78 44 168.7 0 44
79 33 168.7 0 33
80 28 168.7 0 28
81 38 168.7 0 38
82 25 168.7 0 25
83 27 168.7 0 27
84 28 168.7 0 28
85 34 168.7 0 34
86 31 168.7 0 31
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R55_S196_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R55_S196_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.72 s (9 µs/read; 6.34 M reads/minute).
=== Summary ===
Total reads processed: 2,822,468
Reads with adapters: 922,761 (32.7%)
== Read fate breakdown ==
Reads that were too short: 309,129 (11.0%)
Reads written (passing filters): 2,513,339 (89.0%)
Total basepairs processed: 285,069,268 bp
Total written (filtered): 199,446,580 bp (70.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 821460 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.1%
G: 25.8%
T: 26.3%
none/other: 17.8%
Overview of removed sequences
length count expect max.err error counts
3 63932 44101.1 0 63932
4 27664 11025.3 0 27664
5 13013 2756.3 0 13013
6 7966 689.1 0 7966
7 6485 172.3 0 6485
8 5774 43.1 0 5774
9 5851 43.1 0 5851
10 5929 43.1 0 5929
11 5801 43.1 0 5801
12 5671 43.1 0 5671
13 5684 43.1 0 5684
14 6122 43.1 0 6122
15 6131 43.1 0 6131
16 6478 43.1 0 6478
17 6178 43.1 0 6178
18 6371 43.1 0 6371
19 6188 43.1 0 6188
20 5870 43.1 0 5870
21 6076 43.1 0 6076
22 6761 43.1 0 6761
23 6484 43.1 0 6484
24 6140 43.1 0 6140
25 6380 43.1 0 6380
26 6763 43.1 0 6763
27 6340 43.1 0 6340
28 6887 43.1 0 6887
29 7284 43.1 0 7284
30 6520 43.1 0 6520
31 7481 43.1 0 7481
32 6144 43.1 0 6144
33 6625 43.1 0 6625
34 6375 43.1 0 6375
35 6440 43.1 0 6440
36 6313 43.1 0 6313
37 6088 43.1 0 6088
38 6238 43.1 0 6238
39 6640 43.1 0 6640
40 6489 43.1 0 6489
41 6355 43.1 0 6355
42 6683 43.1 0 6683
43 6709 43.1 0 6709
44 6085 43.1 0 6085
45 6840 43.1 0 6840
46 6583 43.1 0 6583
47 6323 43.1 0 6323
48 6616 43.1 0 6616
49 8137 43.1 0 8137
50 9514 43.1 0 9514
51 7347 43.1 0 7347
52 7428 43.1 0 7428
53 7181 43.1 0 7181
54 7110 43.1 0 7110
55 7372 43.1 0 7372
56 7079 43.1 0 7079
57 7224 43.1 0 7224
58 7977 43.1 0 7977
59 7529 43.1 0 7529
60 7701 43.1 0 7701
61 8039 43.1 0 8039
62 7627 43.1 0 7627
63 6962 43.1 0 6962
64 7423 43.1 0 7423
65 7570 43.1 0 7570
66 7280 43.1 0 7280
67 7439 43.1 0 7439
68 7712 43.1 0 7712
69 7305 43.1 0 7305
70 7461 43.1 0 7461
71 9661 43.1 0 9661
72 7810 43.1 0 7810
73 8746 43.1 0 8746
74 8267 43.1 0 8267
75 7172 43.1 0 7172
76 8092 43.1 0 8092
77 9568 43.1 0 9568
78 7079 43.1 0 7079
79 8085 43.1 0 8085
80 6544 43.1 0 6544
81 7592 43.1 0 7592
82 9117 43.1 0 9117
83 10174 43.1 0 10174
84 10632 43.1 0 10632
85 10509 43.1 0 10509
86 146225 43.1 0 146225
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 40480 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.7%
C: 29.3%
G: 0.0%
T: 37.9%
none/other: 4.1%
Overview of removed sequences
length count expect max.err error counts
3 12225 44101.1 0 12225
4 2945 11025.3 0 2945
5 920 2756.3 0 920
6 546 689.1 0 546
7 582 172.3 0 582
8 573 43.1 0 573
9 515 43.1 0 515
10 521 43.1 0 521
11 502 43.1 0 502
12 436 43.1 0 436
13 421 43.1 0 421
14 443 43.1 0 443
15 402 43.1 0 402
16 389 43.1 0 389
17 370 43.1 0 370
18 366 43.1 0 366
19 377 43.1 0 377
20 334 43.1 0 334
21 344 43.1 0 344
22 357 43.1 0 357
23 343 43.1 0 343
24 355 43.1 0 355
25 381 43.1 0 381
26 366 43.1 0 366
27 290 43.1 0 290
28 353 43.1 0 353
29 337 43.1 0 337
30 331 43.1 0 331
31 290 43.1 0 290
32 301 43.1 0 301
33 327 43.1 0 327
34 344 43.1 0 344
35 354 43.1 0 354
36 312 43.1 0 312
37 329 43.1 0 329
38 324 43.1 0 324
39 336 43.1 0 336
40 332 43.1 0 332
41 309 43.1 0 309
42 307 43.1 0 307
43 394 43.1 0 394
44 325 43.1 0 325
45 294 43.1 0 294
46 311 43.1 0 311
47 338 43.1 0 338
48 339 43.1 0 339
49 304 43.1 0 304
50 368 43.1 0 368
51 287 43.1 0 287
52 325 43.1 0 325
53 309 43.1 0 309
54 297 43.1 0 297
55 358 43.1 0 358
56 282 43.1 0 282
57 297 43.1 0 297
58 296 43.1 0 296
59 317 43.1 0 317
60 263 43.1 0 263
61 272 43.1 0 272
62 246 43.1 0 246
63 221 43.1 0 221
64 233 43.1 0 233
65 198 43.1 0 198
66 204 43.1 0 204
67 161 43.1 0 161
68 161 43.1 0 161
69 133 43.1 0 133
70 120 43.1 0 120
71 107 43.1 0 107
72 105 43.1 0 105
73 99 43.1 0 99
74 91 43.1 0 91
75 82 43.1 0 82
76 57 43.1 0 57
77 49 43.1 0 49
78 37 43.1 0 37
79 70 43.1 0 70
80 38 43.1 0 38
81 37 43.1 0 37
82 48 43.1 0 48
83 40 43.1 0 40
84 55 43.1 0 55
85 59 43.1 0 59
86 1664 43.1 0 1664
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60821 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.5%
C: 23.6%
G: 20.7%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45457 44101.1 0 45457
4 10467 11025.3 0 10467
5 1988 2756.3 0 1988
6 214 689.1 0 214
7 17 172.3 0 17
8 34 172.3 0 34
9 31 172.3 0 31
10 30 172.3 0 30
11 26 172.3 0 26
12 23 172.3 0 23
13 29 172.3 0 29
14 30 172.3 0 30
15 18 172.3 0 18
16 21 172.3 0 21
17 31 172.3 0 31
18 24 172.3 0 24
19 38 172.3 0 38
20 29 172.3 0 29
21 26 172.3 0 26
22 24 172.3 0 24
23 23 172.3 0 23
24 22 172.3 0 22
25 41 172.3 0 41
26 49 172.3 0 49
27 31 172.3 0 31
28 26 172.3 0 26
29 34 172.3 0 34
30 31 172.3 0 31
31 20 172.3 0 20
32 55 172.3 0 55
33 29 172.3 0 29
34 23 172.3 0 23
35 33 172.3 0 33
36 33 172.3 0 33
37 39 172.3 0 39
38 38 172.3 0 38
39 47 172.3 0 47
40 43 172.3 0 43
41 47 172.3 0 47
42 28 172.3 0 28
43 39 172.3 0 39
44 34 172.3 0 34
45 42 172.3 0 42
46 46 172.3 0 46
47 53 172.3 0 53
48 41 172.3 0 41
49 33 172.3 0 33
50 28 172.3 0 28
51 43 172.3 0 43
52 40 172.3 0 40
53 26 172.3 0 26
54 46 172.3 0 46
55 26 172.3 0 26
56 26 172.3 0 26
57 34 172.3 0 34
58 19 172.3 0 19
59 34 172.3 0 34
60 30 172.3 0 30
61 31 172.3 0 31
62 36 172.3 0 36
63 33 172.3 0 33
64 35 172.3 0 35
65 43 172.3 0 43
66 28 172.3 0 28
67 25 172.3 0 25
68 27 172.3 0 27
69 43 172.3 0 43
70 35 172.3 0 35
71 34 172.3 0 34
72 30 172.3 0 30
73 40 172.3 0 40
74 24 172.3 0 24
75 40 172.3 0 40
76 33 172.3 0 33
77 100 172.3 0 100
78 40 172.3 0 40
79 25 172.3 0 25
80 27 172.3 0 27
81 24 172.3 0 24
82 30 172.3 0 30
83 42 172.3 0 42
84 31 172.3 0 31
85 46 172.3 0 46
86 30 172.3 0 30
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R56_S197_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R56_S197_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.81 s (9 µs/read; 6.36 M reads/minute).
=== Summary ===
Total reads processed: 2,631,209
Reads with adapters: 786,641 (29.9%)
== Read fate breakdown ==
Reads that were too short: 200,407 (7.6%)
Reads written (passing filters): 2,430,802 (92.4%)
Total basepairs processed: 265,752,109 bp
Total written (filtered): 194,013,396 bp (73.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 696126 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.9%
G: 28.1%
T: 30.0%
none/other: 12.1%
Overview of removed sequences
length count expect max.err error counts
3 63026 41112.6 0 63026
4 26576 10278.2 0 26576
5 13812 2569.5 0 13812
6 9171 642.4 0 9171
7 7163 160.6 0 7163
8 6161 40.1 0 6161
9 6370 40.1 0 6370
10 6395 40.1 0 6395
11 6207 40.1 0 6207
12 6367 40.1 0 6367
13 6191 40.1 0 6191
14 6516 40.1 0 6516
15 6450 40.1 0 6450
16 6536 40.1 0 6536
17 6478 40.1 0 6478
18 6625 40.1 0 6625
19 6260 40.1 0 6260
20 6186 40.1 0 6186
21 6419 40.1 0 6419
22 6353 40.1 0 6353
23 6172 40.1 0 6172
24 6180 40.1 0 6180
25 5969 40.1 0 5969
26 6073 40.1 0 6073
27 6351 40.1 0 6351
28 6509 40.1 0 6509
29 6389 40.1 0 6389
30 6469 40.1 0 6469
31 6904 40.1 0 6904
32 6645 40.1 0 6645
33 7124 40.1 0 7124
34 6753 40.1 0 6753
35 6634 40.1 0 6634
36 6525 40.1 0 6525
37 6391 40.1 0 6391
38 5868 40.1 0 5868
39 6284 40.1 0 6284
40 6188 40.1 0 6188
41 6318 40.1 0 6318
42 6365 40.1 0 6365
43 6485 40.1 0 6485
44 6295 40.1 0 6295
45 6350 40.1 0 6350
46 6859 40.1 0 6859
47 6738 40.1 0 6738
48 6224 40.1 0 6224
49 8763 40.1 0 8763
50 10299 40.1 0 10299
51 6209 40.1 0 6209
52 7169 40.1 0 7169
53 6438 40.1 0 6438
54 5566 40.1 0 5566
55 6078 40.1 0 6078
56 6166 40.1 0 6166
57 5663 40.1 0 5663
58 6258 40.1 0 6258
59 6057 40.1 0 6057
60 5875 40.1 0 5875
61 6230 40.1 0 6230
62 6069 40.1 0 6069
63 5614 40.1 0 5614
64 5852 40.1 0 5852
65 5511 40.1 0 5511
66 5631 40.1 0 5631
67 5378 40.1 0 5378
68 5485 40.1 0 5485
69 5283 40.1 0 5283
70 5003 40.1 0 5003
71 5265 40.1 0 5265
72 5218 40.1 0 5218
73 4930 40.1 0 4930
74 4709 40.1 0 4709
75 4890 40.1 0 4890
76 4733 40.1 0 4733
77 4907 40.1 0 4907
78 5062 40.1 0 5062
79 5884 40.1 0 5884
80 5605 40.1 0 5605
81 6585 40.1 0 6585
82 7855 40.1 0 7855
83 8514 40.1 0 8514
84 9370 40.1 0 9370
85 9774 40.1 0 9774
86 83904 40.1 0 83904
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30288 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.3%
C: 33.8%
G: 0.0%
T: 34.7%
none/other: 2.1%
Overview of removed sequences
length count expect max.err error counts
3 15494 41112.6 0 15494
4 3381 10278.2 0 3381
5 820 2569.5 0 820
6 308 642.4 0 308
7 263 160.6 0 263
8 239 40.1 0 239
9 220 40.1 0 220
10 234 40.1 0 234
11 202 40.1 0 202
12 182 40.1 0 182
13 181 40.1 0 181
14 156 40.1 0 156
15 185 40.1 0 185
16 165 40.1 0 165
17 169 40.1 0 169
18 160 40.1 0 160
19 163 40.1 0 163
20 164 40.1 0 164
21 157 40.1 0 157
22 152 40.1 0 152
23 175 40.1 0 175
24 160 40.1 0 160
25 160 40.1 0 160
26 139 40.1 0 139
27 131 40.1 0 131
28 151 40.1 0 151
29 145 40.1 0 145
30 161 40.1 0 161
31 127 40.1 0 127
32 150 40.1 0 150
33 144 40.1 0 144
34 161 40.1 0 161
35 158 40.1 0 158
36 156 40.1 0 156
37 137 40.1 0 137
38 153 40.1 0 153
39 148 40.1 0 148
40 177 40.1 0 177
41 177 40.1 0 177
42 164 40.1 0 164
43 171 40.1 0 171
44 152 40.1 0 152
45 158 40.1 0 158
46 185 40.1 0 185
47 128 40.1 0 128
48 142 40.1 0 142
49 139 40.1 0 139
50 146 40.1 0 146
51 118 40.1 0 118
52 108 40.1 0 108
53 129 40.1 0 129
54 125 40.1 0 125
55 144 40.1 0 144
56 115 40.1 0 115
57 119 40.1 0 119
58 101 40.1 0 101
59 94 40.1 0 94
60 110 40.1 0 110
61 89 40.1 0 89
62 81 40.1 0 81
63 82 40.1 0 82
64 74 40.1 0 74
65 80 40.1 0 80
66 81 40.1 0 81
67 79 40.1 0 79
68 59 40.1 0 59
69 55 40.1 0 55
70 45 40.1 0 45
71 45 40.1 0 45
72 58 40.1 0 58
73 39 40.1 0 39
74 33 40.1 0 33
75 28 40.1 0 28
76 37 40.1 0 37
77 27 40.1 0 27
78 28 40.1 0 28
79 25 40.1 0 25
80 24 40.1 0 24
81 12 40.1 0 12
82 24 40.1 0 24
83 29 40.1 0 29
84 30 40.1 0 30
85 23 40.1 0 23
86 648 40.1 0 648
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60227 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.1%
C: 23.6%
G: 20.1%
T: 21.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44776 41112.6 0 44776
4 10039 10278.2 0 10039
5 2271 2569.5 0 2271
6 356 642.4 0 356
7 32 160.6 0 32
8 36 160.6 0 36
9 32 160.6 0 32
10 25 160.6 0 25
11 24 160.6 0 24
12 34 160.6 0 34
13 35 160.6 0 35
14 43 160.6 0 43
15 30 160.6 0 30
16 28 160.6 0 28
17 35 160.6 0 35
18 31 160.6 0 31
19 37 160.6 0 37
20 50 160.6 0 50
21 38 160.6 0 38
22 25 160.6 0 25
23 37 160.6 0 37
24 30 160.6 0 30
25 42 160.6 0 42
26 32 160.6 0 32
27 20 160.6 0 20
28 36 160.6 0 36
29 39 160.6 0 39
30 31 160.6 0 31
31 24 160.6 0 24
32 30 160.6 0 30
33 26 160.6 0 26
34 22 160.6 0 22
35 36 160.6 0 36
36 40 160.6 0 40
37 29 160.6 0 29
38 22 160.6 0 22
39 32 160.6 0 32
40 26 160.6 0 26
41 28 160.6 0 28
42 26 160.6 0 26
43 35 160.6 0 35
44 28 160.6 0 28
45 25 160.6 0 25
46 27 160.6 0 27
47 48 160.6 0 48
48 43 160.6 0 43
49 46 160.6 0 46
50 34 160.6 0 34
51 41 160.6 0 41
52 45 160.6 0 45
53 40 160.6 0 40
54 45 160.6 0 45
55 43 160.6 0 43
56 31 160.6 0 31
57 43 160.6 0 43
58 51 160.6 0 51
59 43 160.6 0 43
60 35 160.6 0 35
61 32 160.6 0 32
62 47 160.6 0 47
63 34 160.6 0 34
64 29 160.6 0 29
65 42 160.6 0 42
66 50 160.6 0 50
67 43 160.6 0 43
68 55 160.6 0 55
69 33 160.6 0 33
70 26 160.6 0 26
71 36 160.6 0 36
72 29 160.6 0 29
73 37 160.6 0 37
74 34 160.6 0 34
75 30 160.6 0 30
76 23 160.6 0 23
77 62 160.6 0 62
78 38 160.6 0 38
79 17 160.6 0 17
80 32 160.6 0 32
81 24 160.6 0 24
82 28 160.6 0 28
83 29 160.6 0 29
84 35 160.6 0 35
85 32 160.6 0 32
86 62 160.6 0 62
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R56_S197_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R56_S197_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.31 s (9 µs/read; 6.63 M reads/minute).
=== Summary ===
Total reads processed: 2,686,329
Reads with adapters: 808,032 (30.1%)
== Read fate breakdown ==
Reads that were too short: 210,263 (7.8%)
Reads written (passing filters): 2,476,066 (92.2%)
Total basepairs processed: 271,319,229 bp
Total written (filtered): 197,510,020 bp (72.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 716114 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.8%
G: 28.0%
T: 29.7%
none/other: 12.4%
Overview of removed sequences
length count expect max.err error counts
3 64029 41973.9 0 64029
4 26403 10493.5 0 26403
5 13767 2623.4 0 13767
6 9017 655.8 0 9017
7 7238 164.0 0 7238
8 6410 41.0 0 6410
9 6636 41.0 0 6636
10 6642 41.0 0 6642
11 6377 41.0 0 6377
12 6500 41.0 0 6500
13 6386 41.0 0 6386
14 6377 41.0 0 6377
15 6617 41.0 0 6617
16 6739 41.0 0 6739
17 6573 41.0 0 6573
18 6628 41.0 0 6628
19 6476 41.0 0 6476
20 6362 41.0 0 6362
21 6591 41.0 0 6591
22 6399 41.0 0 6399
23 6256 41.0 0 6256
24 6302 41.0 0 6302
25 6272 41.0 0 6272
26 6357 41.0 0 6357
27 6331 41.0 0 6331
28 6479 41.0 0 6479
29 6548 41.0 0 6548
30 6560 41.0 0 6560
31 6967 41.0 0 6967
32 6650 41.0 0 6650
33 7150 41.0 0 7150
34 6853 41.0 0 6853
35 6651 41.0 0 6651
36 6742 41.0 0 6742
37 6567 41.0 0 6567
38 5954 41.0 0 5954
39 6474 41.0 0 6474
40 6439 41.0 0 6439
41 6411 41.0 0 6411
42 6696 41.0 0 6696
43 6428 41.0 0 6428
44 6482 41.0 0 6482
45 6427 41.0 0 6427
46 6869 41.0 0 6869
47 7052 41.0 0 7052
48 6263 41.0 0 6263
49 9152 41.0 0 9152
50 10726 41.0 0 10726
51 6314 41.0 0 6314
52 7400 41.0 0 7400
53 6735 41.0 0 6735
54 5683 41.0 0 5683
55 6324 41.0 0 6324
56 6407 41.0 0 6407
57 5944 41.0 0 5944
58 6491 41.0 0 6491
59 6208 41.0 0 6208
60 6101 41.0 0 6101
61 6334 41.0 0 6334
62 6189 41.0 0 6189
63 5990 41.0 0 5990
64 5891 41.0 0 5891
65 5970 41.0 0 5970
66 5772 41.0 0 5772
67 5739 41.0 0 5739
68 5743 41.0 0 5743
69 5340 41.0 0 5340
70 5016 41.0 0 5016
71 5576 41.0 0 5576
72 5517 41.0 0 5517
73 5216 41.0 0 5216
74 4887 41.0 0 4887
75 4984 41.0 0 4984
76 4918 41.0 0 4918
77 5041 41.0 0 5041
78 5281 41.0 0 5281
79 5979 41.0 0 5979
80 5865 41.0 0 5865
81 6957 41.0 0 6957
82 8194 41.0 0 8194
83 8938 41.0 0 8938
84 9803 41.0 0 9803
85 10320 41.0 0 10320
86 88822 41.0 0 88822
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30929 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.4%
C: 34.4%
G: 0.0%
T: 34.0%
none/other: 2.2%
Overview of removed sequences
length count expect max.err error counts
3 15947 41973.9 0 15947
4 3321 10493.5 0 3321
5 802 2623.4 0 802
6 287 655.8 0 287
7 269 164.0 0 269
8 233 41.0 0 233
9 247 41.0 0 247
10 204 41.0 0 204
11 206 41.0 0 206
12 203 41.0 0 203
13 191 41.0 0 191
14 150 41.0 0 150
15 185 41.0 0 185
16 152 41.0 0 152
17 147 41.0 0 147
18 166 41.0 0 166
19 181 41.0 0 181
20 171 41.0 0 171
21 177 41.0 0 177
22 150 41.0 0 150
23 146 41.0 0 146
24 161 41.0 0 161
25 172 41.0 0 172
26 150 41.0 0 150
27 139 41.0 0 139
28 161 41.0 0 161
29 132 41.0 0 132
30 154 41.0 0 154
31 160 41.0 0 160
32 158 41.0 0 158
33 179 41.0 0 179
34 171 41.0 0 171
35 156 41.0 0 156
36 157 41.0 0 157
37 157 41.0 0 157
38 162 41.0 0 162
39 157 41.0 0 157
40 173 41.0 0 173
41 157 41.0 0 157
42 174 41.0 0 174
43 169 41.0 0 169
44 196 41.0 0 196
45 132 41.0 0 132
46 181 41.0 0 181
47 129 41.0 0 129
48 139 41.0 0 139
49 139 41.0 0 139
50 128 41.0 0 128
51 115 41.0 0 115
52 126 41.0 0 126
53 143 41.0 0 143
54 111 41.0 0 111
55 135 41.0 0 135
56 114 41.0 0 114
57 99 41.0 0 99
58 120 41.0 0 120
59 119 41.0 0 119
60 126 41.0 0 126
61 87 41.0 0 87
62 87 41.0 0 87
63 100 41.0 0 100
64 92 41.0 0 92
65 94 41.0 0 94
66 92 41.0 0 92
67 69 41.0 0 69
68 71 41.0 0 71
69 64 41.0 0 64
70 46 41.0 0 46
71 52 41.0 0 52
72 47 41.0 0 47
73 43 41.0 0 43
74 41 41.0 0 41
75 37 41.0 0 37
76 27 41.0 0 27
77 19 41.0 0 19
78 16 41.0 0 16
79 16 41.0 0 16
80 33 41.0 0 33
81 20 41.0 0 20
82 35 41.0 0 35
83 30 41.0 0 30
84 26 41.0 0 26
85 24 41.0 0 24
86 675 41.0 0 675
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60989 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.9%
C: 23.5%
G: 20.5%
T: 21.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45262 41973.9 0 45262
4 10263 10493.5 0 10263
5 2293 2623.4 0 2293
6 364 655.8 0 364
7 27 164.0 0 27
8 31 164.0 0 31
9 27 164.0 0 27
10 22 164.0 0 22
11 31 164.0 0 31
12 26 164.0 0 26
13 30 164.0 0 30
14 41 164.0 0 41
15 37 164.0 0 37
16 30 164.0 0 30
17 32 164.0 0 32
18 47 164.0 0 47
19 21 164.0 0 21
20 42 164.0 0 42
21 39 164.0 0 39
22 30 164.0 0 30
23 38 164.0 0 38
24 22 164.0 0 22
25 42 164.0 0 42
26 37 164.0 0 37
27 32 164.0 0 32
28 28 164.0 0 28
29 37 164.0 0 37
30 33 164.0 0 33
31 35 164.0 0 35
32 36 164.0 0 36
33 31 164.0 0 31
34 30 164.0 0 30
35 27 164.0 0 27
36 27 164.0 0 27
37 34 164.0 0 34
38 38 164.0 0 38
39 26 164.0 0 26
40 38 164.0 0 38
41 33 164.0 0 33
42 25 164.0 0 25
43 42 164.0 0 42
44 28 164.0 0 28
45 38 164.0 0 38
46 25 164.0 0 25
47 33 164.0 0 33
48 37 164.0 0 37
49 33 164.0 0 33
50 29 164.0 0 29
51 19 164.0 0 19
52 50 164.0 0 50
53 39 164.0 0 39
54 31 164.0 0 31
55 38 164.0 0 38
56 20 164.0 0 20
57 43 164.0 0 43
58 53 164.0 0 53
59 38 164.0 0 38
60 44 164.0 0 44
61 46 164.0 0 46
62 40 164.0 0 40
63 39 164.0 0 39
64 31 164.0 0 31
65 65 164.0 0 65
66 48 164.0 0 48
67 32 164.0 0 32
68 50 164.0 0 50
69 29 164.0 0 29
70 33 164.0 0 33
71 45 164.0 0 45
72 41 164.0 0 41
73 28 164.0 0 28
74 46 164.0 0 46
75 22 164.0 0 22
76 34 164.0 0 34
77 62 164.0 0 62
78 32 164.0 0 32
79 27 164.0 0 27
80 34 164.0 0 34
81 38 164.0 0 38
82 29 164.0 0 29
83 41 164.0 0 41
84 33 164.0 0 33
85 43 164.0 0 43
86 37 164.0 0 37
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R57_S200_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R57_S200_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.99 s (9 µs/read; 6.37 M reads/minute).
=== Summary ===
Total reads processed: 2,972,763
Reads with adapters: 1,079,300 (36.3%)
== Read fate breakdown ==
Reads that were too short: 258,110 (8.7%)
Reads written (passing filters): 2,714,653 (91.3%)
Total basepairs processed: 300,249,063 bp
Total written (filtered): 211,067,178 bp (70.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 964857 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.9%
G: 28.3%
T: 29.9%
none/other: 10.9%
Overview of removed sequences
length count expect max.err error counts
3 71278 46449.4 0 71278
4 32928 11612.4 0 32928
5 18465 2903.1 0 18465
6 13093 725.8 0 13093
7 11180 181.4 0 11180
8 10096 45.4 0 10096
9 10111 45.4 0 10111
10 10184 45.4 0 10184
11 10044 45.4 0 10044
12 9899 45.4 0 9899
13 9975 45.4 0 9975
14 9930 45.4 0 9930
15 10135 45.4 0 10135
16 10200 45.4 0 10200
17 10266 45.4 0 10266
18 10198 45.4 0 10198
19 10190 45.4 0 10190
20 9783 45.4 0 9783
21 10144 45.4 0 10144
22 10294 45.4 0 10294
23 9772 45.4 0 9772
24 9800 45.4 0 9800
25 9501 45.4 0 9501
26 9565 45.4 0 9565
27 9496 45.4 0 9496
28 9748 45.4 0 9748
29 9792 45.4 0 9792
30 9617 45.4 0 9617
31 10054 45.4 0 10054
32 9553 45.4 0 9553
33 10257 45.4 0 10257
34 9894 45.4 0 9894
35 9289 45.4 0 9289
36 9066 45.4 0 9066
37 9295 45.4 0 9295
38 8728 45.4 0 8728
39 9155 45.4 0 9155
40 9434 45.4 0 9434
41 9112 45.4 0 9112
42 9437 45.4 0 9437
43 9239 45.4 0 9239
44 9007 45.4 0 9007
45 9280 45.4 0 9280
46 9093 45.4 0 9093
47 9533 45.4 0 9533
48 8985 45.4 0 8985
49 11673 45.4 0 11673
50 13873 45.4 0 13873
51 9155 45.4 0 9155
52 9732 45.4 0 9732
53 9455 45.4 0 9455
54 8513 45.4 0 8513
55 8840 45.4 0 8840
56 8764 45.4 0 8764
57 8360 45.4 0 8360
58 9153 45.4 0 9153
59 8552 45.4 0 8552
60 8921 45.4 0 8921
61 8799 45.4 0 8799
62 8962 45.4 0 8962
63 8477 45.4 0 8477
64 8465 45.4 0 8465
65 8319 45.4 0 8319
66 8043 45.4 0 8043
67 7902 45.4 0 7902
68 8049 45.4 0 8049
69 7596 45.4 0 7596
70 7055 45.4 0 7055
71 7570 45.4 0 7570
72 7302 45.4 0 7302
73 7013 45.4 0 7013
74 6658 45.4 0 6658
75 6711 45.4 0 6711
76 6347 45.4 0 6347
77 6385 45.4 0 6385
78 6504 45.4 0 6504
79 7485 45.4 0 7485
80 6913 45.4 0 6913
81 7852 45.4 0 7852
82 9368 45.4 0 9368
83 10164 45.4 0 10164
84 11237 45.4 0 11237
85 11473 45.4 0 11473
86 105122 45.4 0 105122
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 54097 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.2%
C: 34.4%
G: 0.0%
T: 38.9%
none/other: 1.4%
Overview of removed sequences
length count expect max.err error counts
3 13529 46449.4 0 13529
4 3755 11612.4 0 3755
5 1363 2903.1 0 1363
6 853 725.8 0 853
7 737 181.4 0 737
8 771 45.4 0 771
9 706 45.4 0 706
10 665 45.4 0 665
11 664 45.4 0 664
12 647 45.4 0 647
13 671 45.4 0 671
14 696 45.4 0 696
15 652 45.4 0 652
16 613 45.4 0 613
17 610 45.4 0 610
18 634 45.4 0 634
19 623 45.4 0 623
20 602 45.4 0 602
21 572 45.4 0 572
22 581 45.4 0 581
23 561 45.4 0 561
24 561 45.4 0 561
25 607 45.4 0 607
26 587 45.4 0 587
27 553 45.4 0 553
28 558 45.4 0 558
29 537 45.4 0 537
30 570 45.4 0 570
31 510 45.4 0 510
32 528 45.4 0 528
33 633 45.4 0 633
34 557 45.4 0 557
35 594 45.4 0 594
36 597 45.4 0 597
37 524 45.4 0 524
38 578 45.4 0 578
39 527 45.4 0 527
40 555 45.4 0 555
41 537 45.4 0 537
42 520 45.4 0 520
43 585 45.4 0 585
44 531 45.4 0 531
45 498 45.4 0 498
46 532 45.4 0 532
47 526 45.4 0 526
48 519 45.4 0 519
49 481 45.4 0 481
50 490 45.4 0 490
51 435 45.4 0 435
52 448 45.4 0 448
53 439 45.4 0 439
54 416 45.4 0 416
55 447 45.4 0 447
56 424 45.4 0 424
57 402 45.4 0 402
58 372 45.4 0 372
59 433 45.4 0 433
60 379 45.4 0 379
61 334 45.4 0 334
62 340 45.4 0 340
63 333 45.4 0 333
64 315 45.4 0 315
65 279 45.4 0 279
66 256 45.4 0 256
67 238 45.4 0 238
68 206 45.4 0 206
69 196 45.4 0 196
70 161 45.4 0 161
71 146 45.4 0 146
72 158 45.4 0 158
73 127 45.4 0 127
74 116 45.4 0 116
75 91 45.4 0 91
76 76 45.4 0 76
77 75 45.4 0 75
78 58 45.4 0 58
79 56 45.4 0 56
80 53 45.4 0 53
81 44 45.4 0 44
82 35 45.4 0 35
83 34 45.4 0 34
84 36 45.4 0 36
85 57 45.4 0 57
86 782 45.4 0 782
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60346 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.3%
C: 22.4%
G: 21.5%
T: 19.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44972 46449.4 0 44972
4 10412 11612.4 0 10412
5 2093 2903.1 0 2093
6 245 725.8 0 245
7 57 181.4 0 57
8 26 181.4 0 26
9 20 181.4 0 20
10 28 181.4 0 28
11 23 181.4 0 23
12 18 181.4 0 18
13 31 181.4 0 31
14 35 181.4 0 35
15 28 181.4 0 28
16 34 181.4 0 34
17 45 181.4 0 45
18 38 181.4 0 38
19 39 181.4 0 39
20 39 181.4 0 39
21 46 181.4 0 46
22 23 181.4 0 23
23 38 181.4 0 38
24 31 181.4 0 31
25 45 181.4 0 45
26 19 181.4 0 19
27 20 181.4 0 20
28 39 181.4 0 39
29 34 181.4 0 34
30 34 181.4 0 34
31 24 181.4 0 24
32 45 181.4 0 45
33 33 181.4 0 33
34 36 181.4 0 36
35 37 181.4 0 37
36 37 181.4 0 37
37 34 181.4 0 34
38 38 181.4 0 38
39 32 181.4 0 32
40 41 181.4 0 41
41 28 181.4 0 28
42 52 181.4 0 52
43 34 181.4 0 34
44 19 181.4 0 19
45 38 181.4 0 38
46 25 181.4 0 25
47 29 181.4 0 29
48 30 181.4 0 30
49 36 181.4 0 36
50 24 181.4 0 24
51 48 181.4 0 48
52 37 181.4 0 37
53 25 181.4 0 25
54 34 181.4 0 34
55 25 181.4 0 25
56 28 181.4 0 28
57 37 181.4 0 37
58 19 181.4 0 19
59 29 181.4 0 29
60 38 181.4 0 38
61 25 181.4 0 25
62 37 181.4 0 37
63 21 181.4 0 21
64 25 181.4 0 25
65 41 181.4 0 41
66 34 181.4 0 34
67 42 181.4 0 42
68 41 181.4 0 41
69 35 181.4 0 35
70 36 181.4 0 36
71 33 181.4 0 33
72 29 181.4 0 29
73 30 181.4 0 30
74 34 181.4 0 34
75 15 181.4 0 15
76 21 181.4 0 21
77 52 181.4 0 52
78 32 181.4 0 32
79 35 181.4 0 35
80 30 181.4 0 30
81 37 181.4 0 37
82 31 181.4 0 31
83 27 181.4 0 27
84 28 181.4 0 28
85 40 181.4 0 40
86 31 181.4 0 31
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R57_S200_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R57_S200_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 29.13 s (10 µs/read; 6.22 M reads/minute).
=== Summary ===
Total reads processed: 3,021,285
Reads with adapters: 1,109,541 (36.7%)
== Read fate breakdown ==
Reads that were too short: 271,244 (9.0%)
Reads written (passing filters): 2,750,041 (91.0%)
Total basepairs processed: 305,149,785 bp
Total written (filtered): 213,477,391 bp (70.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 992863 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.8%
G: 28.1%
T: 29.8%
none/other: 11.3%
Overview of removed sequences
length count expect max.err error counts
3 71131 47207.6 0 71131
4 33566 11801.9 0 33566
5 18452 2950.5 0 18452
6 13655 737.6 0 13655
7 11232 184.4 0 11232
8 10145 46.1 0 10145
9 10259 46.1 0 10259
10 10319 46.1 0 10319
11 10113 46.1 0 10113
12 9952 46.1 0 9952
13 10320 46.1 0 10320
14 10098 46.1 0 10098
15 10391 46.1 0 10391
16 10766 46.1 0 10766
17 10102 46.1 0 10102
18 10431 46.1 0 10431
19 10259 46.1 0 10259
20 10208 46.1 0 10208
21 10201 46.1 0 10201
22 10558 46.1 0 10558
23 9708 46.1 0 9708
24 10057 46.1 0 10057
25 9695 46.1 0 9695
26 9753 46.1 0 9753
27 9643 46.1 0 9643
28 10074 46.1 0 10074
29 9635 46.1 0 9635
30 9797 46.1 0 9797
31 10331 46.1 0 10331
32 9758 46.1 0 9758
33 10252 46.1 0 10252
34 10012 46.1 0 10012
35 9447 46.1 0 9447
36 9585 46.1 0 9585
37 9312 46.1 0 9312
38 9030 46.1 0 9030
39 9508 46.1 0 9508
40 9511 46.1 0 9511
41 9486 46.1 0 9486
42 9546 46.1 0 9546
43 9530 46.1 0 9530
44 9417 46.1 0 9417
45 9424 46.1 0 9424
46 9597 46.1 0 9597
47 9620 46.1 0 9620
48 9253 46.1 0 9253
49 11930 46.1 0 11930
50 14544 46.1 0 14544
51 9662 46.1 0 9662
52 10019 46.1 0 10019
53 9706 46.1 0 9706
54 8580 46.1 0 8580
55 9116 46.1 0 9116
56 9225 46.1 0 9225
57 8873 46.1 0 8873
58 9438 46.1 0 9438
59 9036 46.1 0 9036
60 9104 46.1 0 9104
61 9232 46.1 0 9232
62 9019 46.1 0 9019
63 8733 46.1 0 8733
64 8832 46.1 0 8832
65 8744 46.1 0 8744
66 8144 46.1 0 8144
67 8418 46.1 0 8418
68 8267 46.1 0 8267
69 7788 46.1 0 7788
70 7556 46.1 0 7556
71 7742 46.1 0 7742
72 7673 46.1 0 7673
73 7231 46.1 0 7231
74 6906 46.1 0 6906
75 6790 46.1 0 6790
76 6724 46.1 0 6724
77 6472 46.1 0 6472
78 6868 46.1 0 6868
79 7798 46.1 0 7798
80 7360 46.1 0 7360
81 8283 46.1 0 8283
82 9614 46.1 0 9614
83 10584 46.1 0 10584
84 11609 46.1 0 11609
85 11986 46.1 0 11986
86 112118 46.1 0 112118
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 55935 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 24.7%
C: 34.7%
G: 0.0%
T: 39.1%
none/other: 1.4%
Overview of removed sequences
length count expect max.err error counts
3 13803 47207.6 0 13803
4 3854 11801.9 0 3854
5 1414 2950.5 0 1414
6 914 737.6 0 914
7 839 184.4 0 839
8 761 46.1 0 761
9 750 46.1 0 750
10 721 46.1 0 721
11 697 46.1 0 697
12 678 46.1 0 678
13 669 46.1 0 669
14 677 46.1 0 677
15 646 46.1 0 646
16 671 46.1 0 671
17 644 46.1 0 644
18 640 46.1 0 640
19 642 46.1 0 642
20 602 46.1 0 602
21 569 46.1 0 569
22 594 46.1 0 594
23 590 46.1 0 590
24 648 46.1 0 648
25 582 46.1 0 582
26 547 46.1 0 547
27 562 46.1 0 562
28 586 46.1 0 586
29 597 46.1 0 597
30 591 46.1 0 591
31 551 46.1 0 551
32 558 46.1 0 558
33 624 46.1 0 624
34 575 46.1 0 575
35 614 46.1 0 614
36 558 46.1 0 558
37 541 46.1 0 541
38 608 46.1 0 608
39 500 46.1 0 500
40 577 46.1 0 577
41 502 46.1 0 502
42 538 46.1 0 538
43 577 46.1 0 577
44 561 46.1 0 561
45 582 46.1 0 582
46 546 46.1 0 546
47 557 46.1 0 557
48 514 46.1 0 514
49 510 46.1 0 510
50 517 46.1 0 517
51 479 46.1 0 479
52 487 46.1 0 487
53 521 46.1 0 521
54 492 46.1 0 492
55 448 46.1 0 448
56 457 46.1 0 457
57 448 46.1 0 448
58 424 46.1 0 424
59 407 46.1 0 407
60 445 46.1 0 445
61 360 46.1 0 360
62 358 46.1 0 358
63 324 46.1 0 324
64 324 46.1 0 324
65 294 46.1 0 294
66 266 46.1 0 266
67 260 46.1 0 260
68 207 46.1 0 207
69 196 46.1 0 196
70 193 46.1 0 193
71 153 46.1 0 153
72 149 46.1 0 149
73 139 46.1 0 139
74 99 46.1 0 99
75 95 46.1 0 95
76 73 46.1 0 73
77 66 46.1 0 66
78 59 46.1 0 59
79 52 46.1 0 52
80 55 46.1 0 55
81 44 46.1 0 44
82 36 46.1 0 36
83 37 46.1 0 37
84 41 46.1 0 41
85 54 46.1 0 54
86 795 46.1 0 795
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60743 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.2%
C: 22.6%
G: 21.4%
T: 19.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45303 47207.6 0 45303
4 10400 11801.9 0 10400
5 2126 2950.5 0 2126
6 255 737.6 0 255
7 37 184.4 0 37
8 36 184.4 0 36
9 21 184.4 0 21
10 28 184.4 0 28
11 38 184.4 0 38
12 22 184.4 0 22
13 40 184.4 0 40
14 36 184.4 0 36
15 25 184.4 0 25
16 34 184.4 0 34
17 35 184.4 0 35
18 31 184.4 0 31
19 37 184.4 0 37
20 44 184.4 0 44
21 38 184.4 0 38
22 39 184.4 0 39
23 35 184.4 0 35
24 33 184.4 0 33
25 36 184.4 0 36
26 30 184.4 0 30
27 22 184.4 0 22
28 37 184.4 0 37
29 27 184.4 0 27
30 39 184.4 0 39
31 36 184.4 0 36
32 33 184.4 0 33
33 22 184.4 0 22
34 34 184.4 0 34
35 37 184.4 0 37
36 30 184.4 0 30
37 42 184.4 0 42
38 20 184.4 0 20
39 30 184.4 0 30
40 40 184.4 0 40
41 36 184.4 0 36
42 44 184.4 0 44
43 22 184.4 0 22
44 25 184.4 0 25
45 39 184.4 0 39
46 27 184.4 0 27
47 27 184.4 0 27
48 40 184.4 0 40
49 29 184.4 0 29
50 38 184.4 0 38
51 41 184.4 0 41
52 28 184.4 0 28
53 42 184.4 0 42
54 45 184.4 0 45
55 32 184.4 0 32
56 33 184.4 0 33
57 36 184.4 0 36
58 36 184.4 0 36
59 30 184.4 0 30
60 37 184.4 0 37
61 36 184.4 0 36
62 41 184.4 0 41
63 27 184.4 0 27
64 28 184.4 0 28
65 29 184.4 0 29
66 33 184.4 0 33
67 23 184.4 0 23
68 44 184.4 0 44
69 29 184.4 0 29
70 34 184.4 0 34
71 33 184.4 0 33
72 31 184.4 0 31
73 32 184.4 0 32
74 30 184.4 0 30
75 25 184.4 0 25
76 21 184.4 0 21
77 42 184.4 0 42
78 46 184.4 0 46
79 33 184.4 0 33
80 29 184.4 0 29
81 35 184.4 0 35
82 30 184.4 0 30
83 39 184.4 0 39
84 33 184.4 0 33
85 32 184.4 0 32
86 33 184.4 0 33
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R58_S198_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R58_S198_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.32 s (10 µs/read; 6.22 M reads/minute).
=== Summary ===
Total reads processed: 2,829,792
Reads with adapters: 900,987 (31.8%)
== Read fate breakdown ==
Reads that were too short: 238,259 (8.4%)
Reads written (passing filters): 2,591,533 (91.6%)
Total basepairs processed: 285,808,992 bp
Total written (filtered): 205,488,426 bp (71.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 798373 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.2%
G: 27.9%
T: 28.2%
none/other: 13.6%
Overview of removed sequences
length count expect max.err error counts
3 66127 44215.5 0 66127
4 28735 11053.9 0 28735
5 15050 2763.5 0 15050
6 9920 690.9 0 9920
7 8286 172.7 0 8286
8 7433 43.2 0 7433
9 7494 43.2 0 7494
10 7394 43.2 0 7394
11 7299 43.2 0 7299
12 7322 43.2 0 7322
13 7484 43.2 0 7484
14 7539 43.2 0 7539
15 7532 43.2 0 7532
16 7685 43.2 0 7685
17 7619 43.2 0 7619
18 7558 43.2 0 7558
19 7362 43.2 0 7362
20 7136 43.2 0 7136
21 7305 43.2 0 7305
22 7558 43.2 0 7558
23 7048 43.2 0 7048
24 7255 43.2 0 7255
25 7220 43.2 0 7220
26 7077 43.2 0 7077
27 7204 43.2 0 7204
28 7408 43.2 0 7408
29 7276 43.2 0 7276
30 7402 43.2 0 7402
31 7780 43.2 0 7780
32 7270 43.2 0 7270
33 7813 43.2 0 7813
34 7514 43.2 0 7514
35 7337 43.2 0 7337
36 7207 43.2 0 7207
37 7292 43.2 0 7292
38 6809 43.2 0 6809
39 7179 43.2 0 7179
40 7252 43.2 0 7252
41 7365 43.2 0 7365
42 7204 43.2 0 7204
43 7556 43.2 0 7556
44 6945 43.2 0 6945
45 7220 43.2 0 7220
46 7451 43.2 0 7451
47 7449 43.2 0 7449
48 7023 43.2 0 7023
49 10369 43.2 0 10369
50 12633 43.2 0 12633
51 7428 43.2 0 7428
52 8051 43.2 0 8051
53 7756 43.2 0 7756
54 6678 43.2 0 6678
55 6878 43.2 0 6878
56 7029 43.2 0 7029
57 6706 43.2 0 6706
58 7085 43.2 0 7085
59 6808 43.2 0 6808
60 6970 43.2 0 6970
61 6903 43.2 0 6903
62 6607 43.2 0 6607
63 6454 43.2 0 6454
64 6478 43.2 0 6478
65 6504 43.2 0 6504
66 6309 43.2 0 6309
67 6212 43.2 0 6212
68 6257 43.2 0 6257
69 5872 43.2 0 5872
70 5701 43.2 0 5701
71 6105 43.2 0 6105
72 6072 43.2 0 6072
73 5649 43.2 0 5649
74 5523 43.2 0 5523
75 5770 43.2 0 5770
76 5305 43.2 0 5305
77 5335 43.2 0 5335
78 5297 43.2 0 5297
79 6053 43.2 0 6053
80 6156 43.2 0 6156
81 6873 43.2 0 6873
82 8458 43.2 0 8458
83 9354 43.2 0 9354
84 10053 43.2 0 10053
85 10438 43.2 0 10438
86 108850 43.2 0 108850
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38095 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.6%
C: 31.7%
G: 0.0%
T: 36.9%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 15204 44215.5 0 15204
4 3241 11053.9 0 3241
5 967 2763.5 0 967
6 466 690.9 0 466
7 444 172.7 0 444
8 425 43.2 0 425
9 381 43.2 0 381
10 361 43.2 0 361
11 315 43.2 0 315
12 328 43.2 0 328
13 331 43.2 0 331
14 314 43.2 0 314
15 291 43.2 0 291
16 294 43.2 0 294
17 257 43.2 0 257
18 259 43.2 0 259
19 306 43.2 0 306
20 284 43.2 0 284
21 279 43.2 0 279
22 310 43.2 0 310
23 304 43.2 0 304
24 269 43.2 0 269
25 285 43.2 0 285
26 277 43.2 0 277
27 272 43.2 0 272
28 259 43.2 0 259
29 259 43.2 0 259
30 259 43.2 0 259
31 274 43.2 0 274
32 287 43.2 0 287
33 287 43.2 0 287
34 287 43.2 0 287
35 249 43.2 0 249
36 276 43.2 0 276
37 280 43.2 0 280
38 259 43.2 0 259
39 248 43.2 0 248
40 282 43.2 0 282
41 263 43.2 0 263
42 261 43.2 0 261
43 265 43.2 0 265
44 279 43.2 0 279
45 265 43.2 0 265
46 265 43.2 0 265
47 254 43.2 0 254
48 262 43.2 0 262
49 250 43.2 0 250
50 264 43.2 0 264
51 227 43.2 0 227
52 253 43.2 0 253
53 234 43.2 0 234
54 221 43.2 0 221
55 229 43.2 0 229
56 203 43.2 0 203
57 236 43.2 0 236
58 256 43.2 0 256
59 225 43.2 0 225
60 225 43.2 0 225
61 216 43.2 0 216
62 176 43.2 0 176
63 188 43.2 0 188
64 163 43.2 0 163
65 150 43.2 0 150
66 145 43.2 0 145
67 137 43.2 0 137
68 106 43.2 0 106
69 98 43.2 0 98
70 112 43.2 0 112
71 86 43.2 0 86
72 66 43.2 0 66
73 64 43.2 0 64
74 63 43.2 0 63
75 43 43.2 0 43
76 38 43.2 0 38
77 32 43.2 0 32
78 23 43.2 0 23
79 34 43.2 0 34
80 22 43.2 0 22
81 36 43.2 0 36
82 25 43.2 0 25
83 42 43.2 0 42
84 31 43.2 0 31
85 51 43.2 0 51
86 1041 43.2 0 1041
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 64519 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 23.0%
G: 21.9%
T: 19.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 48359 44215.5 0 48359
4 10513 11053.9 0 10513
5 2310 2763.5 0 2310
6 341 690.9 0 341
7 27 172.7 0 27
8 37 172.7 0 37
9 39 172.7 0 39
10 35 172.7 0 35
11 42 172.7 0 42
12 28 172.7 0 28
13 27 172.7 0 27
14 35 172.7 0 35
15 40 172.7 0 40
16 43 172.7 0 43
17 35 172.7 0 35
18 35 172.7 0 35
19 44 172.7 0 44
20 32 172.7 0 32
21 41 172.7 0 41
22 35 172.7 0 35
23 28 172.7 0 28
24 39 172.7 0 39
25 31 172.7 0 31
26 42 172.7 0 42
27 24 172.7 0 24
28 34 172.7 0 34
29 25 172.7 0 25
30 37 172.7 0 37
31 47 172.7 0 47
32 35 172.7 0 35
33 40 172.7 0 40
34 26 172.7 0 26
35 31 172.7 0 31
36 57 172.7 0 57
37 29 172.7 0 29
38 49 172.7 0 49
39 32 172.7 0 32
40 47 172.7 0 47
41 43 172.7 0 43
42 38 172.7 0 38
43 32 172.7 0 32
44 41 172.7 0 41
45 32 172.7 0 32
46 36 172.7 0 36
47 25 172.7 0 25
48 34 172.7 0 34
49 37 172.7 0 37
50 45 172.7 0 45
51 38 172.7 0 38
52 42 172.7 0 42
53 35 172.7 0 35
54 39 172.7 0 39
55 40 172.7 0 40
56 34 172.7 0 34
57 44 172.7 0 44
58 32 172.7 0 32
59 36 172.7 0 36
60 41 172.7 0 41
61 36 172.7 0 36
62 51 172.7 0 51
63 34 172.7 0 34
64 39 172.7 0 39
65 51 172.7 0 51
66 37 172.7 0 37
67 39 172.7 0 39
68 28 172.7 0 28
69 44 172.7 0 44
70 35 172.7 0 35
71 49 172.7 0 49
72 31 172.7 0 31
73 39 172.7 0 39
74 42 172.7 0 42
75 21 172.7 0 21
76 24 172.7 0 24
77 95 172.7 0 95
78 57 172.7 0 57
79 26 172.7 0 26
80 23 172.7 0 23
81 27 172.7 0 27
82 35 172.7 0 35
83 47 172.7 0 47
84 41 172.7 0 41
85 40 172.7 0 40
86 33 172.7 0 33
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R58_S198_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R58_S198_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.36 s (9 µs/read; 6.34 M reads/minute).
=== Summary ===
Total reads processed: 2,892,630
Reads with adapters: 929,610 (32.1%)
== Read fate breakdown ==
Reads that were too short: 251,505 (8.7%)
Reads written (passing filters): 2,641,125 (91.3%)
Total basepairs processed: 292,155,630 bp
Total written (filtered): 209,215,921 bp (71.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 824909 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.1%
G: 27.8%
T: 28.0%
none/other: 14.1%
Overview of removed sequences
length count expect max.err error counts
3 66722 45197.3 0 66722
4 29032 11299.3 0 29032
5 15253 2824.8 0 15253
6 10164 706.2 0 10164
7 8297 176.6 0 8297
8 7437 44.1 0 7437
9 7438 44.1 0 7438
10 7576 44.1 0 7576
11 7495 44.1 0 7495
12 7391 44.1 0 7391
13 7430 44.1 0 7430
14 7636 44.1 0 7636
15 7601 44.1 0 7601
16 7968 44.1 0 7968
17 7870 44.1 0 7870
18 7675 44.1 0 7675
19 7630 44.1 0 7630
20 7496 44.1 0 7496
21 7578 44.1 0 7578
22 7703 44.1 0 7703
23 7230 44.1 0 7230
24 7368 44.1 0 7368
25 7476 44.1 0 7476
26 7072 44.1 0 7072
27 7350 44.1 0 7350
28 7498 44.1 0 7498
29 7449 44.1 0 7449
30 7404 44.1 0 7404
31 8044 44.1 0 8044
32 7608 44.1 0 7608
33 7872 44.1 0 7872
34 7810 44.1 0 7810
35 7558 44.1 0 7558
36 7324 44.1 0 7324
37 7477 44.1 0 7477
38 7085 44.1 0 7085
39 7534 44.1 0 7534
40 7657 44.1 0 7657
41 7437 44.1 0 7437
42 7542 44.1 0 7542
43 7781 44.1 0 7781
44 7307 44.1 0 7307
45 7247 44.1 0 7247
46 7610 44.1 0 7610
47 7634 44.1 0 7634
48 7436 44.1 0 7436
49 10637 44.1 0 10637
50 13051 44.1 0 13051
51 7822 44.1 0 7822
52 8398 44.1 0 8398
53 8038 44.1 0 8038
54 7071 44.1 0 7071
55 7242 44.1 0 7242
56 7129 44.1 0 7129
57 6992 44.1 0 6992
58 7371 44.1 0 7371
59 7039 44.1 0 7039
60 7022 44.1 0 7022
61 7146 44.1 0 7146
62 6921 44.1 0 6921
63 6574 44.1 0 6574
64 6793 44.1 0 6793
65 6676 44.1 0 6676
66 6453 44.1 0 6453
67 6533 44.1 0 6533
68 6629 44.1 0 6629
69 6057 44.1 0 6057
70 5820 44.1 0 5820
71 6327 44.1 0 6327
72 6283 44.1 0 6283
73 5934 44.1 0 5934
74 5803 44.1 0 5803
75 5761 44.1 0 5761
76 5463 44.1 0 5463
77 5607 44.1 0 5607
78 5566 44.1 0 5566
79 6576 44.1 0 6576
80 6402 44.1 0 6402
81 7337 44.1 0 7337
82 8810 44.1 0 8810
83 9759 44.1 0 9759
84 10483 44.1 0 10483
85 10955 44.1 0 10955
86 116227 44.1 0 116227
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39539 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.8%
C: 32.2%
G: 0.0%
T: 36.5%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 15518 45197.3 0 15518
4 3437 11299.3 0 3437
5 959 2824.8 0 959
6 468 706.2 0 468
7 473 176.6 0 473
8 423 44.1 0 423
9 434 44.1 0 434
10 383 44.1 0 383
11 345 44.1 0 345
12 336 44.1 0 336
13 321 44.1 0 321
14 322 44.1 0 322
15 287 44.1 0 287
16 299 44.1 0 299
17 323 44.1 0 323
18 302 44.1 0 302
19 301 44.1 0 301
20 275 44.1 0 275
21 308 44.1 0 308
22 294 44.1 0 294
23 301 44.1 0 301
24 270 44.1 0 270
25 325 44.1 0 325
26 309 44.1 0 309
27 264 44.1 0 264
28 321 44.1 0 321
29 273 44.1 0 273
30 307 44.1 0 307
31 292 44.1 0 292
32 239 44.1 0 239
33 314 44.1 0 314
34 309 44.1 0 309
35 262 44.1 0 262
36 285 44.1 0 285
37 284 44.1 0 284
38 276 44.1 0 276
39 255 44.1 0 255
40 315 44.1 0 315
41 258 44.1 0 258
42 304 44.1 0 304
43 243 44.1 0 243
44 278 44.1 0 278
45 267 44.1 0 267
46 246 44.1 0 246
47 279 44.1 0 279
48 269 44.1 0 269
49 264 44.1 0 264
50 281 44.1 0 281
51 232 44.1 0 232
52 252 44.1 0 252
53 274 44.1 0 274
54 247 44.1 0 247
55 240 44.1 0 240
56 250 44.1 0 250
57 250 44.1 0 250
58 226 44.1 0 226
59 217 44.1 0 217
60 221 44.1 0 221
61 179 44.1 0 179
62 214 44.1 0 214
63 206 44.1 0 206
64 196 44.1 0 196
65 170 44.1 0 170
66 158 44.1 0 158
67 167 44.1 0 167
68 133 44.1 0 133
69 132 44.1 0 132
70 100 44.1 0 100
71 78 44.1 0 78
72 72 44.1 0 72
73 69 44.1 0 69
74 61 44.1 0 61
75 50 44.1 0 50
76 50 44.1 0 50
77 42 44.1 0 42
78 48 44.1 0 48
79 37 44.1 0 37
80 29 44.1 0 29
81 30 44.1 0 30
82 45 44.1 0 45
83 31 44.1 0 31
84 39 44.1 0 39
85 61 44.1 0 61
86 1035 44.1 0 1035
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 65162 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 22.7%
G: 21.9%
T: 19.4%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 48310 45197.3 0 48310
4 10958 11299.3 0 10958
5 2413 2824.8 0 2413
6 320 706.2 0 320
7 37 176.6 0 37
8 31 176.6 0 31
9 23 176.6 0 23
10 33 176.6 0 33
11 37 176.6 0 37
12 28 176.6 0 28
13 41 176.6 0 41
14 50 176.6 0 50
15 46 176.6 0 46
16 32 176.6 0 32
17 37 176.6 0 37
18 46 176.6 0 46
19 33 176.6 0 33
20 43 176.6 0 43
21 48 176.6 0 48
22 37 176.6 0 37
23 38 176.6 0 38
24 28 176.6 0 28
25 25 176.6 0 25
26 38 176.6 0 38
27 33 176.6 0 33
28 36 176.6 0 36
29 33 176.6 0 33
30 31 176.6 0 31
31 40 176.6 0 40
32 52 176.6 0 52
33 44 176.6 0 44
34 29 176.6 0 29
35 29 176.6 0 29
36 42 176.6 0 42
37 37 176.6 0 37
38 40 176.6 0 40
39 46 176.6 0 46
40 44 176.6 0 44
41 58 176.6 0 58
42 30 176.6 0 30
43 46 176.6 0 46
44 24 176.6 0 24
45 31 176.6 0 31
46 31 176.6 0 31
47 39 176.6 0 39
48 44 176.6 0 44
49 38 176.6 0 38
50 35 176.6 0 35
51 33 176.6 0 33
52 35 176.6 0 35
53 35 176.6 0 35
54 49 176.6 0 49
55 49 176.6 0 49
56 25 176.6 0 25
57 36 176.6 0 36
58 40 176.6 0 40
59 50 176.6 0 50
60 54 176.6 0 54
61 39 176.6 0 39
62 43 176.6 0 43
63 31 176.6 0 31
64 40 176.6 0 40
65 45 176.6 0 45
66 50 176.6 0 50
67 29 176.6 0 29
68 39 176.6 0 39
69 38 176.6 0 38
70 43 176.6 0 43
71 54 176.6 0 54
72 32 176.6 0 32
73 37 176.6 0 37
74 43 176.6 0 43
75 31 176.6 0 31
76 31 176.6 0 31
77 101 176.6 0 101
78 59 176.6 0 59
79 34 176.6 0 34
80 41 176.6 0 41
81 34 176.6 0 34
82 43 176.6 0 43
83 39 176.6 0 39
84 55 176.6 0 55
85 41 176.6 0 41
86 40 176.6 0 40
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R59_S202_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R59_S202_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 20.37 s (10 µs/read; 5.82 M reads/minute).
=== Summary ===
Total reads processed: 1,977,716
Reads with adapters: 580,201 (29.3%)
== Read fate breakdown ==
Reads that were too short: 173,439 (8.8%)
Reads written (passing filters): 1,804,277 (91.2%)
Total basepairs processed: 199,749,316 bp
Total written (filtered): 144,646,902 bp (72.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 509974 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.4%
G: 26.6%
T: 29.5%
none/other: 14.4%
Overview of removed sequences
length count expect max.err error counts
3 46940 30901.8 0 46940
4 18950 7725.5 0 18950
5 9110 1931.4 0 9110
6 5682 482.8 0 5682
7 4517 120.7 0 4517
8 3859 30.2 0 3859
9 3636 30.2 0 3636
10 3892 30.2 0 3892
11 3807 30.2 0 3807
12 3849 30.2 0 3849
13 3779 30.2 0 3779
14 3872 30.2 0 3872
15 4042 30.2 0 4042
16 4223 30.2 0 4223
17 3895 30.2 0 3895
18 4114 30.2 0 4114
19 4157 30.2 0 4157
20 3961 30.2 0 3961
21 4084 30.2 0 4084
22 4269 30.2 0 4269
23 3895 30.2 0 3895
24 3971 30.2 0 3971
25 3901 30.2 0 3901
26 3969 30.2 0 3969
27 3780 30.2 0 3780
28 4051 30.2 0 4051
29 4117 30.2 0 4117
30 3885 30.2 0 3885
31 4208 30.2 0 4208
32 4061 30.2 0 4061
33 4137 30.2 0 4137
34 4041 30.2 0 4041
35 4116 30.2 0 4116
36 4050 30.2 0 4050
37 4059 30.2 0 4059
38 3972 30.2 0 3972
39 4014 30.2 0 4014
40 4139 30.2 0 4139
41 4071 30.2 0 4071
42 4251 30.2 0 4251
43 4386 30.2 0 4386
44 3993 30.2 0 3993
45 4217 30.2 0 4217
46 4527 30.2 0 4527
47 4392 30.2 0 4392
48 4328 30.2 0 4328
49 5938 30.2 0 5938
50 6649 30.2 0 6649
51 4614 30.2 0 4614
52 4888 30.2 0 4888
53 4640 30.2 0 4640
54 4386 30.2 0 4386
55 4706 30.2 0 4706
56 4779 30.2 0 4779
57 4550 30.2 0 4550
58 4930 30.2 0 4930
59 4728 30.2 0 4728
60 4735 30.2 0 4735
61 4769 30.2 0 4769
62 4832 30.2 0 4832
63 4602 30.2 0 4602
64 4691 30.2 0 4691
65 4526 30.2 0 4526
66 4530 30.2 0 4530
67 4536 30.2 0 4536
68 4516 30.2 0 4516
69 4215 30.2 0 4215
70 4318 30.2 0 4318
71 4673 30.2 0 4673
72 4468 30.2 0 4468
73 4345 30.2 0 4345
74 4127 30.2 0 4127
75 4174 30.2 0 4174
76 4137 30.2 0 4137
77 4436 30.2 0 4436
78 4388 30.2 0 4388
79 4983 30.2 0 4983
80 4687 30.2 0 4687
81 5398 30.2 0 5398
82 6604 30.2 0 6604
83 7443 30.2 0 7443
84 7988 30.2 0 7988
85 8227 30.2 0 8227
86 73649 30.2 0 73649
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 22250 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 32.5%
C: 27.7%
G: 0.0%
T: 35.6%
none/other: 4.2%
Overview of removed sequences
length count expect max.err error counts
3 10697 30901.8 0 10697
4 2394 7725.5 0 2394
5 554 1931.4 0 554
6 255 482.8 0 255
7 213 120.7 0 213
8 146 30.2 0 146
9 177 30.2 0 177
10 170 30.2 0 170
11 125 30.2 0 125
12 151 30.2 0 151
13 116 30.2 0 116
14 125 30.2 0 125
15 140 30.2 0 140
16 123 30.2 0 123
17 121 30.2 0 121
18 124 30.2 0 124
19 126 30.2 0 126
20 117 30.2 0 117
21 120 30.2 0 120
22 111 30.2 0 111
23 127 30.2 0 127
24 119 30.2 0 119
25 127 30.2 0 127
26 125 30.2 0 125
27 120 30.2 0 120
28 116 30.2 0 116
29 106 30.2 0 106
30 103 30.2 0 103
31 110 30.2 0 110
32 107 30.2 0 107
33 140 30.2 0 140
34 105 30.2 0 105
35 121 30.2 0 121
36 125 30.2 0 125
37 103 30.2 0 103
38 97 30.2 0 97
39 106 30.2 0 106
40 139 30.2 0 139
41 121 30.2 0 121
42 114 30.2 0 114
43 122 30.2 0 122
44 117 30.2 0 117
45 113 30.2 0 113
46 124 30.2 0 124
47 110 30.2 0 110
48 74 30.2 0 74
49 94 30.2 0 94
50 101 30.2 0 101
51 90 30.2 0 90
52 105 30.2 0 105
53 92 30.2 0 92
54 108 30.2 0 108
55 101 30.2 0 101
56 87 30.2 0 87
57 98 30.2 0 98
58 91 30.2 0 91
59 109 30.2 0 109
60 94 30.2 0 94
61 60 30.2 0 60
62 61 30.2 0 61
63 73 30.2 0 73
64 69 30.2 0 69
65 62 30.2 0 62
66 65 30.2 0 65
67 54 30.2 0 54
68 46 30.2 0 46
69 54 30.2 0 54
70 48 30.2 0 48
71 40 30.2 0 40
72 41 30.2 0 41
73 30 30.2 0 30
74 34 30.2 0 34
75 41 30.2 0 41
76 20 30.2 0 20
77 21 30.2 0 21
78 32 30.2 0 32
79 29 30.2 0 29
80 26 30.2 0 26
81 18 30.2 0 18
82 31 30.2 0 31
83 28 30.2 0 28
84 31 30.2 0 31
85 38 30.2 0 38
86 932 30.2 0 932
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 47977 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.4%
C: 22.3%
G: 22.0%
T: 21.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 35757 30901.8 0 35757
4 8274 7725.5 0 8274
5 1541 1931.4 0 1541
6 178 482.8 0 178
7 27 120.7 0 27
8 25 120.7 0 25
9 19 120.7 0 19
10 28 120.7 0 28
11 34 120.7 0 34
12 28 120.7 0 28
13 22 120.7 0 22
14 28 120.7 0 28
15 26 120.7 0 26
16 26 120.7 0 26
17 16 120.7 0 16
18 27 120.7 0 27
19 23 120.7 0 23
20 27 120.7 0 27
21 23 120.7 0 23
22 32 120.7 0 32
23 23 120.7 0 23
24 17 120.7 0 17
25 37 120.7 0 37
26 50 120.7 0 50
27 26 120.7 0 26
28 31 120.7 0 31
29 39 120.7 0 39
30 35 120.7 0 35
31 22 120.7 0 22
32 45 120.7 0 45
33 34 120.7 0 34
34 23 120.7 0 23
35 26 120.7 0 26
36 28 120.7 0 28
37 26 120.7 0 26
38 33 120.7 0 33
39 26 120.7 0 26
40 28 120.7 0 28
41 24 120.7 0 24
42 32 120.7 0 32
43 30 120.7 0 30
44 20 120.7 0 20
45 21 120.7 0 21
46 30 120.7 0 30
47 35 120.7 0 35
48 30 120.7 0 30
49 26 120.7 0 26
50 36 120.7 0 36
51 28 120.7 0 28
52 22 120.7 0 22
53 32 120.7 0 32
54 31 120.7 0 31
55 33 120.7 0 33
56 23 120.7 0 23
57 21 120.7 0 21
58 24 120.7 0 24
59 20 120.7 0 20
60 34 120.7 0 34
61 20 120.7 0 20
62 36 120.7 0 36
63 32 120.7 0 32
64 32 120.7 0 32
65 34 120.7 0 34
66 28 120.7 0 28
67 15 120.7 0 15
68 20 120.7 0 20
69 25 120.7 0 25
70 23 120.7 0 23
71 18 120.7 0 18
72 24 120.7 0 24
73 37 120.7 0 37
74 17 120.7 0 17
75 16 120.7 0 16
76 26 120.7 0 26
77 52 120.7 0 52
78 29 120.7 0 29
79 31 120.7 0 31
80 28 120.7 0 28
81 24 120.7 0 24
82 32 120.7 0 32
83 37 120.7 0 37
84 22 120.7 0 22
85 24 120.7 0 24
86 33 120.7 0 33
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R59_S202_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R59_S202_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 18.31 s (9 µs/read; 6.58 M reads/minute).
=== Summary ===
Total reads processed: 2,008,559
Reads with adapters: 594,963 (29.6%)
== Read fate breakdown ==
Reads that were too short: 180,448 (9.0%)
Reads written (passing filters): 1,828,111 (91.0%)
Total basepairs processed: 202,864,459 bp
Total written (filtered): 146,421,228 bp (72.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 523838 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.4%
G: 26.6%
T: 29.3%
none/other: 14.7%
Overview of removed sequences
length count expect max.err error counts
3 47299 31383.7 0 47299
4 19022 7845.9 0 19022
5 9399 1961.5 0 9399
6 5465 490.4 0 5465
7 4523 122.6 0 4523
8 3902 30.6 0 3902
9 3874 30.6 0 3874
10 3942 30.6 0 3942
11 3899 30.6 0 3899
12 3993 30.6 0 3993
13 3813 30.6 0 3813
14 4054 30.6 0 4054
15 4017 30.6 0 4017
16 4296 30.6 0 4296
17 4124 30.6 0 4124
18 4203 30.6 0 4203
19 4219 30.6 0 4219
20 3978 30.6 0 3978
21 4106 30.6 0 4106
22 4287 30.6 0 4287
23 4033 30.6 0 4033
24 3839 30.6 0 3839
25 3871 30.6 0 3871
26 4132 30.6 0 4132
27 3820 30.6 0 3820
28 4013 30.6 0 4013
29 4123 30.6 0 4123
30 4060 30.6 0 4060
31 4361 30.6 0 4361
32 4082 30.6 0 4082
33 4328 30.6 0 4328
34 4167 30.6 0 4167
35 4144 30.6 0 4144
36 4124 30.6 0 4124
37 4117 30.6 0 4117
38 3909 30.6 0 3909
39 4219 30.6 0 4219
40 4174 30.6 0 4174
41 4278 30.6 0 4278
42 4339 30.6 0 4339
43 4660 30.6 0 4660
44 4182 30.6 0 4182
45 4442 30.6 0 4442
46 4543 30.6 0 4543
47 4449 30.6 0 4449
48 4365 30.6 0 4365
49 6158 30.6 0 6158
50 6908 30.6 0 6908
51 4792 30.6 0 4792
52 5018 30.6 0 5018
53 4827 30.6 0 4827
54 4496 30.6 0 4496
55 4792 30.6 0 4792
56 4728 30.6 0 4728
57 4755 30.6 0 4755
58 5064 30.6 0 5064
59 4792 30.6 0 4792
60 4750 30.6 0 4750
61 5062 30.6 0 5062
62 5087 30.6 0 5087
63 4568 30.6 0 4568
64 4841 30.6 0 4841
65 4928 30.6 0 4928
66 4693 30.6 0 4693
67 4796 30.6 0 4796
68 4642 30.6 0 4642
69 4400 30.6 0 4400
70 4330 30.6 0 4330
71 4950 30.6 0 4950
72 4751 30.6 0 4751
73 4623 30.6 0 4623
74 4214 30.6 0 4214
75 4409 30.6 0 4409
76 4251 30.6 0 4251
77 4593 30.6 0 4593
78 4392 30.6 0 4392
79 5152 30.6 0 5152
80 4868 30.6 0 4868
81 5565 30.6 0 5565
82 6776 30.6 0 6776
83 7788 30.6 0 7788
84 8292 30.6 0 8292
85 8449 30.6 0 8449
86 77149 30.6 0 77149
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 22697 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 33.1%
C: 27.6%
G: 0.0%
T: 35.3%
none/other: 4.0%
Overview of removed sequences
length count expect max.err error counts
3 10881 31383.7 0 10881
4 2410 7845.9 0 2410
5 606 1961.5 0 606
6 226 490.4 0 226
7 186 122.6 0 186
8 169 30.6 0 169
9 173 30.6 0 173
10 153 30.6 0 153
11 154 30.6 0 154
12 145 30.6 0 145
13 140 30.6 0 140
14 136 30.6 0 136
15 131 30.6 0 131
16 156 30.6 0 156
17 133 30.6 0 133
18 133 30.6 0 133
19 113 30.6 0 113
20 147 30.6 0 147
21 122 30.6 0 122
22 123 30.6 0 123
23 112 30.6 0 112
24 133 30.6 0 133
25 130 30.6 0 130
26 114 30.6 0 114
27 142 30.6 0 142
28 123 30.6 0 123
29 119 30.6 0 119
30 114 30.6 0 114
31 127 30.6 0 127
32 114 30.6 0 114
33 148 30.6 0 148
34 105 30.6 0 105
35 107 30.6 0 107
36 113 30.6 0 113
37 112 30.6 0 112
38 133 30.6 0 133
39 110 30.6 0 110
40 120 30.6 0 120
41 118 30.6 0 118
42 114 30.6 0 114
43 107 30.6 0 107
44 129 30.6 0 129
45 102 30.6 0 102
46 111 30.6 0 111
47 107 30.6 0 107
48 117 30.6 0 117
49 112 30.6 0 112
50 109 30.6 0 109
51 106 30.6 0 106
52 115 30.6 0 115
53 107 30.6 0 107
54 97 30.6 0 97
55 98 30.6 0 98
56 99 30.6 0 99
57 95 30.6 0 95
58 83 30.6 0 83
59 90 30.6 0 90
60 79 30.6 0 79
61 78 30.6 0 78
62 86 30.6 0 86
63 72 30.6 0 72
64 86 30.6 0 86
65 68 30.6 0 68
66 59 30.6 0 59
67 55 30.6 0 55
68 61 30.6 0 61
69 49 30.6 0 49
70 48 30.6 0 48
71 38 30.6 0 38
72 38 30.6 0 38
73 37 30.6 0 37
74 24 30.6 0 24
75 35 30.6 0 35
76 31 30.6 0 31
77 26 30.6 0 26
78 14 30.6 0 14
79 30 30.6 0 30
80 20 30.6 0 20
81 20 30.6 0 20
82 24 30.6 0 24
83 31 30.6 0 31
84 28 30.6 0 28
85 35 30.6 0 35
86 896 30.6 0 896
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 48428 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.1%
C: 22.5%
G: 21.9%
T: 21.4%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 36159 31383.7 0 36159
4 8267 7845.9 0 8267
5 1658 1961.5 0 1658
6 186 490.4 0 186
7 21 122.6 0 21
8 20 122.6 0 20
9 18 122.6 0 18
10 16 122.6 0 16
11 18 122.6 0 18
12 30 122.6 0 30
13 21 122.6 0 21
14 30 122.6 0 30
15 27 122.6 0 27
16 17 122.6 0 17
17 25 122.6 0 25
18 21 122.6 0 21
19 22 122.6 0 22
20 34 122.6 0 34
21 25 122.6 0 25
22 18 122.6 0 18
23 28 122.6 0 28
24 10 122.6 0 10
25 29 122.6 0 29
26 40 122.6 0 40
27 31 122.6 0 31
28 30 122.6 0 30
29 40 122.6 0 40
30 37 122.6 0 37
31 25 122.6 0 25
32 35 122.6 0 35
33 30 122.6 0 30
34 18 122.6 0 18
35 27 122.6 0 27
36 21 122.6 0 21
37 19 122.6 0 19
38 28 122.6 0 28
39 24 122.6 0 24
40 25 122.6 0 25
41 32 122.6 0 32
42 42 122.6 0 42
43 34 122.6 0 34
44 23 122.6 0 23
45 28 122.6 0 28
46 31 122.6 0 31
47 26 122.6 0 26
48 30 122.6 0 30
49 26 122.6 0 26
50 41 122.6 0 41
51 31 122.6 0 31
52 29 122.6 0 29
53 30 122.6 0 30
54 33 122.6 0 33
55 36 122.6 0 36
56 17 122.6 0 17
57 25 122.6 0 25
58 21 122.6 0 21
59 34 122.6 0 34
60 25 122.6 0 25
61 30 122.6 0 30
62 36 122.6 0 36
63 31 122.6 0 31
64 22 122.6 0 22
65 50 122.6 0 50
66 17 122.6 0 17
67 27 122.6 0 27
68 22 122.6 0 22
69 27 122.6 0 27
70 19 122.6 0 19
71 31 122.6 0 31
72 16 122.6 0 16
73 33 122.6 0 33
74 28 122.6 0 28
75 24 122.6 0 24
76 22 122.6 0 22
77 40 122.6 0 40
78 27 122.6 0 27
79 17 122.6 0 17
80 24 122.6 0 24
81 27 122.6 0 27
82 24 122.6 0 24
83 31 122.6 0 31
84 19 122.6 0 19
85 31 122.6 0 31
86 29 122.6 0 29
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R60_S201_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R60_S201_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 22.28 s (9 µs/read; 6.89 M reads/minute).
=== Summary ===
Total reads processed: 2,557,306
Reads with adapters: 575,874 (22.5%)
== Read fate breakdown ==
Reads that were too short: 145,425 (5.7%)
Reads written (passing filters): 2,411,881 (94.3%)
Total basepairs processed: 258,287,906 bp
Total written (filtered): 198,007,515 bp (76.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 482402 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.1%
G: 29.6%
T: 29.1%
none/other: 13.3%
Overview of removed sequences
length count expect max.err error counts
3 62362 39957.9 0 62362
4 23892 9989.5 0 23892
5 11235 2497.4 0 11235
6 6146 624.3 0 6146
7 4578 156.1 0 4578
8 3868 39.0 0 3868
9 4008 39.0 0 4008
10 3865 39.0 0 3865
11 4035 39.0 0 4035
12 3911 39.0 0 3911
13 4048 39.0 0 4048
14 4003 39.0 0 4003
15 4023 39.0 0 4023
16 4057 39.0 0 4057
17 3987 39.0 0 3987
18 4179 39.0 0 4179
19 3891 39.0 0 3891
20 3845 39.0 0 3845
21 3845 39.0 0 3845
22 3906 39.0 0 3906
23 3736 39.0 0 3736
24 3863 39.0 0 3863
25 3639 39.0 0 3639
26 3702 39.0 0 3702
27 3825 39.0 0 3825
28 3784 39.0 0 3784
29 3952 39.0 0 3952
30 3624 39.0 0 3624
31 4055 39.0 0 4055
32 3891 39.0 0 3891
33 3856 39.0 0 3856
34 3802 39.0 0 3802
35 3725 39.0 0 3725
36 3765 39.0 0 3765
37 3662 39.0 0 3662
38 3513 39.0 0 3513
39 3738 39.0 0 3738
40 3661 39.0 0 3661
41 3762 39.0 0 3762
42 3778 39.0 0 3778
43 3855 39.0 0 3855
44 3606 39.0 0 3606
45 3706 39.0 0 3706
46 3764 39.0 0 3764
47 3887 39.0 0 3887
48 3660 39.0 0 3660
49 5696 39.0 0 5696
50 7395 39.0 0 7395
51 3935 39.0 0 3935
52 4327 39.0 0 4327
53 4111 39.0 0 4111
54 3499 39.0 0 3499
55 3859 39.0 0 3859
56 3817 39.0 0 3817
57 3594 39.0 0 3594
58 4050 39.0 0 4050
59 3728 39.0 0 3728
60 3789 39.0 0 3789
61 3750 39.0 0 3750
62 3688 39.0 0 3688
63 3581 39.0 0 3581
64 3644 39.0 0 3644
65 3631 39.0 0 3631
66 3418 39.0 0 3418
67 3587 39.0 0 3587
68 3640 39.0 0 3640
69 3469 39.0 0 3469
70 3197 39.0 0 3197
71 3531 39.0 0 3531
72 3760 39.0 0 3760
73 3459 39.0 0 3459
74 3405 39.0 0 3405
75 3300 39.0 0 3300
76 3331 39.0 0 3331
77 3255 39.0 0 3255
78 3619 39.0 0 3619
79 4164 39.0 0 4164
80 3942 39.0 0 3942
81 4826 39.0 0 4826
82 5588 39.0 0 5588
83 6025 39.0 0 6025
84 6538 39.0 0 6538
85 6672 39.0 0 6672
86 64087 39.0 0 64087
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 26501 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 33.7%
C: 31.1%
G: 0.0%
T: 31.6%
none/other: 3.6%
Overview of removed sequences
length count expect max.err error counts
3 17262 39957.9 0 17262
4 3580 9989.5 0 3580
5 684 2497.4 0 684
6 166 624.3 0 166
7 120 156.1 0 120
8 105 39.0 0 105
9 104 39.0 0 104
10 76 39.0 0 76
11 91 39.0 0 91
12 86 39.0 0 86
13 70 39.0 0 70
14 69 39.0 0 69
15 66 39.0 0 66
16 59 39.0 0 59
17 74 39.0 0 74
18 56 39.0 0 56
19 61 39.0 0 61
20 65 39.0 0 65
21 51 39.0 0 51
22 56 39.0 0 56
23 68 39.0 0 68
24 57 39.0 0 57
25 54 39.0 0 54
26 59 39.0 0 59
27 54 39.0 0 54
28 53 39.0 0 53
29 54 39.0 0 54
30 48 39.0 0 48
31 45 39.0 0 45
32 52 39.0 0 52
33 57 39.0 0 57
34 56 39.0 0 56
35 53 39.0 0 53
36 60 39.0 0 60
37 43 39.0 0 43
38 52 39.0 0 52
39 46 39.0 0 46
40 54 39.0 0 54
41 66 39.0 0 66
42 65 39.0 0 65
43 72 39.0 0 72
44 51 39.0 0 51
45 64 39.0 0 64
46 56 39.0 0 56
47 45 39.0 0 45
48 63 39.0 0 63
49 61 39.0 0 61
50 50 39.0 0 50
51 55 39.0 0 55
52 51 39.0 0 51
53 40 39.0 0 40
54 36 39.0 0 36
55 40 39.0 0 40
56 55 39.0 0 55
57 52 39.0 0 52
58 40 39.0 0 40
59 55 39.0 0 55
60 47 39.0 0 47
61 50 39.0 0 50
62 39 39.0 0 39
63 23 39.0 0 23
64 33 39.0 0 33
65 44 39.0 0 44
66 37 39.0 0 37
67 21 39.0 0 21
68 37 39.0 0 37
69 25 39.0 0 25
70 10 39.0 0 10
71 28 39.0 0 28
72 21 39.0 0 21
73 16 39.0 0 16
74 21 39.0 0 21
75 20 39.0 0 20
76 12 39.0 0 12
77 16 39.0 0 16
78 25 39.0 0 25
79 14 39.0 0 14
80 13 39.0 0 13
81 8 39.0 0 8
82 23 39.0 0 23
83 26 39.0 0 26
84 28 39.0 0 28
85 35 39.0 0 35
86 946 39.0 0 946
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 66971 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.3%
C: 23.0%
G: 22.0%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 49441 39957.9 0 49441
4 11811 9989.5 0 11811
5 2531 2497.4 0 2531
6 367 624.3 0 367
7 37 156.1 0 37
8 26 156.1 0 26
9 26 156.1 0 26
10 30 156.1 0 30
11 28 156.1 0 28
12 33 156.1 0 33
13 32 156.1 0 32
14 28 156.1 0 28
15 29 156.1 0 29
16 31 156.1 0 31
17 41 156.1 0 41
18 38 156.1 0 38
19 32 156.1 0 32
20 26 156.1 0 26
21 48 156.1 0 48
22 22 156.1 0 22
23 18 156.1 0 18
24 32 156.1 0 32
25 34 156.1 0 34
26 68 156.1 0 68
27 27 156.1 0 27
28 35 156.1 0 35
29 55 156.1 0 55
30 38 156.1 0 38
31 18 156.1 0 18
32 82 156.1 0 82
33 32 156.1 0 32
34 31 156.1 0 31
35 20 156.1 0 20
36 48 156.1 0 48
37 24 156.1 0 24
38 20 156.1 0 20
39 35 156.1 0 35
40 30 156.1 0 30
41 49 156.1 0 49
42 38 156.1 0 38
43 36 156.1 0 36
44 40 156.1 0 40
45 31 156.1 0 31
46 30 156.1 0 30
47 36 156.1 0 36
48 38 156.1 0 38
49 41 156.1 0 41
50 38 156.1 0 38
51 29 156.1 0 29
52 55 156.1 0 55
53 28 156.1 0 28
54 39 156.1 0 39
55 42 156.1 0 42
56 32 156.1 0 32
57 32 156.1 0 32
58 34 156.1 0 34
59 36 156.1 0 36
60 42 156.1 0 42
61 24 156.1 0 24
62 45 156.1 0 45
63 36 156.1 0 36
64 34 156.1 0 34
65 54 156.1 0 54
66 43 156.1 0 43
67 41 156.1 0 41
68 35 156.1 0 35
69 23 156.1 0 23
70 35 156.1 0 35
71 48 156.1 0 48
72 16 156.1 0 16
73 27 156.1 0 27
74 10 156.1 0 10
75 27 156.1 0 27
76 33 156.1 0 33
77 52 156.1 0 52
78 33 156.1 0 33
79 32 156.1 0 32
80 25 156.1 0 25
81 32 156.1 0 32
82 39 156.1 0 39
83 56 156.1 0 56
84 36 156.1 0 36
85 42 156.1 0 42
86 43 156.1 0 43
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R60_S201_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R60_S201_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.44 s (9 µs/read; 6.40 M reads/minute).
=== Summary ===
Total reads processed: 2,606,820
Reads with adapters: 590,113 (22.6%)
== Read fate breakdown ==
Reads that were too short: 150,662 (5.8%)
Reads written (passing filters): 2,456,158 (94.2%)
Total basepairs processed: 263,288,820 bp
Total written (filtered): 201,599,963 bp (76.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 494719 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.1%
G: 29.5%
T: 28.9%
none/other: 13.5%
Overview of removed sequences
length count expect max.err error counts
3 64012 40731.6 0 64012
4 24360 10182.9 0 24360
5 11481 2545.7 0 11481
6 6184 636.4 0 6184
7 4680 159.1 0 4680
8 3998 39.8 0 3998
9 3983 39.8 0 3983
10 3966 39.8 0 3966
11 3914 39.8 0 3914
12 4059 39.8 0 4059
13 3944 39.8 0 3944
14 3926 39.8 0 3926
15 3964 39.8 0 3964
16 4153 39.8 0 4153
17 4195 39.8 0 4195
18 4131 39.8 0 4131
19 3856 39.8 0 3856
20 3835 39.8 0 3835
21 3990 39.8 0 3990
22 3983 39.8 0 3983
23 3890 39.8 0 3890
24 3789 39.8 0 3789
25 3831 39.8 0 3831
26 3727 39.8 0 3727
27 3899 39.8 0 3899
28 3980 39.8 0 3980
29 3979 39.8 0 3979
30 3880 39.8 0 3880
31 4015 39.8 0 4015
32 3890 39.8 0 3890
33 3867 39.8 0 3867
34 3770 39.8 0 3770
35 3780 39.8 0 3780
36 3906 39.8 0 3906
37 3789 39.8 0 3789
38 3595 39.8 0 3595
39 3799 39.8 0 3799
40 3907 39.8 0 3907
41 3810 39.8 0 3810
42 3872 39.8 0 3872
43 3943 39.8 0 3943
44 3707 39.8 0 3707
45 3856 39.8 0 3856
46 4122 39.8 0 4122
47 3974 39.8 0 3974
48 3656 39.8 0 3656
49 5859 39.8 0 5859
50 7478 39.8 0 7478
51 3931 39.8 0 3931
52 4482 39.8 0 4482
53 4345 39.8 0 4345
54 3550 39.8 0 3550
55 3898 39.8 0 3898
56 3781 39.8 0 3781
57 3744 39.8 0 3744
58 4128 39.8 0 4128
59 3826 39.8 0 3826
60 3814 39.8 0 3814
61 4054 39.8 0 4054
62 3831 39.8 0 3831
63 3675 39.8 0 3675
64 3720 39.8 0 3720
65 3714 39.8 0 3714
66 3473 39.8 0 3473
67 3516 39.8 0 3516
68 3629 39.8 0 3629
69 3511 39.8 0 3511
70 3317 39.8 0 3317
71 3705 39.8 0 3705
72 3731 39.8 0 3731
73 3548 39.8 0 3548
74 3449 39.8 0 3449
75 3567 39.8 0 3567
76 3461 39.8 0 3461
77 3486 39.8 0 3486
78 3818 39.8 0 3818
79 4237 39.8 0 4237
80 4188 39.8 0 4188
81 5211 39.8 0 5211
82 5761 39.8 0 5761
83 6082 39.8 0 6082
84 6734 39.8 0 6734
85 6970 39.8 0 6970
86 66648 39.8 0 66648
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27111 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 33.8%
C: 30.5%
G: 0.0%
T: 32.4%
none/other: 3.3%
Overview of removed sequences
length count expect max.err error counts
3 17724 40731.6 0 17724
4 3617 10182.9 0 3617
5 667 2545.7 0 667
6 194 636.4 0 194
7 124 159.1 0 124
8 124 39.8 0 124
9 108 39.8 0 108
10 107 39.8 0 107
11 77 39.8 0 77
12 88 39.8 0 88
13 76 39.8 0 76
14 64 39.8 0 64
15 73 39.8 0 73
16 56 39.8 0 56
17 54 39.8 0 54
18 61 39.8 0 61
19 64 39.8 0 64
20 61 39.8 0 61
21 57 39.8 0 57
22 49 39.8 0 49
23 61 39.8 0 61
24 65 39.8 0 65
25 75 39.8 0 75
26 80 39.8 0 80
27 54 39.8 0 54
28 61 39.8 0 61
29 50 39.8 0 50
30 54 39.8 0 54
31 54 39.8 0 54
32 55 39.8 0 55
33 74 39.8 0 74
34 58 39.8 0 58
35 62 39.8 0 62
36 51 39.8 0 51
37 60 39.8 0 60
38 53 39.8 0 53
39 41 39.8 0 41
40 56 39.8 0 56
41 54 39.8 0 54
42 60 39.8 0 60
43 52 39.8 0 52
44 56 39.8 0 56
45 57 39.8 0 57
46 61 39.8 0 61
47 66 39.8 0 66
48 53 39.8 0 53
49 52 39.8 0 52
50 63 39.8 0 63
51 56 39.8 0 56
52 54 39.8 0 54
53 48 39.8 0 48
54 53 39.8 0 53
55 42 39.8 0 42
56 49 39.8 0 49
57 47 39.8 0 47
58 46 39.8 0 46
59 39 39.8 0 39
60 31 39.8 0 31
61 43 39.8 0 43
62 28 39.8 0 28
63 32 39.8 0 32
64 47 39.8 0 47
65 38 39.8 0 38
66 36 39.8 0 36
67 31 39.8 0 31
68 23 39.8 0 23
69 28 39.8 0 28
70 24 39.8 0 24
71 29 39.8 0 29
72 30 39.8 0 30
73 21 39.8 0 21
74 27 39.8 0 27
75 11 39.8 0 11
76 13 39.8 0 13
77 22 39.8 0 22
78 21 39.8 0 21
79 27 39.8 0 27
80 29 39.8 0 29
81 19 39.8 0 19
82 20 39.8 0 20
83 26 39.8 0 26
84 19 39.8 0 19
85 32 39.8 0 32
86 887 39.8 0 887
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 68283 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.0%
C: 23.0%
G: 21.9%
T: 21.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 50291 40731.6 0 50291
4 12026 10182.9 0 12026
5 2677 2545.7 0 2677
6 399 636.4 0 399
7 38 159.1 0 38
8 31 159.1 0 31
9 31 159.1 0 31
10 23 159.1 0 23
11 42 159.1 0 42
12 29 159.1 0 29
13 26 159.1 0 26
14 26 159.1 0 26
15 34 159.1 0 34
16 36 159.1 0 36
17 34 159.1 0 34
18 36 159.1 0 36
19 52 159.1 0 52
20 37 159.1 0 37
21 36 159.1 0 36
22 35 159.1 0 35
23 27 159.1 0 27
24 19 159.1 0 19
25 22 159.1 0 22
26 61 159.1 0 61
27 25 159.1 0 25
28 33 159.1 0 33
29 59 159.1 0 59
30 36 159.1 0 36
31 31 159.1 0 31
32 84 159.1 0 84
33 38 159.1 0 38
34 21 159.1 0 21
35 22 159.1 0 22
36 31 159.1 0 31
37 26 159.1 0 26
38 37 159.1 0 37
39 39 159.1 0 39
40 33 159.1 0 33
41 40 159.1 0 40
42 29 159.1 0 29
43 22 159.1 0 22
44 45 159.1 0 45
45 34 159.1 0 34
46 29 159.1 0 29
47 37 159.1 0 37
48 30 159.1 0 30
49 33 159.1 0 33
50 40 159.1 0 40
51 43 159.1 0 43
52 37 159.1 0 37
53 21 159.1 0 21
54 45 159.1 0 45
55 40 159.1 0 40
56 24 159.1 0 24
57 38 159.1 0 38
58 30 159.1 0 30
59 36 159.1 0 36
60 41 159.1 0 41
61 31 159.1 0 31
62 52 159.1 0 52
63 50 159.1 0 50
64 30 159.1 0 30
65 50 159.1 0 50
66 39 159.1 0 39
67 28 159.1 0 28
68 43 159.1 0 43
69 31 159.1 0 31
70 43 159.1 0 43
71 38 159.1 0 38
72 27 159.1 0 27
73 29 159.1 0 29
74 40 159.1 0 40
75 19 159.1 0 19
76 29 159.1 0 29
77 56 159.1 0 56
78 39 159.1 0 39
79 32 159.1 0 32
80 22 159.1 0 22
81 41 159.1 0 41
82 44 159.1 0 44
83 32 159.1 0 32
84 50 159.1 0 50
85 48 159.1 0 48
86 63 159.1 0 63
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R61_S207_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R61_S207_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 22.26 s (10 µs/read; 6.00 M reads/minute).
=== Summary ===
Total reads processed: 2,226,641
Reads with adapters: 748,620 (33.6%)
== Read fate breakdown ==
Reads that were too short: 230,407 (10.3%)
Reads written (passing filters): 1,996,234 (89.7%)
Total basepairs processed: 224,890,741 bp
Total written (filtered): 157,575,306 bp (70.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 672051 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.9%
G: 26.7%
T: 29.0%
none/other: 15.4%
Overview of removed sequences
length count expect max.err error counts
3 51405 34791.3 0 51405
4 22476 8697.8 0 22476
5 11597 2174.5 0 11597
6 7813 543.6 0 7813
7 6280 135.9 0 6280
8 5579 34.0 0 5579
9 5577 34.0 0 5577
10 5444 34.0 0 5444
11 5417 34.0 0 5417
12 5365 34.0 0 5365
13 5591 34.0 0 5591
14 5443 34.0 0 5443
15 5580 34.0 0 5580
16 5730 34.0 0 5730
17 5552 34.0 0 5552
18 5538 34.0 0 5538
19 5586 34.0 0 5586
20 5416 34.0 0 5416
21 5780 34.0 0 5780
22 5601 34.0 0 5601
23 5326 34.0 0 5326
24 5471 34.0 0 5471
25 5328 34.0 0 5328
26 5298 34.0 0 5298
27 5314 34.0 0 5314
28 5575 34.0 0 5575
29 5621 34.0 0 5621
30 5557 34.0 0 5557
31 5942 34.0 0 5942
32 5631 34.0 0 5631
33 5889 34.0 0 5889
34 5594 34.0 0 5594
35 5471 34.0 0 5471
36 5546 34.0 0 5546
37 5497 34.0 0 5497
38 5383 34.0 0 5383
39 5556 34.0 0 5556
40 5480 34.0 0 5480
41 5687 34.0 0 5687
42 5754 34.0 0 5754
43 6097 34.0 0 6097
44 5686 34.0 0 5686
45 5773 34.0 0 5773
46 6149 34.0 0 6149
47 6092 34.0 0 6092
48 5812 34.0 0 5812
49 8494 34.0 0 8494
50 10159 34.0 0 10159
51 5994 34.0 0 5994
52 6533 34.0 0 6533
53 6327 34.0 0 6327
54 5833 34.0 0 5833
55 5942 34.0 0 5942
56 6053 34.0 0 6053
57 5671 34.0 0 5671
58 6233 34.0 0 6233
59 6087 34.0 0 6087
60 6076 34.0 0 6076
61 6199 34.0 0 6199
62 6067 34.0 0 6067
63 5736 34.0 0 5736
64 5975 34.0 0 5975
65 5787 34.0 0 5787
66 5760 34.0 0 5760
67 5773 34.0 0 5773
68 5620 34.0 0 5620
69 5413 34.0 0 5413
70 5154 34.0 0 5154
71 5255 34.0 0 5255
72 5367 34.0 0 5367
73 5117 34.0 0 5117
74 4965 34.0 0 4965
75 5006 34.0 0 5006
76 5066 34.0 0 5066
77 5034 34.0 0 5034
78 5249 34.0 0 5249
79 6232 34.0 0 6232
80 6029 34.0 0 6029
81 7162 34.0 0 7162
82 8828 34.0 0 8828
83 10129 34.0 0 10129
84 10926 34.0 0 10926
85 11769 34.0 0 11769
86 103732 34.0 0 103732
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29776 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.1%
C: 32.1%
G: 0.0%
T: 36.6%
none/other: 3.1%
Overview of removed sequences
length count expect max.err error counts
3 11487 34791.3 0 11487
4 2583 8697.8 0 2583
5 821 2174.5 0 821
6 372 543.6 0 372
7 313 135.9 0 313
8 318 34.0 0 318
9 280 34.0 0 280
10 266 34.0 0 266
11 318 34.0 0 318
12 243 34.0 0 243
13 269 34.0 0 269
14 241 34.0 0 241
15 251 34.0 0 251
16 218 34.0 0 218
17 220 34.0 0 220
18 232 34.0 0 232
19 233 34.0 0 233
20 215 34.0 0 215
21 233 34.0 0 233
22 216 34.0 0 216
23 230 34.0 0 230
24 239 34.0 0 239
25 196 34.0 0 196
26 208 34.0 0 208
27 241 34.0 0 241
28 208 34.0 0 208
29 209 34.0 0 209
30 209 34.0 0 209
31 201 34.0 0 201
32 222 34.0 0 222
33 240 34.0 0 240
34 194 34.0 0 194
35 242 34.0 0 242
36 194 34.0 0 194
37 224 34.0 0 224
38 229 34.0 0 229
39 215 34.0 0 215
40 234 34.0 0 234
41 197 34.0 0 197
42 231 34.0 0 231
43 209 34.0 0 209
44 208 34.0 0 208
45 210 34.0 0 210
46 209 34.0 0 209
47 201 34.0 0 201
48 184 34.0 0 184
49 183 34.0 0 183
50 165 34.0 0 165
51 192 34.0 0 192
52 193 34.0 0 193
53 172 34.0 0 172
54 182 34.0 0 182
55 172 34.0 0 172
56 160 34.0 0 160
57 154 34.0 0 154
58 159 34.0 0 159
59 155 34.0 0 155
60 179 34.0 0 179
61 176 34.0 0 176
62 158 34.0 0 158
63 139 34.0 0 139
64 114 34.0 0 114
65 96 34.0 0 96
66 115 34.0 0 115
67 111 34.0 0 111
68 116 34.0 0 116
69 104 34.0 0 104
70 90 34.0 0 90
71 63 34.0 0 63
72 68 34.0 0 68
73 53 34.0 0 53
74 63 34.0 0 63
75 53 34.0 0 53
76 44 34.0 0 44
77 40 34.0 0 40
78 40 34.0 0 40
79 31 34.0 0 31
80 38 34.0 0 38
81 33 34.0 0 33
82 29 34.0 0 29
83 31 34.0 0 31
84 32 34.0 0 32
85 34 34.0 0 34
86 926 34.0 0 926
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 46793 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 23.1%
G: 21.1%
T: 20.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 34616 34791.3 0 34616
4 7911 8697.8 0 7911
5 1702 2174.5 0 1702
6 250 543.6 0 250
7 23 135.9 0 23
8 40 135.9 0 40
9 26 135.9 0 26
10 29 135.9 0 29
11 35 135.9 0 35
12 30 135.9 0 30
13 34 135.9 0 34
14 35 135.9 0 35
15 32 135.9 0 32
16 28 135.9 0 28
17 35 135.9 0 35
18 39 135.9 0 39
19 34 135.9 0 34
20 42 135.9 0 42
21 31 135.9 0 31
22 27 135.9 0 27
23 27 135.9 0 27
24 27 135.9 0 27
25 44 135.9 0 44
26 25 135.9 0 25
27 24 135.9 0 24
28 22 135.9 0 22
29 23 135.9 0 23
30 25 135.9 0 25
31 23 135.9 0 23
32 31 135.9 0 31
33 22 135.9 0 22
34 23 135.9 0 23
35 27 135.9 0 27
36 29 135.9 0 29
37 25 135.9 0 25
38 30 135.9 0 30
39 20 135.9 0 20
40 31 135.9 0 31
41 27 135.9 0 27
42 28 135.9 0 28
43 27 135.9 0 27
44 19 135.9 0 19
45 22 135.9 0 22
46 21 135.9 0 21
47 18 135.9 0 18
48 30 135.9 0 30
49 34 135.9 0 34
50 35 135.9 0 35
51 27 135.9 0 27
52 35 135.9 0 35
53 30 135.9 0 30
54 25 135.9 0 25
55 15 135.9 0 15
56 28 135.9 0 28
57 40 135.9 0 40
58 31 135.9 0 31
59 30 135.9 0 30
60 26 135.9 0 26
61 31 135.9 0 31
62 30 135.9 0 30
63 30 135.9 0 30
64 32 135.9 0 32
65 30 135.9 0 30
66 33 135.9 0 33
67 22 135.9 0 22
68 13 135.9 0 13
69 21 135.9 0 21
70 22 135.9 0 22
71 37 135.9 0 37
72 16 135.9 0 16
73 28 135.9 0 28
74 27 135.9 0 27
75 26 135.9 0 26
76 18 135.9 0 18
77 69 135.9 0 69
78 39 135.9 0 39
79 28 135.9 0 28
80 32 135.9 0 32
81 25 135.9 0 25
82 24 135.9 0 24
83 32 135.9 0 32
84 34 135.9 0 34
85 30 135.9 0 30
86 39 135.9 0 39
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R61_S207_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R61_S207_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 21.67 s (10 µs/read; 6.29 M reads/minute).
=== Summary ===
Total reads processed: 2,272,675
Reads with adapters: 771,236 (33.9%)
== Read fate breakdown ==
Reads that were too short: 240,773 (10.6%)
Reads written (passing filters): 2,031,902 (89.4%)
Total basepairs processed: 229,540,175 bp
Total written (filtered): 160,206,021 bp (69.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 692816 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.0%
G: 26.5%
T: 28.7%
none/other: 15.7%
Overview of removed sequences
length count expect max.err error counts
3 51726 35510.5 0 51726
4 23010 8877.6 0 23010
5 11705 2219.4 0 11705
6 7821 554.9 0 7821
7 6229 138.7 0 6229
8 5539 34.7 0 5539
9 5666 34.7 0 5666
10 5540 34.7 0 5540
11 5408 34.7 0 5408
12 5413 34.7 0 5413
13 5609 34.7 0 5609
14 5507 34.7 0 5507
15 5695 34.7 0 5695
16 5688 34.7 0 5688
17 5744 34.7 0 5744
18 5812 34.7 0 5812
19 5830 34.7 0 5830
20 5474 34.7 0 5474
21 5632 34.7 0 5632
22 5707 34.7 0 5707
23 5561 34.7 0 5561
24 5483 34.7 0 5483
25 5477 34.7 0 5477
26 5410 34.7 0 5410
27 5656 34.7 0 5656
28 5776 34.7 0 5776
29 5711 34.7 0 5711
30 5720 34.7 0 5720
31 6293 34.7 0 6293
32 5761 34.7 0 5761
33 6067 34.7 0 6067
34 5815 34.7 0 5815
35 5858 34.7 0 5858
36 5639 34.7 0 5639
37 5705 34.7 0 5705
38 5500 34.7 0 5500
39 5674 34.7 0 5674
40 5823 34.7 0 5823
41 5785 34.7 0 5785
42 5963 34.7 0 5963
43 6307 34.7 0 6307
44 5672 34.7 0 5672
45 5978 34.7 0 5978
46 6309 34.7 0 6309
47 6150 34.7 0 6150
48 5961 34.7 0 5961
49 8949 34.7 0 8949
50 10279 34.7 0 10279
51 6414 34.7 0 6414
52 6782 34.7 0 6782
53 6593 34.7 0 6593
54 5869 34.7 0 5869
55 6138 34.7 0 6138
56 6320 34.7 0 6320
57 6111 34.7 0 6111
58 6389 34.7 0 6389
59 6171 34.7 0 6171
60 6346 34.7 0 6346
61 6273 34.7 0 6273
62 6305 34.7 0 6305
63 6038 34.7 0 6038
64 5962 34.7 0 5962
65 6000 34.7 0 6000
66 6054 34.7 0 6054
67 5878 34.7 0 5878
68 6026 34.7 0 6026
69 5579 34.7 0 5579
70 5316 34.7 0 5316
71 5564 34.7 0 5564
72 5703 34.7 0 5703
73 5241 34.7 0 5241
74 4978 34.7 0 4978
75 5352 34.7 0 5352
76 5102 34.7 0 5102
77 5322 34.7 0 5322
78 5600 34.7 0 5600
79 6361 34.7 0 6361
80 6250 34.7 0 6250
81 7319 34.7 0 7319
82 9281 34.7 0 9281
83 10323 34.7 0 10323
84 11575 34.7 0 11575
85 12204 34.7 0 12204
86 109040 34.7 0 109040
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30630 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.7%
C: 31.8%
G: 0.0%
T: 36.9%
none/other: 3.5%
Overview of removed sequences
length count expect max.err error counts
3 11604 35510.5 0 11604
4 2592 8877.6 0 2592
5 786 2219.4 0 786
6 382 554.9 0 382
7 328 138.7 0 328
8 315 34.7 0 315
9 288 34.7 0 288
10 302 34.7 0 302
11 292 34.7 0 292
12 266 34.7 0 266
13 261 34.7 0 261
14 262 34.7 0 262
15 259 34.7 0 259
16 237 34.7 0 237
17 231 34.7 0 231
18 230 34.7 0 230
19 268 34.7 0 268
20 218 34.7 0 218
21 231 34.7 0 231
22 215 34.7 0 215
23 228 34.7 0 228
24 230 34.7 0 230
25 233 34.7 0 233
26 231 34.7 0 231
27 227 34.7 0 227
28 245 34.7 0 245
29 229 34.7 0 229
30 229 34.7 0 229
31 225 34.7 0 225
32 216 34.7 0 216
33 258 34.7 0 258
34 240 34.7 0 240
35 202 34.7 0 202
36 227 34.7 0 227
37 229 34.7 0 229
38 199 34.7 0 199
39 240 34.7 0 240
40 214 34.7 0 214
41 248 34.7 0 248
42 223 34.7 0 223
43 248 34.7 0 248
44 202 34.7 0 202
45 197 34.7 0 197
46 244 34.7 0 244
47 208 34.7 0 208
48 216 34.7 0 216
49 197 34.7 0 197
50 185 34.7 0 185
51 182 34.7 0 182
52 200 34.7 0 200
53 197 34.7 0 197
54 178 34.7 0 178
55 198 34.7 0 198
56 177 34.7 0 177
57 179 34.7 0 179
58 181 34.7 0 181
59 182 34.7 0 182
60 170 34.7 0 170
61 155 34.7 0 155
62 131 34.7 0 131
63 133 34.7 0 133
64 144 34.7 0 144
65 131 34.7 0 131
66 116 34.7 0 116
67 103 34.7 0 103
68 97 34.7 0 97
69 87 34.7 0 87
70 79 34.7 0 79
71 76 34.7 0 76
72 64 34.7 0 64
73 56 34.7 0 56
74 47 34.7 0 47
75 49 34.7 0 49
76 51 34.7 0 51
77 43 34.7 0 43
78 43 34.7 0 43
79 36 34.7 0 36
80 38 34.7 0 38
81 24 34.7 0 24
82 42 34.7 0 42
83 34 34.7 0 34
84 49 34.7 0 49
85 44 34.7 0 44
86 1077 34.7 0 1077
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 47790 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.9%
C: 23.1%
G: 21.1%
T: 20.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 35457 35510.5 0 35457
4 7930 8877.6 0 7930
5 1729 2219.4 0 1729
6 253 554.9 0 253
7 22 138.7 0 22
8 23 138.7 0 23
9 35 138.7 0 35
10 37 138.7 0 37
11 30 138.7 0 30
12 28 138.7 0 28
13 46 138.7 0 46
14 37 138.7 0 37
15 32 138.7 0 32
16 45 138.7 0 45
17 37 138.7 0 37
18 22 138.7 0 22
19 34 138.7 0 34
20 28 138.7 0 28
21 27 138.7 0 27
22 30 138.7 0 30
23 35 138.7 0 35
24 24 138.7 0 24
25 48 138.7 0 48
26 32 138.7 0 32
27 17 138.7 0 17
28 29 138.7 0 29
29 37 138.7 0 37
30 26 138.7 0 26
31 35 138.7 0 35
32 38 138.7 0 38
33 29 138.7 0 29
34 26 138.7 0 26
35 26 138.7 0 26
36 32 138.7 0 32
37 23 138.7 0 23
38 21 138.7 0 21
39 27 138.7 0 27
40 26 138.7 0 26
41 27 138.7 0 27
42 27 138.7 0 27
43 28 138.7 0 28
44 33 138.7 0 33
45 21 138.7 0 21
46 21 138.7 0 21
47 37 138.7 0 37
48 28 138.7 0 28
49 34 138.7 0 34
50 39 138.7 0 39
51 34 138.7 0 34
52 31 138.7 0 31
53 31 138.7 0 31
54 43 138.7 0 43
55 31 138.7 0 31
56 22 138.7 0 22
57 26 138.7 0 26
58 28 138.7 0 28
59 28 138.7 0 28
60 39 138.7 0 39
61 21 138.7 0 21
62 23 138.7 0 23
63 30 138.7 0 30
64 21 138.7 0 21
65 26 138.7 0 26
66 28 138.7 0 28
67 25 138.7 0 25
68 26 138.7 0 26
69 20 138.7 0 20
70 40 138.7 0 40
71 42 138.7 0 42
72 24 138.7 0 24
73 26 138.7 0 26
74 23 138.7 0 23
75 39 138.7 0 39
76 17 138.7 0 17
77 65 138.7 0 65
78 38 138.7 0 38
79 33 138.7 0 33
80 25 138.7 0 25
81 35 138.7 0 35
82 28 138.7 0 28
83 28 138.7 0 28
84 29 138.7 0 29
85 30 138.7 0 30
86 27 138.7 0 27
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R62_S203_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R62_S203_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 15.49 s (10 µs/read; 5.86 M reads/minute).
=== Summary ===
Total reads processed: 1,513,989
Reads with adapters: 388,720 (25.7%)
== Read fate breakdown ==
Reads that were too short: 113,615 (7.5%)
Reads written (passing filters): 1,400,374 (92.5%)
Total basepairs processed: 152,912,889 bp
Total written (filtered): 113,712,834 bp (74.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 328363 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.7%
G: 25.4%
T: 27.4%
none/other: 18.4%
Overview of removed sequences
length count expect max.err error counts
3 37615 23656.1 0 37615
4 15628 5914.0 0 15628
5 7012 1478.5 0 7012
6 3641 369.6 0 3641
7 2823 92.4 0 2823
8 2315 23.1 0 2315
9 2344 23.1 0 2344
10 2243 23.1 0 2243
11 2245 23.1 0 2245
12 2218 23.1 0 2218
13 2357 23.1 0 2357
14 2401 23.1 0 2401
15 2345 23.1 0 2345
16 2409 23.1 0 2409
17 2358 23.1 0 2358
18 2405 23.1 0 2405
19 2375 23.1 0 2375
20 2383 23.1 0 2383
21 2469 23.1 0 2469
22 2444 23.1 0 2444
23 2414 23.1 0 2414
24 2324 23.1 0 2324
25 2449 23.1 0 2449
26 2432 23.1 0 2432
27 2469 23.1 0 2469
28 2508 23.1 0 2508
29 2529 23.1 0 2529
30 2475 23.1 0 2475
31 2521 23.1 0 2521
32 2294 23.1 0 2294
33 2439 23.1 0 2439
34 2535 23.1 0 2535
35 2411 23.1 0 2411
36 2473 23.1 0 2473
37 2391 23.1 0 2391
38 2235 23.1 0 2235
39 2458 23.1 0 2458
40 2517 23.1 0 2517
41 2572 23.1 0 2572
42 2561 23.1 0 2561
43 2512 23.1 0 2512
44 2334 23.1 0 2334
45 2614 23.1 0 2614
46 2530 23.1 0 2530
47 2528 23.1 0 2528
48 2528 23.1 0 2528
49 2744 23.1 0 2744
50 3167 23.1 0 3167
51 2882 23.1 0 2882
52 2639 23.1 0 2639
53 2696 23.1 0 2696
54 2695 23.1 0 2695
55 2853 23.1 0 2853
56 2605 23.1 0 2605
57 2842 23.1 0 2842
58 2735 23.1 0 2735
59 2872 23.1 0 2872
60 2975 23.1 0 2975
61 3002 23.1 0 3002
62 2891 23.1 0 2891
63 2871 23.1 0 2871
64 2866 23.1 0 2866
65 2953 23.1 0 2953
66 2815 23.1 0 2815
67 2833 23.1 0 2833
68 2732 23.1 0 2732
69 2727 23.1 0 2727
70 2724 23.1 0 2724
71 3094 23.1 0 3094
72 2729 23.1 0 2729
73 2656 23.1 0 2656
74 2638 23.1 0 2638
75 2394 23.1 0 2394
76 2235 23.1 0 2235
77 2619 23.1 0 2619
78 2115 23.1 0 2115
79 2408 23.1 0 2408
80 2156 23.1 0 2156
81 2369 23.1 0 2369
82 2658 23.1 0 2658
83 3097 23.1 0 3097
84 3314 23.1 0 3314
85 3217 23.1 0 3217
86 60462 23.1 0 60462
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27947 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.6%
C: 30.9%
G: 0.0%
T: 38.3%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 6805 23656.1 0 6805
4 1969 5914.0 0 1969
5 762 1478.5 0 762
6 420 369.6 0 420
7 431 92.4 0 431
8 381 23.1 0 381
9 353 23.1 0 353
10 345 23.1 0 345
11 367 23.1 0 367
12 366 23.1 0 366
13 369 23.1 0 369
14 319 23.1 0 319
15 318 23.1 0 318
16 323 23.1 0 323
17 274 23.1 0 274
18 274 23.1 0 274
19 326 23.1 0 326
20 267 23.1 0 267
21 308 23.1 0 308
22 266 23.1 0 266
23 268 23.1 0 268
24 266 23.1 0 266
25 294 23.1 0 294
26 281 23.1 0 281
27 245 23.1 0 245
28 232 23.1 0 232
29 305 23.1 0 305
30 244 23.1 0 244
31 296 23.1 0 296
32 293 23.1 0 293
33 289 23.1 0 289
34 283 23.1 0 283
35 285 23.1 0 285
36 272 23.1 0 272
37 248 23.1 0 248
38 267 23.1 0 267
39 278 23.1 0 278
40 257 23.1 0 257
41 241 23.1 0 241
42 257 23.1 0 257
43 282 23.1 0 282
44 236 23.1 0 236
45 230 23.1 0 230
46 273 23.1 0 273
47 246 23.1 0 246
48 257 23.1 0 257
49 223 23.1 0 223
50 243 23.1 0 243
51 225 23.1 0 225
52 228 23.1 0 228
53 270 23.1 0 270
54 215 23.1 0 215
55 262 23.1 0 262
56 239 23.1 0 239
57 209 23.1 0 209
58 235 23.1 0 235
59 222 23.1 0 222
60 184 23.1 0 184
61 168 23.1 0 168
62 196 23.1 0 196
63 183 23.1 0 183
64 189 23.1 0 189
65 159 23.1 0 159
66 122 23.1 0 122
67 115 23.1 0 115
68 127 23.1 0 127
69 93 23.1 0 93
70 93 23.1 0 93
71 87 23.1 0 87
72 83 23.1 0 83
73 67 23.1 0 67
74 71 23.1 0 71
75 53 23.1 0 53
76 30 23.1 0 30
77 40 23.1 0 40
78 41 23.1 0 41
79 47 23.1 0 47
80 29 23.1 0 29
81 31 23.1 0 31
82 22 23.1 0 22
83 24 23.1 0 24
84 28 23.1 0 28
85 28 23.1 0 28
86 898 23.1 0 898
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 32410 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 33.9%
C: 22.7%
G: 21.2%
T: 22.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 23390 23656.1 0 23390
4 6220 5914.0 0 6220
5 1016 1478.5 0 1016
6 141 369.6 0 141
7 22 92.4 0 22
8 21 92.4 0 21
9 16 92.4 0 16
10 16 92.4 0 16
11 21 92.4 0 21
12 11 92.4 0 11
13 20 92.4 0 20
14 23 92.4 0 23
15 12 92.4 0 12
16 21 92.4 0 21
17 29 92.4 0 29
18 21 92.4 0 21
19 15 92.4 0 15
20 19 92.4 0 19
21 17 92.4 0 17
22 16 92.4 0 16
23 26 92.4 0 26
24 21 92.4 0 21
25 28 92.4 0 28
26 16 92.4 0 16
27 15 92.4 0 15
28 24 92.4 0 24
29 21 92.4 0 21
30 12 92.4 0 12
31 18 92.4 0 18
32 20 92.4 0 20
33 11 92.4 0 11
34 19 92.4 0 19
35 11 92.4 0 11
36 15 92.4 0 15
37 27 92.4 0 27
38 20 92.4 0 20
39 9 92.4 0 9
40 30 92.4 0 30
41 30 92.4 0 30
42 12 92.4 0 12
43 30 92.4 0 30
44 28 92.4 0 28
45 18 92.4 0 18
46 19 92.4 0 19
47 28 92.4 0 28
48 18 92.4 0 18
49 30 92.4 0 30
50 17 92.4 0 17
51 33 92.4 0 33
52 21 92.4 0 21
53 15 92.4 0 15
54 23 92.4 0 23
55 22 92.4 0 22
56 13 92.4 0 13
57 19 92.4 0 19
58 13 92.4 0 13
59 27 92.4 0 27
60 18 92.4 0 18
61 19 92.4 0 19
62 25 92.4 0 25
63 25 92.4 0 25
64 19 92.4 0 19
65 28 92.4 0 28
66 19 92.4 0 19
67 14 92.4 0 14
68 21 92.4 0 21
69 24 92.4 0 24
70 31 92.4 0 31
71 17 92.4 0 17
72 30 92.4 0 30
73 15 92.4 0 15
74 11 92.4 0 11
75 19 92.4 0 19
76 15 92.4 0 15
77 47 92.4 0 47
78 32 92.4 0 32
79 12 92.4 0 12
80 21 92.4 0 21
81 13 92.4 0 13
82 26 92.4 0 26
83 28 92.4 0 28
84 20 92.4 0 20
85 19 92.4 0 19
86 16 92.4 0 16
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R62_S203_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R62_S203_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 11.96 s (8 µs/read; 7.76 M reads/minute).
=== Summary ===
Total reads processed: 1,547,598
Reads with adapters: 401,057 (25.9%)
== Read fate breakdown ==
Reads that were too short: 120,194 (7.8%)
Reads written (passing filters): 1,427,404 (92.2%)
Total basepairs processed: 156,307,398 bp
Total written (filtered): 115,861,442 bp (74.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 339338 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 28.6%
G: 25.4%
T: 27.1%
none/other: 18.9%
Overview of removed sequences
length count expect max.err error counts
3 37972 24181.2 0 37972
4 16009 6045.3 0 16009
5 7005 1511.3 0 7005
6 3604 377.8 0 3604
7 2795 94.5 0 2795
8 2456 23.6 0 2456
9 2410 23.6 0 2410
10 2292 23.6 0 2292
11 2255 23.6 0 2255
12 2333 23.6 0 2333
13 2378 23.6 0 2378
14 2417 23.6 0 2417
15 2511 23.6 0 2511
16 2430 23.6 0 2430
17 2533 23.6 0 2533
18 2419 23.6 0 2419
19 2353 23.6 0 2353
20 2428 23.6 0 2428
21 2545 23.6 0 2545
22 2590 23.6 0 2590
23 2302 23.6 0 2302
24 2492 23.6 0 2492
25 2495 23.6 0 2495
26 2506 23.6 0 2506
27 2403 23.6 0 2403
28 2556 23.6 0 2556
29 2556 23.6 0 2556
30 2481 23.6 0 2481
31 2620 23.6 0 2620
32 2418 23.6 0 2418
33 2518 23.6 0 2518
34 2531 23.6 0 2531
35 2429 23.6 0 2429
36 2495 23.6 0 2495
37 2466 23.6 0 2466
38 2420 23.6 0 2420
39 2491 23.6 0 2491
40 2543 23.6 0 2543
41 2488 23.6 0 2488
42 2644 23.6 0 2644
43 2587 23.6 0 2587
44 2397 23.6 0 2397
45 2522 23.6 0 2522
46 2512 23.6 0 2512
47 2420 23.6 0 2420
48 2694 23.6 0 2694
49 2826 23.6 0 2826
50 3354 23.6 0 3354
51 2985 23.6 0 2985
52 2755 23.6 0 2755
53 2696 23.6 0 2696
54 2829 23.6 0 2829
55 2851 23.6 0 2851
56 2809 23.6 0 2809
57 2859 23.6 0 2859
58 2864 23.6 0 2864
59 2929 23.6 0 2929
60 3192 23.6 0 3192
61 3142 23.6 0 3142
62 2977 23.6 0 2977
63 3040 23.6 0 3040
64 3031 23.6 0 3031
65 2930 23.6 0 2930
66 2912 23.6 0 2912
67 2885 23.6 0 2885
68 3051 23.6 0 3051
69 2973 23.6 0 2973
70 2739 23.6 0 2739
71 3189 23.6 0 3189
72 2845 23.6 0 2845
73 2844 23.6 0 2844
74 2738 23.6 0 2738
75 2578 23.6 0 2578
76 2385 23.6 0 2385
77 2838 23.6 0 2838
78 2176 23.6 0 2176
79 2514 23.6 0 2514
80 2214 23.6 0 2214
81 2531 23.6 0 2531
82 2816 23.6 0 2816
83 3197 23.6 0 3197
84 3444 23.6 0 3444
85 3413 23.6 0 3413
86 64266 23.6 0 64266
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28725 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.8%
C: 30.6%
G: 0.0%
T: 38.2%
none/other: 3.3%
Overview of removed sequences
length count expect max.err error counts
3 6978 24181.2 0 6978
4 2046 6045.3 0 2046
5 717 1511.3 0 717
6 426 377.8 0 426
7 391 94.5 0 391
8 426 23.6 0 426
9 399 23.6 0 399
10 371 23.6 0 371
11 361 23.6 0 361
12 383 23.6 0 383
13 338 23.6 0 338
14 352 23.6 0 352
15 334 23.6 0 334
16 288 23.6 0 288
17 282 23.6 0 282
18 334 23.6 0 334
19 310 23.6 0 310
20 283 23.6 0 283
21 329 23.6 0 329
22 270 23.6 0 270
23 289 23.6 0 289
24 304 23.6 0 304
25 304 23.6 0 304
26 294 23.6 0 294
27 273 23.6 0 273
28 274 23.6 0 274
29 220 23.6 0 220
30 262 23.6 0 262
31 241 23.6 0 241
32 272 23.6 0 272
33 269 23.6 0 269
34 279 23.6 0 279
35 304 23.6 0 304
36 300 23.6 0 300
37 273 23.6 0 273
38 273 23.6 0 273
39 256 23.6 0 256
40 291 23.6 0 291
41 265 23.6 0 265
42 281 23.6 0 281
43 276 23.6 0 276
44 259 23.6 0 259
45 246 23.6 0 246
46 293 23.6 0 293
47 237 23.6 0 237
48 256 23.6 0 256
49 232 23.6 0 232
50 251 23.6 0 251
51 253 23.6 0 253
52 237 23.6 0 237
53 270 23.6 0 270
54 227 23.6 0 227
55 242 23.6 0 242
56 228 23.6 0 228
57 248 23.6 0 248
58 202 23.6 0 202
59 216 23.6 0 216
60 229 23.6 0 229
61 177 23.6 0 177
62 187 23.6 0 187
63 182 23.6 0 182
64 164 23.6 0 164
65 172 23.6 0 172
66 149 23.6 0 149
67 131 23.6 0 131
68 149 23.6 0 149
69 132 23.6 0 132
70 78 23.6 0 78
71 88 23.6 0 88
72 80 23.6 0 80
73 69 23.6 0 69
74 65 23.6 0 65
75 52 23.6 0 52
76 47 23.6 0 47
77 46 23.6 0 46
78 43 23.6 0 43
79 43 23.6 0 43
80 31 23.6 0 31
81 31 23.6 0 31
82 28 23.6 0 28
83 23 23.6 0 23
84 26 23.6 0 26
85 31 23.6 0 31
86 957 23.6 0 957
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 32994 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.1%
C: 22.7%
G: 20.8%
T: 22.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 23895 24181.2 0 23895
4 6187 6045.3 0 6187
5 1065 1511.3 0 1065
6 148 377.8 0 148
7 23 94.5 0 23
8 33 94.5 0 33
9 16 94.5 0 16
10 25 94.5 0 25
11 25 94.5 0 25
12 13 94.5 0 13
13 22 94.5 0 22
14 15 94.5 0 15
15 24 94.5 0 24
16 24 94.5 0 24
17 23 94.5 0 23
18 13 94.5 0 13
19 15 94.5 0 15
20 22 94.5 0 22
21 23 94.5 0 23
22 28 94.5 0 28
23 31 94.5 0 31
24 24 94.5 0 24
25 20 94.5 0 20
26 21 94.5 0 21
27 5 94.5 0 5
28 15 94.5 0 15
29 23 94.5 0 23
30 11 94.5 0 11
31 21 94.5 0 21
32 23 94.5 0 23
33 14 94.5 0 14
34 23 94.5 0 23
35 18 94.5 0 18
36 22 94.5 0 22
37 17 94.5 0 17
38 20 94.5 0 20
39 15 94.5 0 15
40 29 94.5 0 29
41 36 94.5 0 36
42 16 94.5 0 16
43 30 94.5 0 30
44 29 94.5 0 29
45 32 94.5 0 32
46 15 94.5 0 15
47 20 94.5 0 20
48 30 94.5 0 30
49 32 94.5 0 32
50 15 94.5 0 15
51 30 94.5 0 30
52 16 94.5 0 16
53 20 94.5 0 20
54 21 94.5 0 21
55 24 94.5 0 24
56 12 94.5 0 12
57 17 94.5 0 17
58 18 94.5 0 18
59 30 94.5 0 30
60 14 94.5 0 14
61 27 94.5 0 27
62 28 94.5 0 28
63 18 94.5 0 18
64 25 94.5 0 25
65 25 94.5 0 25
66 15 94.5 0 15
67 14 94.5 0 14
68 14 94.5 0 14
69 18 94.5 0 18
70 21 94.5 0 21
71 12 94.5 0 12
72 11 94.5 0 11
73 18 94.5 0 18
74 14 94.5 0 14
75 28 94.5 0 28
76 25 94.5 0 25
77 58 94.5 0 58
78 26 94.5 0 26
79 20 94.5 0 20
80 18 94.5 0 18
81 13 94.5 0 13
82 28 94.5 0 28
83 23 94.5 0 23
84 16 94.5 0 16
85 13 94.5 0 13
86 18 94.5 0 18
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R78_S180_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R78_S180_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.25 s (10 µs/read; 6.30 M reads/minute).
=== Summary ===
Total reads processed: 2,858,686
Reads with adapters: 1,043,494 (36.5%)
== Read fate breakdown ==
Reads that were too short: 296,239 (10.4%)
Reads written (passing filters): 2,562,447 (89.6%)
Total basepairs processed: 288,727,286 bp
Total written (filtered): 199,469,487 bp (69.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 951770 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.3%
G: 27.0%
T: 30.3%
none/other: 12.4%
Overview of removed sequences
length count expect max.err error counts
3 66263 44667.0 0 66263
4 28625 11166.7 0 28625
5 15983 2791.7 0 15983
6 11175 697.9 0 11175
7 9303 174.5 0 9303
8 8411 43.6 0 8411
9 8656 43.6 0 8656
10 8601 43.6 0 8601
11 8675 43.6 0 8675
12 8614 43.6 0 8614
13 8566 43.6 0 8566
14 8768 43.6 0 8768
15 8744 43.6 0 8744
16 9007 43.6 0 9007
17 8638 43.6 0 8638
18 8602 43.6 0 8602
19 8722 43.6 0 8722
20 8625 43.6 0 8625
21 8733 43.6 0 8733
22 8615 43.6 0 8615
23 8391 43.6 0 8391
24 8725 43.6 0 8725
25 8278 43.6 0 8278
26 8592 43.6 0 8592
27 8483 43.6 0 8483
28 8657 43.6 0 8657
29 8893 43.6 0 8893
30 9080 43.6 0 9080
31 9275 43.6 0 9275
32 8877 43.6 0 8877
33 9489 43.6 0 9489
34 9166 43.6 0 9166
35 8701 43.6 0 8701
36 8982 43.6 0 8982
37 9278 43.6 0 9278
38 8522 43.6 0 8522
39 8494 43.6 0 8494
40 8894 43.6 0 8894
41 8908 43.6 0 8908
42 9040 43.6 0 9040
43 9146 43.6 0 9146
44 8731 43.6 0 8731
45 8802 43.6 0 8802
46 9247 43.6 0 9247
47 9077 43.6 0 9077
48 9012 43.6 0 9012
49 11275 43.6 0 11275
50 12504 43.6 0 12504
51 8940 43.6 0 8940
52 9664 43.6 0 9664
53 9327 43.6 0 9327
54 8509 43.6 0 8509
55 8901 43.6 0 8901
56 8866 43.6 0 8866
57 8719 43.6 0 8719
58 9289 43.6 0 9289
59 8797 43.6 0 8797
60 8825 43.6 0 8825
61 9047 43.6 0 9047
62 8938 43.6 0 8938
63 8659 43.6 0 8659
64 8595 43.6 0 8595
65 8731 43.6 0 8731
66 8166 43.6 0 8166
67 8193 43.6 0 8193
68 8339 43.6 0 8339
69 7728 43.6 0 7728
70 7595 43.6 0 7595
71 7868 43.6 0 7868
72 7423 43.6 0 7423
73 7324 43.6 0 7324
74 6821 43.6 0 6821
75 6916 43.6 0 6916
76 7012 43.6 0 7012
77 7037 43.6 0 7037
78 7532 43.6 0 7532
79 8767 43.6 0 8767
80 8842 43.6 0 8842
81 10265 43.6 0 10265
82 12702 43.6 0 12702
83 13753 43.6 0 13753
84 15462 43.6 0 15462
85 16087 43.6 0 16087
86 118286 43.6 0 118286
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 33639 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.8%
C: 35.8%
G: 0.0%
T: 35.3%
none/other: 2.1%
Overview of removed sequences
length count expect max.err error counts
3 14671 44667.0 0 14671
4 3351 11166.7 0 3351
5 893 2791.7 0 893
6 382 697.9 0 382
7 306 174.5 0 306
8 320 43.6 0 320
9 267 43.6 0 267
10 287 43.6 0 287
11 256 43.6 0 256
12 239 43.6 0 239
13 259 43.6 0 259
14 234 43.6 0 234
15 255 43.6 0 255
16 263 43.6 0 263
17 238 43.6 0 238
18 240 43.6 0 240
19 222 43.6 0 222
20 239 43.6 0 239
21 234 43.6 0 234
22 202 43.6 0 202
23 225 43.6 0 225
24 279 43.6 0 279
25 255 43.6 0 255
26 238 43.6 0 238
27 228 43.6 0 228
28 205 43.6 0 205
29 210 43.6 0 210
30 228 43.6 0 228
31 224 43.6 0 224
32 195 43.6 0 195
33 229 43.6 0 229
34 210 43.6 0 210
35 218 43.6 0 218
36 185 43.6 0 185
37 232 43.6 0 232
38 241 43.6 0 241
39 231 43.6 0 231
40 200 43.6 0 200
41 212 43.6 0 212
42 237 43.6 0 237
43 190 43.6 0 190
44 196 43.6 0 196
45 203 43.6 0 203
46 203 43.6 0 203
47 220 43.6 0 220
48 214 43.6 0 214
49 200 43.6 0 200
50 187 43.6 0 187
51 168 43.6 0 168
52 196 43.6 0 196
53 167 43.6 0 167
54 177 43.6 0 177
55 173 43.6 0 173
56 193 43.6 0 193
57 176 43.6 0 176
58 154 43.6 0 154
59 179 43.6 0 179
60 149 43.6 0 149
61 135 43.6 0 135
62 152 43.6 0 152
63 146 43.6 0 146
64 140 43.6 0 140
65 133 43.6 0 133
66 112 43.6 0 112
67 110 43.6 0 110
68 94 43.6 0 94
69 72 43.6 0 72
70 85 43.6 0 85
71 62 43.6 0 62
72 67 43.6 0 67
73 66 43.6 0 66
74 51 43.6 0 51
75 44 43.6 0 44
76 35 43.6 0 35
77 30 43.6 0 30
78 32 43.6 0 32
79 31 43.6 0 31
80 21 43.6 0 21
81 27 43.6 0 27
82 23 43.6 0 23
83 24 43.6 0 24
84 22 43.6 0 22
85 36 43.6 0 36
86 704 43.6 0 704
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 58085 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 23.2%
G: 20.2%
T: 21.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 43655 44667.0 0 43655
4 9570 11166.7 0 9570
5 2029 2791.7 0 2029
6 305 697.9 0 305
7 33 174.5 0 33
8 20 174.5 0 20
9 23 174.5 0 23
10 24 174.5 0 24
11 34 174.5 0 34
12 37 174.5 0 37
13 36 174.5 0 36
14 30 174.5 0 30
15 31 174.5 0 31
16 30 174.5 0 30
17 51 174.5 0 51
18 32 174.5 0 32
19 32 174.5 0 32
20 35 174.5 0 35
21 37 174.5 0 37
22 28 174.5 0 28
23 27 174.5 0 27
24 21 174.5 0 21
25 40 174.5 0 40
26 39 174.5 0 39
27 32 174.5 0 32
28 36 174.5 0 36
29 28 174.5 0 28
30 28 174.5 0 28
31 28 174.5 0 28
32 30 174.5 0 30
33 29 174.5 0 29
34 36 174.5 0 36
35 25 174.5 0 25
36 36 174.5 0 36
37 30 174.5 0 30
38 27 174.5 0 27
39 32 174.5 0 32
40 23 174.5 0 23
41 28 174.5 0 28
42 27 174.5 0 27
43 24 174.5 0 24
44 23 174.5 0 23
45 28 174.5 0 28
46 23 174.5 0 23
47 33 174.5 0 33
48 35 174.5 0 35
49 26 174.5 0 26
50 23 174.5 0 23
51 29 174.5 0 29
52 39 174.5 0 39
53 27 174.5 0 27
54 45 174.5 0 45
55 36 174.5 0 36
56 32 174.5 0 32
57 30 174.5 0 30
58 36 174.5 0 36
59 33 174.5 0 33
60 30 174.5 0 30
61 25 174.5 0 25
62 35 174.5 0 35
63 36 174.5 0 36
64 29 174.5 0 29
65 41 174.5 0 41
66 42 174.5 0 42
67 36 174.5 0 36
68 42 174.5 0 42
69 18 174.5 0 18
70 38 174.5 0 38
71 35 174.5 0 35
72 19 174.5 0 19
73 28 174.5 0 28
74 26 174.5 0 26
75 22 174.5 0 22
76 25 174.5 0 25
77 47 174.5 0 47
78 50 174.5 0 50
79 38 174.5 0 38
80 26 174.5 0 26
81 24 174.5 0 24
82 31 174.5 0 31
83 40 174.5 0 40
84 35 174.5 0 35
85 28 174.5 0 28
86 43 174.5 0 43
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: R78_S180_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/R78_S180_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.28 s (9 µs/read; 6.67 M reads/minute).
=== Summary ===
Total reads processed: 2,919,255
Reads with adapters: 1,073,566 (36.8%)
== Read fate breakdown ==
Reads that were too short: 308,776 (10.6%)
Reads written (passing filters): 2,610,479 (89.4%)
Total basepairs processed: 294,844,755 bp
Total written (filtered): 202,980,955 bp (68.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 980970 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.3%
G: 26.9%
T: 30.2%
none/other: 12.6%
Overview of removed sequences
length count expect max.err error counts
3 67714 45613.4 0 67714
4 28686 11403.3 0 28686
5 16190 2850.8 0 16190
6 11601 712.7 0 11601
7 9457 178.2 0 9457
8 8654 44.5 0 8654
9 8799 44.5 0 8799
10 8794 44.5 0 8794
11 8785 44.5 0 8785
12 8813 44.5 0 8813
13 8640 44.5 0 8640
14 8907 44.5 0 8907
15 8928 44.5 0 8928
16 9125 44.5 0 9125
17 9028 44.5 0 9028
18 8868 44.5 0 8868
19 8898 44.5 0 8898
20 8797 44.5 0 8797
21 8907 44.5 0 8907
22 8869 44.5 0 8869
23 8573 44.5 0 8573
24 8769 44.5 0 8769
25 8408 44.5 0 8408
26 8674 44.5 0 8674
27 8706 44.5 0 8706
28 8886 44.5 0 8886
29 8857 44.5 0 8857
30 9359 44.5 0 9359
31 9244 44.5 0 9244
32 9114 44.5 0 9114
33 9565 44.5 0 9565
34 9662 44.5 0 9662
35 9115 44.5 0 9115
36 9318 44.5 0 9318
37 9422 44.5 0 9422
38 8675 44.5 0 8675
39 9132 44.5 0 9132
40 9339 44.5 0 9339
41 9145 44.5 0 9145
42 9438 44.5 0 9438
43 9327 44.5 0 9327
44 9208 44.5 0 9208
45 9050 44.5 0 9050
46 9417 44.5 0 9417
47 9404 44.5 0 9404
48 8884 44.5 0 8884
49 11502 44.5 0 11502
50 13004 44.5 0 13004
51 9023 44.5 0 9023
52 9760 44.5 0 9760
53 9552 44.5 0 9552
54 8729 44.5 0 8729
55 9050 44.5 0 9050
56 9193 44.5 0 9193
57 8859 44.5 0 8859
58 9571 44.5 0 9571
59 9321 44.5 0 9321
60 9267 44.5 0 9267
61 9622 44.5 0 9622
62 9302 44.5 0 9302
63 8860 44.5 0 8860
64 9130 44.5 0 9130
65 8976 44.5 0 8976
66 8707 44.5 0 8707
67 8526 44.5 0 8526
68 8613 44.5 0 8613
69 8227 44.5 0 8227
70 7781 44.5 0 7781
71 7997 44.5 0 7997
72 7825 44.5 0 7825
73 7525 44.5 0 7525
74 6930 44.5 0 6930
75 7052 44.5 0 7052
76 7299 44.5 0 7299
77 7355 44.5 0 7355
78 8115 44.5 0 8115
79 9293 44.5 0 9293
80 9350 44.5 0 9350
81 10732 44.5 0 10732
82 13148 44.5 0 13148
83 14238 44.5 0 14238
84 16033 44.5 0 16033
85 16768 44.5 0 16768
86 123584 44.5 0 123584
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34348 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.7%
C: 35.5%
G: 0.0%
T: 35.7%
none/other: 2.1%
Overview of removed sequences
length count expect max.err error counts
3 15067 45613.4 0 15067
4 3337 11403.3 0 3337
5 822 2850.8 0 822
6 385 712.7 0 385
7 284 178.2 0 284
8 277 44.5 0 277
9 298 44.5 0 298
10 262 44.5 0 262
11 286 44.5 0 286
12 262 44.5 0 262
13 265 44.5 0 265
14 266 44.5 0 266
15 262 44.5 0 262
16 270 44.5 0 270
17 229 44.5 0 229
18 240 44.5 0 240
19 226 44.5 0 226
20 214 44.5 0 214
21 251 44.5 0 251
22 232 44.5 0 232
23 243 44.5 0 243
24 219 44.5 0 219
25 246 44.5 0 246
26 242 44.5 0 242
27 213 44.5 0 213
28 241 44.5 0 241
29 249 44.5 0 249
30 245 44.5 0 245
31 216 44.5 0 216
32 217 44.5 0 217
33 224 44.5 0 224
34 246 44.5 0 246
35 235 44.5 0 235
36 229 44.5 0 229
37 246 44.5 0 246
38 241 44.5 0 241
39 206 44.5 0 206
40 206 44.5 0 206
41 195 44.5 0 195
42 218 44.5 0 218
43 211 44.5 0 211
44 228 44.5 0 228
45 188 44.5 0 188
46 201 44.5 0 201
47 185 44.5 0 185
48 202 44.5 0 202
49 183 44.5 0 183
50 203 44.5 0 203
51 184 44.5 0 184
52 207 44.5 0 207
53 177 44.5 0 177
54 207 44.5 0 207
55 178 44.5 0 178
56 171 44.5 0 171
57 177 44.5 0 177
58 187 44.5 0 187
59 189 44.5 0 189
60 171 44.5 0 171
61 138 44.5 0 138
62 150 44.5 0 150
63 124 44.5 0 124
64 159 44.5 0 159
65 118 44.5 0 118
66 120 44.5 0 120
67 133 44.5 0 133
68 98 44.5 0 98
69 93 44.5 0 93
70 93 44.5 0 93
71 87 44.5 0 87
72 71 44.5 0 71
73 53 44.5 0 53
74 56 44.5 0 56
75 57 44.5 0 57
76 36 44.5 0 36
77 41 44.5 0 41
78 42 44.5 0 42
79 35 44.5 0 35
80 25 44.5 0 25
81 26 44.5 0 26
82 22 44.5 0 22
83 22 44.5 0 22
84 33 44.5 0 33
85 45 44.5 0 45
86 710 44.5 0 710
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 58248 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.5%
C: 23.3%
G: 20.1%
T: 21.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 43909 45613.4 0 43909
4 9517 11403.3 0 9517
5 1983 2850.8 0 1983
6 343 712.7 0 343
7 24 178.2 0 24
8 25 178.2 0 25
9 15 178.2 0 15
10 28 178.2 0 28
11 27 178.2 0 27
12 22 178.2 0 22
13 33 178.2 0 33
14 33 178.2 0 33
15 22 178.2 0 22
16 29 178.2 0 29
17 31 178.2 0 31
18 30 178.2 0 30
19 39 178.2 0 39
20 42 178.2 0 42
21 34 178.2 0 34
22 46 178.2 0 46
23 26 178.2 0 26
24 28 178.2 0 28
25 39 178.2 0 39
26 38 178.2 0 38
27 44 178.2 0 44
28 36 178.2 0 36
29 33 178.2 0 33
30 30 178.2 0 30
31 25 178.2 0 25
32 35 178.2 0 35
33 37 178.2 0 37
34 33 178.2 0 33
35 31 178.2 0 31
36 28 178.2 0 28
37 27 178.2 0 27
38 25 178.2 0 25
39 30 178.2 0 30
40 30 178.2 0 30
41 36 178.2 0 36
42 32 178.2 0 32
43 24 178.2 0 24
44 32 178.2 0 32
45 25 178.2 0 25
46 28 178.2 0 28
47 26 178.2 0 26
48 23 178.2 0 23
49 30 178.2 0 30
50 45 178.2 0 45
51 25 178.2 0 25
52 31 178.2 0 31
53 22 178.2 0 22
54 30 178.2 0 30
55 38 178.2 0 38
56 32 178.2 0 32
57 34 178.2 0 34
58 31 178.2 0 31
59 35 178.2 0 35
60 20 178.2 0 20
61 31 178.2 0 31
62 49 178.2 0 49
63 38 178.2 0 38
64 33 178.2 0 33
65 56 178.2 0 56
66 28 178.2 0 28
67 30 178.2 0 30
68 49 178.2 0 49
69 21 178.2 0 21
70 21 178.2 0 21
71 33 178.2 0 33
72 24 178.2 0 24
73 22 178.2 0 22
74 26 178.2 0 26
75 15 178.2 0 15
76 19 178.2 0 19
77 67 178.2 0 67
78 33 178.2 0 33
79 23 178.2 0 23
80 30 178.2 0 30
81 35 178.2 0 35
82 18 178.2 0 18
83 34 178.2 0 34
84 33 178.2 0 33
85 28 178.2 0 28
86 46 178.2 0 46
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T55_S158_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T55_S158_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.15 s (9 µs/read; 6.58 M reads/minute).
=== Summary ===
Total reads processed: 2,757,658
Reads with adapters: 839,250 (30.4%)
== Read fate breakdown ==
Reads that were too short: 208,934 (7.6%)
Reads written (passing filters): 2,548,724 (92.4%)
Total basepairs processed: 278,523,458 bp
Total written (filtered): 202,838,658 bp (72.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 738650 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.5%
G: 27.7%
T: 30.2%
none/other: 11.7%
Overview of removed sequences
length count expect max.err error counts
3 65833 43088.4 0 65833
4 28780 10772.1 0 28780
5 14806 2693.0 0 14806
6 9553 673.3 0 9553
7 7660 168.3 0 7660
8 6767 42.1 0 6767
9 6763 42.1 0 6763
10 6884 42.1 0 6884
11 6806 42.1 0 6806
12 6985 42.1 0 6985
13 6832 42.1 0 6832
14 7019 42.1 0 7019
15 7109 42.1 0 7109
16 7025 42.1 0 7025
17 7133 42.1 0 7133
18 7168 42.1 0 7168
19 7113 42.1 0 7113
20 6934 42.1 0 6934
21 7179 42.1 0 7179
22 6796 42.1 0 6796
23 6646 42.1 0 6646
24 6782 42.1 0 6782
25 6545 42.1 0 6545
26 6468 42.1 0 6468
27 6612 42.1 0 6612
28 7027 42.1 0 7027
29 7177 42.1 0 7177
30 7043 42.1 0 7043
31 7365 42.1 0 7365
32 7210 42.1 0 7210
33 6708 42.1 0 6708
34 6686 42.1 0 6686
35 7113 42.1 0 7113
36 6589 42.1 0 6589
37 6485 42.1 0 6485
38 6316 42.1 0 6316
39 6635 42.1 0 6635
40 6693 42.1 0 6693
41 6523 42.1 0 6523
42 6966 42.1 0 6966
43 6945 42.1 0 6945
44 6425 42.1 0 6425
45 6854 42.1 0 6854
46 6814 42.1 0 6814
47 6714 42.1 0 6714
48 6647 42.1 0 6647
49 9211 42.1 0 9211
50 10836 42.1 0 10836
51 6878 42.1 0 6878
52 7529 42.1 0 7529
53 7125 42.1 0 7125
54 6311 42.1 0 6311
55 6742 42.1 0 6742
56 6650 42.1 0 6650
57 6354 42.1 0 6354
58 6920 42.1 0 6920
59 6631 42.1 0 6631
60 6539 42.1 0 6539
61 6805 42.1 0 6805
62 6440 42.1 0 6440
63 6266 42.1 0 6266
64 6231 42.1 0 6231
65 6138 42.1 0 6138
66 5922 42.1 0 5922
67 6036 42.1 0 6036
68 5991 42.1 0 5991
69 5601 42.1 0 5601
70 5421 42.1 0 5421
71 5688 42.1 0 5688
72 5816 42.1 0 5816
73 5383 42.1 0 5383
74 5206 42.1 0 5206
75 5190 42.1 0 5190
76 4922 42.1 0 4922
77 5090 42.1 0 5090
78 5364 42.1 0 5364
79 5894 42.1 0 5894
80 5766 42.1 0 5766
81 6643 42.1 0 6643
82 7967 42.1 0 7967
83 8664 42.1 0 8664
84 9285 42.1 0 9285
85 9898 42.1 0 9898
86 86164 42.1 0 86164
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39129 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.3%
C: 33.4%
G: 0.0%
T: 36.6%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 15210 43088.4 0 15210
4 3410 10772.1 0 3410
5 1001 2693.0 0 1001
6 502 673.3 0 502
7 455 168.3 0 455
8 417 42.1 0 417
9 391 42.1 0 391
10 371 42.1 0 371
11 392 42.1 0 392
12 366 42.1 0 366
13 326 42.1 0 326
14 297 42.1 0 297
15 334 42.1 0 334
16 300 42.1 0 300
17 294 42.1 0 294
18 321 42.1 0 321
19 324 42.1 0 324
20 267 42.1 0 267
21 323 42.1 0 323
22 302 42.1 0 302
23 278 42.1 0 278
24 318 42.1 0 318
25 310 42.1 0 310
26 305 42.1 0 305
27 324 42.1 0 324
28 333 42.1 0 333
29 286 42.1 0 286
30 297 42.1 0 297
31 258 42.1 0 258
32 258 42.1 0 258
33 298 42.1 0 298
34 301 42.1 0 301
35 285 42.1 0 285
36 265 42.1 0 265
37 280 42.1 0 280
38 235 42.1 0 235
39 286 42.1 0 286
40 291 42.1 0 291
41 277 42.1 0 277
42 264 42.1 0 264
43 257 42.1 0 257
44 264 42.1 0 264
45 235 42.1 0 235
46 303 42.1 0 303
47 260 42.1 0 260
48 273 42.1 0 273
49 240 42.1 0 240
50 264 42.1 0 264
51 263 42.1 0 263
52 229 42.1 0 229
53 262 42.1 0 262
54 249 42.1 0 249
55 221 42.1 0 221
56 229 42.1 0 229
57 237 42.1 0 237
58 235 42.1 0 235
59 257 42.1 0 257
60 212 42.1 0 212
61 200 42.1 0 200
62 174 42.1 0 174
63 178 42.1 0 178
64 174 42.1 0 174
65 145 42.1 0 145
66 172 42.1 0 172
67 128 42.1 0 128
68 113 42.1 0 113
69 95 42.1 0 95
70 91 42.1 0 91
71 88 42.1 0 88
72 80 42.1 0 80
73 79 42.1 0 79
74 72 42.1 0 72
75 47 42.1 0 47
76 67 42.1 0 67
77 38 42.1 0 38
78 46 42.1 0 46
79 30 42.1 0 30
80 37 42.1 0 37
81 38 42.1 0 38
82 30 42.1 0 30
83 34 42.1 0 34
84 27 42.1 0 27
85 44 42.1 0 44
86 1060 42.1 0 1060
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61471 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 22.9%
G: 21.4%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45175 43088.4 0 45175
4 10841 10772.1 0 10841
5 2232 2693.0 0 2232
6 319 673.3 0 319
7 31 168.3 0 31
8 33 168.3 0 33
9 23 168.3 0 23
10 29 168.3 0 29
11 35 168.3 0 35
12 22 168.3 0 22
13 36 168.3 0 36
14 44 168.3 0 44
15 39 168.3 0 39
16 41 168.3 0 41
17 49 168.3 0 49
18 28 168.3 0 28
19 39 168.3 0 39
20 48 168.3 0 48
21 39 168.3 0 39
22 38 168.3 0 38
23 35 168.3 0 35
24 44 168.3 0 44
25 33 168.3 0 33
26 49 168.3 0 49
27 35 168.3 0 35
28 34 168.3 0 34
29 39 168.3 0 39
30 32 168.3 0 32
31 31 168.3 0 31
32 51 168.3 0 51
33 36 168.3 0 36
34 29 168.3 0 29
35 35 168.3 0 35
36 39 168.3 0 39
37 39 168.3 0 39
38 27 168.3 0 27
39 31 168.3 0 31
40 30 168.3 0 30
41 35 168.3 0 35
42 22 168.3 0 22
43 26 168.3 0 26
44 42 168.3 0 42
45 37 168.3 0 37
46 33 168.3 0 33
47 37 168.3 0 37
48 48 168.3 0 48
49 46 168.3 0 46
50 45 168.3 0 45
51 37 168.3 0 37
52 47 168.3 0 47
53 24 168.3 0 24
54 35 168.3 0 35
55 51 168.3 0 51
56 23 168.3 0 23
57 43 168.3 0 43
58 50 168.3 0 50
59 26 168.3 0 26
60 43 168.3 0 43
61 30 168.3 0 30
62 41 168.3 0 41
63 39 168.3 0 39
64 30 168.3 0 30
65 52 168.3 0 52
66 38 168.3 0 38
67 25 168.3 0 25
68 40 168.3 0 40
69 37 168.3 0 37
70 38 168.3 0 38
71 39 168.3 0 39
72 33 168.3 0 33
73 32 168.3 0 32
74 33 168.3 0 33
75 27 168.3 0 27
76 20 168.3 0 20
77 45 168.3 0 45
78 36 168.3 0 36
79 27 168.3 0 27
80 40 168.3 0 40
81 36 168.3 0 36
82 26 168.3 0 26
83 53 168.3 0 53
84 42 168.3 0 42
85 38 168.3 0 38
86 34 168.3 0 34
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T55_S158_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T55_S158_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.52 s (9 µs/read; 6.37 M reads/minute).
=== Summary ===
Total reads processed: 2,816,628
Reads with adapters: 865,052 (30.7%)
== Read fate breakdown ==
Reads that were too short: 218,400 (7.8%)
Reads written (passing filters): 2,598,228 (92.2%)
Total basepairs processed: 284,479,428 bp
Total written (filtered): 206,532,243 bp (72.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 763221 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.4%
G: 27.6%
T: 30.0%
none/other: 12.0%
Overview of removed sequences
length count expect max.err error counts
3 66816 44009.8 0 66816
4 29581 11002.5 0 29581
5 15054 2750.6 0 15054
6 9627 687.7 0 9627
7 7965 171.9 0 7965
8 7056 43.0 0 7056
9 7076 43.0 0 7076
10 7181 43.0 0 7181
11 7024 43.0 0 7024
12 6859 43.0 0 6859
13 6848 43.0 0 6848
14 7272 43.0 0 7272
15 7226 43.0 0 7226
16 7136 43.0 0 7136
17 7306 43.0 0 7306
18 7273 43.0 0 7273
19 7094 43.0 0 7094
20 7048 43.0 0 7048
21 7397 43.0 0 7397
22 7049 43.0 0 7049
23 6723 43.0 0 6723
24 6715 43.0 0 6715
25 6717 43.0 0 6717
26 6856 43.0 0 6856
27 6782 43.0 0 6782
28 7113 43.0 0 7113
29 7397 43.0 0 7397
30 6981 43.0 0 6981
31 7552 43.0 0 7552
32 7231 43.0 0 7231
33 6956 43.0 0 6956
34 6963 43.0 0 6963
35 7311 43.0 0 7311
36 7130 43.0 0 7130
37 6731 43.0 0 6731
38 6398 43.0 0 6398
39 6987 43.0 0 6987
40 6892 43.0 0 6892
41 6781 43.0 0 6781
42 7096 43.0 0 7096
43 7044 43.0 0 7044
44 6722 43.0 0 6722
45 6940 43.0 0 6940
46 7242 43.0 0 7242
47 7009 43.0 0 7009
48 6865 43.0 0 6865
49 9615 43.0 0 9615
50 11336 43.0 0 11336
51 7231 43.0 0 7231
52 7661 43.0 0 7661
53 7329 43.0 0 7329
54 6566 43.0 0 6566
55 6933 43.0 0 6933
56 7115 43.0 0 7115
57 6648 43.0 0 6648
58 7288 43.0 0 7288
59 6841 43.0 0 6841
60 6848 43.0 0 6848
61 7080 43.0 0 7080
62 6691 43.0 0 6691
63 6450 43.0 0 6450
64 6624 43.0 0 6624
65 6622 43.0 0 6622
66 6047 43.0 0 6047
67 6125 43.0 0 6125
68 6189 43.0 0 6189
69 5800 43.0 0 5800
70 5653 43.0 0 5653
71 5933 43.0 0 5933
72 5946 43.0 0 5946
73 5537 43.0 0 5537
74 5381 43.0 0 5381
75 5412 43.0 0 5412
76 5176 43.0 0 5176
77 5288 43.0 0 5288
78 5446 43.0 0 5446
79 5995 43.0 0 5995
80 6115 43.0 0 6115
81 6774 43.0 0 6774
82 8412 43.0 0 8412
83 8988 43.0 0 8988
84 9710 43.0 0 9710
85 10194 43.0 0 10194
86 91200 43.0 0 91200
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 40042 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.2%
C: 33.9%
G: 0.0%
T: 36.1%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 15231 44009.8 0 15231
4 3560 11002.5 0 3560
5 1017 2750.6 0 1017
6 499 687.7 0 499
7 396 171.9 0 396
8 411 43.0 0 411
9 406 43.0 0 406
10 367 43.0 0 367
11 356 43.0 0 356
12 353 43.0 0 353
13 374 43.0 0 374
14 355 43.0 0 355
15 322 43.0 0 322
16 330 43.0 0 330
17 299 43.0 0 299
18 348 43.0 0 348
19 327 43.0 0 327
20 324 43.0 0 324
21 333 43.0 0 333
22 312 43.0 0 312
23 299 43.0 0 299
24 330 43.0 0 330
25 338 43.0 0 338
26 323 43.0 0 323
27 343 43.0 0 343
28 348 43.0 0 348
29 287 43.0 0 287
30 284 43.0 0 284
31 301 43.0 0 301
32 293 43.0 0 293
33 307 43.0 0 307
34 308 43.0 0 308
35 303 43.0 0 303
36 338 43.0 0 338
37 319 43.0 0 319
38 285 43.0 0 285
39 268 43.0 0 268
40 277 43.0 0 277
41 281 43.0 0 281
42 269 43.0 0 269
43 274 43.0 0 274
44 247 43.0 0 247
45 273 43.0 0 273
46 283 43.0 0 283
47 265 43.0 0 265
48 274 43.0 0 274
49 241 43.0 0 241
50 271 43.0 0 271
51 230 43.0 0 230
52 266 43.0 0 266
53 259 43.0 0 259
54 263 43.0 0 263
55 250 43.0 0 250
56 256 43.0 0 256
57 270 43.0 0 270
58 235 43.0 0 235
59 235 43.0 0 235
60 220 43.0 0 220
61 190 43.0 0 190
62 186 43.0 0 186
63 173 43.0 0 173
64 172 43.0 0 172
65 158 43.0 0 158
66 143 43.0 0 143
67 147 43.0 0 147
68 114 43.0 0 114
69 120 43.0 0 120
70 97 43.0 0 97
71 79 43.0 0 79
72 87 43.0 0 87
73 82 43.0 0 82
74 69 43.0 0 69
75 61 43.0 0 61
76 53 43.0 0 53
77 46 43.0 0 46
78 48 43.0 0 48
79 52 43.0 0 52
80 36 43.0 0 36
81 33 43.0 0 33
82 33 43.0 0 33
83 29 43.0 0 29
84 43 43.0 0 43
85 41 43.0 0 41
86 1117 43.0 0 1117
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61789 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 22.8%
G: 21.1%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 45449 44009.8 0 45449
4 10702 11002.5 0 10702
5 2360 2750.6 0 2360
6 367 687.7 0 367
7 25 171.9 0 25
8 37 171.9 0 37
9 33 171.9 0 33
10 36 171.9 0 36
11 35 171.9 0 35
12 39 171.9 0 39
13 53 171.9 0 53
14 34 171.9 0 34
15 29 171.9 0 29
16 34 171.9 0 34
17 50 171.9 0 50
18 38 171.9 0 38
19 41 171.9 0 41
20 36 171.9 0 36
21 41 171.9 0 41
22 23 171.9 0 23
23 39 171.9 0 39
24 28 171.9 0 28
25 46 171.9 0 46
26 35 171.9 0 35
27 34 171.9 0 34
28 27 171.9 0 27
29 36 171.9 0 36
30 42 171.9 0 42
31 31 171.9 0 31
32 36 171.9 0 36
33 34 171.9 0 34
34 23 171.9 0 23
35 34 171.9 0 34
36 44 171.9 0 44
37 29 171.9 0 29
38 39 171.9 0 39
39 30 171.9 0 30
40 16 171.9 0 16
41 31 171.9 0 31
42 32 171.9 0 32
43 36 171.9 0 36
44 26 171.9 0 26
45 35 171.9 0 35
46 35 171.9 0 35
47 42 171.9 0 42
48 37 171.9 0 37
49 29 171.9 0 29
50 30 171.9 0 30
51 49 171.9 0 49
52 48 171.9 0 48
53 31 171.9 0 31
54 36 171.9 0 36
55 40 171.9 0 40
56 31 171.9 0 31
57 38 171.9 0 38
58 30 171.9 0 30
59 51 171.9 0 51
60 44 171.9 0 44
61 41 171.9 0 41
62 41 171.9 0 41
63 33 171.9 0 33
64 36 171.9 0 36
65 58 171.9 0 58
66 45 171.9 0 45
67 32 171.9 0 32
68 23 171.9 0 23
69 35 171.9 0 35
70 43 171.9 0 43
71 36 171.9 0 36
72 36 171.9 0 36
73 27 171.9 0 27
74 22 171.9 0 22
75 43 171.9 0 43
76 31 171.9 0 31
77 60 171.9 0 60
78 45 171.9 0 45
79 23 171.9 0 23
80 27 171.9 0 27
81 34 171.9 0 34
82 35 171.9 0 35
83 53 171.9 0 53
84 43 171.9 0 43
85 42 171.9 0 42
86 49 171.9 0 49
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T56_S155_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T56_S155_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.85 s (10 µs/read; 6.29 M reads/minute).
=== Summary ===
Total reads processed: 2,709,059
Reads with adapters: 949,883 (35.1%)
== Read fate breakdown ==
Reads that were too short: 256,725 (9.5%)
Reads written (passing filters): 2,452,334 (90.5%)
Total basepairs processed: 273,614,959 bp
Total written (filtered): 191,583,951 bp (70.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 852168 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.8%
G: 27.1%
T: 29.7%
none/other: 12.5%
Overview of removed sequences
length count expect max.err error counts
3 62773 42329.0 0 62773
4 28299 10582.3 0 28299
5 14937 2645.6 0 14937
6 9934 661.4 0 9934
7 8536 165.3 0 8536
8 7589 41.3 0 7589
9 7594 41.3 0 7594
10 7611 41.3 0 7611
11 7373 41.3 0 7373
12 7528 41.3 0 7528
13 7704 41.3 0 7704
14 7680 41.3 0 7680
15 7840 41.3 0 7840
16 7917 41.3 0 7917
17 7933 41.3 0 7933
18 8040 41.3 0 8040
19 7769 41.3 0 7769
20 7662 41.3 0 7662
21 8017 41.3 0 8017
22 7734 41.3 0 7734
23 7440 41.3 0 7440
24 7794 41.3 0 7794
25 7548 41.3 0 7548
26 7555 41.3 0 7555
27 7646 41.3 0 7646
28 7808 41.3 0 7808
29 7672 41.3 0 7672
30 7783 41.3 0 7783
31 8258 41.3 0 8258
32 8047 41.3 0 8047
33 7858 41.3 0 7858
34 8102 41.3 0 8102
35 7994 41.3 0 7994
36 7967 41.3 0 7967
37 7639 41.3 0 7639
38 7263 41.3 0 7263
39 7639 41.3 0 7639
40 7683 41.3 0 7683
41 7730 41.3 0 7730
42 8022 41.3 0 8022
43 7866 41.3 0 7866
44 7754 41.3 0 7754
45 7659 41.3 0 7659
46 8298 41.3 0 8298
47 7978 41.3 0 7978
48 7947 41.3 0 7947
49 11047 41.3 0 11047
50 12957 41.3 0 12957
51 8580 41.3 0 8580
52 8989 41.3 0 8989
53 8475 41.3 0 8475
54 7608 41.3 0 7608
55 8065 41.3 0 8065
56 8226 41.3 0 8226
57 7947 41.3 0 7947
58 8618 41.3 0 8618
59 8084 41.3 0 8084
60 8124 41.3 0 8124
61 8534 41.3 0 8534
62 8480 41.3 0 8480
63 7865 41.3 0 7865
64 7942 41.3 0 7942
65 7858 41.3 0 7858
66 7566 41.3 0 7566
67 7688 41.3 0 7688
68 7813 41.3 0 7813
69 7200 41.3 0 7200
70 6913 41.3 0 6913
71 7259 41.3 0 7259
72 7058 41.3 0 7058
73 6648 41.3 0 6648
74 6455 41.3 0 6455
75 6206 41.3 0 6206
76 6143 41.3 0 6143
77 6357 41.3 0 6357
78 6336 41.3 0 6336
79 7307 41.3 0 7307
80 6781 41.3 0 6781
81 8010 41.3 0 8010
82 9458 41.3 0 9458
83 10389 41.3 0 10389
84 11556 41.3 0 11556
85 12133 41.3 0 12133
86 106073 41.3 0 106073
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 41502 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.7%
C: 33.6%
G: 0.0%
T: 37.6%
none/other: 2.1%
Overview of removed sequences
length count expect max.err error counts
3 13077 42329.0 0 13077
4 3293 10582.3 0 3293
5 1042 2645.6 0 1042
6 558 661.4 0 558
7 501 165.3 0 501
8 505 41.3 0 505
9 470 41.3 0 470
10 423 41.3 0 423
11 493 41.3 0 493
12 377 41.3 0 377
13 423 41.3 0 423
14 435 41.3 0 435
15 393 41.3 0 393
16 403 41.3 0 403
17 416 41.3 0 416
18 416 41.3 0 416
19 380 41.3 0 380
20 420 41.3 0 420
21 408 41.3 0 408
22 373 41.3 0 373
23 384 41.3 0 384
24 407 41.3 0 407
25 403 41.3 0 403
26 393 41.3 0 393
27 340 41.3 0 340
28 378 41.3 0 378
29 347 41.3 0 347
30 356 41.3 0 356
31 346 41.3 0 346
32 380 41.3 0 380
33 358 41.3 0 358
34 332 41.3 0 332
35 366 41.3 0 366
36 336 41.3 0 336
37 364 41.3 0 364
38 334 41.3 0 334
39 349 41.3 0 349
40 318 41.3 0 318
41 364 41.3 0 364
42 322 41.3 0 322
43 334 41.3 0 334
44 323 41.3 0 323
45 341 41.3 0 341
46 369 41.3 0 369
47 349 41.3 0 349
48 367 41.3 0 367
49 337 41.3 0 337
50 321 41.3 0 321
51 312 41.3 0 312
52 308 41.3 0 308
53 305 41.3 0 305
54 313 41.3 0 313
55 326 41.3 0 326
56 331 41.3 0 331
57 302 41.3 0 302
58 318 41.3 0 318
59 325 41.3 0 325
60 271 41.3 0 271
61 279 41.3 0 279
62 222 41.3 0 222
63 228 41.3 0 228
64 234 41.3 0 234
65 197 41.3 0 197
66 191 41.3 0 191
67 155 41.3 0 155
68 149 41.3 0 149
69 141 41.3 0 141
70 125 41.3 0 125
71 113 41.3 0 113
72 106 41.3 0 106
73 91 41.3 0 91
74 75 41.3 0 75
75 74 41.3 0 74
76 69 41.3 0 69
77 49 41.3 0 49
78 49 41.3 0 49
79 24 41.3 0 24
80 42 41.3 0 42
81 25 41.3 0 25
82 33 41.3 0 33
83 45 41.3 0 45
84 39 41.3 0 39
85 51 41.3 0 51
86 861 41.3 0 861
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 56213 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 22.9%
G: 21.3%
T: 20.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41674 42329.0 0 41674
4 9698 10582.3 0 9698
5 2063 2645.6 0 2063
6 272 661.4 0 272
7 27 165.3 0 27
8 32 165.3 0 32
9 26 165.3 0 26
10 25 165.3 0 25
11 30 165.3 0 30
12 33 165.3 0 33
13 27 165.3 0 27
14 35 165.3 0 35
15 33 165.3 0 33
16 30 165.3 0 30
17 39 165.3 0 39
18 32 165.3 0 32
19 30 165.3 0 30
20 32 165.3 0 32
21 33 165.3 0 33
22 28 165.3 0 28
23 29 165.3 0 29
24 29 165.3 0 29
25 48 165.3 0 48
26 42 165.3 0 42
27 24 165.3 0 24
28 37 165.3 0 37
29 46 165.3 0 46
30 39 165.3 0 39
31 20 165.3 0 20
32 59 165.3 0 59
33 31 165.3 0 31
34 41 165.3 0 41
35 22 165.3 0 22
36 26 165.3 0 26
37 18 165.3 0 18
38 30 165.3 0 30
39 23 165.3 0 23
40 30 165.3 0 30
41 43 165.3 0 43
42 21 165.3 0 21
43 23 165.3 0 23
44 28 165.3 0 28
45 31 165.3 0 31
46 26 165.3 0 26
47 27 165.3 0 27
48 28 165.3 0 28
49 30 165.3 0 30
50 40 165.3 0 40
51 33 165.3 0 33
52 34 165.3 0 34
53 24 165.3 0 24
54 23 165.3 0 23
55 42 165.3 0 42
56 20 165.3 0 20
57 24 165.3 0 24
58 30 165.3 0 30
59 39 165.3 0 39
60 25 165.3 0 25
61 32 165.3 0 32
62 45 165.3 0 45
63 23 165.3 0 23
64 25 165.3 0 25
65 46 165.3 0 46
66 32 165.3 0 32
67 29 165.3 0 29
68 26 165.3 0 26
69 20 165.3 0 20
70 29 165.3 0 29
71 33 165.3 0 33
72 27 165.3 0 27
73 27 165.3 0 27
74 27 165.3 0 27
75 33 165.3 0 33
76 21 165.3 0 21
77 66 165.3 0 66
78 36 165.3 0 36
79 27 165.3 0 27
80 39 165.3 0 39
81 21 165.3 0 21
82 28 165.3 0 28
83 37 165.3 0 37
84 31 165.3 0 31
85 38 165.3 0 38
86 31 165.3 0 31
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T56_S155_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T56_S155_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.12 s (9 µs/read; 6.35 M reads/minute).
=== Summary ===
Total reads processed: 2,762,774
Reads with adapters: 978,280 (35.4%)
== Read fate breakdown ==
Reads that were too short: 269,401 (9.8%)
Reads written (passing filters): 2,493,373 (90.2%)
Total basepairs processed: 279,040,174 bp
Total written (filtered): 194,523,832 bp (69.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 879164 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.8%
G: 27.1%
T: 29.3%
none/other: 12.7%
Overview of removed sequences
length count expect max.err error counts
3 63157 43168.3 0 63157
4 28350 10792.1 0 28350
5 15099 2698.0 0 15099
6 10207 674.5 0 10207
7 8603 168.6 0 8603
8 7772 42.2 0 7772
9 7678 42.2 0 7678
10 7731 42.2 0 7731
11 7491 42.2 0 7491
12 7602 42.2 0 7602
13 7595 42.2 0 7595
14 7887 42.2 0 7887
15 7960 42.2 0 7960
16 8165 42.2 0 8165
17 8123 42.2 0 8123
18 8049 42.2 0 8049
19 7924 42.2 0 7924
20 7803 42.2 0 7803
21 8234 42.2 0 8234
22 7788 42.2 0 7788
23 7587 42.2 0 7587
24 7739 42.2 0 7739
25 7834 42.2 0 7834
26 7714 42.2 0 7714
27 7598 42.2 0 7598
28 8270 42.2 0 8270
29 8173 42.2 0 8173
30 8136 42.2 0 8136
31 8372 42.2 0 8372
32 8156 42.2 0 8156
33 8369 42.2 0 8369
34 8149 42.2 0 8149
35 8097 42.2 0 8097
36 8175 42.2 0 8175
37 8038 42.2 0 8038
38 7662 42.2 0 7662
39 7985 42.2 0 7985
40 8016 42.2 0 8016
41 7983 42.2 0 7983
42 8154 42.2 0 8154
43 8338 42.2 0 8338
44 7808 42.2 0 7808
45 7963 42.2 0 7963
46 8462 42.2 0 8462
47 8170 42.2 0 8170
48 8134 42.2 0 8134
49 11290 42.2 0 11290
50 13546 42.2 0 13546
51 8694 42.2 0 8694
52 9306 42.2 0 9306
53 8661 42.2 0 8661
54 7965 42.2 0 7965
55 8604 42.2 0 8604
56 8524 42.2 0 8524
57 8081 42.2 0 8081
58 8965 42.2 0 8965
59 8509 42.2 0 8509
60 8468 42.2 0 8468
61 8762 42.2 0 8762
62 8601 42.2 0 8601
63 8102 42.2 0 8102
64 8238 42.2 0 8238
65 8177 42.2 0 8177
66 7934 42.2 0 7934
67 7817 42.2 0 7817
68 8187 42.2 0 8187
69 7536 42.2 0 7536
70 6855 42.2 0 6855
71 7697 42.2 0 7697
72 7482 42.2 0 7482
73 6982 42.2 0 6982
74 6977 42.2 0 6977
75 6804 42.2 0 6804
76 6507 42.2 0 6507
77 6720 42.2 0 6720
78 6638 42.2 0 6638
79 7662 42.2 0 7662
80 7408 42.2 0 7408
81 8224 42.2 0 8224
82 9715 42.2 0 9715
83 10908 42.2 0 10908
84 11855 42.2 0 11855
85 12638 42.2 0 12638
86 111825 42.2 0 111825
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 42212 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.5%
C: 33.8%
G: 0.0%
T: 37.7%
none/other: 2.0%
Overview of removed sequences
length count expect max.err error counts
3 13195 43168.3 0 13195
4 3215 10792.1 0 3215
5 1023 2698.0 0 1023
6 559 674.5 0 559
7 500 168.6 0 500
8 486 42.2 0 486
9 470 42.2 0 470
10 451 42.2 0 451
11 495 42.2 0 495
12 439 42.2 0 439
13 421 42.2 0 421
14 432 42.2 0 432
15 378 42.2 0 378
16 423 42.2 0 423
17 424 42.2 0 424
18 394 42.2 0 394
19 444 42.2 0 444
20 396 42.2 0 396
21 361 42.2 0 361
22 421 42.2 0 421
23 418 42.2 0 418
24 416 42.2 0 416
25 376 42.2 0 376
26 393 42.2 0 393
27 371 42.2 0 371
28 359 42.2 0 359
29 397 42.2 0 397
30 386 42.2 0 386
31 325 42.2 0 325
32 360 42.2 0 360
33 421 42.2 0 421
34 413 42.2 0 413
35 356 42.2 0 356
36 382 42.2 0 382
37 377 42.2 0 377
38 371 42.2 0 371
39 362 42.2 0 362
40 345 42.2 0 345
41 384 42.2 0 384
42 363 42.2 0 363
43 365 42.2 0 365
44 318 42.2 0 318
45 357 42.2 0 357
46 360 42.2 0 360
47 385 42.2 0 385
48 364 42.2 0 364
49 306 42.2 0 306
50 354 42.2 0 354
51 313 42.2 0 313
52 370 42.2 0 370
53 360 42.2 0 360
54 342 42.2 0 342
55 337 42.2 0 337
56 294 42.2 0 294
57 326 42.2 0 326
58 310 42.2 0 310
59 304 42.2 0 304
60 264 42.2 0 264
61 242 42.2 0 242
62 258 42.2 0 258
63 238 42.2 0 238
64 223 42.2 0 223
65 178 42.2 0 178
66 222 42.2 0 222
67 174 42.2 0 174
68 148 42.2 0 148
69 141 42.2 0 141
70 143 42.2 0 143
71 134 42.2 0 134
72 111 42.2 0 111
73 96 42.2 0 96
74 53 42.2 0 53
75 59 42.2 0 59
76 73 42.2 0 73
77 40 42.2 0 40
78 42 42.2 0 42
79 43 42.2 0 43
80 40 42.2 0 40
81 31 42.2 0 31
82 43 42.2 0 43
83 36 42.2 0 36
84 35 42.2 0 35
85 41 42.2 0 41
86 837 42.2 0 837
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 56904 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 22.5%
G: 21.5%
T: 20.5%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 42213 43168.3 0 42213
4 9978 10792.1 0 9978
5 2020 2698.0 0 2020
6 239 674.5 0 239
7 26 168.6 0 26
8 34 168.6 0 34
9 32 168.6 0 32
10 30 168.6 0 30
11 39 168.6 0 39
12 24 168.6 0 24
13 23 168.6 0 23
14 39 168.6 0 39
15 21 168.6 0 21
16 28 168.6 0 28
17 27 168.6 0 27
18 32 168.6 0 32
19 40 168.6 0 40
20 40 168.6 0 40
21 31 168.6 0 31
22 37 168.6 0 37
23 20 168.6 0 20
24 23 168.6 0 23
25 38 168.6 0 38
26 54 168.6 0 54
27 23 168.6 0 23
28 38 168.6 0 38
29 53 168.6 0 53
30 27 168.6 0 27
31 27 168.6 0 27
32 41 168.6 0 41
33 41 168.6 0 41
34 28 168.6 0 28
35 17 168.6 0 17
36 29 168.6 0 29
37 27 168.6 0 27
38 22 168.6 0 22
39 27 168.6 0 27
40 24 168.6 0 24
41 38 168.6 0 38
42 32 168.6 0 32
43 28 168.6 0 28
44 28 168.6 0 28
45 26 168.6 0 26
46 15 168.6 0 15
47 29 168.6 0 29
48 33 168.6 0 33
49 26 168.6 0 26
50 35 168.6 0 35
51 30 168.6 0 30
52 22 168.6 0 22
53 21 168.6 0 21
54 34 168.6 0 34
55 40 168.6 0 40
56 25 168.6 0 25
57 17 168.6 0 17
58 44 168.6 0 44
59 38 168.6 0 38
60 24 168.6 0 24
61 28 168.6 0 28
62 28 168.6 0 28
63 31 168.6 0 31
64 13 168.6 0 13
65 27 168.6 0 27
66 36 168.6 0 36
67 35 168.6 0 35
68 24 168.6 0 24
69 30 168.6 0 30
70 19 168.6 0 19
71 38 168.6 0 38
72 17 168.6 0 17
73 21 168.6 0 21
74 34 168.6 0 34
75 20 168.6 0 20
76 25 168.6 0 25
77 74 168.6 0 74
78 45 168.6 0 45
79 28 168.6 0 28
80 27 168.6 0 27
81 31 168.6 0 31
82 24 168.6 0 24
83 50 168.6 0 50
84 19 168.6 0 19
85 35 168.6 0 35
86 48 168.6 0 48
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T57_S157_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T57_S157_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 31.33 s (9 µs/read; 6.79 M reads/minute).
=== Summary ===
Total reads processed: 3,545,695
Reads with adapters: 1,178,537 (33.2%)
== Read fate breakdown ==
Reads that were too short: 316,511 (8.9%)
Reads written (passing filters): 3,229,184 (91.1%)
Total basepairs processed: 358,115,195 bp
Total written (filtered): 254,237,094 bp (71.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1067409 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.6%
G: 27.6%
T: 30.3%
none/other: 11.5%
Overview of removed sequences
length count expect max.err error counts
3 80457 55401.5 0 80457
4 35106 13850.4 0 35106
5 19245 3462.6 0 19245
6 13141 865.6 0 13141
7 11010 216.4 0 11010
8 9650 54.1 0 9650
9 9851 54.1 0 9851
10 9988 54.1 0 9988
11 9827 54.1 0 9827
12 9837 54.1 0 9837
13 9654 54.1 0 9654
14 9844 54.1 0 9844
15 9856 54.1 0 9856
16 10156 54.1 0 10156
17 9692 54.1 0 9692
18 9672 54.1 0 9672
19 9686 54.1 0 9686
20 9613 54.1 0 9613
21 9756 54.1 0 9756
22 9587 54.1 0 9587
23 9236 54.1 0 9236
24 9602 54.1 0 9602
25 9377 54.1 0 9377
26 9436 54.1 0 9436
27 9283 54.1 0 9283
28 9788 54.1 0 9788
29 10238 54.1 0 10238
30 10008 54.1 0 10008
31 10357 54.1 0 10357
32 10290 54.1 0 10290
33 10088 54.1 0 10088
34 10038 54.1 0 10038
35 10691 54.1 0 10691
36 10089 54.1 0 10089
37 9773 54.1 0 9773
38 9463 54.1 0 9463
39 9737 54.1 0 9737
40 9791 54.1 0 9791
41 9866 54.1 0 9866
42 10649 54.1 0 10649
43 10853 54.1 0 10853
44 9819 54.1 0 9819
45 10017 54.1 0 10017
46 10578 54.1 0 10578
47 10205 54.1 0 10205
48 9860 54.1 0 9860
49 14249 54.1 0 14249
50 16972 54.1 0 16972
51 10281 54.1 0 10281
52 10764 54.1 0 10764
53 10512 54.1 0 10512
54 9117 54.1 0 9117
55 9688 54.1 0 9688
56 9918 54.1 0 9918
57 9337 54.1 0 9337
58 10348 54.1 0 10348
59 9797 54.1 0 9797
60 9702 54.1 0 9702
61 10176 54.1 0 10176
62 9792 54.1 0 9792
63 9328 54.1 0 9328
64 9772 54.1 0 9772
65 9596 54.1 0 9596
66 9110 54.1 0 9110
67 9379 54.1 0 9379
68 9149 54.1 0 9149
69 9028 54.1 0 9028
70 8533 54.1 0 8533
71 8799 54.1 0 8799
72 8922 54.1 0 8922
73 8331 54.1 0 8331
74 8065 54.1 0 8065
75 8106 54.1 0 8106
76 7959 54.1 0 7959
77 7968 54.1 0 7968
78 8637 54.1 0 8637
79 9918 54.1 0 9918
80 9293 54.1 0 9293
81 10858 54.1 0 10858
82 12883 54.1 0 12883
83 13797 54.1 0 13797
84 15494 54.1 0 15494
85 16218 54.1 0 16218
86 122853 54.1 0 122853
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34495 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.5%
C: 35.9%
G: 0.0%
T: 32.4%
none/other: 2.2%
Overview of removed sequences
length count expect max.err error counts
3 19660 55401.5 0 19660
4 4404 13850.4 0 4404
5 937 3462.6 0 937
6 315 865.6 0 315
7 232 216.4 0 232
8 190 54.1 0 190
9 209 54.1 0 209
10 175 54.1 0 175
11 171 54.1 0 171
12 182 54.1 0 182
13 176 54.1 0 176
14 159 54.1 0 159
15 129 54.1 0 129
16 143 54.1 0 143
17 132 54.1 0 132
18 138 54.1 0 138
19 155 54.1 0 155
20 176 54.1 0 176
21 132 54.1 0 132
22 128 54.1 0 128
23 130 54.1 0 130
24 145 54.1 0 145
25 138 54.1 0 138
26 126 54.1 0 126
27 130 54.1 0 130
28 128 54.1 0 128
29 139 54.1 0 139
30 115 54.1 0 115
31 116 54.1 0 116
32 112 54.1 0 112
33 138 54.1 0 138
34 142 54.1 0 142
35 124 54.1 0 124
36 127 54.1 0 127
37 115 54.1 0 115
38 132 54.1 0 132
39 128 54.1 0 128
40 125 54.1 0 125
41 127 54.1 0 127
42 143 54.1 0 143
43 137 54.1 0 137
44 118 54.1 0 118
45 106 54.1 0 106
46 141 54.1 0 141
47 138 54.1 0 138
48 110 54.1 0 110
49 116 54.1 0 116
50 112 54.1 0 112
51 103 54.1 0 103
52 116 54.1 0 116
53 120 54.1 0 120
54 113 54.1 0 113
55 110 54.1 0 110
56 110 54.1 0 110
57 105 54.1 0 105
58 102 54.1 0 102
59 91 54.1 0 91
60 94 54.1 0 94
61 94 54.1 0 94
62 98 54.1 0 98
63 71 54.1 0 71
64 80 54.1 0 80
65 88 54.1 0 88
66 58 54.1 0 58
67 68 54.1 0 68
68 64 54.1 0 64
69 56 54.1 0 56
70 58 54.1 0 58
71 57 54.1 0 57
72 46 54.1 0 46
73 28 54.1 0 28
74 39 54.1 0 39
75 31 54.1 0 31
76 44 54.1 0 44
77 20 54.1 0 20
78 18 54.1 0 18
79 26 54.1 0 26
80 24 54.1 0 24
81 20 54.1 0 20
82 19 54.1 0 19
83 30 54.1 0 30
84 25 54.1 0 25
85 27 54.1 0 27
86 741 54.1 0 741
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 76633 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 23.7%
G: 20.4%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 57047 55401.5 0 57047
4 12679 13850.4 0 12679
5 2942 3462.6 0 2942
6 451 865.6 0 451
7 42 216.4 0 42
8 30 216.4 0 30
9 46 216.4 0 46
10 51 216.4 0 51
11 52 216.4 0 52
12 41 216.4 0 41
13 33 216.4 0 33
14 41 216.4 0 41
15 39 216.4 0 39
16 37 216.4 0 37
17 37 216.4 0 37
18 45 216.4 0 45
19 48 216.4 0 48
20 54 216.4 0 54
21 39 216.4 0 39
22 35 216.4 0 35
23 34 216.4 0 34
24 41 216.4 0 41
25 48 216.4 0 48
26 53 216.4 0 53
27 40 216.4 0 40
28 44 216.4 0 44
29 45 216.4 0 45
30 34 216.4 0 34
31 41 216.4 0 41
32 57 216.4 0 57
33 38 216.4 0 38
34 47 216.4 0 47
35 46 216.4 0 46
36 35 216.4 0 35
37 45 216.4 0 45
38 46 216.4 0 46
39 34 216.4 0 34
40 44 216.4 0 44
41 50 216.4 0 50
42 44 216.4 0 44
43 42 216.4 0 42
44 37 216.4 0 37
45 40 216.4 0 40
46 44 216.4 0 44
47 48 216.4 0 48
48 46 216.4 0 46
49 28 216.4 0 28
50 63 216.4 0 63
51 47 216.4 0 47
52 54 216.4 0 54
53 42 216.4 0 42
54 47 216.4 0 47
55 67 216.4 0 67
56 46 216.4 0 46
57 39 216.4 0 39
58 69 216.4 0 69
59 39 216.4 0 39
60 39 216.4 0 39
61 51 216.4 0 51
62 33 216.4 0 33
63 47 216.4 0 47
64 31 216.4 0 31
65 58 216.4 0 58
66 41 216.4 0 41
67 48 216.4 0 48
68 46 216.4 0 46
69 38 216.4 0 38
70 35 216.4 0 35
71 51 216.4 0 51
72 18 216.4 0 18
73 44 216.4 0 44
74 48 216.4 0 48
75 42 216.4 0 42
76 24 216.4 0 24
77 59 216.4 0 59
78 39 216.4 0 39
79 37 216.4 0 37
80 36 216.4 0 36
81 43 216.4 0 43
82 41 216.4 0 41
83 69 216.4 0 69
84 49 216.4 0 49
85 45 216.4 0 45
86 68 216.4 0 68
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T57_S157_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T57_S157_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 32.79 s (9 µs/read; 6.59 M reads/minute).
=== Summary ===
Total reads processed: 3,599,191
Reads with adapters: 1,206,377 (33.5%)
== Read fate breakdown ==
Reads that were too short: 328,401 (9.1%)
Reads written (passing filters): 3,270,790 (90.9%)
Total basepairs processed: 363,518,291 bp
Total written (filtered): 257,299,487 bp (70.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1092897 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.6%
G: 27.6%
T: 30.1%
none/other: 11.8%
Overview of removed sequences
length count expect max.err error counts
3 81233 56237.4 0 81233
4 35260 14059.3 0 35260
5 19590 3514.8 0 19590
6 13378 878.7 0 13378
7 11290 219.7 0 11290
8 9966 54.9 0 9966
9 10028 54.9 0 10028
10 10280 54.9 0 10280
11 9944 54.9 0 9944
12 9800 54.9 0 9800
13 9990 54.9 0 9990
14 10191 54.9 0 10191
15 9933 54.9 0 9933
16 10233 54.9 0 10233
17 9839 54.9 0 9839
18 9926 54.9 0 9926
19 9854 54.9 0 9854
20 9787 54.9 0 9787
21 9689 54.9 0 9689
22 9587 54.9 0 9587
23 9529 54.9 0 9529
24 9572 54.9 0 9572
25 9347 54.9 0 9347
26 9674 54.9 0 9674
27 9493 54.9 0 9493
28 9938 54.9 0 9938
29 10409 54.9 0 10409
30 9753 54.9 0 9753
31 10607 54.9 0 10607
32 10670 54.9 0 10670
33 10355 54.9 0 10355
34 10103 54.9 0 10103
35 10816 54.9 0 10816
36 10053 54.9 0 10053
37 9989 54.9 0 9989
38 9497 54.9 0 9497
39 10078 54.9 0 10078
40 9938 54.9 0 9938
41 10123 54.9 0 10123
42 10527 54.9 0 10527
43 10832 54.9 0 10832
44 9856 54.9 0 9856
45 10487 54.9 0 10487
46 10673 54.9 0 10673
47 10639 54.9 0 10639
48 10184 54.9 0 10184
49 14979 54.9 0 14979
50 17402 54.9 0 17402
51 10759 54.9 0 10759
52 11306 54.9 0 11306
53 10766 54.9 0 10766
54 9470 54.9 0 9470
55 9900 54.9 0 9900
56 10182 54.9 0 10182
57 9480 54.9 0 9480
58 10613 54.9 0 10613
59 9967 54.9 0 9967
60 9858 54.9 0 9858
61 10294 54.9 0 10294
62 10274 54.9 0 10274
63 9578 54.9 0 9578
64 9876 54.9 0 9876
65 9955 54.9 0 9955
66 9309 54.9 0 9309
67 9624 54.9 0 9624
68 9662 54.9 0 9662
69 9298 54.9 0 9298
70 8593 54.9 0 8593
71 9287 54.9 0 9287
72 9156 54.9 0 9156
73 8809 54.9 0 8809
74 8408 54.9 0 8408
75 8443 54.9 0 8443
76 8287 54.9 0 8287
77 8357 54.9 0 8357
78 8926 54.9 0 8926
79 10179 54.9 0 10179
80 9443 54.9 0 9443
81 10975 54.9 0 10975
82 13202 54.9 0 13202
83 14394 54.9 0 14394
84 15898 54.9 0 15898
85 16650 54.9 0 16650
86 128398 54.9 0 128398
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35346 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.3%
C: 35.9%
G: 0.0%
T: 32.6%
none/other: 2.3%
Overview of removed sequences
length count expect max.err error counts
3 20051 56237.4 0 20051
4 4415 14059.3 0 4415
5 897 3514.8 0 897
6 320 878.7 0 320
7 244 219.7 0 244
8 232 54.9 0 232
9 212 54.9 0 212
10 170 54.9 0 170
11 183 54.9 0 183
12 165 54.9 0 165
13 188 54.9 0 188
14 159 54.9 0 159
15 180 54.9 0 180
16 150 54.9 0 150
17 146 54.9 0 146
18 139 54.9 0 139
19 144 54.9 0 144
20 149 54.9 0 149
21 148 54.9 0 148
22 152 54.9 0 152
23 155 54.9 0 155
24 123 54.9 0 123
25 133 54.9 0 133
26 151 54.9 0 151
27 148 54.9 0 148
28 152 54.9 0 152
29 142 54.9 0 142
30 130 54.9 0 130
31 122 54.9 0 122
32 135 54.9 0 135
33 142 54.9 0 142
34 123 54.9 0 123
35 148 54.9 0 148
36 125 54.9 0 125
37 131 54.9 0 131
38 146 54.9 0 146
39 136 54.9 0 136
40 119 54.9 0 119
41 130 54.9 0 130
42 145 54.9 0 145
43 143 54.9 0 143
44 127 54.9 0 127
45 131 54.9 0 131
46 110 54.9 0 110
47 120 54.9 0 120
48 118 54.9 0 118
49 101 54.9 0 101
50 103 54.9 0 103
51 121 54.9 0 121
52 120 54.9 0 120
53 118 54.9 0 118
54 114 54.9 0 114
55 117 54.9 0 117
56 113 54.9 0 113
57 131 54.9 0 131
58 129 54.9 0 129
59 107 54.9 0 107
60 108 54.9 0 108
61 91 54.9 0 91
62 77 54.9 0 77
63 87 54.9 0 87
64 78 54.9 0 78
65 77 54.9 0 77
66 59 54.9 0 59
67 66 54.9 0 66
68 72 54.9 0 72
69 77 54.9 0 77
70 54 54.9 0 54
71 54 54.9 0 54
72 54 54.9 0 54
73 34 54.9 0 34
74 41 54.9 0 41
75 26 54.9 0 26
76 39 54.9 0 39
77 26 54.9 0 26
78 29 54.9 0 29
79 28 54.9 0 28
80 30 54.9 0 30
81 25 54.9 0 25
82 22 54.9 0 22
83 22 54.9 0 22
84 29 54.9 0 29
85 44 54.9 0 44
86 794 54.9 0 794
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 78134 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 24.0%
G: 20.5%
T: 19.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 57884 56237.4 0 57884
4 13205 14059.3 0 13205
5 3022 3514.8 0 3022
6 486 878.7 0 486
7 40 219.7 0 40
8 33 219.7 0 33
9 42 219.7 0 42
10 44 219.7 0 44
11 36 219.7 0 36
12 55 219.7 0 55
13 52 219.7 0 52
14 36 219.7 0 36
15 42 219.7 0 42
16 45 219.7 0 45
17 45 219.7 0 45
18 32 219.7 0 32
19 51 219.7 0 51
20 52 219.7 0 52
21 50 219.7 0 50
22 45 219.7 0 45
23 34 219.7 0 34
24 51 219.7 0 51
25 49 219.7 0 49
26 31 219.7 0 31
27 50 219.7 0 50
28 44 219.7 0 44
29 47 219.7 0 47
30 45 219.7 0 45
31 41 219.7 0 41
32 43 219.7 0 43
33 47 219.7 0 47
34 44 219.7 0 44
35 29 219.7 0 29
36 51 219.7 0 51
37 47 219.7 0 47
38 43 219.7 0 43
39 48 219.7 0 48
40 43 219.7 0 43
41 32 219.7 0 32
42 30 219.7 0 30
43 33 219.7 0 33
44 39 219.7 0 39
45 40 219.7 0 40
46 45 219.7 0 45
47 47 219.7 0 47
48 40 219.7 0 40
49 54 219.7 0 54
50 52 219.7 0 52
51 54 219.7 0 54
52 51 219.7 0 51
53 40 219.7 0 40
54 46 219.7 0 46
55 52 219.7 0 52
56 51 219.7 0 51
57 46 219.7 0 46
58 57 219.7 0 57
59 40 219.7 0 40
60 52 219.7 0 52
61 44 219.7 0 44
62 57 219.7 0 57
63 45 219.7 0 45
64 47 219.7 0 47
65 56 219.7 0 56
66 54 219.7 0 54
67 35 219.7 0 35
68 39 219.7 0 39
69 29 219.7 0 29
70 33 219.7 0 33
71 52 219.7 0 52
72 41 219.7 0 41
73 41 219.7 0 41
74 33 219.7 0 33
75 43 219.7 0 43
76 21 219.7 0 21
77 67 219.7 0 67
78 28 219.7 0 28
79 38 219.7 0 38
80 35 219.7 0 35
81 51 219.7 0 51
82 59 219.7 0 59
83 55 219.7 0 55
84 39 219.7 0 39
85 50 219.7 0 50
86 57 219.7 0 57
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T58_S152_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T58_S152_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 21.71 s (10 µs/read; 6.05 M reads/minute).
=== Summary ===
Total reads processed: 2,188,761
Reads with adapters: 783,340 (35.8%)
== Read fate breakdown ==
Reads that were too short: 338,728 (15.5%)
Reads written (passing filters): 1,850,033 (84.5%)
Total basepairs processed: 221,064,861 bp
Total written (filtered): 146,486,828 bp (66.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 711744 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 27.3%
G: 23.5%
T: 21.4%
none/other: 27.8%
Overview of removed sequences
length count expect max.err error counts
3 46252 34199.4 0 46252
4 20387 8549.8 0 20387
5 9508 2137.5 0 9508
6 5783 534.4 0 5783
7 4521 133.6 0 4521
8 3695 33.4 0 3695
9 3906 33.4 0 3906
10 3854 33.4 0 3854
11 3759 33.4 0 3759
12 3751 33.4 0 3751
13 3858 33.4 0 3858
14 4084 33.4 0 4084
15 4105 33.4 0 4105
16 4014 33.4 0 4014
17 4018 33.4 0 4018
18 4225 33.4 0 4225
19 4044 33.4 0 4044
20 3884 33.4 0 3884
21 4034 33.4 0 4034
22 4003 33.4 0 4003
23 4254 33.4 0 4254
24 4044 33.4 0 4044
25 4223 33.4 0 4223
26 4411 33.4 0 4411
27 4149 33.4 0 4149
28 4532 33.4 0 4532
29 4910 33.4 0 4910
30 4613 33.4 0 4613
31 4678 33.4 0 4678
32 4219 33.4 0 4219
33 4233 33.4 0 4233
34 4460 33.4 0 4460
35 4307 33.4 0 4307
36 4389 33.4 0 4389
37 4257 33.4 0 4257
38 4107 33.4 0 4107
39 4577 33.4 0 4577
40 4433 33.4 0 4433
41 4399 33.4 0 4399
42 4615 33.4 0 4615
43 4818 33.4 0 4818
44 4356 33.4 0 4356
45 4922 33.4 0 4922
46 4903 33.4 0 4903
47 4621 33.4 0 4621
48 5089 33.4 0 5089
49 6185 33.4 0 6185
50 7486 33.4 0 7486
51 6193 33.4 0 6193
52 5785 33.4 0 5785
53 5776 33.4 0 5776
54 5709 33.4 0 5709
55 6050 33.4 0 6050
56 5983 33.4 0 5983
57 6114 33.4 0 6114
58 6542 33.4 0 6542
59 6413 33.4 0 6413
60 6547 33.4 0 6547
61 6552 33.4 0 6552
62 6860 33.4 0 6860
63 6199 33.4 0 6199
64 6676 33.4 0 6676
65 6948 33.4 0 6948
66 6054 33.4 0 6054
67 6567 33.4 0 6567
68 7045 33.4 0 7045
69 6102 33.4 0 6102
70 6150 33.4 0 6150
71 7472 33.4 0 7472
72 6592 33.4 0 6592
73 6778 33.4 0 6778
74 6250 33.4 0 6250
75 5875 33.4 0 5875
76 5937 33.4 0 5937
77 6802 33.4 0 6802
78 5552 33.4 0 5552
79 6655 33.4 0 6655
80 6062 33.4 0 6062
81 7110 33.4 0 7110
82 8557 33.4 0 8557
83 10521 33.4 0 10521
84 10839 33.4 0 10839
85 11141 33.4 0 11141
86 197461 33.4 0 197461
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28291 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.8%
C: 27.4%
G: 0.0%
T: 35.9%
none/other: 5.9%
Overview of removed sequences
length count expect max.err error counts
3 8963 34199.4 0 8963
4 2040 8549.8 0 2040
5 667 2137.5 0 667
6 387 534.4 0 387
7 591 133.6 0 591
8 610 33.4 0 610
9 513 33.4 0 513
10 396 33.4 0 396
11 378 33.4 0 378
12 346 33.4 0 346
13 315 33.4 0 315
14 289 33.4 0 289
15 282 33.4 0 282
16 254 33.4 0 254
17 261 33.4 0 261
18 473 33.4 0 473
19 241 33.4 0 241
20 190 33.4 0 190
21 205 33.4 0 205
22 181 33.4 0 181
23 204 33.4 0 204
24 213 33.4 0 213
25 229 33.4 0 229
26 231 33.4 0 231
27 198 33.4 0 198
28 221 33.4 0 221
29 185 33.4 0 185
30 206 33.4 0 206
31 174 33.4 0 174
32 188 33.4 0 188
33 223 33.4 0 223
34 196 33.4 0 196
35 231 33.4 0 231
36 231 33.4 0 231
37 183 33.4 0 183
38 214 33.4 0 214
39 201 33.4 0 201
40 183 33.4 0 183
41 200 33.4 0 200
42 158 33.4 0 158
43 190 33.4 0 190
44 217 33.4 0 217
45 182 33.4 0 182
46 210 33.4 0 210
47 187 33.4 0 187
48 174 33.4 0 174
49 192 33.4 0 192
50 181 33.4 0 181
51 173 33.4 0 173
52 193 33.4 0 193
53 200 33.4 0 200
54 187 33.4 0 187
55 182 33.4 0 182
56 177 33.4 0 177
57 183 33.4 0 183
58 163 33.4 0 163
59 154 33.4 0 154
60 170 33.4 0 170
61 134 33.4 0 134
62 141 33.4 0 141
63 139 33.4 0 139
64 114 33.4 0 114
65 128 33.4 0 128
66 124 33.4 0 124
67 84 33.4 0 84
68 91 33.4 0 91
69 88 33.4 0 88
70 76 33.4 0 76
71 64 33.4 0 64
72 71 33.4 0 71
73 47 33.4 0 47
74 43 33.4 0 43
75 39 33.4 0 39
76 31 33.4 0 31
77 31 33.4 0 31
78 27 33.4 0 27
79 30 33.4 0 30
80 30 33.4 0 30
81 22 33.4 0 22
82 26 33.4 0 26
83 25 33.4 0 25
84 22 33.4 0 22
85 32 33.4 0 32
86 1666 33.4 0 1666
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 43305 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 23.7%
G: 20.3%
T: 20.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 31940 34199.4 0 31940
4 7541 8549.8 0 7541
5 1428 2137.5 0 1428
6 168 534.4 0 168
7 22 133.6 0 22
8 26 133.6 0 26
9 21 133.6 0 21
10 23 133.6 0 23
11 30 133.6 0 30
12 19 133.6 0 19
13 18 133.6 0 18
14 25 133.6 0 25
15 25 133.6 0 25
16 18 133.6 0 18
17 22 133.6 0 22
18 12 133.6 0 12
19 36 133.6 0 36
20 24 133.6 0 24
21 20 133.6 0 20
22 38 133.6 0 38
23 19 133.6 0 19
24 29 133.6 0 29
25 38 133.6 0 38
26 38 133.6 0 38
27 21 133.6 0 21
28 28 133.6 0 28
29 40 133.6 0 40
30 22 133.6 0 22
31 23 133.6 0 23
32 46 133.6 0 46
33 27 133.6 0 27
34 19 133.6 0 19
35 24 133.6 0 24
36 27 133.6 0 27
37 21 133.6 0 21
38 24 133.6 0 24
39 30 133.6 0 30
40 25 133.6 0 25
41 35 133.6 0 35
42 25 133.6 0 25
43 23 133.6 0 23
44 19 133.6 0 19
45 30 133.6 0 30
46 27 133.6 0 27
47 28 133.6 0 28
48 26 133.6 0 26
49 25 133.6 0 25
50 16 133.6 0 16
51 25 133.6 0 25
52 25 133.6 0 25
53 37 133.6 0 37
54 17 133.6 0 17
55 35 133.6 0 35
56 24 133.6 0 24
57 16 133.6 0 16
58 22 133.6 0 22
59 22 133.6 0 22
60 19 133.6 0 19
61 22 133.6 0 22
62 24 133.6 0 24
63 21 133.6 0 21
64 18 133.6 0 18
65 25 133.6 0 25
66 27 133.6 0 27
67 20 133.6 0 20
68 14 133.6 0 14
69 37 133.6 0 37
70 36 133.6 0 36
71 46 133.6 0 46
72 33 133.6 0 33
73 24 133.6 0 24
74 28 133.6 0 28
75 21 133.6 0 21
76 25 133.6 0 25
77 151 133.6 0 151
78 53 133.6 0 53
79 20 133.6 0 20
80 23 133.6 0 23
81 25 133.6 0 25
82 28 133.6 0 28
83 47 133.6 0 47
84 23 133.6 0 23
85 25 133.6 0 25
86 36 133.6 0 36
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T58_S152_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T58_S152_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 20.39 s (9 µs/read; 6.61 M reads/minute).
=== Summary ===
Total reads processed: 2,244,163
Reads with adapters: 812,370 (36.2%)
== Read fate breakdown ==
Reads that were too short: 357,363 (15.9%)
Reads written (passing filters): 1,886,800 (84.1%)
Total basepairs processed: 226,660,463 bp
Total written (filtered): 149,253,978 bp (65.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 739202 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 27.2%
G: 23.4%
T: 21.1%
none/other: 28.3%
Overview of removed sequences
length count expect max.err error counts
3 46870 35065.0 0 46870
4 20723 8766.3 0 20723
5 9643 2191.6 0 9643
6 5856 547.9 0 5856
7 4490 137.0 0 4490
8 3778 34.2 0 3778
9 3908 34.2 0 3908
10 3938 34.2 0 3938
11 3789 34.2 0 3789
12 3749 34.2 0 3749
13 3873 34.2 0 3873
14 4166 34.2 0 4166
15 3993 34.2 0 3993
16 4087 34.2 0 4087
17 4115 34.2 0 4115
18 4373 34.2 0 4373
19 3988 34.2 0 3988
20 3975 34.2 0 3975
21 4157 34.2 0 4157
22 4248 34.2 0 4248
23 4212 34.2 0 4212
24 4151 34.2 0 4151
25 4214 34.2 0 4214
26 4389 34.2 0 4389
27 4208 34.2 0 4208
28 4730 34.2 0 4730
29 4885 34.2 0 4885
30 4550 34.2 0 4550
31 4875 34.2 0 4875
32 4251 34.2 0 4251
33 4332 34.2 0 4332
34 4318 34.2 0 4318
35 4451 34.2 0 4451
36 4458 34.2 0 4458
37 4352 34.2 0 4352
38 4351 34.2 0 4351
39 4466 34.2 0 4466
40 4672 34.2 0 4672
41 4470 34.2 0 4470
42 4845 34.2 0 4845
43 4883 34.2 0 4883
44 4568 34.2 0 4568
45 5120 34.2 0 5120
46 5149 34.2 0 5149
47 4872 34.2 0 4872
48 5132 34.2 0 5132
49 6383 34.2 0 6383
50 7662 34.2 0 7662
51 6390 34.2 0 6390
52 6016 34.2 0 6016
53 5923 34.2 0 5923
54 6173 34.2 0 6173
55 6201 34.2 0 6201
56 6114 34.2 0 6114
57 6420 34.2 0 6420
58 6696 34.2 0 6696
59 6725 34.2 0 6725
60 6720 34.2 0 6720
61 6681 34.2 0 6681
62 7269 34.2 0 7269
63 6500 34.2 0 6500
64 6910 34.2 0 6910
65 7174 34.2 0 7174
66 6593 34.2 0 6593
67 6781 34.2 0 6781
68 7461 34.2 0 7461
69 6542 34.2 0 6542
70 6705 34.2 0 6705
71 7640 34.2 0 7640
72 6627 34.2 0 6627
73 7205 34.2 0 7205
74 6461 34.2 0 6461
75 6064 34.2 0 6064
76 6298 34.2 0 6298
77 7536 34.2 0 7536
78 5901 34.2 0 5901
79 6902 34.2 0 6902
80 6422 34.2 0 6422
81 7375 34.2 0 7375
82 9094 34.2 0 9094
83 10891 34.2 0 10891
84 11353 34.2 0 11353
85 11896 34.2 0 11896
86 208875 34.2 0 208875
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29119 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.7%
C: 27.4%
G: 0.0%
T: 36.1%
none/other: 5.9%
Overview of removed sequences
length count expect max.err error counts
3 9132 35065.0 0 9132
4 2180 8766.3 0 2180
5 692 2191.6 0 692
6 396 547.9 0 396
7 609 137.0 0 609
8 622 34.2 0 622
9 515 34.2 0 515
10 465 34.2 0 465
11 414 34.2 0 414
12 381 34.2 0 381
13 336 34.2 0 336
14 312 34.2 0 312
15 296 34.2 0 296
16 242 34.2 0 242
17 233 34.2 0 233
18 435 34.2 0 435
19 226 34.2 0 226
20 203 34.2 0 203
21 173 34.2 0 173
22 233 34.2 0 233
23 206 34.2 0 206
24 221 34.2 0 221
25 227 34.2 0 227
26 228 34.2 0 228
27 187 34.2 0 187
28 208 34.2 0 208
29 209 34.2 0 209
30 216 34.2 0 216
31 189 34.2 0 189
32 215 34.2 0 215
33 205 34.2 0 205
34 216 34.2 0 216
35 213 34.2 0 213
36 213 34.2 0 213
37 207 34.2 0 207
38 203 34.2 0 203
39 174 34.2 0 174
40 198 34.2 0 198
41 182 34.2 0 182
42 206 34.2 0 206
43 209 34.2 0 209
44 168 34.2 0 168
45 207 34.2 0 207
46 200 34.2 0 200
47 191 34.2 0 191
48 207 34.2 0 207
49 201 34.2 0 201
50 202 34.2 0 202
51 214 34.2 0 214
52 207 34.2 0 207
53 181 34.2 0 181
54 196 34.2 0 196
55 211 34.2 0 211
56 180 34.2 0 180
57 197 34.2 0 197
58 196 34.2 0 196
59 162 34.2 0 162
60 179 34.2 0 179
61 161 34.2 0 161
62 127 34.2 0 127
63 133 34.2 0 133
64 140 34.2 0 140
65 121 34.2 0 121
66 104 34.2 0 104
67 103 34.2 0 103
68 97 34.2 0 97
69 79 34.2 0 79
70 50 34.2 0 50
71 65 34.2 0 65
72 61 34.2 0 61
73 41 34.2 0 41
74 49 34.2 0 49
75 39 34.2 0 39
76 45 34.2 0 45
77 35 34.2 0 35
78 40 34.2 0 40
79 19 34.2 0 19
80 27 34.2 0 27
81 25 34.2 0 25
82 25 34.2 0 25
83 23 34.2 0 23
84 32 34.2 0 32
85 31 34.2 0 31
86 1721 34.2 0 1721
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 44049 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 23.6%
G: 20.3%
T: 20.8%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 32555 35065.0 0 32555
4 7684 8766.3 0 7684
5 1401 2191.6 0 1401
6 165 547.9 0 165
7 14 137.0 0 14
8 21 137.0 0 21
9 24 137.0 0 24
10 23 137.0 0 23
11 16 137.0 0 16
12 27 137.0 0 27
13 29 137.0 0 29
14 37 137.0 0 37
15 18 137.0 0 18
16 21 137.0 0 21
17 32 137.0 0 32
18 21 137.0 0 21
19 33 137.0 0 33
20 22 137.0 0 22
21 24 137.0 0 24
22 36 137.0 0 36
23 17 137.0 0 17
24 15 137.0 0 15
25 40 137.0 0 40
26 42 137.0 0 42
27 23 137.0 0 23
28 31 137.0 0 31
29 31 137.0 0 31
30 14 137.0 0 14
31 21 137.0 0 21
32 43 137.0 0 43
33 24 137.0 0 24
34 10 137.0 0 10
35 18 137.0 0 18
36 24 137.0 0 24
37 31 137.0 0 31
38 22 137.0 0 22
39 27 137.0 0 27
40 27 137.0 0 27
41 31 137.0 0 31
42 26 137.0 0 26
43 33 137.0 0 33
44 23 137.0 0 23
45 17 137.0 0 17
46 30 137.0 0 30
47 37 137.0 0 37
48 26 137.0 0 26
49 28 137.0 0 28
50 25 137.0 0 25
51 28 137.0 0 28
52 34 137.0 0 34
53 19 137.0 0 19
54 34 137.0 0 34
55 31 137.0 0 31
56 18 137.0 0 18
57 9 137.0 0 9
58 28 137.0 0 28
59 26 137.0 0 26
60 22 137.0 0 22
61 20 137.0 0 20
62 21 137.0 0 21
63 20 137.0 0 20
64 22 137.0 0 22
65 23 137.0 0 23
66 28 137.0 0 28
67 24 137.0 0 24
68 19 137.0 0 19
69 44 137.0 0 44
70 39 137.0 0 39
71 44 137.0 0 44
72 27 137.0 0 27
73 24 137.0 0 24
74 22 137.0 0 22
75 29 137.0 0 29
76 25 137.0 0 25
77 166 137.0 0 166
78 59 137.0 0 59
79 19 137.0 0 19
80 28 137.0 0 28
81 19 137.0 0 19
82 23 137.0 0 23
83 35 137.0 0 35
84 11 137.0 0 11
85 28 137.0 0 28
86 42 137.0 0 42
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T59_S151_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T59_S151_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 20.74 s (9 µs/read; 6.38 M reads/minute).
=== Summary ===
Total reads processed: 2,205,475
Reads with adapters: 792,238 (35.9%)
== Read fate breakdown ==
Reads that were too short: 255,769 (11.6%)
Reads written (passing filters): 1,949,706 (88.4%)
Total basepairs processed: 222,752,975 bp
Total written (filtered): 152,699,780 bp (68.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 721449 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.5%
G: 26.3%
T: 27.8%
none/other: 16.4%
Overview of removed sequences
length count expect max.err error counts
3 49591 34460.5 0 49591
4 21783 8615.1 0 21783
5 11336 2153.8 0 11336
6 7954 538.4 0 7954
7 6537 134.6 0 6537
8 5705 33.7 0 5705
9 5718 33.7 0 5718
10 5802 33.7 0 5802
11 5696 33.7 0 5696
12 5554 33.7 0 5554
13 5748 33.7 0 5748
14 5766 33.7 0 5766
15 5861 33.7 0 5861
16 6166 33.7 0 6166
17 5984 33.7 0 5984
18 6185 33.7 0 6185
19 6132 33.7 0 6132
20 5586 33.7 0 5586
21 6205 33.7 0 6205
22 6050 33.7 0 6050
23 5590 33.7 0 5590
24 5594 33.7 0 5594
25 5675 33.7 0 5675
26 5541 33.7 0 5541
27 5661 33.7 0 5661
28 6081 33.7 0 6081
29 5945 33.7 0 5945
30 5824 33.7 0 5824
31 6268 33.7 0 6268
32 6042 33.7 0 6042
33 6298 33.7 0 6298
34 6142 33.7 0 6142
35 6029 33.7 0 6029
36 5906 33.7 0 5906
37 5961 33.7 0 5961
38 5573 33.7 0 5573
39 5982 33.7 0 5982
40 5814 33.7 0 5814
41 5948 33.7 0 5948
42 6225 33.7 0 6225
43 6230 33.7 0 6230
44 5874 33.7 0 5874
45 6142 33.7 0 6142
46 6547 33.7 0 6547
47 6310 33.7 0 6310
48 5990 33.7 0 5990
49 9914 33.7 0 9914
50 11861 33.7 0 11861
51 6680 33.7 0 6680
52 7503 33.7 0 7503
53 7036 33.7 0 7036
54 5973 33.7 0 5973
55 6728 33.7 0 6728
56 6475 33.7 0 6475
57 6280 33.7 0 6280
58 6931 33.7 0 6931
59 6659 33.7 0 6659
60 6605 33.7 0 6605
61 6761 33.7 0 6761
62 6550 33.7 0 6550
63 6585 33.7 0 6585
64 6427 33.7 0 6427
65 6287 33.7 0 6287
66 6095 33.7 0 6095
67 6133 33.7 0 6133
68 6388 33.7 0 6388
69 5969 33.7 0 5969
70 5596 33.7 0 5596
71 6362 33.7 0 6362
72 6384 33.7 0 6384
73 5864 33.7 0 5864
74 5888 33.7 0 5888
75 5900 33.7 0 5900
76 5680 33.7 0 5680
77 6092 33.7 0 6092
78 5916 33.7 0 5916
79 6989 33.7 0 6989
80 6618 33.7 0 6618
81 7665 33.7 0 7665
82 9282 33.7 0 9282
83 10391 33.7 0 10391
84 10863 33.7 0 10863
85 11432 33.7 0 11432
86 118136 33.7 0 118136
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 22603 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.6%
C: 29.6%
G: 0.0%
T: 34.7%
none/other: 4.2%
Overview of removed sequences
length count expect max.err error counts
3 10922 34460.5 0 10922
4 2438 8615.1 0 2438
5 593 2153.8 0 593
6 251 538.4 0 251
7 227 134.6 0 227
8 288 33.7 0 288
9 224 33.7 0 224
10 190 33.7 0 190
11 174 33.7 0 174
12 156 33.7 0 156
13 151 33.7 0 151
14 133 33.7 0 133
15 133 33.7 0 133
16 105 33.7 0 105
17 140 33.7 0 140
18 124 33.7 0 124
19 124 33.7 0 124
20 116 33.7 0 116
21 117 33.7 0 117
22 115 33.7 0 115
23 117 33.7 0 117
24 122 33.7 0 122
25 114 33.7 0 114
26 127 33.7 0 127
27 109 33.7 0 109
28 128 33.7 0 128
29 105 33.7 0 105
30 124 33.7 0 124
31 112 33.7 0 112
32 95 33.7 0 95
33 124 33.7 0 124
34 90 33.7 0 90
35 108 33.7 0 108
36 116 33.7 0 116
37 101 33.7 0 101
38 106 33.7 0 106
39 117 33.7 0 117
40 114 33.7 0 114
41 107 33.7 0 107
42 100 33.7 0 100
43 91 33.7 0 91
44 87 33.7 0 87
45 106 33.7 0 106
46 103 33.7 0 103
47 91 33.7 0 91
48 103 33.7 0 103
49 99 33.7 0 99
50 91 33.7 0 91
51 90 33.7 0 90
52 109 33.7 0 109
53 101 33.7 0 101
54 90 33.7 0 90
55 92 33.7 0 92
56 83 33.7 0 83
57 88 33.7 0 88
58 98 33.7 0 98
59 76 33.7 0 76
60 82 33.7 0 82
61 88 33.7 0 88
62 68 33.7 0 68
63 59 33.7 0 59
64 61 33.7 0 61
65 67 33.7 0 67
66 70 33.7 0 70
67 60 33.7 0 60
68 48 33.7 0 48
69 45 33.7 0 45
70 38 33.7 0 38
71 41 33.7 0 41
72 39 33.7 0 39
73 34 33.7 0 34
74 33 33.7 0 33
75 43 33.7 0 43
76 23 33.7 0 23
77 21 33.7 0 21
78 25 33.7 0 25
79 24 33.7 0 24
80 17 33.7 0 17
81 11 33.7 0 11
82 32 33.7 0 32
83 23 33.7 0 23
84 24 33.7 0 24
85 29 33.7 0 29
86 943 33.7 0 943
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 48186 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 23.2%
G: 22.1%
T: 19.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 36478 34460.5 0 36478
4 7599 8615.1 0 7599
5 1543 2153.8 0 1543
6 204 538.4 0 204
7 19 134.6 0 19
8 29 134.6 0 29
9 32 134.6 0 32
10 29 134.6 0 29
11 25 134.6 0 25
12 22 134.6 0 22
13 29 134.6 0 29
14 25 134.6 0 25
15 27 134.6 0 27
16 18 134.6 0 18
17 25 134.6 0 25
18 31 134.6 0 31
19 28 134.6 0 28
20 21 134.6 0 21
21 26 134.6 0 26
22 29 134.6 0 29
23 29 134.6 0 29
24 18 134.6 0 18
25 29 134.6 0 29
26 30 134.6 0 30
27 25 134.6 0 25
28 30 134.6 0 30
29 22 134.6 0 22
30 28 134.6 0 28
31 33 134.6 0 33
32 45 134.6 0 45
33 31 134.6 0 31
34 30 134.6 0 30
35 24 134.6 0 24
36 25 134.6 0 25
37 32 134.6 0 32
38 28 134.6 0 28
39 42 134.6 0 42
40 32 134.6 0 32
41 31 134.6 0 31
42 30 134.6 0 30
43 29 134.6 0 29
44 27 134.6 0 27
45 23 134.6 0 23
46 17 134.6 0 17
47 33 134.6 0 33
48 23 134.6 0 23
49 28 134.6 0 28
50 36 134.6 0 36
51 34 134.6 0 34
52 33 134.6 0 33
53 21 134.6 0 21
54 26 134.6 0 26
55 26 134.6 0 26
56 25 134.6 0 25
57 36 134.6 0 36
58 31 134.6 0 31
59 24 134.6 0 24
60 29 134.6 0 29
61 24 134.6 0 24
62 41 134.6 0 41
63 24 134.6 0 24
64 31 134.6 0 31
65 34 134.6 0 34
66 30 134.6 0 30
67 29 134.6 0 29
68 29 134.6 0 29
69 33 134.6 0 33
70 32 134.6 0 32
71 59 134.6 0 59
72 19 134.6 0 19
73 28 134.6 0 28
74 18 134.6 0 18
75 14 134.6 0 14
76 21 134.6 0 21
77 97 134.6 0 97
78 39 134.6 0 39
79 27 134.6 0 27
80 24 134.6 0 24
81 28 134.6 0 28
82 36 134.6 0 36
83 26 134.6 0 26
84 24 134.6 0 24
85 46 134.6 0 46
86 39 134.6 0 39
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T59_S151_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T59_S151_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 21.10 s (9 µs/read; 6.36 M reads/minute).
=== Summary ===
Total reads processed: 2,237,957
Reads with adapters: 810,651 (36.2%)
== Read fate breakdown ==
Reads that were too short: 266,026 (11.9%)
Reads written (passing filters): 1,971,931 (88.1%)
Total basepairs processed: 226,033,657 bp
Total written (filtered): 154,295,842 bp (68.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 739113 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.5%
G: 26.1%
T: 27.7%
none/other: 16.8%
Overview of removed sequences
length count expect max.err error counts
3 49455 34968.1 0 49455
4 22182 8742.0 0 22182
5 11475 2185.5 0 11475
6 7870 546.4 0 7870
7 6471 136.6 0 6471
8 5793 34.1 0 5793
9 5729 34.1 0 5729
10 5951 34.1 0 5951
11 5702 34.1 0 5702
12 5724 34.1 0 5724
13 5678 34.1 0 5678
14 5966 34.1 0 5966
15 5968 34.1 0 5968
16 6370 34.1 0 6370
17 6037 34.1 0 6037
18 6390 34.1 0 6390
19 5972 34.1 0 5972
20 5773 34.1 0 5773
21 6380 34.1 0 6380
22 6136 34.1 0 6136
23 5693 34.1 0 5693
24 5544 34.1 0 5544
25 5685 34.1 0 5685
26 5490 34.1 0 5490
27 5535 34.1 0 5535
28 6017 34.1 0 6017
29 5965 34.1 0 5965
30 5918 34.1 0 5918
31 6288 34.1 0 6288
32 6140 34.1 0 6140
33 6459 34.1 0 6459
34 6232 34.1 0 6232
35 6177 34.1 0 6177
36 5998 34.1 0 5998
37 6036 34.1 0 6036
38 5616 34.1 0 5616
39 6166 34.1 0 6166
40 6107 34.1 0 6107
41 6207 34.1 0 6207
42 6261 34.1 0 6261
43 6566 34.1 0 6566
44 5979 34.1 0 5979
45 6247 34.1 0 6247
46 6756 34.1 0 6756
47 6563 34.1 0 6563
48 6193 34.1 0 6193
49 10069 34.1 0 10069
50 12318 34.1 0 12318
51 6778 34.1 0 6778
52 7479 34.1 0 7479
53 7223 34.1 0 7223
54 6190 34.1 0 6190
55 6756 34.1 0 6756
56 6816 34.1 0 6816
57 6391 34.1 0 6391
58 7178 34.1 0 7178
59 6911 34.1 0 6911
60 6724 34.1 0 6724
61 6967 34.1 0 6967
62 6777 34.1 0 6777
63 6679 34.1 0 6679
64 6613 34.1 0 6613
65 6442 34.1 0 6442
66 6180 34.1 0 6180
67 6350 34.1 0 6350
68 6405 34.1 0 6405
69 6167 34.1 0 6167
70 5991 34.1 0 5991
71 6711 34.1 0 6711
72 6674 34.1 0 6674
73 6067 34.1 0 6067
74 6000 34.1 0 6000
75 6236 34.1 0 6236
76 5807 34.1 0 5807
77 6397 34.1 0 6397
78 6220 34.1 0 6220
79 7045 34.1 0 7045
80 6718 34.1 0 6718
81 7849 34.1 0 7849
82 9616 34.1 0 9616
83 10711 34.1 0 10711
84 10999 34.1 0 10999
85 11991 34.1 0 11991
86 123808 34.1 0 123808
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 22947 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.4%
C: 29.9%
G: 0.0%
T: 34.5%
none/other: 4.2%
Overview of removed sequences
length count expect max.err error counts
3 11204 34968.1 0 11204
4 2472 8742.0 0 2472
5 587 2185.5 0 587
6 222 546.4 0 222
7 248 136.6 0 248
8 267 34.1 0 267
9 234 34.1 0 234
10 203 34.1 0 203
11 204 34.1 0 204
12 160 34.1 0 160
13 161 34.1 0 161
14 139 34.1 0 139
15 136 34.1 0 136
16 128 34.1 0 128
17 115 34.1 0 115
18 127 34.1 0 127
19 138 34.1 0 138
20 109 34.1 0 109
21 105 34.1 0 105
22 103 34.1 0 103
23 119 34.1 0 119
24 114 34.1 0 114
25 106 34.1 0 106
26 127 34.1 0 127
27 108 34.1 0 108
28 139 34.1 0 139
29 105 34.1 0 105
30 111 34.1 0 111
31 108 34.1 0 108
32 104 34.1 0 104
33 119 34.1 0 119
34 95 34.1 0 95
35 101 34.1 0 101
36 118 34.1 0 118
37 110 34.1 0 110
38 116 34.1 0 116
39 90 34.1 0 90
40 100 34.1 0 100
41 81 34.1 0 81
42 94 34.1 0 94
43 96 34.1 0 96
44 106 34.1 0 106
45 101 34.1 0 101
46 106 34.1 0 106
47 90 34.1 0 90
48 117 34.1 0 117
49 90 34.1 0 90
50 93 34.1 0 93
51 96 34.1 0 96
52 111 34.1 0 111
53 88 34.1 0 88
54 116 34.1 0 116
55 108 34.1 0 108
56 81 34.1 0 81
57 104 34.1 0 104
58 86 34.1 0 86
59 76 34.1 0 76
60 94 34.1 0 94
61 69 34.1 0 69
62 61 34.1 0 61
63 68 34.1 0 68
64 68 34.1 0 68
65 43 34.1 0 43
66 81 34.1 0 81
67 55 34.1 0 55
68 64 34.1 0 64
69 54 34.1 0 54
70 44 34.1 0 44
71 42 34.1 0 42
72 35 34.1 0 35
73 30 34.1 0 30
74 31 34.1 0 31
75 31 34.1 0 31
76 19 34.1 0 19
77 31 34.1 0 31
78 23 34.1 0 23
79 24 34.1 0 24
80 27 34.1 0 27
81 14 34.1 0 14
82 22 34.1 0 22
83 22 34.1 0 22
84 15 34.1 0 15
85 26 34.1 0 26
86 962 34.1 0 962
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 48591 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 23.5%
G: 22.2%
T: 19.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 36802 34968.1 0 36802
4 7615 8742.0 0 7615
5 1510 2185.5 0 1510
6 212 546.4 0 212
7 24 136.6 0 24
8 30 136.6 0 30
9 15 136.6 0 15
10 40 136.6 0 40
11 25 136.6 0 25
12 44 136.6 0 44
13 36 136.6 0 36
14 26 136.6 0 26
15 22 136.6 0 22
16 24 136.6 0 24
17 33 136.6 0 33
18 35 136.6 0 35
19 37 136.6 0 37
20 27 136.6 0 27
21 35 136.6 0 35
22 28 136.6 0 28
23 27 136.6 0 27
24 31 136.6 0 31
25 40 136.6 0 40
26 23 136.6 0 23
27 16 136.6 0 16
28 40 136.6 0 40
29 25 136.6 0 25
30 30 136.6 0 30
31 19 136.6 0 19
32 24 136.6 0 24
33 37 136.6 0 37
34 35 136.6 0 35
35 27 136.6 0 27
36 30 136.6 0 30
37 24 136.6 0 24
38 30 136.6 0 30
39 33 136.6 0 33
40 31 136.6 0 31
41 33 136.6 0 33
42 31 136.6 0 31
43 23 136.6 0 23
44 20 136.6 0 20
45 15 136.6 0 15
46 27 136.6 0 27
47 38 136.6 0 38
48 21 136.6 0 21
49 23 136.6 0 23
50 28 136.6 0 28
51 25 136.6 0 25
52 26 136.6 0 26
53 26 136.6 0 26
54 39 136.6 0 39
55 19 136.6 0 19
56 14 136.6 0 14
57 28 136.6 0 28
58 38 136.6 0 38
59 39 136.6 0 39
60 31 136.6 0 31
61 39 136.6 0 39
62 29 136.6 0 29
63 42 136.6 0 42
64 19 136.6 0 19
65 53 136.6 0 53
66 30 136.6 0 30
67 32 136.6 0 32
68 25 136.6 0 25
69 26 136.6 0 26
70 28 136.6 0 28
71 33 136.6 0 33
72 24 136.6 0 24
73 32 136.6 0 32
74 36 136.6 0 36
75 26 136.6 0 26
76 19 136.6 0 19
77 113 136.6 0 113
78 49 136.6 0 49
79 28 136.6 0 28
80 29 136.6 0 29
81 30 136.6 0 30
82 26 136.6 0 26
83 33 136.6 0 33
84 38 136.6 0 38
85 30 136.6 0 30
86 36 136.6 0 36
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T60_S149_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T60_S149_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.71 s (9 µs/read; 6.38 M reads/minute).
=== Summary ===
Total reads processed: 2,732,178
Reads with adapters: 946,952 (34.7%)
== Read fate breakdown ==
Reads that were too short: 268,033 (9.8%)
Reads written (passing filters): 2,464,145 (90.2%)
Total basepairs processed: 275,949,978 bp
Total written (filtered): 193,012,578 bp (69.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 832947 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.6%
G: 26.3%
T: 28.5%
none/other: 14.6%
Overview of removed sequences
length count expect max.err error counts
3 64270 42690.3 0 64270
4 28944 10672.6 0 28944
5 14712 2668.1 0 14712
6 9647 667.0 0 9647
7 7441 166.8 0 7441
8 7028 41.7 0 7028
9 6930 41.7 0 6930
10 6879 41.7 0 6879
11 6840 41.7 0 6840
12 6707 41.7 0 6707
13 6928 41.7 0 6928
14 7056 41.7 0 7056
15 7013 41.7 0 7013
16 7255 41.7 0 7255
17 7134 41.7 0 7134
18 7242 41.7 0 7242
19 7041 41.7 0 7041
20 6929 41.7 0 6929
21 7229 41.7 0 7229
22 7434 41.7 0 7434
23 6761 41.7 0 6761
24 7119 41.7 0 7119
25 7088 41.7 0 7088
26 7027 41.7 0 7027
27 6997 41.7 0 6997
28 7314 41.7 0 7314
29 7453 41.7 0 7453
30 7373 41.7 0 7373
31 7547 41.7 0 7547
32 7269 41.7 0 7269
33 7346 41.7 0 7346
34 7363 41.7 0 7363
35 7249 41.7 0 7249
36 7209 41.7 0 7209
37 7394 41.7 0 7394
38 7107 41.7 0 7107
39 7315 41.7 0 7315
40 7355 41.7 0 7355
41 7349 41.7 0 7349
42 7437 41.7 0 7437
43 7448 41.7 0 7448
44 7154 41.7 0 7154
45 7482 41.7 0 7482
46 7557 41.7 0 7557
47 7498 41.7 0 7498
48 7636 41.7 0 7636
49 9230 41.7 0 9230
50 10302 41.7 0 10302
51 8095 41.7 0 8095
52 8129 41.7 0 8129
53 8098 41.7 0 8098
54 7731 41.7 0 7731
55 8024 41.7 0 8024
56 8135 41.7 0 8135
57 8008 41.7 0 8008
58 8311 41.7 0 8311
59 8375 41.7 0 8375
60 8276 41.7 0 8276
61 8285 41.7 0 8285
62 8293 41.7 0 8293
63 8062 41.7 0 8062
64 8196 41.7 0 8196
65 7985 41.7 0 7985
66 7900 41.7 0 7900
67 7869 41.7 0 7869
68 7611 41.7 0 7611
69 7440 41.7 0 7440
70 7127 41.7 0 7127
71 7569 41.7 0 7569
72 7293 41.7 0 7293
73 7064 41.7 0 7064
74 6465 41.7 0 6465
75 6283 41.7 0 6283
76 6272 41.7 0 6272
77 6551 41.7 0 6551
78 5842 41.7 0 5842
79 6515 41.7 0 6515
80 6264 41.7 0 6264
81 6892 41.7 0 6892
82 8399 41.7 0 8399
83 9521 41.7 0 9521
84 9981 41.7 0 9981
85 10474 41.7 0 10474
86 121574 41.7 0 121574
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 57000 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.5%
C: 32.3%
G: 0.0%
T: 39.0%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 12217 42690.3 0 12217
4 3406 10672.6 0 3406
5 1271 2668.1 0 1271
6 850 667.0 0 850
7 831 166.8 0 831
8 889 41.7 0 889
9 856 41.7 0 856
10 741 41.7 0 741
11 756 41.7 0 756
12 788 41.7 0 788
13 727 41.7 0 727
14 664 41.7 0 664
15 638 41.7 0 638
16 653 41.7 0 653
17 663 41.7 0 663
18 653 41.7 0 653
19 626 41.7 0 626
20 618 41.7 0 618
21 604 41.7 0 604
22 577 41.7 0 577
23 576 41.7 0 576
24 645 41.7 0 645
25 612 41.7 0 612
26 656 41.7 0 656
27 610 41.7 0 610
28 593 41.7 0 593
29 566 41.7 0 566
30 573 41.7 0 573
31 580 41.7 0 580
32 572 41.7 0 572
33 632 41.7 0 632
34 605 41.7 0 605
35 630 41.7 0 630
36 567 41.7 0 567
37 584 41.7 0 584
38 535 41.7 0 535
39 591 41.7 0 591
40 535 41.7 0 535
41 573 41.7 0 573
42 560 41.7 0 560
43 592 41.7 0 592
44 552 41.7 0 552
45 579 41.7 0 579
46 574 41.7 0 574
47 597 41.7 0 597
48 575 41.7 0 575
49 561 41.7 0 561
50 541 41.7 0 541
51 519 41.7 0 519
52 538 41.7 0 538
53 487 41.7 0 487
54 517 41.7 0 517
55 481 41.7 0 481
56 542 41.7 0 542
57 480 41.7 0 480
58 517 41.7 0 517
59 508 41.7 0 508
60 423 41.7 0 423
61 464 41.7 0 464
62 390 41.7 0 390
63 418 41.7 0 418
64 362 41.7 0 362
65 342 41.7 0 342
66 301 41.7 0 301
67 301 41.7 0 301
68 262 41.7 0 262
69 244 41.7 0 244
70 219 41.7 0 219
71 207 41.7 0 207
72 185 41.7 0 185
73 168 41.7 0 168
74 142 41.7 0 142
75 106 41.7 0 106
76 98 41.7 0 98
77 82 41.7 0 82
78 77 41.7 0 77
79 63 41.7 0 63
80 65 41.7 0 65
81 50 41.7 0 50
82 46 41.7 0 46
83 48 41.7 0 48
84 59 41.7 0 59
85 54 41.7 0 54
86 1841 41.7 0 1841
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 57005 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 22.1%
G: 21.5%
T: 20.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 42392 42690.3 0 42392
4 9742 10672.6 0 9742
5 1830 2668.1 0 1830
6 189 667.0 0 189
7 43 166.8 0 43
8 42 166.8 0 42
9 36 166.8 0 36
10 39 166.8 0 39
11 38 166.8 0 38
12 35 166.8 0 35
13 40 166.8 0 40
14 36 166.8 0 36
15 29 166.8 0 29
16 39 166.8 0 39
17 39 166.8 0 39
18 37 166.8 0 37
19 58 166.8 0 58
20 45 166.8 0 45
21 25 166.8 0 25
22 43 166.8 0 43
23 33 166.8 0 33
24 32 166.8 0 32
25 66 166.8 0 66
26 35 166.8 0 35
27 36 166.8 0 36
28 27 166.8 0 27
29 44 166.8 0 44
30 32 166.8 0 32
31 39 166.8 0 39
32 33 166.8 0 33
33 43 166.8 0 43
34 34 166.8 0 34
35 34 166.8 0 34
36 29 166.8 0 29
37 30 166.8 0 30
38 35 166.8 0 35
39 34 166.8 0 34
40 22 166.8 0 22
41 44 166.8 0 44
42 29 166.8 0 29
43 32 166.8 0 32
44 35 166.8 0 35
45 38 166.8 0 38
46 39 166.8 0 39
47 51 166.8 0 51
48 38 166.8 0 38
49 30 166.8 0 30
50 42 166.8 0 42
51 51 166.8 0 51
52 29 166.8 0 29
53 25 166.8 0 25
54 36 166.8 0 36
55 29 166.8 0 29
56 28 166.8 0 28
57 36 166.8 0 36
58 31 166.8 0 31
59 31 166.8 0 31
60 34 166.8 0 34
61 29 166.8 0 29
62 23 166.8 0 23
63 19 166.8 0 19
64 34 166.8 0 34
65 40 166.8 0 40
66 27 166.8 0 27
67 30 166.8 0 30
68 31 166.8 0 31
69 29 166.8 0 29
70 36 166.8 0 36
71 51 166.8 0 51
72 17 166.8 0 17
73 29 166.8 0 29
74 48 166.8 0 48
75 28 166.8 0 28
76 35 166.8 0 35
77 77 166.8 0 77
78 37 166.8 0 37
79 31 166.8 0 31
80 29 166.8 0 29
81 38 166.8 0 38
82 17 166.8 0 17
83 29 166.8 0 29
84 46 166.8 0 46
85 35 166.8 0 35
86 37 166.8 0 37
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T60_S149_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T60_S149_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.98 s (9 µs/read; 6.45 M reads/minute).
=== Summary ===
Total reads processed: 2,793,864
Reads with adapters: 976,729 (35.0%)
== Read fate breakdown ==
Reads that were too short: 281,623 (10.1%)
Reads written (passing filters): 2,512,241 (89.9%)
Total basepairs processed: 282,180,264 bp
Total written (filtered): 196,570,529 bp (69.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 859666 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.5%
G: 26.3%
T: 28.1%
none/other: 15.1%
Overview of removed sequences
length count expect max.err error counts
3 65080 43654.1 0 65080
4 29218 10913.5 0 29218
5 14952 2728.4 0 14952
6 9676 682.1 0 9676
7 7629 170.5 0 7629
8 6830 42.6 0 6830
9 6839 42.6 0 6839
10 7036 42.6 0 7036
11 7104 42.6 0 7104
12 6976 42.6 0 6976
13 6890 42.6 0 6890
14 7187 42.6 0 7187
15 7242 42.6 0 7242
16 7265 42.6 0 7265
17 7199 42.6 0 7199
18 7513 42.6 0 7513
19 7114 42.6 0 7114
20 7166 42.6 0 7166
21 7449 42.6 0 7449
22 7410 42.6 0 7410
23 7296 42.6 0 7296
24 7156 42.6 0 7156
25 7271 42.6 0 7271
26 7214 42.6 0 7214
27 7054 42.6 0 7054
28 7504 42.6 0 7504
29 7629 42.6 0 7629
30 7438 42.6 0 7438
31 7833 42.6 0 7833
32 7492 42.6 0 7492
33 7631 42.6 0 7631
34 7363 42.6 0 7363
35 7576 42.6 0 7576
36 7469 42.6 0 7469
37 7423 42.6 0 7423
38 7242 42.6 0 7242
39 7591 42.6 0 7591
40 7357 42.6 0 7357
41 7474 42.6 0 7474
42 7504 42.6 0 7504
43 7621 42.6 0 7621
44 7282 42.6 0 7282
45 7597 42.6 0 7597
46 7719 42.6 0 7719
47 7707 42.6 0 7707
48 7895 42.6 0 7895
49 9560 42.6 0 9560
50 10600 42.6 0 10600
51 8412 42.6 0 8412
52 8446 42.6 0 8446
53 8352 42.6 0 8352
54 7943 42.6 0 7943
55 8564 42.6 0 8564
56 8298 42.6 0 8298
57 8270 42.6 0 8270
58 8640 42.6 0 8640
59 8636 42.6 0 8636
60 8684 42.6 0 8684
61 8762 42.6 0 8762
62 8612 42.6 0 8612
63 8320 42.6 0 8320
64 8558 42.6 0 8558
65 8390 42.6 0 8390
66 8079 42.6 0 8079
67 8237 42.6 0 8237
68 7891 42.6 0 7891
69 7812 42.6 0 7812
70 7463 42.6 0 7463
71 8039 42.6 0 8039
72 7379 42.6 0 7379
73 7055 42.6 0 7055
74 6789 42.6 0 6789
75 6534 42.6 0 6534
76 6389 42.6 0 6389
77 6815 42.6 0 6815
78 6210 42.6 0 6210
79 6890 42.6 0 6890
80 6583 42.6 0 6583
81 6966 42.6 0 6966
82 8401 42.6 0 8401
83 9695 42.6 0 9695
84 10439 42.6 0 10439
85 10756 42.6 0 10756
86 130084 42.6 0 130084
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 58964 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.5%
C: 32.7%
G: 0.0%
T: 38.6%
none/other: 3.3%
Overview of removed sequences
length count expect max.err error counts
3 12502 43654.1 0 12502
4 3459 10913.5 0 3459
5 1280 2728.4 0 1280
6 884 682.1 0 884
7 860 170.5 0 860
8 801 42.6 0 801
9 859 42.6 0 859
10 757 42.6 0 757
11 787 42.6 0 787
12 759 42.6 0 759
13 739 42.6 0 739
14 723 42.6 0 723
15 663 42.6 0 663
16 637 42.6 0 637
17 665 42.6 0 665
18 720 42.6 0 720
19 683 42.6 0 683
20 674 42.6 0 674
21 650 42.6 0 650
22 621 42.6 0 621
23 633 42.6 0 633
24 656 42.6 0 656
25 667 42.6 0 667
26 611 42.6 0 611
27 619 42.6 0 619
28 596 42.6 0 596
29 636 42.6 0 636
30 596 42.6 0 596
31 628 42.6 0 628
32 617 42.6 0 617
33 601 42.6 0 601
34 607 42.6 0 607
35 658 42.6 0 658
36 588 42.6 0 588
37 605 42.6 0 605
38 624 42.6 0 624
39 589 42.6 0 589
40 587 42.6 0 587
41 636 42.6 0 636
42 570 42.6 0 570
43 602 42.6 0 602
44 582 42.6 0 582
45 574 42.6 0 574
46 629 42.6 0 629
47 608 42.6 0 608
48 592 42.6 0 592
49 548 42.6 0 548
50 560 42.6 0 560
51 584 42.6 0 584
52 521 42.6 0 521
53 567 42.6 0 567
54 496 42.6 0 496
55 547 42.6 0 547
56 555 42.6 0 555
57 520 42.6 0 520
58 513 42.6 0 513
59 517 42.6 0 517
60 504 42.6 0 504
61 473 42.6 0 473
62 452 42.6 0 452
63 412 42.6 0 412
64 365 42.6 0 365
65 361 42.6 0 361
66 333 42.6 0 333
67 278 42.6 0 278
68 265 42.6 0 265
69 244 42.6 0 244
70 233 42.6 0 233
71 200 42.6 0 200
72 178 42.6 0 178
73 152 42.6 0 152
74 130 42.6 0 130
75 126 42.6 0 126
76 116 42.6 0 116
77 114 42.6 0 114
78 81 42.6 0 81
79 72 42.6 0 72
80 67 42.6 0 67
81 69 42.6 0 69
82 72 42.6 0 72
83 46 42.6 0 46
84 63 42.6 0 63
85 72 42.6 0 72
86 1924 42.6 0 1924
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 58099 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 22.4%
G: 21.1%
T: 20.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 43121 43654.1 0 43121
4 10140 10913.5 0 10140
5 1733 2728.4 0 1733
6 202 682.1 0 202
7 32 170.5 0 32
8 41 170.5 0 41
9 42 170.5 0 42
10 34 170.5 0 34
11 50 170.5 0 50
12 34 170.5 0 34
13 32 170.5 0 32
14 37 170.5 0 37
15 46 170.5 0 46
16 45 170.5 0 45
17 40 170.5 0 40
18 34 170.5 0 34
19 45 170.5 0 45
20 35 170.5 0 35
21 34 170.5 0 34
22 68 170.5 0 68
23 40 170.5 0 40
24 37 170.5 0 37
25 39 170.5 0 39
26 46 170.5 0 46
27 35 170.5 0 35
28 45 170.5 0 45
29 54 170.5 0 54
30 22 170.5 0 22
31 32 170.5 0 32
32 46 170.5 0 46
33 33 170.5 0 33
34 15 170.5 0 15
35 36 170.5 0 36
36 31 170.5 0 31
37 26 170.5 0 26
38 33 170.5 0 33
39 32 170.5 0 32
40 37 170.5 0 37
41 45 170.5 0 45
42 25 170.5 0 25
43 34 170.5 0 34
44 33 170.5 0 33
45 34 170.5 0 34
46 30 170.5 0 30
47 46 170.5 0 46
48 34 170.5 0 34
49 52 170.5 0 52
50 33 170.5 0 33
51 51 170.5 0 51
52 38 170.5 0 38
53 26 170.5 0 26
54 40 170.5 0 40
55 46 170.5 0 46
56 35 170.5 0 35
57 32 170.5 0 32
58 38 170.5 0 38
59 37 170.5 0 37
60 34 170.5 0 34
61 24 170.5 0 24
62 37 170.5 0 37
63 16 170.5 0 16
64 32 170.5 0 32
65 34 170.5 0 34
66 35 170.5 0 35
67 23 170.5 0 23
68 33 170.5 0 33
69 22 170.5 0 22
70 35 170.5 0 35
71 44 170.5 0 44
72 26 170.5 0 26
73 35 170.5 0 35
74 34 170.5 0 34
75 37 170.5 0 37
76 14 170.5 0 14
77 83 170.5 0 83
78 59 170.5 0 59
79 32 170.5 0 32
80 33 170.5 0 33
81 28 170.5 0 28
82 26 170.5 0 26
83 29 170.5 0 29
84 34 170.5 0 34
85 27 170.5 0 27
86 40 170.5 0 40
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T61_S156_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T61_S156_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 31.03 s (9 µs/read; 6.73 M reads/minute).
=== Summary ===
Total reads processed: 3,481,089
Reads with adapters: 1,327,338 (38.1%)
== Read fate breakdown ==
Reads that were too short: 425,178 (12.2%)
Reads written (passing filters): 3,055,911 (87.8%)
Total basepairs processed: 351,589,989 bp
Total written (filtered): 236,511,373 bp (67.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1189410 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.9%
G: 24.5%
T: 27.7%
none/other: 17.0%
Overview of removed sequences
length count expect max.err error counts
3 77270 54392.0 0 77270
4 36063 13598.0 0 36063
5 18202 3399.5 0 18202
6 12230 849.9 0 12230
7 10071 212.5 0 10071
8 9000 53.1 0 9000
9 9129 53.1 0 9129
10 9137 53.1 0 9137
11 9037 53.1 0 9037
12 8899 53.1 0 8899
13 8956 53.1 0 8956
14 9345 53.1 0 9345
15 9533 53.1 0 9533
16 9527 53.1 0 9527
17 9607 53.1 0 9607
18 9743 53.1 0 9743
19 9373 53.1 0 9373
20 9163 53.1 0 9163
21 9492 53.1 0 9492
22 9891 53.1 0 9891
23 9752 53.1 0 9752
24 9387 53.1 0 9387
25 9639 53.1 0 9639
26 9585 53.1 0 9585
27 9399 53.1 0 9399
28 10390 53.1 0 10390
29 10775 53.1 0 10775
30 9933 53.1 0 9933
31 11017 53.1 0 11017
32 9727 53.1 0 9727
33 9889 53.1 0 9889
34 9861 53.1 0 9861
35 9874 53.1 0 9874
36 9871 53.1 0 9871
37 9693 53.1 0 9693
38 9770 53.1 0 9770
39 9841 53.1 0 9841
40 9529 53.1 0 9529
41 9757 53.1 0 9757
42 10301 53.1 0 10301
43 10178 53.1 0 10178
44 9594 53.1 0 9594
45 10421 53.1 0 10421
46 10632 53.1 0 10632
47 10267 53.1 0 10267
48 10841 53.1 0 10841
49 12614 53.1 0 12614
50 13681 53.1 0 13681
51 11469 53.1 0 11469
52 11528 53.1 0 11528
53 11259 53.1 0 11259
54 10795 53.1 0 10795
55 11758 53.1 0 11758
56 11304 53.1 0 11304
57 11449 53.1 0 11449
58 12552 53.1 0 12552
59 12246 53.1 0 12246
60 12030 53.1 0 12030
61 12424 53.1 0 12424
62 12252 53.1 0 12252
63 12184 53.1 0 12184
64 12390 53.1 0 12390
65 12565 53.1 0 12565
66 11877 53.1 0 11877
67 11821 53.1 0 11821
68 11662 53.1 0 11662
69 11359 53.1 0 11359
70 11202 53.1 0 11202
71 12547 53.1 0 12547
72 11080 53.1 0 11080
73 11313 53.1 0 11313
74 10740 53.1 0 10740
75 9778 53.1 0 9778
76 10201 53.1 0 10201
77 11147 53.1 0 11147
78 9427 53.1 0 9427
79 10505 53.1 0 10505
80 9452 53.1 0 9452
81 10138 53.1 0 10138
82 12125 53.1 0 12125
83 14050 53.1 0 14050
84 14434 53.1 0 14434
85 14949 53.1 0 14949
86 201512 53.1 0 201512
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 69652 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 24.3%
C: 32.9%
G: 0.0%
T: 39.7%
none/other: 3.0%
Overview of removed sequences
length count expect max.err error counts
3 13608 54392.0 0 13608
4 3973 13598.0 0 3973
5 1684 3399.5 0 1684
6 1055 849.9 0 1055
7 976 212.5 0 976
8 1033 53.1 0 1033
9 1044 53.1 0 1044
10 904 53.1 0 904
11 909 53.1 0 909
12 893 53.1 0 893
13 847 53.1 0 847
14 894 53.1 0 894
15 838 53.1 0 838
16 818 53.1 0 818
17 776 53.1 0 776
18 937 53.1 0 937
19 834 53.1 0 834
20 758 53.1 0 758
21 767 53.1 0 767
22 747 53.1 0 747
23 746 53.1 0 746
24 821 53.1 0 821
25 785 53.1 0 785
26 819 53.1 0 819
27 784 53.1 0 784
28 746 53.1 0 746
29 815 53.1 0 815
30 745 53.1 0 745
31 788 53.1 0 788
32 765 53.1 0 765
33 798 53.1 0 798
34 783 53.1 0 783
35 819 53.1 0 819
36 696 53.1 0 696
37 722 53.1 0 722
38 763 53.1 0 763
39 687 53.1 0 687
40 765 53.1 0 765
41 713 53.1 0 713
42 711 53.1 0 711
43 702 53.1 0 702
44 742 53.1 0 742
45 744 53.1 0 744
46 737 53.1 0 737
47 720 53.1 0 720
48 766 53.1 0 766
49 713 53.1 0 713
50 645 53.1 0 645
51 650 53.1 0 650
52 654 53.1 0 654
53 733 53.1 0 733
54 665 53.1 0 665
55 654 53.1 0 654
56 662 53.1 0 662
57 615 53.1 0 615
58 639 53.1 0 639
59 635 53.1 0 635
60 609 53.1 0 609
61 527 53.1 0 527
62 510 53.1 0 510
63 549 53.1 0 549
64 473 53.1 0 473
65 455 53.1 0 455
66 423 53.1 0 423
67 338 53.1 0 338
68 301 53.1 0 301
69 306 53.1 0 306
70 262 53.1 0 262
71 219 53.1 0 219
72 185 53.1 0 185
73 182 53.1 0 182
74 140 53.1 0 140
75 117 53.1 0 117
76 99 53.1 0 99
77 101 53.1 0 101
78 55 53.1 0 55
79 49 53.1 0 49
80 60 53.1 0 60
81 65 53.1 0 65
82 81 53.1 0 81
83 68 53.1 0 68
84 60 53.1 0 60
85 74 53.1 0 74
86 2102 53.1 0 2102
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 68276 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 23.5%
G: 20.1%
T: 20.4%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51028 54392.0 0 51028
4 11903 13598.0 0 11903
5 2054 3399.5 0 2054
6 228 849.9 0 228
7 38 212.5 0 38
8 43 212.5 0 43
9 37 212.5 0 37
10 33 212.5 0 33
11 32 212.5 0 32
12 26 212.5 0 26
13 43 212.5 0 43
14 41 212.5 0 41
15 35 212.5 0 35
16 41 212.5 0 41
17 39 212.5 0 39
18 35 212.5 0 35
19 59 212.5 0 59
20 34 212.5 0 34
21 34 212.5 0 34
22 43 212.5 0 43
23 40 212.5 0 40
24 39 212.5 0 39
25 56 212.5 0 56
26 46 212.5 0 46
27 35 212.5 0 35
28 53 212.5 0 53
29 52 212.5 0 52
30 32 212.5 0 32
31 33 212.5 0 33
32 44 212.5 0 44
33 36 212.5 0 36
34 43 212.5 0 43
35 26 212.5 0 26
36 33 212.5 0 33
37 43 212.5 0 43
38 36 212.5 0 36
39 32 212.5 0 32
40 29 212.5 0 29
41 39 212.5 0 39
42 29 212.5 0 29
43 46 212.5 0 46
44 35 212.5 0 35
45 46 212.5 0 46
46 25 212.5 0 25
47 39 212.5 0 39
48 36 212.5 0 36
49 34 212.5 0 34
50 32 212.5 0 32
51 45 212.5 0 45
52 35 212.5 0 35
53 24 212.5 0 24
54 31 212.5 0 31
55 34 212.5 0 34
56 27 212.5 0 27
57 22 212.5 0 22
58 29 212.5 0 29
59 42 212.5 0 42
60 26 212.5 0 26
61 32 212.5 0 32
62 45 212.5 0 45
63 23 212.5 0 23
64 30 212.5 0 30
65 36 212.5 0 36
66 28 212.5 0 28
67 34 212.5 0 34
68 23 212.5 0 23
69 31 212.5 0 31
70 29 212.5 0 29
71 43 212.5 0 43
72 25 212.5 0 25
73 38 212.5 0 38
74 38 212.5 0 38
75 31 212.5 0 31
76 23 212.5 0 23
77 153 212.5 0 153
78 97 212.5 0 97
79 58 212.5 0 58
80 34 212.5 0 34
81 35 212.5 0 35
82 19 212.5 0 19
83 40 212.5 0 40
84 42 212.5 0 42
85 35 212.5 0 35
86 44 212.5 0 44
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T61_S156_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T61_S156_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 37.13 s (10 µs/read; 5.74 M reads/minute).
=== Summary ===
Total reads processed: 3,552,753
Reads with adapters: 1,371,355 (38.6%)
== Read fate breakdown ==
Reads that were too short: 445,844 (12.5%)
Reads written (passing filters): 3,106,909 (87.5%)
Total basepairs processed: 358,828,053 bp
Total written (filtered): 240,049,219 bp (66.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1229104 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.8%
G: 24.3%
T: 27.5%
none/other: 17.3%
Overview of removed sequences
length count expect max.err error counts
3 78785 55511.8 0 78785
4 36001 13877.9 0 36001
5 18286 3469.5 0 18286
6 12292 867.4 0 12292
7 10039 216.8 0 10039
8 9129 54.2 0 9129
9 9173 54.2 0 9173
10 9522 54.2 0 9522
11 8865 54.2 0 8865
12 9123 54.2 0 9123
13 9028 54.2 0 9028
14 9466 54.2 0 9466
15 9723 54.2 0 9723
16 9708 54.2 0 9708
17 9563 54.2 0 9563
18 10110 54.2 0 10110
19 9806 54.2 0 9806
20 9463 54.2 0 9463
21 9821 54.2 0 9821
22 10013 54.2 0 10013
23 10026 54.2 0 10026
24 9633 54.2 0 9633
25 9858 54.2 0 9858
26 9977 54.2 0 9977
27 9656 54.2 0 9656
28 10476 54.2 0 10476
29 11236 54.2 0 11236
30 9921 54.2 0 9921
31 11296 54.2 0 11296
32 10028 54.2 0 10028
33 10065 54.2 0 10065
34 10094 54.2 0 10094
35 10205 54.2 0 10205
36 10339 54.2 0 10339
37 9967 54.2 0 9967
38 9797 54.2 0 9797
39 10183 54.2 0 10183
40 10204 54.2 0 10204
41 10081 54.2 0 10081
42 10419 54.2 0 10419
43 10544 54.2 0 10544
44 10157 54.2 0 10157
45 10689 54.2 0 10689
46 10823 54.2 0 10823
47 10377 54.2 0 10377
48 10884 54.2 0 10884
49 12966 54.2 0 12966
50 14239 54.2 0 14239
51 11940 54.2 0 11940
52 11564 54.2 0 11564
53 11466 54.2 0 11466
54 11373 54.2 0 11373
55 12118 54.2 0 12118
56 11820 54.2 0 11820
57 11888 54.2 0 11888
58 12763 54.2 0 12763
59 12427 54.2 0 12427
60 12630 54.2 0 12630
61 13093 54.2 0 13093
62 12846 54.2 0 12846
63 12455 54.2 0 12455
64 12896 54.2 0 12896
65 13093 54.2 0 13093
66 12680 54.2 0 12680
67 12564 54.2 0 12564
68 12317 54.2 0 12317
69 11895 54.2 0 11895
70 11916 54.2 0 11916
71 13003 54.2 0 13003
72 11584 54.2 0 11584
73 11616 54.2 0 11616
74 11388 54.2 0 11388
75 10441 54.2 0 10441
76 10644 54.2 0 10644
77 11815 54.2 0 11815
78 9673 54.2 0 9673
79 10978 54.2 0 10978
80 9679 54.2 0 9679
81 10445 54.2 0 10445
82 12488 54.2 0 12488
83 14700 54.2 0 14700
84 14917 54.2 0 14917
85 15490 54.2 0 15490
86 212443 54.2 0 212443
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 72934 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 24.2%
C: 33.0%
G: 0.0%
T: 40.0%
none/other: 2.8%
Overview of removed sequences
length count expect max.err error counts
3 14115 55511.8 0 14115
4 4144 13877.9 0 4144
5 1667 3469.5 0 1667
6 1057 867.4 0 1057
7 1025 216.8 0 1025
8 1038 54.2 0 1038
9 1021 54.2 0 1021
10 1030 54.2 0 1030
11 961 54.2 0 961
12 949 54.2 0 949
13 945 54.2 0 945
14 925 54.2 0 925
15 924 54.2 0 924
16 910 54.2 0 910
17 882 54.2 0 882
18 995 54.2 0 995
19 932 54.2 0 932
20 804 54.2 0 804
21 852 54.2 0 852
22 793 54.2 0 793
23 838 54.2 0 838
24 888 54.2 0 888
25 850 54.2 0 850
26 875 54.2 0 875
27 805 54.2 0 805
28 795 54.2 0 795
29 772 54.2 0 772
30 850 54.2 0 850
31 777 54.2 0 777
32 780 54.2 0 780
33 818 54.2 0 818
34 826 54.2 0 826
35 772 54.2 0 772
36 782 54.2 0 782
37 747 54.2 0 747
38 776 54.2 0 776
39 745 54.2 0 745
40 765 54.2 0 765
41 692 54.2 0 692
42 794 54.2 0 794
43 767 54.2 0 767
44 740 54.2 0 740
45 806 54.2 0 806
46 715 54.2 0 715
47 798 54.2 0 798
48 754 54.2 0 754
49 798 54.2 0 798
50 718 54.2 0 718
51 715 54.2 0 715
52 696 54.2 0 696
53 744 54.2 0 744
54 698 54.2 0 698
55 711 54.2 0 711
56 667 54.2 0 667
57 678 54.2 0 678
58 674 54.2 0 674
59 648 54.2 0 648
60 646 54.2 0 646
61 581 54.2 0 581
62 553 54.2 0 553
63 510 54.2 0 510
64 490 54.2 0 490
65 507 54.2 0 507
66 435 54.2 0 435
67 419 54.2 0 419
68 371 54.2 0 371
69 276 54.2 0 276
70 253 54.2 0 253
71 217 54.2 0 217
72 175 54.2 0 175
73 187 54.2 0 187
74 162 54.2 0 162
75 133 54.2 0 133
76 101 54.2 0 101
77 92 54.2 0 92
78 82 54.2 0 82
79 67 54.2 0 67
80 47 54.2 0 47
81 39 54.2 0 39
82 59 54.2 0 59
83 71 54.2 0 71
84 64 54.2 0 64
85 82 54.2 0 82
86 2072 54.2 0 2072
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69317 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.1%
C: 23.6%
G: 20.0%
T: 20.3%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51779 55511.8 0 51779
4 12031 13877.9 0 12031
5 2105 3469.5 0 2105
6 222 867.4 0 222
7 37 216.8 0 37
8 34 216.8 0 34
9 19 216.8 0 19
10 42 216.8 0 42
11 48 216.8 0 48
12 37 216.8 0 37
13 48 216.8 0 48
14 40 216.8 0 40
15 41 216.8 0 41
16 46 216.8 0 46
17 43 216.8 0 43
18 51 216.8 0 51
19 72 216.8 0 72
20 40 216.8 0 40
21 33 216.8 0 33
22 50 216.8 0 50
23 34 216.8 0 34
24 21 216.8 0 21
25 64 216.8 0 64
26 45 216.8 0 45
27 44 216.8 0 44
28 36 216.8 0 36
29 57 216.8 0 57
30 32 216.8 0 32
31 38 216.8 0 38
32 50 216.8 0 50
33 38 216.8 0 38
34 22 216.8 0 22
35 37 216.8 0 37
36 27 216.8 0 27
37 26 216.8 0 26
38 29 216.8 0 29
39 39 216.8 0 39
40 25 216.8 0 25
41 48 216.8 0 48
42 30 216.8 0 30
43 42 216.8 0 42
44 38 216.8 0 38
45 41 216.8 0 41
46 34 216.8 0 34
47 45 216.8 0 45
48 38 216.8 0 38
49 46 216.8 0 46
50 37 216.8 0 37
51 50 216.8 0 50
52 43 216.8 0 43
53 26 216.8 0 26
54 32 216.8 0 32
55 44 216.8 0 44
56 26 216.8 0 26
57 46 216.8 0 46
58 26 216.8 0 26
59 26 216.8 0 26
60 25 216.8 0 25
61 50 216.8 0 50
62 38 216.8 0 38
63 20 216.8 0 20
64 32 216.8 0 32
65 44 216.8 0 44
66 29 216.8 0 29
67 32 216.8 0 32
68 21 216.8 0 21
69 28 216.8 0 28
70 41 216.8 0 41
71 39 216.8 0 39
72 31 216.8 0 31
73 32 216.8 0 32
74 41 216.8 0 41
75 32 216.8 0 32
76 26 216.8 0 26
77 172 216.8 0 172
78 107 216.8 0 107
79 50 216.8 0 50
80 27 216.8 0 27
81 36 216.8 0 36
82 26 216.8 0 26
83 39 216.8 0 39
84 38 216.8 0 38
85 28 216.8 0 28
86 33 216.8 0 33
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T62_S148_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T62_S148_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 16.76 s (8 µs/read; 7.70 M reads/minute).
=== Summary ===
Total reads processed: 2,151,807
Reads with adapters: 435,061 (20.2%)
== Read fate breakdown ==
Reads that were too short: 161,546 (7.5%)
Reads written (passing filters): 1,990,261 (92.5%)
Total basepairs processed: 217,332,507 bp
Total written (filtered): 165,963,063 bp (76.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 355920 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 21.7%
G: 21.3%
T: 24.3%
none/other: 32.7%
Overview of removed sequences
length count expect max.err error counts
3 51482 33622.0 0 51482
4 20539 8405.5 0 20539
5 8235 2101.4 0 8235
6 3896 525.3 0 3896
7 2396 131.3 0 2396
8 1859 32.8 0 1859
9 1790 32.8 0 1790
10 1814 32.8 0 1814
11 1770 32.8 0 1770
12 1918 32.8 0 1918
13 1840 32.8 0 1840
14 1864 32.8 0 1864
15 1877 32.8 0 1877
16 1783 32.8 0 1783
17 1891 32.8 0 1891
18 1968 32.8 0 1968
19 1943 32.8 0 1943
20 1901 32.8 0 1901
21 1991 32.8 0 1991
22 1886 32.8 0 1886
23 1971 32.8 0 1971
24 1881 32.8 0 1881
25 1842 32.8 0 1842
26 1933 32.8 0 1933
27 1822 32.8 0 1822
28 1965 32.8 0 1965
29 2027 32.8 0 2027
30 1779 32.8 0 1779
31 1739 32.8 0 1739
32 1693 32.8 0 1693
33 1688 32.8 0 1688
34 1728 32.8 0 1728
35 1588 32.8 0 1588
36 1748 32.8 0 1748
37 1609 32.8 0 1609
38 1583 32.8 0 1583
39 1594 32.8 0 1594
40 1652 32.8 0 1652
41 1648 32.8 0 1648
42 1704 32.8 0 1704
43 1736 32.8 0 1736
44 1717 32.8 0 1717
45 1865 32.8 0 1865
46 1828 32.8 0 1828
47 1785 32.8 0 1785
48 1736 32.8 0 1736
49 1957 32.8 0 1957
50 1888 32.8 0 1888
51 1983 32.8 0 1983
52 1949 32.8 0 1949
53 2000 32.8 0 2000
54 2000 32.8 0 2000
55 2134 32.8 0 2134
56 1998 32.8 0 1998
57 2010 32.8 0 2010
58 2236 32.8 0 2236
59 2138 32.8 0 2138
60 2261 32.8 0 2261
61 2240 32.8 0 2240
62 2186 32.8 0 2186
63 2784 32.8 0 2784
64 2351 32.8 0 2351
65 2105 32.8 0 2105
66 2152 32.8 0 2152
67 2124 32.8 0 2124
68 2158 32.8 0 2158
69 2007 32.8 0 2007
70 2092 32.8 0 2092
71 2478 32.8 0 2478
72 2040 32.8 0 2040
73 2146 32.8 0 2146
74 2027 32.8 0 2027
75 2016 32.8 0 2016
76 2043 32.8 0 2043
77 2360 32.8 0 2360
78 1790 32.8 0 1790
79 2094 32.8 0 2094
80 1708 32.8 0 1708
81 1897 32.8 0 1897
82 2295 32.8 0 2295
83 2403 32.8 0 2403
84 2432 32.8 0 2432
85 2565 32.8 0 2565
86 116369 32.8 0 116369
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29924 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 33.5%
C: 22.2%
G: 0.0%
T: 35.3%
none/other: 9.1%
Overview of removed sequences
length count expect max.err error counts
3 10343 33622.0 0 10343
4 2617 8405.5 0 2617
5 789 2101.4 0 789
6 388 525.3 0 388
7 560 131.3 0 560
8 577 32.8 0 577
9 496 32.8 0 496
10 408 32.8 0 408
11 385 32.8 0 385
12 328 32.8 0 328
13 320 32.8 0 320
14 337 32.8 0 337
15 255 32.8 0 255
16 226 32.8 0 226
17 224 32.8 0 224
18 616 32.8 0 616
19 255 32.8 0 255
20 211 32.8 0 211
21 214 32.8 0 214
22 218 32.8 0 218
23 190 32.8 0 190
24 207 32.8 0 207
25 172 32.8 0 172
26 205 32.8 0 205
27 195 32.8 0 195
28 185 32.8 0 185
29 173 32.8 0 173
30 173 32.8 0 173
31 180 32.8 0 180
32 186 32.8 0 186
33 173 32.8 0 173
34 189 32.8 0 189
35 189 32.8 0 189
36 172 32.8 0 172
37 133 32.8 0 133
38 149 32.8 0 149
39 153 32.8 0 153
40 156 32.8 0 156
41 166 32.8 0 166
42 137 32.8 0 137
43 161 32.8 0 161
44 132 32.8 0 132
45 132 32.8 0 132
46 144 32.8 0 144
47 137 32.8 0 137
48 138 32.8 0 138
49 153 32.8 0 153
50 146 32.8 0 146
51 117 32.8 0 117
52 133 32.8 0 133
53 133 32.8 0 133
54 144 32.8 0 144
55 151 32.8 0 151
56 164 32.8 0 164
57 123 32.8 0 123
58 132 32.8 0 132
59 125 32.8 0 125
60 117 32.8 0 117
61 105 32.8 0 105
62 103 32.8 0 103
63 94 32.8 0 94
64 97 32.8 0 97
65 105 32.8 0 105
66 82 32.8 0 82
67 74 32.8 0 74
68 81 32.8 0 81
69 74 32.8 0 74
70 68 32.8 0 68
71 48 32.8 0 48
72 35 32.8 0 35
73 52 32.8 0 52
74 42 32.8 0 42
75 21 32.8 0 21
76 46 32.8 0 46
77 22 32.8 0 22
78 42 32.8 0 42
79 37 32.8 0 37
80 34 32.8 0 34
81 29 32.8 0 29
82 29 32.8 0 29
83 34 32.8 0 34
84 70 32.8 0 70
85 45 32.8 0 45
86 2723 32.8 0 2723
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 49217 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 33.7%
C: 23.9%
G: 20.0%
T: 22.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 35420 33622.0 0 35420
4 9368 8405.5 0 9368
5 1501 2101.4 0 1501
6 182 525.3 0 182
7 24 131.3 0 24
8 28 131.3 0 28
9 27 131.3 0 27
10 32 131.3 0 32
11 40 131.3 0 40
12 13 131.3 0 13
13 29 131.3 0 29
14 25 131.3 0 25
15 24 131.3 0 24
16 19 131.3 0 19
17 40 131.3 0 40
18 29 131.3 0 29
19 21 131.3 0 21
20 22 131.3 0 22
21 17 131.3 0 17
22 15 131.3 0 15
23 21 131.3 0 21
24 16 131.3 0 16
25 22 131.3 0 22
26 28 131.3 0 28
27 26 131.3 0 26
28 28 131.3 0 28
29 37 131.3 0 37
30 34 131.3 0 34
31 33 131.3 0 33
32 68 131.3 0 68
33 32 131.3 0 32
34 31 131.3 0 31
35 15 131.3 0 15
36 23 131.3 0 23
37 29 131.3 0 29
38 26 131.3 0 26
39 23 131.3 0 23
40 44 131.3 0 44
41 55 131.3 0 55
42 38 131.3 0 38
43 28 131.3 0 28
44 48 131.3 0 48
45 53 131.3 0 53
46 37 131.3 0 37
47 34 131.3 0 34
48 40 131.3 0 40
49 39 131.3 0 39
50 31 131.3 0 31
51 39 131.3 0 39
52 25 131.3 0 25
53 39 131.3 0 39
54 19 131.3 0 19
55 43 131.3 0 43
56 25 131.3 0 25
57 20 131.3 0 20
58 24 131.3 0 24
59 30 131.3 0 30
60 31 131.3 0 31
61 40 131.3 0 40
62 34 131.3 0 34
63 25 131.3 0 25
64 32 131.3 0 32
65 42 131.3 0 42
66 38 131.3 0 38
67 28 131.3 0 28
68 17 131.3 0 17
69 37 131.3 0 37
70 53 131.3 0 53
71 33 131.3 0 33
72 45 131.3 0 45
73 66 131.3 0 66
74 39 131.3 0 39
75 20 131.3 0 20
76 43 131.3 0 43
77 165 131.3 0 165
78 50 131.3 0 50
79 38 131.3 0 38
80 39 131.3 0 39
81 30 131.3 0 30
82 25 131.3 0 25
83 42 131.3 0 42
84 24 131.3 0 24
85 50 131.3 0 50
86 52 131.3 0 52
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: T62_S148_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/T62_S148_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 20.81 s (9 µs/read; 6.38 M reads/minute).
=== Summary ===
Total reads processed: 2,213,907
Reads with adapters: 452,918 (20.5%)
== Read fate breakdown ==
Reads that were too short: 171,116 (7.7%)
Reads written (passing filters): 2,042,791 (92.3%)
Total basepairs processed: 223,604,607 bp
Total written (filtered): 170,307,742 bp (76.2%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 371241 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 21.4%
G: 21.1%
T: 23.9%
none/other: 33.5%
Overview of removed sequences
length count expect max.err error counts
3 53233 34592.3 0 53233
4 21116 8648.1 0 21116
5 8608 2162.0 0 8608
6 3937 540.5 0 3937
7 2590 135.1 0 2590
8 1956 33.8 0 1956
9 1827 33.8 0 1827
10 1826 33.8 0 1826
11 1875 33.8 0 1875
12 1846 33.8 0 1846
13 1843 33.8 0 1843
14 1950 33.8 0 1950
15 1932 33.8 0 1932
16 1896 33.8 0 1896
17 2012 33.8 0 2012
18 1859 33.8 0 1859
19 1947 33.8 0 1947
20 1911 33.8 0 1911
21 1931 33.8 0 1931
22 1806 33.8 0 1806
23 1893 33.8 0 1893
24 1959 33.8 0 1959
25 1929 33.8 0 1929
26 1931 33.8 0 1931
27 1901 33.8 0 1901
28 1955 33.8 0 1955
29 2070 33.8 0 2070
30 1777 33.8 0 1777
31 1835 33.8 0 1835
32 1654 33.8 0 1654
33 1731 33.8 0 1731
34 1690 33.8 0 1690
35 1739 33.8 0 1739
36 1762 33.8 0 1762
37 1640 33.8 0 1640
38 1653 33.8 0 1653
39 1770 33.8 0 1770
40 1690 33.8 0 1690
41 1639 33.8 0 1639
42 1810 33.8 0 1810
43 1785 33.8 0 1785
44 1679 33.8 0 1679
45 2081 33.8 0 2081
46 1821 33.8 0 1821
47 1917 33.8 0 1917
48 1891 33.8 0 1891
49 2126 33.8 0 2126
50 2074 33.8 0 2074
51 2176 33.8 0 2176
52 2027 33.8 0 2027
53 2050 33.8 0 2050
54 2138 33.8 0 2138
55 2176 33.8 0 2176
56 1971 33.8 0 1971
57 2094 33.8 0 2094
58 2127 33.8 0 2127
59 2125 33.8 0 2125
60 2342 33.8 0 2342
61 2383 33.8 0 2383
62 2272 33.8 0 2272
63 2885 33.8 0 2885
64 2352 33.8 0 2352
65 2339 33.8 0 2339
66 2230 33.8 0 2230
67 2280 33.8 0 2280
68 2110 33.8 0 2110
69 2013 33.8 0 2013
70 2125 33.8 0 2125
71 2480 33.8 0 2480
72 2107 33.8 0 2107
73 2243 33.8 0 2243
74 2290 33.8 0 2290
75 2140 33.8 0 2140
76 2123 33.8 0 2123
77 2386 33.8 0 2386
78 1831 33.8 0 1831
79 2048 33.8 0 2048
80 1752 33.8 0 1752
81 2112 33.8 0 2112
82 2323 33.8 0 2323
83 2384 33.8 0 2384
84 2475 33.8 0 2475
85 2621 33.8 0 2621
86 124408 33.8 0 124408
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 31056 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 33.6%
C: 22.3%
G: 0.0%
T: 34.7%
none/other: 9.5%
Overview of removed sequences
length count expect max.err error counts
3 10647 34592.3 0 10647
4 2604 8648.1 0 2604
5 791 2162.0 0 791
6 362 540.5 0 362
7 591 135.1 0 591
8 605 33.8 0 605
9 535 33.8 0 535
10 467 33.8 0 467
11 422 33.8 0 422
12 334 33.8 0 334
13 374 33.8 0 374
14 357 33.8 0 357
15 266 33.8 0 266
16 227 33.8 0 227
17 279 33.8 0 279
18 597 33.8 0 597
19 241 33.8 0 241
20 218 33.8 0 218
21 219 33.8 0 219
22 206 33.8 0 206
23 171 33.8 0 171
24 184 33.8 0 184
25 198 33.8 0 198
26 214 33.8 0 214
27 167 33.8 0 167
28 222 33.8 0 222
29 196 33.8 0 196
30 184 33.8 0 184
31 200 33.8 0 200
32 208 33.8 0 208
33 202 33.8 0 202
34 199 33.8 0 199
35 170 33.8 0 170
36 203 33.8 0 203
37 179 33.8 0 179
38 184 33.8 0 184
39 189 33.8 0 189
40 157 33.8 0 157
41 162 33.8 0 162
42 177 33.8 0 177
43 167 33.8 0 167
44 142 33.8 0 142
45 147 33.8 0 147
46 143 33.8 0 143
47 142 33.8 0 142
48 143 33.8 0 143
49 139 33.8 0 139
50 137 33.8 0 137
51 143 33.8 0 143
52 133 33.8 0 133
53 152 33.8 0 152
54 126 33.8 0 126
55 142 33.8 0 142
56 139 33.8 0 139
57 129 33.8 0 129
58 120 33.8 0 120
59 127 33.8 0 127
60 107 33.8 0 107
61 126 33.8 0 126
62 136 33.8 0 136
63 99 33.8 0 99
64 80 33.8 0 80
65 89 33.8 0 89
66 85 33.8 0 85
67 86 33.8 0 86
68 56 33.8 0 56
69 65 33.8 0 65
70 65 33.8 0 65
71 50 33.8 0 50
72 48 33.8 0 48
73 49 33.8 0 49
74 40 33.8 0 40
75 42 33.8 0 42
76 28 33.8 0 28
77 28 33.8 0 28
78 41 33.8 0 41
79 30 33.8 0 30
80 39 33.8 0 39
81 34 33.8 0 34
82 40 33.8 0 40
83 41 33.8 0 41
84 79 33.8 0 79
85 45 33.8 0 45
86 2949 33.8 0 2949
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 50621 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 33.4%
C: 23.7%
G: 20.4%
T: 22.4%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 36395 34592.3 0 36395
4 9540 8648.1 0 9540
5 1544 2162.0 0 1544
6 200 540.5 0 200
7 50 135.1 0 50
8 24 135.1 0 24
9 35 135.1 0 35
10 20 135.1 0 20
11 26 135.1 0 26
12 18 135.1 0 18
13 30 135.1 0 30
14 24 135.1 0 24
15 29 135.1 0 29
16 27 135.1 0 27
17 30 135.1 0 30
18 15 135.1 0 15
19 33 135.1 0 33
20 27 135.1 0 27
21 20 135.1 0 20
22 16 135.1 0 16
23 20 135.1 0 20
24 30 135.1 0 30
25 25 135.1 0 25
26 42 135.1 0 42
27 23 135.1 0 23
28 40 135.1 0 40
29 52 135.1 0 52
30 22 135.1 0 22
31 34 135.1 0 34
32 70 135.1 0 70
33 37 135.1 0 37
34 30 135.1 0 30
35 21 135.1 0 21
36 33 135.1 0 33
37 38 135.1 0 38
38 27 135.1 0 27
39 30 135.1 0 30
40 43 135.1 0 43
41 50 135.1 0 50
42 60 135.1 0 60
43 31 135.1 0 31
44 44 135.1 0 44
45 56 135.1 0 56
46 31 135.1 0 31
47 33 135.1 0 33
48 37 135.1 0 37
49 32 135.1 0 32
50 27 135.1 0 27
51 38 135.1 0 38
52 38 135.1 0 38
53 27 135.1 0 27
54 26 135.1 0 26
55 33 135.1 0 33
56 20 135.1 0 20
57 17 135.1 0 17
58 24 135.1 0 24
59 32 135.1 0 32
60 37 135.1 0 37
61 39 135.1 0 39
62 35 135.1 0 35
63 20 135.1 0 20
64 31 135.1 0 31
65 43 135.1 0 43
66 30 135.1 0 30
67 35 135.1 0 35
68 34 135.1 0 34
69 52 135.1 0 52
70 54 135.1 0 54
71 30 135.1 0 30
72 55 135.1 0 55
73 63 135.1 0 63
74 45 135.1 0 45
75 23 135.1 0 23
76 51 135.1 0 51
77 164 135.1 0 164
78 49 135.1 0 49
79 37 135.1 0 37
80 50 135.1 0 50
81 50 135.1 0 50
82 37 135.1 0 37
83 40 135.1 0 40
84 36 135.1 0 36
85 46 135.1 0 46
86 59 135.1 0 59
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X41_S183_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X41_S183_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.34 s (9 µs/read; 6.46 M reads/minute).
=== Summary ===
Total reads processed: 2,835,284
Reads with adapters: 1,038,256 (36.6%)
== Read fate breakdown ==
Reads that were too short: 321,704 (11.3%)
Reads written (passing filters): 2,513,580 (88.7%)
Total basepairs processed: 286,363,684 bp
Total written (filtered): 196,148,137 bp (68.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 942033 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.0%
G: 26.2%
T: 29.7%
none/other: 15.1%
Overview of removed sequences
length count expect max.err error counts
3 64169 44301.3 0 64169
4 28373 11075.3 0 28373
5 15318 2768.8 0 15318
6 10579 692.2 0 10579
7 8917 173.1 0 8917
8 7944 43.3 0 7944
9 7935 43.3 0 7935
10 7851 43.3 0 7851
11 7995 43.3 0 7995
12 8104 43.3 0 8104
13 7828 43.3 0 7828
14 7999 43.3 0 7999
15 8096 43.3 0 8096
16 8368 43.3 0 8368
17 8069 43.3 0 8069
18 8130 43.3 0 8130
19 8386 43.3 0 8386
20 8271 43.3 0 8271
21 8232 43.3 0 8232
22 8100 43.3 0 8100
23 7899 43.3 0 7899
24 7920 43.3 0 7920
25 7659 43.3 0 7659
26 7909 43.3 0 7909
27 8058 43.3 0 8058
28 7764 43.3 0 7764
29 7952 43.3 0 7952
30 8145 43.3 0 8145
31 8513 43.3 0 8513
32 8078 43.3 0 8078
33 8666 43.3 0 8666
34 8512 43.3 0 8512
35 7932 43.3 0 7932
36 8185 43.3 0 8185
37 8817 43.3 0 8817
38 7723 43.3 0 7723
39 8228 43.3 0 8228
40 8426 43.3 0 8426
41 8236 43.3 0 8236
42 8446 43.3 0 8446
43 8738 43.3 0 8738
44 8297 43.3 0 8297
45 8207 43.3 0 8207
46 8489 43.3 0 8489
47 8491 43.3 0 8491
48 8194 43.3 0 8194
49 10577 43.3 0 10577
50 12233 43.3 0 12233
51 8433 43.3 0 8433
52 9028 43.3 0 9028
53 8663 43.3 0 8663
54 8107 43.3 0 8107
55 8812 43.3 0 8812
56 8603 43.3 0 8603
57 8459 43.3 0 8459
58 9021 43.3 0 9021
59 8787 43.3 0 8787
60 8775 43.3 0 8775
61 9111 43.3 0 9111
62 8815 43.3 0 8815
63 8577 43.3 0 8577
64 8346 43.3 0 8346
65 8354 43.3 0 8354
66 8221 43.3 0 8221
67 7644 43.3 0 7644
68 8061 43.3 0 8061
69 7449 43.3 0 7449
70 7240 43.3 0 7240
71 7286 43.3 0 7286
72 7491 43.3 0 7491
73 6903 43.3 0 6903
74 6674 43.3 0 6674
75 6848 43.3 0 6848
76 7059 43.3 0 7059
77 7167 43.3 0 7167
78 7631 43.3 0 7631
79 9217 43.3 0 9217
80 8923 43.3 0 8923
81 10496 43.3 0 10496
82 12980 43.3 0 12980
83 14601 43.3 0 14601
84 16268 43.3 0 16268
85 17257 43.3 0 17257
86 141768 43.3 0 141768
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 37513 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.6%
C: 33.7%
G: 0.0%
T: 36.4%
none/other: 2.4%
Overview of removed sequences
length count expect max.err error counts
3 14062 44301.3 0 14062
4 3433 11075.3 0 3433
5 1015 2768.8 0 1015
6 478 692.2 0 478
7 394 173.1 0 394
8 407 43.3 0 407
9 392 43.3 0 392
10 355 43.3 0 355
11 351 43.3 0 351
12 349 43.3 0 349
13 303 43.3 0 303
14 316 43.3 0 316
15 293 43.3 0 293
16 295 43.3 0 295
17 296 43.3 0 296
18 291 43.3 0 291
19 300 43.3 0 300
20 283 43.3 0 283
21 302 43.3 0 302
22 291 43.3 0 291
23 319 43.3 0 319
24 283 43.3 0 283
25 308 43.3 0 308
26 315 43.3 0 315
27 288 43.3 0 288
28 252 43.3 0 252
29 272 43.3 0 272
30 280 43.3 0 280
31 287 43.3 0 287
32 285 43.3 0 285
33 285 43.3 0 285
34 289 43.3 0 289
35 301 43.3 0 301
36 270 43.3 0 270
37 292 43.3 0 292
38 281 43.3 0 281
39 251 43.3 0 251
40 285 43.3 0 285
41 275 43.3 0 275
42 316 43.3 0 316
43 294 43.3 0 294
44 266 43.3 0 266
45 270 43.3 0 270
46 274 43.3 0 274
47 243 43.3 0 243
48 265 43.3 0 265
49 302 43.3 0 302
50 261 43.3 0 261
51 246 43.3 0 246
52 221 43.3 0 221
53 231 43.3 0 231
54 223 43.3 0 223
55 258 43.3 0 258
56 228 43.3 0 228
57 235 43.3 0 235
58 208 43.3 0 208
59 214 43.3 0 214
60 200 43.3 0 200
61 185 43.3 0 185
62 169 43.3 0 169
63 189 43.3 0 189
64 171 43.3 0 171
65 171 43.3 0 171
66 167 43.3 0 167
67 120 43.3 0 120
68 128 43.3 0 128
69 98 43.3 0 98
70 104 43.3 0 104
71 105 43.3 0 105
72 79 43.3 0 79
73 69 43.3 0 69
74 68 43.3 0 68
75 57 43.3 0 57
76 52 43.3 0 52
77 25 43.3 0 25
78 26 43.3 0 26
79 46 43.3 0 46
80 37 43.3 0 37
81 22 43.3 0 22
82 37 43.3 0 37
83 32 43.3 0 32
84 43 43.3 0 43
85 35 43.3 0 35
86 899 43.3 0 899
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 58710 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.2%
C: 22.8%
G: 21.0%
T: 20.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44243 44301.3 0 44243
4 9756 11075.3 0 9756
5 1910 2768.8 0 1910
6 265 692.2 0 265
7 23 173.1 0 23
8 38 173.1 0 38
9 28 173.1 0 28
10 30 173.1 0 30
11 38 173.1 0 38
12 33 173.1 0 33
13 36 173.1 0 36
14 42 173.1 0 42
15 28 173.1 0 28
16 34 173.1 0 34
17 35 173.1 0 35
18 39 173.1 0 39
19 39 173.1 0 39
20 33 173.1 0 33
21 35 173.1 0 35
22 32 173.1 0 32
23 28 173.1 0 28
24 31 173.1 0 31
25 40 173.1 0 40
26 28 173.1 0 28
27 24 173.1 0 24
28 24 173.1 0 24
29 27 173.1 0 27
30 32 173.1 0 32
31 25 173.1 0 25
32 39 173.1 0 39
33 42 173.1 0 42
34 20 173.1 0 20
35 28 173.1 0 28
36 30 173.1 0 30
37 21 173.1 0 21
38 21 173.1 0 21
39 27 173.1 0 27
40 34 173.1 0 34
41 24 173.1 0 24
42 36 173.1 0 36
43 22 173.1 0 22
44 24 173.1 0 24
45 36 173.1 0 36
46 27 173.1 0 27
47 28 173.1 0 28
48 27 173.1 0 27
49 37 173.1 0 37
50 36 173.1 0 36
51 43 173.1 0 43
52 30 173.1 0 30
53 21 173.1 0 21
54 46 173.1 0 46
55 37 173.1 0 37
56 26 173.1 0 26
57 34 173.1 0 34
58 38 173.1 0 38
59 31 173.1 0 31
60 30 173.1 0 30
61 25 173.1 0 25
62 24 173.1 0 24
63 38 173.1 0 38
64 29 173.1 0 29
65 30 173.1 0 30
66 34 173.1 0 34
67 32 173.1 0 32
68 37 173.1 0 37
69 25 173.1 0 25
70 43 173.1 0 43
71 35 173.1 0 35
72 26 173.1 0 26
73 30 173.1 0 30
74 29 173.1 0 29
75 21 173.1 0 21
76 24 173.1 0 24
77 63 173.1 0 63
78 50 173.1 0 50
79 33 173.1 0 33
80 32 173.1 0 32
81 27 173.1 0 27
82 28 173.1 0 28
83 25 173.1 0 25
84 25 173.1 0 25
85 32 173.1 0 32
86 42 173.1 0 42
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X41_S183_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X41_S183_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 26.74 s (9 µs/read; 6.46 M reads/minute).
=== Summary ===
Total reads processed: 2,878,791
Reads with adapters: 1,062,804 (36.9%)
== Read fate breakdown ==
Reads that were too short: 333,327 (11.6%)
Reads written (passing filters): 2,545,464 (88.4%)
Total basepairs processed: 290,757,891 bp
Total written (filtered): 198,448,973 bp (68.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 965247 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.0%
G: 26.2%
T: 29.6%
none/other: 15.3%
Overview of removed sequences
length count expect max.err error counts
3 65207 44981.1 0 65207
4 29017 11245.3 0 29017
5 15415 2811.3 0 15415
6 10783 702.8 0 10783
7 8753 175.7 0 8753
8 7872 43.9 0 7872
9 7976 43.9 0 7976
10 7812 43.9 0 7812
11 8028 43.9 0 8028
12 8152 43.9 0 8152
13 7923 43.9 0 7923
14 8087 43.9 0 8087
15 8344 43.9 0 8344
16 8355 43.9 0 8355
17 8306 43.9 0 8306
18 8262 43.9 0 8262
19 8537 43.9 0 8537
20 8168 43.9 0 8168
21 8208 43.9 0 8208
22 8598 43.9 0 8598
23 7839 43.9 0 7839
24 8073 43.9 0 8073
25 7872 43.9 0 7872
26 7932 43.9 0 7932
27 8226 43.9 0 8226
28 8088 43.9 0 8088
29 8165 43.9 0 8165
30 8378 43.9 0 8378
31 8857 43.9 0 8857
32 8140 43.9 0 8140
33 8989 43.9 0 8989
34 8572 43.9 0 8572
35 8073 43.9 0 8073
36 8160 43.9 0 8160
37 8955 43.9 0 8955
38 8077 43.9 0 8077
39 8379 43.9 0 8379
40 8702 43.9 0 8702
41 8588 43.9 0 8588
42 8802 43.9 0 8802
43 8958 43.9 0 8958
44 8362 43.9 0 8362
45 8291 43.9 0 8291
46 8337 43.9 0 8337
47 8678 43.9 0 8678
48 8490 43.9 0 8490
49 10917 43.9 0 10917
50 12692 43.9 0 12692
51 8586 43.9 0 8586
52 9144 43.9 0 9144
53 8906 43.9 0 8906
54 8442 43.9 0 8442
55 9015 43.9 0 9015
56 8877 43.9 0 8877
57 8649 43.9 0 8649
58 9423 43.9 0 9423
59 8858 43.9 0 8858
60 8969 43.9 0 8969
61 9235 43.9 0 9235
62 8929 43.9 0 8929
63 8640 43.9 0 8640
64 8683 43.9 0 8683
65 8624 43.9 0 8624
66 8391 43.9 0 8391
67 8116 43.9 0 8116
68 8286 43.9 0 8286
69 7627 43.9 0 7627
70 7433 43.9 0 7433
71 7694 43.9 0 7694
72 7474 43.9 0 7474
73 7185 43.9 0 7185
74 6979 43.9 0 6979
75 7023 43.9 0 7023
76 7412 43.9 0 7412
77 7388 43.9 0 7388
78 7970 43.9 0 7970
79 9560 43.9 0 9560
80 9067 43.9 0 9067
81 10841 43.9 0 10841
82 13075 43.9 0 13075
83 15228 43.9 0 15228
84 16798 43.9 0 16798
85 17926 43.9 0 17926
86 147399 43.9 0 147399
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38150 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 27.3%
C: 33.3%
G: 0.0%
T: 37.0%
none/other: 2.4%
Overview of removed sequences
length count expect max.err error counts
3 14190 44981.1 0 14190
4 3441 11245.3 0 3441
5 940 2811.3 0 940
6 457 702.8 0 457
7 411 175.7 0 411
8 392 43.9 0 392
9 408 43.9 0 408
10 383 43.9 0 383
11 356 43.9 0 356
12 341 43.9 0 341
13 363 43.9 0 363
14 336 43.9 0 336
15 330 43.9 0 330
16 331 43.9 0 331
17 328 43.9 0 328
18 314 43.9 0 314
19 314 43.9 0 314
20 316 43.9 0 316
21 303 43.9 0 303
22 318 43.9 0 318
23 265 43.9 0 265
24 313 43.9 0 313
25 346 43.9 0 346
26 289 43.9 0 289
27 295 43.9 0 295
28 293 43.9 0 293
29 284 43.9 0 284
30 306 43.9 0 306
31 273 43.9 0 273
32 277 43.9 0 277
33 293 43.9 0 293
34 273 43.9 0 273
35 270 43.9 0 270
36 304 43.9 0 304
37 289 43.9 0 289
38 294 43.9 0 294
39 283 43.9 0 283
40 279 43.9 0 279
41 268 43.9 0 268
42 274 43.9 0 274
43 289 43.9 0 289
44 289 43.9 0 289
45 270 43.9 0 270
46 277 43.9 0 277
47 267 43.9 0 267
48 292 43.9 0 292
49 270 43.9 0 270
50 283 43.9 0 283
51 261 43.9 0 261
52 284 43.9 0 284
53 240 43.9 0 240
54 220 43.9 0 220
55 250 43.9 0 250
56 236 43.9 0 236
57 205 43.9 0 205
58 257 43.9 0 257
59 232 43.9 0 232
60 215 43.9 0 215
61 184 43.9 0 184
62 181 43.9 0 181
63 189 43.9 0 189
64 181 43.9 0 181
65 142 43.9 0 142
66 144 43.9 0 144
67 119 43.9 0 119
68 120 43.9 0 120
69 110 43.9 0 110
70 98 43.9 0 98
71 93 43.9 0 93
72 71 43.9 0 71
73 75 43.9 0 75
74 66 43.9 0 66
75 63 43.9 0 63
76 52 43.9 0 52
77 39 43.9 0 39
78 28 43.9 0 28
79 42 43.9 0 42
80 39 43.9 0 39
81 32 43.9 0 32
82 37 43.9 0 37
83 39 43.9 0 39
84 56 43.9 0 56
85 52 43.9 0 52
86 921 43.9 0 921
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 59407 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 22.7%
G: 20.9%
T: 20.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 44757 44981.1 0 44757
4 9773 11245.3 0 9773
5 1968 2811.3 0 1968
6 253 702.8 0 253
7 36 175.7 0 36
8 29 175.7 0 29
9 33 175.7 0 33
10 28 175.7 0 28
11 26 175.7 0 26
12 30 175.7 0 30
13 48 175.7 0 48
14 35 175.7 0 35
15 30 175.7 0 30
16 37 175.7 0 37
17 37 175.7 0 37
18 45 175.7 0 45
19 29 175.7 0 29
20 27 175.7 0 27
21 28 175.7 0 28
22 29 175.7 0 29
23 39 175.7 0 39
24 29 175.7 0 29
25 39 175.7 0 39
26 36 175.7 0 36
27 23 175.7 0 23
28 41 175.7 0 41
29 25 175.7 0 25
30 36 175.7 0 36
31 28 175.7 0 28
32 34 175.7 0 34
33 35 175.7 0 35
34 24 175.7 0 24
35 27 175.7 0 27
36 27 175.7 0 27
37 19 175.7 0 19
38 20 175.7 0 20
39 41 175.7 0 41
40 49 175.7 0 49
41 25 175.7 0 25
42 43 175.7 0 43
43 22 175.7 0 22
44 20 175.7 0 20
45 34 175.7 0 34
46 36 175.7 0 36
47 43 175.7 0 43
48 35 175.7 0 35
49 35 175.7 0 35
50 33 175.7 0 33
51 38 175.7 0 38
52 41 175.7 0 41
53 36 175.7 0 36
54 37 175.7 0 37
55 27 175.7 0 27
56 28 175.7 0 28
57 30 175.7 0 30
58 24 175.7 0 24
59 34 175.7 0 34
60 24 175.7 0 24
61 36 175.7 0 36
62 39 175.7 0 39
63 27 175.7 0 27
64 28 175.7 0 28
65 51 175.7 0 51
66 37 175.7 0 37
67 24 175.7 0 24
68 43 175.7 0 43
69 23 175.7 0 23
70 30 175.7 0 30
71 28 175.7 0 28
72 21 175.7 0 21
73 18 175.7 0 18
74 43 175.7 0 43
75 32 175.7 0 32
76 21 175.7 0 21
77 78 175.7 0 78
78 49 175.7 0 49
79 34 175.7 0 34
80 29 175.7 0 29
81 33 175.7 0 33
82 37 175.7 0 37
83 39 175.7 0 39
84 33 175.7 0 33
85 30 175.7 0 30
86 49 175.7 0 49
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X42_S182_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X42_S182_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 18.93 s (10 µs/read; 6.15 M reads/minute).
=== Summary ===
Total reads processed: 1,938,834
Reads with adapters: 379,424 (19.6%)
== Read fate breakdown ==
Reads that were too short: 137,570 (7.1%)
Reads written (passing filters): 1,801,264 (92.9%)
Total basepairs processed: 195,822,234 bp
Total written (filtered): 150,648,857 bp (76.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 302398 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 19.6%
G: 18.3%
T: 25.3%
none/other: 36.7%
Overview of removed sequences
length count expect max.err error counts
3 47572 30294.3 0 47572
4 20291 7573.6 0 20291
5 7364 1893.4 0 7364
6 3479 473.3 0 3479
7 2373 118.3 0 2373
8 1768 29.6 0 1768
9 1609 29.6 0 1609
10 1638 29.6 0 1638
11 1585 29.6 0 1585
12 1597 29.6 0 1597
13 1551 29.6 0 1551
14 1740 29.6 0 1740
15 1641 29.6 0 1641
16 1599 29.6 0 1599
17 1656 29.6 0 1656
18 1675 29.6 0 1675
19 1516 29.6 0 1516
20 1601 29.6 0 1601
21 1545 29.6 0 1545
22 2324 29.6 0 2324
23 1591 29.6 0 1591
24 1594 29.6 0 1594
25 1529 29.6 0 1529
26 1587 29.6 0 1587
27 1552 29.6 0 1552
28 1415 29.6 0 1415
29 1497 29.6 0 1497
30 1449 29.6 0 1449
31 1549 29.6 0 1549
32 1339 29.6 0 1339
33 1503 29.6 0 1503
34 1560 29.6 0 1560
35 1652 29.6 0 1652
36 1323 29.6 0 1323
37 1444 29.6 0 1444
38 1587 29.6 0 1587
39 1478 29.6 0 1478
40 1316 29.6 0 1316
41 1484 29.6 0 1484
42 1225 29.6 0 1225
43 1309 29.6 0 1309
44 1200 29.6 0 1200
45 1462 29.6 0 1462
46 1316 29.6 0 1316
47 1318 29.6 0 1318
48 1429 29.6 0 1429
49 1286 29.6 0 1286
50 1281 29.6 0 1281
51 1426 29.6 0 1426
52 1204 29.6 0 1204
53 1287 29.6 0 1287
54 1358 29.6 0 1358
55 1248 29.6 0 1248
56 1192 29.6 0 1192
57 1237 29.6 0 1237
58 1345 29.6 0 1345
59 1320 29.6 0 1320
60 1371 29.6 0 1371
61 1368 29.6 0 1368
62 1289 29.6 0 1289
63 1323 29.6 0 1323
64 1399 29.6 0 1399
65 1451 29.6 0 1451
66 1352 29.6 0 1352
67 1324 29.6 0 1324
68 1401 29.6 0 1401
69 1290 29.6 0 1290
70 1180 29.6 0 1180
71 1371 29.6 0 1371
72 1257 29.6 0 1257
73 1070 29.6 0 1070
74 1263 29.6 0 1263
75 1404 29.6 0 1404
76 1220 29.6 0 1220
77 1083 29.6 0 1083
78 1473 29.6 0 1473
79 1121 29.6 0 1121
80 1107 29.6 0 1107
81 1197 29.6 0 1197
82 1242 29.6 0 1242
83 1099 29.6 0 1099
84 1149 29.6 0 1149
85 1495 29.6 0 1495
86 111083 29.6 0 111083
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35728 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 30.2%
C: 28.8%
G: 0.0%
T: 39.1%
none/other: 1.8%
Overview of removed sequences
length count expect max.err error counts
3 8204 30294.3 0 8204
4 2499 7573.6 0 2499
5 1074 1893.4 0 1074
6 662 473.3 0 662
7 778 118.3 0 778
8 833 29.6 0 833
9 677 29.6 0 677
10 608 29.6 0 608
11 561 29.6 0 561
12 503 29.6 0 503
13 489 29.6 0 489
14 540 29.6 0 540
15 461 29.6 0 461
16 474 29.6 0 474
17 452 29.6 0 452
18 474 29.6 0 474
19 485 29.6 0 485
20 442 29.6 0 442
21 423 29.6 0 423
22 384 29.6 0 384
23 387 29.6 0 387
24 427 29.6 0 427
25 421 29.6 0 421
26 418 29.6 0 418
27 356 29.6 0 356
28 344 29.6 0 344
29 347 29.6 0 347
30 393 29.6 0 393
31 339 29.6 0 339
32 332 29.6 0 332
33 394 29.6 0 394
34 386 29.6 0 386
35 381 29.6 0 381
36 387 29.6 0 387
37 354 29.6 0 354
38 348 29.6 0 348
39 322 29.6 0 322
40 333 29.6 0 333
41 286 29.6 0 286
42 328 29.6 0 328
43 304 29.6 0 304
44 310 29.6 0 310
45 283 29.6 0 283
46 297 29.6 0 297
47 253 29.6 0 253
48 257 29.6 0 257
49 272 29.6 0 272
50 308 29.6 0 308
51 228 29.6 0 228
52 203 29.6 0 203
53 242 29.6 0 242
54 211 29.6 0 211
55 229 29.6 0 229
56 237 29.6 0 237
57 220 29.6 0 220
58 203 29.6 0 203
59 212 29.6 0 212
60 194 29.6 0 194
61 203 29.6 0 203
62 159 29.6 0 159
63 176 29.6 0 176
64 185 29.6 0 185
65 159 29.6 0 159
66 137 29.6 0 137
67 140 29.6 0 140
68 133 29.6 0 133
69 117 29.6 0 117
70 101 29.6 0 101
71 88 29.6 0 88
72 64 29.6 0 64
73 81 29.6 0 81
74 68 29.6 0 68
75 51 29.6 0 51
76 64 29.6 0 64
77 62 29.6 0 62
78 48 29.6 0 48
79 45 29.6 0 45
80 47 29.6 0 47
81 24 29.6 0 24
82 34 29.6 0 34
83 42 29.6 0 42
84 27 29.6 0 27
85 46 29.6 0 46
86 658 29.6 0 658
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 41298 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 33.4%
C: 22.9%
G: 20.4%
T: 23.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 29362 30294.3 0 29362
4 7729 7573.6 0 7729
5 1197 1893.4 0 1197
6 197 473.3 0 197
7 18 118.3 0 18
8 24 118.3 0 24
9 14 118.3 0 14
10 26 118.3 0 26
11 29 118.3 0 29
12 27 118.3 0 27
13 31 118.3 0 31
14 16 118.3 0 16
15 18 118.3 0 18
16 25 118.3 0 25
17 14 118.3 0 14
18 33 118.3 0 33
19 14 118.3 0 14
20 15 118.3 0 15
21 25 118.3 0 25
22 14 118.3 0 14
23 15 118.3 0 15
24 29 118.3 0 29
25 34 118.3 0 34
26 54 118.3 0 54
27 26 118.3 0 26
28 38 118.3 0 38
29 61 118.3 0 61
30 17 118.3 0 17
31 24 118.3 0 24
32 80 118.3 0 80
33 19 118.3 0 19
34 20 118.3 0 20
35 19 118.3 0 19
36 19 118.3 0 19
37 43 118.3 0 43
38 36 118.3 0 36
39 60 118.3 0 60
40 59 118.3 0 59
41 42 118.3 0 42
42 72 118.3 0 72
43 57 118.3 0 57
44 27 118.3 0 27
45 108 118.3 0 108
46 35 118.3 0 35
47 26 118.3 0 26
48 40 118.3 0 40
49 47 118.3 0 47
50 15 118.3 0 15
51 28 118.3 0 28
52 29 118.3 0 29
53 50 118.3 0 50
54 17 118.3 0 17
55 48 118.3 0 48
56 36 118.3 0 36
57 28 118.3 0 28
58 25 118.3 0 25
59 33 118.3 0 33
60 23 118.3 0 23
61 31 118.3 0 31
62 47 118.3 0 47
63 23 118.3 0 23
64 41 118.3 0 41
65 51 118.3 0 51
66 37 118.3 0 37
67 28 118.3 0 28
68 36 118.3 0 36
69 38 118.3 0 38
70 46 118.3 0 46
71 33 118.3 0 33
72 22 118.3 0 22
73 30 118.3 0 30
74 24 118.3 0 24
75 39 118.3 0 39
76 29 118.3 0 29
77 185 118.3 0 185
78 80 118.3 0 80
79 28 118.3 0 28
80 32 118.3 0 32
81 32 118.3 0 32
82 18 118.3 0 18
83 40 118.3 0 40
84 13 118.3 0 13
85 28 118.3 0 28
86 20 118.3 0 20
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X42_S182_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X42_S182_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 17.85 s (9 µs/read; 6.63 M reads/minute).
=== Summary ===
Total reads processed: 1,973,393
Reads with adapters: 388,873 (19.7%)
== Read fate breakdown ==
Reads that were too short: 143,366 (7.3%)
Reads written (passing filters): 1,830,027 (92.7%)
Total basepairs processed: 199,312,693 bp
Total written (filtered): 153,032,255 bp (76.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 310044 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 19.3%
G: 18.3%
T: 24.9%
none/other: 37.6%
Overview of removed sequences
length count expect max.err error counts
3 48031 30834.3 0 48031
4 20084 7708.6 0 20084
5 7552 1927.1 0 7552
6 3523 481.8 0 3523
7 2420 120.4 0 2420
8 1821 30.1 0 1821
9 1600 30.1 0 1600
10 1718 30.1 0 1718
11 1588 30.1 0 1588
12 1719 30.1 0 1719
13 1636 30.1 0 1636
14 1819 30.1 0 1819
15 1650 30.1 0 1650
16 1630 30.1 0 1630
17 1638 30.1 0 1638
18 1693 30.1 0 1693
19 1449 30.1 0 1449
20 1719 30.1 0 1719
21 1554 30.1 0 1554
22 2347 30.1 0 2347
23 1634 30.1 0 1634
24 1515 30.1 0 1515
25 1559 30.1 0 1559
26 1598 30.1 0 1598
27 1531 30.1 0 1531
28 1505 30.1 0 1505
29 1463 30.1 0 1463
30 1436 30.1 0 1436
31 1534 30.1 0 1534
32 1353 30.1 0 1353
33 1505 30.1 0 1505
34 1634 30.1 0 1634
35 1648 30.1 0 1648
36 1367 30.1 0 1367
37 1487 30.1 0 1487
38 1618 30.1 0 1618
39 1402 30.1 0 1402
40 1303 30.1 0 1303
41 1492 30.1 0 1492
42 1253 30.1 0 1253
43 1343 30.1 0 1343
44 1193 30.1 0 1193
45 1509 30.1 0 1509
46 1396 30.1 0 1396
47 1314 30.1 0 1314
48 1386 30.1 0 1386
49 1259 30.1 0 1259
50 1402 30.1 0 1402
51 1489 30.1 0 1489
52 1258 30.1 0 1258
53 1311 30.1 0 1311
54 1451 30.1 0 1451
55 1209 30.1 0 1209
56 1222 30.1 0 1222
57 1250 30.1 0 1250
58 1410 30.1 0 1410
59 1345 30.1 0 1345
60 1455 30.1 0 1455
61 1332 30.1 0 1332
62 1327 30.1 0 1327
63 1411 30.1 0 1411
64 1420 30.1 0 1420
65 1473 30.1 0 1473
66 1371 30.1 0 1371
67 1331 30.1 0 1331
68 1400 30.1 0 1400
69 1280 30.1 0 1280
70 1279 30.1 0 1279
71 1319 30.1 0 1319
72 1239 30.1 0 1239
73 1142 30.1 0 1142
74 1178 30.1 0 1178
75 1385 30.1 0 1385
76 1207 30.1 0 1207
77 1134 30.1 0 1134
78 1496 30.1 0 1496
79 1128 30.1 0 1128
80 1127 30.1 0 1127
81 1166 30.1 0 1166
82 1324 30.1 0 1324
83 1116 30.1 0 1116
84 1162 30.1 0 1162
85 1514 30.1 0 1514
86 116553 30.1 0 116553
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 36827 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 29.8%
C: 28.9%
G: 0.0%
T: 39.3%
none/other: 2.0%
Overview of removed sequences
length count expect max.err error counts
3 8216 30834.3 0 8216
4 2559 7708.6 0 2559
5 1165 1927.1 0 1165
6 641 481.8 0 641
7 863 120.4 0 863
8 876 30.1 0 876
9 642 30.1 0 642
10 666 30.1 0 666
11 591 30.1 0 591
12 519 30.1 0 519
13 507 30.1 0 507
14 545 30.1 0 545
15 464 30.1 0 464
16 464 30.1 0 464
17 425 30.1 0 425
18 484 30.1 0 484
19 449 30.1 0 449
20 464 30.1 0 464
21 419 30.1 0 419
22 427 30.1 0 427
23 402 30.1 0 402
24 438 30.1 0 438
25 393 30.1 0 393
26 403 30.1 0 403
27 334 30.1 0 334
28 388 30.1 0 388
29 384 30.1 0 384
30 466 30.1 0 466
31 321 30.1 0 321
32 373 30.1 0 373
33 436 30.1 0 436
34 385 30.1 0 385
35 331 30.1 0 331
36 413 30.1 0 413
37 387 30.1 0 387
38 323 30.1 0 323
39 325 30.1 0 325
40 342 30.1 0 342
41 328 30.1 0 328
42 310 30.1 0 310
43 336 30.1 0 336
44 354 30.1 0 354
45 265 30.1 0 265
46 300 30.1 0 300
47 285 30.1 0 285
48 288 30.1 0 288
49 294 30.1 0 294
50 291 30.1 0 291
51 277 30.1 0 277
52 221 30.1 0 221
53 262 30.1 0 262
54 223 30.1 0 223
55 199 30.1 0 199
56 254 30.1 0 254
57 239 30.1 0 239
58 238 30.1 0 238
59 197 30.1 0 197
60 208 30.1 0 208
61 202 30.1 0 202
62 199 30.1 0 199
63 175 30.1 0 175
64 209 30.1 0 209
65 183 30.1 0 183
66 129 30.1 0 129
67 136 30.1 0 136
68 159 30.1 0 159
69 149 30.1 0 149
70 101 30.1 0 101
71 89 30.1 0 89
72 92 30.1 0 92
73 82 30.1 0 82
74 83 30.1 0 83
75 58 30.1 0 58
76 57 30.1 0 57
77 64 30.1 0 64
78 73 30.1 0 73
79 31 30.1 0 31
80 40 30.1 0 40
81 25 30.1 0 25
82 37 30.1 0 37
83 36 30.1 0 36
84 38 30.1 0 38
85 38 30.1 0 38
86 743 30.1 0 743
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 42002 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 33.3%
C: 22.8%
G: 20.5%
T: 23.3%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
3 29782 30834.3 0 29782
4 7936 7708.6 0 7936
5 1215 1927.1 0 1215
6 219 481.8 0 219
7 20 120.4 0 20
8 14 120.4 0 14
9 21 120.4 0 21
10 40 120.4 0 40
11 36 120.4 0 36
12 22 120.4 0 22
13 23 120.4 0 23
14 19 120.4 0 19
15 17 120.4 0 17
16 28 120.4 0 28
17 16 120.4 0 16
18 16 120.4 0 16
19 13 120.4 0 13
20 29 120.4 0 29
21 22 120.4 0 22
22 9 120.4 0 9
23 21 120.4 0 21
24 32 120.4 0 32
25 30 120.4 0 30
26 61 120.4 0 61
27 14 120.4 0 14
28 53 120.4 0 53
29 71 120.4 0 71
30 13 120.4 0 13
31 24 120.4 0 24
32 78 120.4 0 78
33 14 120.4 0 14
34 31 120.4 0 31
35 24 120.4 0 24
36 20 120.4 0 20
37 29 120.4 0 29
38 27 120.4 0 27
39 78 120.4 0 78
40 53 120.4 0 53
41 51 120.4 0 51
42 74 120.4 0 74
43 51 120.4 0 51
44 35 120.4 0 35
45 124 120.4 0 124
46 28 120.4 0 28
47 30 120.4 0 30
48 33 120.4 0 33
49 49 120.4 0 49
50 15 120.4 0 15
51 27 120.4 0 27
52 46 120.4 0 46
53 76 120.4 0 76
54 27 120.4 0 27
55 42 120.4 0 42
56 23 120.4 0 23
57 29 120.4 0 29
58 19 120.4 0 19
59 44 120.4 0 44
60 19 120.4 0 19
61 41 120.4 0 41
62 52 120.4 0 52
63 26 120.4 0 26
64 37 120.4 0 37
65 45 120.4 0 45
66 34 120.4 0 34
67 25 120.4 0 25
68 18 120.4 0 18
69 27 120.4 0 27
70 54 120.4 0 54
71 32 120.4 0 32
72 40 120.4 0 40
73 25 120.4 0 25
74 23 120.4 0 23
75 39 120.4 0 39
76 32 120.4 0 32
77 172 120.4 0 172
78 63 120.4 0 63
79 30 120.4 0 30
80 30 120.4 0 30
81 42 120.4 0 42
82 15 120.4 0 15
83 41 120.4 0 41
84 10 120.4 0 10
85 20 120.4 0 20
86 17 120.4 0 17
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X43_S173_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X43_S173_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.24 s (9 µs/read; 6.44 M reads/minute).
=== Summary ===
Total reads processed: 2,492,327
Reads with adapters: 790,430 (31.7%)
== Read fate breakdown ==
Reads that were too short: 213,992 (8.6%)
Reads written (passing filters): 2,278,335 (91.4%)
Total basepairs processed: 251,725,027 bp
Total written (filtered): 180,452,805 bp (71.7%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 692402 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.6%
G: 27.0%
T: 28.7%
none/other: 13.6%
Overview of removed sequences
length count expect max.err error counts
3 59449 38942.6 0 59449
4 25758 9735.7 0 25758
5 12984 2433.9 0 12984
6 8215 608.5 0 8215
7 6601 152.1 0 6601
8 5748 38.0 0 5748
9 5783 38.0 0 5783
10 5706 38.0 0 5706
11 5823 38.0 0 5823
12 5752 38.0 0 5752
13 5838 38.0 0 5838
14 5933 38.0 0 5933
15 5867 38.0 0 5867
16 5914 38.0 0 5914
17 5983 38.0 0 5983
18 6103 38.0 0 6103
19 6052 38.0 0 6052
20 5919 38.0 0 5919
21 6028 38.0 0 6028
22 5797 38.0 0 5797
23 5921 38.0 0 5921
24 5807 38.0 0 5807
25 5983 38.0 0 5983
26 5950 38.0 0 5950
27 5897 38.0 0 5897
28 6223 38.0 0 6223
29 6299 38.0 0 6299
30 6066 38.0 0 6066
31 6344 38.0 0 6344
32 6106 38.0 0 6106
33 6498 38.0 0 6498
34 6246 38.0 0 6246
35 6043 38.0 0 6043
36 5946 38.0 0 5946
37 5818 38.0 0 5818
38 5827 38.0 0 5827
39 5981 38.0 0 5981
40 6175 38.0 0 6175
41 6045 38.0 0 6045
42 6108 38.0 0 6108
43 6296 38.0 0 6296
44 5915 38.0 0 5915
45 6137 38.0 0 6137
46 6451 38.0 0 6451
47 6310 38.0 0 6310
48 6389 38.0 0 6389
49 7704 38.0 0 7704
50 8611 38.0 0 8611
51 6666 38.0 0 6666
52 7070 38.0 0 7070
53 6656 38.0 0 6656
54 6611 38.0 0 6611
55 6623 38.0 0 6623
56 6643 38.0 0 6643
57 6609 38.0 0 6609
58 6698 38.0 0 6698
59 6445 38.0 0 6445
60 6779 38.0 0 6779
61 6793 38.0 0 6793
62 6604 38.0 0 6604
63 6466 38.0 0 6466
64 6468 38.0 0 6468
65 6455 38.0 0 6455
66 6387 38.0 0 6387
67 6171 38.0 0 6171
68 6097 38.0 0 6097
69 5918 38.0 0 5918
70 5623 38.0 0 5623
71 6196 38.0 0 6196
72 5736 38.0 0 5736
73 5586 38.0 0 5586
74 5293 38.0 0 5293
75 5121 38.0 0 5121
76 4984 38.0 0 4984
77 5618 38.0 0 5618
78 4890 38.0 0 4890
79 5359 38.0 0 5359
80 5014 38.0 0 5014
81 5883 38.0 0 5883
82 6895 38.0 0 6895
83 7999 38.0 0 7999
84 8447 38.0 0 8447
85 8839 38.0 0 8839
86 94411 38.0 0 94411
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 42671 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.7%
C: 32.3%
G: 0.0%
T: 37.3%
none/other: 3.8%
Overview of removed sequences
length count expect max.err error counts
3 12013 38942.6 0 12013
4 3143 9735.7 0 3143
5 1051 2433.9 0 1051
6 637 608.5 0 637
7 512 152.1 0 512
8 545 38.0 0 545
9 528 38.0 0 528
10 520 38.0 0 520
11 464 38.0 0 464
12 447 38.0 0 447
13 442 38.0 0 442
14 458 38.0 0 458
15 402 38.0 0 402
16 403 38.0 0 403
17 438 38.0 0 438
18 441 38.0 0 441
19 420 38.0 0 420
20 420 38.0 0 420
21 454 38.0 0 454
22 375 38.0 0 375
23 419 38.0 0 419
24 443 38.0 0 443
25 439 38.0 0 439
26 434 38.0 0 434
27 399 38.0 0 399
28 423 38.0 0 423
29 400 38.0 0 400
30 383 38.0 0 383
31 374 38.0 0 374
32 362 38.0 0 362
33 421 38.0 0 421
34 387 38.0 0 387
35 385 38.0 0 385
36 382 38.0 0 382
37 406 38.0 0 406
38 376 38.0 0 376
39 391 38.0 0 391
40 388 38.0 0 388
41 389 38.0 0 389
42 404 38.0 0 404
43 413 38.0 0 413
44 348 38.0 0 348
45 375 38.0 0 375
46 348 38.0 0 348
47 367 38.0 0 367
48 344 38.0 0 344
49 372 38.0 0 372
50 347 38.0 0 347
51 342 38.0 0 342
52 341 38.0 0 341
53 343 38.0 0 343
54 336 38.0 0 336
55 299 38.0 0 299
56 289 38.0 0 289
57 313 38.0 0 313
58 317 38.0 0 317
59 321 38.0 0 321
60 304 38.0 0 304
61 245 38.0 0 245
62 232 38.0 0 232
63 245 38.0 0 245
64 217 38.0 0 217
65 200 38.0 0 200
66 200 38.0 0 200
67 190 38.0 0 190
68 129 38.0 0 129
69 139 38.0 0 139
70 139 38.0 0 139
71 109 38.0 0 109
72 99 38.0 0 99
73 77 38.0 0 77
74 73 38.0 0 73
75 64 38.0 0 64
76 56 38.0 0 56
77 62 38.0 0 62
78 50 38.0 0 50
79 45 38.0 0 45
80 46 38.0 0 46
81 37 38.0 0 37
82 36 38.0 0 36
83 56 38.0 0 56
84 39 38.0 0 39
85 50 38.0 0 50
86 1599 38.0 0 1599
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 55357 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.9%
C: 22.5%
G: 20.8%
T: 20.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41063 38942.6 0 41063
4 9529 9735.7 0 9529
5 1730 2433.9 0 1730
6 238 608.5 0 238
7 34 152.1 0 34
8 28 152.1 0 28
9 26 152.1 0 26
10 35 152.1 0 35
11 26 152.1 0 26
12 23 152.1 0 23
13 36 152.1 0 36
14 32 152.1 0 32
15 32 152.1 0 32
16 28 152.1 0 28
17 22 152.1 0 22
18 27 152.1 0 27
19 38 152.1 0 38
20 29 152.1 0 29
21 25 152.1 0 25
22 40 152.1 0 40
23 32 152.1 0 32
24 20 152.1 0 20
25 44 152.1 0 44
26 52 152.1 0 52
27 25 152.1 0 25
28 32 152.1 0 32
29 36 152.1 0 36
30 29 152.1 0 29
31 27 152.1 0 27
32 41 152.1 0 41
33 26 152.1 0 26
34 29 152.1 0 29
35 26 152.1 0 26
36 37 152.1 0 37
37 31 152.1 0 31
38 51 152.1 0 51
39 34 152.1 0 34
40 30 152.1 0 30
41 33 152.1 0 33
42 29 152.1 0 29
43 30 152.1 0 30
44 28 152.1 0 28
45 47 152.1 0 47
46 28 152.1 0 28
47 36 152.1 0 36
48 26 152.1 0 26
49 48 152.1 0 48
50 29 152.1 0 29
51 28 152.1 0 28
52 37 152.1 0 37
53 31 152.1 0 31
54 27 152.1 0 27
55 42 152.1 0 42
56 33 152.1 0 33
57 22 152.1 0 22
58 31 152.1 0 31
59 40 152.1 0 40
60 30 152.1 0 30
61 33 152.1 0 33
62 42 152.1 0 42
63 42 152.1 0 42
64 37 152.1 0 37
65 55 152.1 0 55
66 33 152.1 0 33
67 34 152.1 0 34
68 36 152.1 0 36
69 32 152.1 0 32
70 37 152.1 0 37
71 40 152.1 0 40
72 32 152.1 0 32
73 39 152.1 0 39
74 23 152.1 0 23
75 31 152.1 0 31
76 22 152.1 0 22
77 78 152.1 0 78
78 86 152.1 0 86
79 33 152.1 0 33
80 37 152.1 0 37
81 47 152.1 0 47
82 39 152.1 0 39
83 59 152.1 0 59
84 24 152.1 0 24
85 40 152.1 0 40
86 48 152.1 0 48
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X43_S173_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X43_S173_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 24.28 s (10 µs/read; 6.28 M reads/minute).
=== Summary ===
Total reads processed: 2,542,443
Reads with adapters: 817,192 (32.1%)
== Read fate breakdown ==
Reads that were too short: 226,295 (8.9%)
Reads written (passing filters): 2,316,148 (91.1%)
Total basepairs processed: 256,786,743 bp
Total written (filtered): 183,232,362 bp (71.4%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 717379 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.6%
G: 26.9%
T: 28.5%
none/other: 14.0%
Overview of removed sequences
length count expect max.err error counts
3 60261 39725.7 0 60261
4 26383 9931.4 0 26383
5 13350 2482.9 0 13350
6 8254 620.7 0 8254
7 6617 155.2 0 6617
8 5694 38.8 0 5694
9 5878 38.8 0 5878
10 5866 38.8 0 5866
11 5827 38.8 0 5827
12 6021 38.8 0 6021
13 5942 38.8 0 5942
14 6037 38.8 0 6037
15 6017 38.8 0 6017
16 6137 38.8 0 6137
17 6166 38.8 0 6166
18 6466 38.8 0 6466
19 6082 38.8 0 6082
20 6093 38.8 0 6093
21 6208 38.8 0 6208
22 6043 38.8 0 6043
23 6165 38.8 0 6165
24 6065 38.8 0 6065
25 6030 38.8 0 6030
26 6122 38.8 0 6122
27 6062 38.8 0 6062
28 6333 38.8 0 6333
29 6635 38.8 0 6635
30 6243 38.8 0 6243
31 6466 38.8 0 6466
32 6243 38.8 0 6243
33 6374 38.8 0 6374
34 6313 38.8 0 6313
35 6315 38.8 0 6315
36 6168 38.8 0 6168
37 6123 38.8 0 6123
38 6087 38.8 0 6087
39 6213 38.8 0 6213
40 6437 38.8 0 6437
41 6111 38.8 0 6111
42 6321 38.8 0 6321
43 6539 38.8 0 6539
44 6201 38.8 0 6201
45 6356 38.8 0 6356
46 6524 38.8 0 6524
47 6421 38.8 0 6421
48 6676 38.8 0 6676
49 7839 38.8 0 7839
50 8813 38.8 0 8813
51 7062 38.8 0 7062
52 7400 38.8 0 7400
53 6850 38.8 0 6850
54 6562 38.8 0 6562
55 6719 38.8 0 6719
56 6850 38.8 0 6850
57 6767 38.8 0 6767
58 6908 38.8 0 6908
59 6811 38.8 0 6811
60 7014 38.8 0 7014
61 6955 38.8 0 6955
62 6852 38.8 0 6852
63 6832 38.8 0 6832
64 6860 38.8 0 6860
65 6637 38.8 0 6637
66 6579 38.8 0 6579
67 6635 38.8 0 6635
68 6222 38.8 0 6222
69 6075 38.8 0 6075
70 5991 38.8 0 5991
71 6467 38.8 0 6467
72 6009 38.8 0 6009
73 5904 38.8 0 5904
74 5604 38.8 0 5604
75 5469 38.8 0 5469
76 5180 38.8 0 5180
77 5836 38.8 0 5836
78 5216 38.8 0 5216
79 5585 38.8 0 5585
80 5359 38.8 0 5359
81 6362 38.8 0 6362
82 7308 38.8 0 7308
83 8355 38.8 0 8355
84 8940 38.8 0 8940
85 9135 38.8 0 9135
86 100532 38.8 0 100532
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 43680 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.7%
C: 32.0%
G: 0.0%
T: 37.4%
none/other: 3.8%
Overview of removed sequences
length count expect max.err error counts
3 12317 39725.7 0 12317
4 3102 9931.4 0 3102
5 1020 2482.9 0 1020
6 576 620.7 0 576
7 531 155.2 0 531
8 568 38.8 0 568
9 554 38.8 0 554
10 520 38.8 0 520
11 457 38.8 0 457
12 508 38.8 0 508
13 493 38.8 0 493
14 445 38.8 0 445
15 492 38.8 0 492
16 436 38.8 0 436
17 390 38.8 0 390
18 459 38.8 0 459
19 466 38.8 0 466
20 422 38.8 0 422
21 433 38.8 0 433
22 399 38.8 0 399
23 460 38.8 0 460
24 477 38.8 0 477
25 449 38.8 0 449
26 453 38.8 0 453
27 445 38.8 0 445
28 423 38.8 0 423
29 425 38.8 0 425
30 409 38.8 0 409
31 388 38.8 0 388
32 385 38.8 0 385
33 415 38.8 0 415
34 432 38.8 0 432
35 380 38.8 0 380
36 404 38.8 0 404
37 356 38.8 0 356
38 374 38.8 0 374
39 359 38.8 0 359
40 408 38.8 0 408
41 385 38.8 0 385
42 393 38.8 0 393
43 391 38.8 0 391
44 365 38.8 0 365
45 341 38.8 0 341
46 382 38.8 0 382
47 372 38.8 0 372
48 358 38.8 0 358
49 359 38.8 0 359
50 347 38.8 0 347
51 347 38.8 0 347
52 354 38.8 0 354
53 370 38.8 0 370
54 303 38.8 0 303
55 358 38.8 0 358
56 345 38.8 0 345
57 291 38.8 0 291
58 323 38.8 0 323
59 296 38.8 0 296
60 286 38.8 0 286
61 238 38.8 0 238
62 251 38.8 0 251
63 254 38.8 0 254
64 239 38.8 0 239
65 213 38.8 0 213
66 226 38.8 0 226
67 208 38.8 0 208
68 187 38.8 0 187
69 144 38.8 0 144
70 132 38.8 0 132
71 117 38.8 0 117
72 123 38.8 0 123
73 69 38.8 0 69
74 78 38.8 0 78
75 77 38.8 0 77
76 56 38.8 0 56
77 38 38.8 0 38
78 41 38.8 0 41
79 49 38.8 0 49
80 36 38.8 0 36
81 41 38.8 0 41
82 38 38.8 0 38
83 46 38.8 0 46
84 63 38.8 0 63
85 49 38.8 0 49
86 1671 38.8 0 1671
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 56133 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 22.4%
G: 20.9%
T: 21.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41738 39725.7 0 41738
4 9506 9931.4 0 9506
5 1740 2482.9 0 1740
6 237 620.7 0 237
7 32 155.2 0 32
8 37 155.2 0 37
9 24 155.2 0 24
10 21 155.2 0 21
11 32 155.2 0 32
12 21 155.2 0 21
13 34 155.2 0 34
14 41 155.2 0 41
15 28 155.2 0 28
16 27 155.2 0 27
17 32 155.2 0 32
18 29 155.2 0 29
19 43 155.2 0 43
20 42 155.2 0 42
21 27 155.2 0 27
22 26 155.2 0 26
23 35 155.2 0 35
24 34 155.2 0 34
25 39 155.2 0 39
26 40 155.2 0 40
27 34 155.2 0 34
28 37 155.2 0 37
29 44 155.2 0 44
30 31 155.2 0 31
31 31 155.2 0 31
32 62 155.2 0 62
33 34 155.2 0 34
34 15 155.2 0 15
35 22 155.2 0 22
36 37 155.2 0 37
37 30 155.2 0 30
38 35 155.2 0 35
39 34 155.2 0 34
40 27 155.2 0 27
41 38 155.2 0 38
42 46 155.2 0 46
43 45 155.2 0 45
44 30 155.2 0 30
45 27 155.2 0 27
46 32 155.2 0 32
47 33 155.2 0 33
48 41 155.2 0 41
49 37 155.2 0 37
50 35 155.2 0 35
51 28 155.2 0 28
52 38 155.2 0 38
53 25 155.2 0 25
54 52 155.2 0 52
55 42 155.2 0 42
56 25 155.2 0 25
57 13 155.2 0 13
58 30 155.2 0 30
59 45 155.2 0 45
60 37 155.2 0 37
61 30 155.2 0 30
62 41 155.2 0 41
63 37 155.2 0 37
64 47 155.2 0 47
65 56 155.2 0 56
66 37 155.2 0 37
67 41 155.2 0 41
68 29 155.2 0 29
69 32 155.2 0 32
70 45 155.2 0 45
71 26 155.2 0 26
72 41 155.2 0 41
73 31 155.2 0 31
74 33 155.2 0 33
75 25 155.2 0 25
76 45 155.2 0 45
77 93 155.2 0 93
78 86 155.2 0 86
79 46 155.2 0 46
80 30 155.2 0 30
81 48 155.2 0 48
82 46 155.2 0 46
83 45 155.2 0 45
84 24 155.2 0 24
85 40 155.2 0 40
86 42 155.2 0 42
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X44_S172_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X44_S172_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 4.06 s (7 µs/read; 8.08 M reads/minute).
=== Summary ===
Total reads processed: 546,473
Reads with adapters: 102,233 (18.7%)
== Read fate breakdown ==
Reads that were too short: 49,006 (9.0%)
Reads written (passing filters): 497,467 (91.0%)
Total basepairs processed: 55,193,773 bp
Total written (filtered): 42,024,538 bp (76.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 84013 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 13.2%
G: 14.2%
T: 20.6%
none/other: 52.0%
Overview of removed sequences
length count expect max.err error counts
3 12672 8538.6 0 12672
4 5080 2134.7 0 5080
5 1810 533.7 0 1810
6 788 133.4 0 788
7 961 33.4 0 961
8 314 8.3 0 314
9 241 8.3 0 241
10 357 8.3 0 357
11 225 8.3 0 225
12 354 8.3 0 354
13 266 8.3 0 266
14 325 8.3 0 325
15 263 8.3 0 263
16 304 8.3 0 304
17 277 8.3 0 277
18 381 8.3 0 381
19 244 8.3 0 244
20 242 8.3 0 242
21 245 8.3 0 245
22 220 8.3 0 220
23 201 8.3 0 201
24 251 8.3 0 251
25 274 8.3 0 274
26 307 8.3 0 307
27 250 8.3 0 250
28 215 8.3 0 215
29 189 8.3 0 189
30 241 8.3 0 241
31 355 8.3 0 355
32 248 8.3 0 248
33 269 8.3 0 269
34 254 8.3 0 254
35 190 8.3 0 190
36 254 8.3 0 254
37 240 8.3 0 240
38 258 8.3 0 258
39 183 8.3 0 183
40 229 8.3 0 229
41 244 8.3 0 244
42 209 8.3 0 209
43 188 8.3 0 188
44 182 8.3 0 182
45 240 8.3 0 240
46 189 8.3 0 189
47 210 8.3 0 210
48 240 8.3 0 240
49 328 8.3 0 328
50 208 8.3 0 208
51 345 8.3 0 345
52 303 8.3 0 303
53 182 8.3 0 182
54 186 8.3 0 186
55 226 8.3 0 226
56 193 8.3 0 193
57 190 8.3 0 190
58 209 8.3 0 209
59 190 8.3 0 190
60 198 8.3 0 198
61 256 8.3 0 256
62 196 8.3 0 196
63 205 8.3 0 205
64 255 8.3 0 255
65 304 8.3 0 304
66 257 8.3 0 257
67 177 8.3 0 177
68 221 8.3 0 221
69 190 8.3 0 190
70 381 8.3 0 381
71 306 8.3 0 306
72 166 8.3 0 166
73 435 8.3 0 435
74 214 8.3 0 214
75 237 8.3 0 237
76 224 8.3 0 224
77 222 8.3 0 222
78 250 8.3 0 250
79 247 8.3 0 247
80 185 8.3 0 185
81 185 8.3 0 185
82 198 8.3 0 198
83 197 8.3 0 197
84 181 8.3 0 181
85 216 8.3 0 216
86 43671 8.3 0 43671
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 7048 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 35.3%
C: 21.6%
G: 0.0%
T: 37.4%
none/other: 5.7%
Overview of removed sequences
length count expect max.err error counts
3 2029 8538.6 0 2029
4 606 2134.7 0 606
5 275 533.7 0 275
6 139 133.4 0 139
7 211 33.4 0 211
8 200 8.3 0 200
9 163 8.3 0 163
10 128 8.3 0 128
11 102 8.3 0 102
12 66 8.3 0 66
13 81 8.3 0 81
14 157 8.3 0 157
15 66 8.3 0 66
16 62 8.3 0 62
17 39 8.3 0 39
18 43 8.3 0 43
19 67 8.3 0 67
20 46 8.3 0 46
21 58 8.3 0 58
22 44 8.3 0 44
23 37 8.3 0 37
24 39 8.3 0 39
25 37 8.3 0 37
26 43 8.3 0 43
27 47 8.3 0 47
28 69 8.3 0 69
29 57 8.3 0 57
30 72 8.3 0 72
31 42 8.3 0 42
32 48 8.3 0 48
33 42 8.3 0 42
34 44 8.3 0 44
35 52 8.3 0 52
36 56 8.3 0 56
37 38 8.3 0 38
38 39 8.3 0 39
39 46 8.3 0 46
40 37 8.3 0 37
41 46 8.3 0 46
42 49 8.3 0 49
43 30 8.3 0 30
44 62 8.3 0 62
45 24 8.3 0 24
46 61 8.3 0 61
47 30 8.3 0 30
48 35 8.3 0 35
49 41 8.3 0 41
50 52 8.3 0 52
51 46 8.3 0 46
52 56 8.3 0 56
53 40 8.3 0 40
54 29 8.3 0 29
55 40 8.3 0 40
56 41 8.3 0 41
57 31 8.3 0 31
58 17 8.3 0 17
59 23 8.3 0 23
60 29 8.3 0 29
61 17 8.3 0 17
62 25 8.3 0 25
63 27 8.3 0 27
64 40 8.3 0 40
65 23 8.3 0 23
66 13 8.3 0 13
67 23 8.3 0 23
68 41 8.3 0 41
69 33 8.3 0 33
70 33 8.3 0 33
71 23 8.3 0 23
72 7 8.3 0 7
73 7 8.3 0 7
74 11 8.3 0 11
75 9 8.3 0 9
76 10 8.3 0 10
77 20 8.3 0 20
78 8 8.3 0 8
79 5 8.3 0 5
80 7 8.3 0 7
81 6 8.3 0 6
82 7 8.3 0 7
83 15 8.3 0 15
84 13 8.3 0 13
85 15 8.3 0 15
86 401 8.3 0 401
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 11172 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.0%
C: 22.3%
G: 20.8%
T: 21.9%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
3 7971 8538.6 0 7971
4 2052 2134.7 0 2052
5 362 533.7 0 362
6 43 133.4 0 43
8 2 33.4 0 2
9 10 33.4 0 10
10 5 33.4 0 5
11 8 33.4 0 8
12 1 33.4 0 1
13 4 33.4 0 4
14 11 33.4 0 11
15 4 33.4 0 4
16 4 33.4 0 4
17 6 33.4 0 6
18 5 33.4 0 5
19 3 33.4 0 3
20 10 33.4 0 10
21 5 33.4 0 5
22 4 33.4 0 4
23 9 33.4 0 9
24 9 33.4 0 9
25 1 33.4 0 1
26 9 33.4 0 9
27 4 33.4 0 4
28 21 33.4 0 21
29 34 33.4 0 34
30 4 33.4 0 4
31 4 33.4 0 4
32 20 33.4 0 20
33 12 33.4 0 12
34 10 33.4 0 10
35 12 33.4 0 12
36 6 33.4 0 6
37 13 33.4 0 13
38 16 33.4 0 16
39 2 33.4 0 2
40 17 33.4 0 17
41 10 33.4 0 10
42 8 33.4 0 8
43 7 33.4 0 7
44 2 33.4 0 2
45 4 33.4 0 4
46 3 33.4 0 3
47 7 33.4 0 7
48 16 33.4 0 16
49 18 33.4 0 18
50 2 33.4 0 2
51 14 33.4 0 14
52 3 33.4 0 3
53 42 33.4 0 42
54 15 33.4 0 15
55 2 33.4 0 2
56 4 33.4 0 4
57 4 33.4 0 4
58 5 33.4 0 5
59 9 33.4 0 9
60 8 33.4 0 8
61 13 33.4 0 13
62 20 33.4 0 20
63 13 33.4 0 13
64 14 33.4 0 14
65 3 33.4 0 3
66 4 33.4 0 4
67 6 33.4 0 6
68 1 33.4 0 1
69 8 33.4 0 8
70 14 33.4 0 14
71 3 33.4 0 3
72 13 33.4 0 13
73 2 33.4 0 2
74 6 33.4 0 6
75 5 33.4 0 5
76 12 33.4 0 12
77 51 33.4 0 51
78 29 33.4 0 29
79 4 33.4 0 4
80 3 33.4 0 3
81 11 33.4 0 11
82 19 33.4 0 19
83 2 33.4 0 2
84 8 33.4 0 8
85 7 33.4 0 7
86 5 33.4 0 5
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X44_S172_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X44_S172_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 4.32 s (8 µs/read; 7.79 M reads/minute).
=== Summary ===
Total reads processed: 560,455
Reads with adapters: 106,768 (19.1%)
== Read fate breakdown ==
Reads that were too short: 52,193 (9.3%)
Reads written (passing filters): 508,262 (90.7%)
Total basepairs processed: 56,605,955 bp
Total written (filtered): 42,937,875 bp (75.9%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 87822 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 12.8%
G: 13.7%
T: 20.1%
none/other: 53.4%
Overview of removed sequences
length count expect max.err error counts
3 12970 8757.1 0 12970
4 5392 2189.3 0 5392
5 1840 547.3 0 1840
6 780 136.8 0 780
7 991 34.2 0 991
8 304 8.6 0 304
9 256 8.6 0 256
10 331 8.6 0 331
11 270 8.6 0 270
12 317 8.6 0 317
13 231 8.6 0 231
14 298 8.6 0 298
15 266 8.6 0 266
16 309 8.6 0 309
17 249 8.6 0 249
18 368 8.6 0 368
19 277 8.6 0 277
20 247 8.6 0 247
21 280 8.6 0 280
22 212 8.6 0 212
23 193 8.6 0 193
24 258 8.6 0 258
25 305 8.6 0 305
26 334 8.6 0 334
27 249 8.6 0 249
28 189 8.6 0 189
29 190 8.6 0 190
30 243 8.6 0 243
31 326 8.6 0 326
32 232 8.6 0 232
33 277 8.6 0 277
34 231 8.6 0 231
35 219 8.6 0 219
36 240 8.6 0 240
37 267 8.6 0 267
38 250 8.6 0 250
39 177 8.6 0 177
40 222 8.6 0 222
41 238 8.6 0 238
42 207 8.6 0 207
43 182 8.6 0 182
44 171 8.6 0 171
45 257 8.6 0 257
46 187 8.6 0 187
47 231 8.6 0 231
48 227 8.6 0 227
49 321 8.6 0 321
50 214 8.6 0 214
51 314 8.6 0 314
52 306 8.6 0 306
53 195 8.6 0 195
54 212 8.6 0 212
55 233 8.6 0 233
56 173 8.6 0 173
57 196 8.6 0 196
58 222 8.6 0 222
59 202 8.6 0 202
60 230 8.6 0 230
61 244 8.6 0 244
62 182 8.6 0 182
63 229 8.6 0 229
64 247 8.6 0 247
65 351 8.6 0 351
66 236 8.6 0 236
67 188 8.6 0 188
68 238 8.6 0 238
69 197 8.6 0 197
70 339 8.6 0 339
71 296 8.6 0 296
72 181 8.6 0 181
73 403 8.6 0 403
74 190 8.6 0 190
75 254 8.6 0 254
76 184 8.6 0 184
77 242 8.6 0 242
78 249 8.6 0 249
79 220 8.6 0 220
80 176 8.6 0 176
81 176 8.6 0 176
82 237 8.6 0 237
83 178 8.6 0 178
84 194 8.6 0 194
85 204 8.6 0 204
86 46879 8.6 0 46879
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 7526 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 35.8%
C: 21.0%
G: 0.0%
T: 37.9%
none/other: 5.3%
Overview of removed sequences
length count expect max.err error counts
3 2108 8757.1 0 2108
4 690 2189.3 0 690
5 293 547.3 0 293
6 148 136.8 0 148
7 230 34.2 0 230
8 238 8.6 0 238
9 180 8.6 0 180
10 138 8.6 0 138
11 117 8.6 0 117
12 80 8.6 0 80
13 51 8.6 0 51
14 169 8.6 0 169
15 90 8.6 0 90
16 58 8.6 0 58
17 68 8.6 0 68
18 46 8.6 0 46
19 66 8.6 0 66
20 34 8.6 0 34
21 61 8.6 0 61
22 36 8.6 0 36
23 34 8.6 0 34
24 43 8.6 0 43
25 34 8.6 0 34
26 38 8.6 0 38
27 55 8.6 0 55
28 64 8.6 0 64
29 52 8.6 0 52
30 69 8.6 0 69
31 49 8.6 0 49
32 45 8.6 0 45
33 49 8.6 0 49
34 41 8.6 0 41
35 69 8.6 0 69
36 53 8.6 0 53
37 35 8.6 0 35
38 47 8.6 0 47
39 47 8.6 0 47
40 49 8.6 0 49
41 62 8.6 0 62
42 57 8.6 0 57
43 39 8.6 0 39
44 53 8.6 0 53
45 40 8.6 0 40
46 49 8.6 0 49
47 35 8.6 0 35
48 45 8.6 0 45
49 56 8.6 0 56
50 38 8.6 0 38
51 38 8.6 0 38
52 64 8.6 0 64
53 47 8.6 0 47
54 34 8.6 0 34
55 36 8.6 0 36
56 44 8.6 0 44
57 36 8.6 0 36
58 18 8.6 0 18
59 23 8.6 0 23
60 44 8.6 0 44
61 27 8.6 0 27
62 39 8.6 0 39
63 15 8.6 0 15
64 33 8.6 0 33
65 34 8.6 0 34
66 15 8.6 0 15
67 17 8.6 0 17
68 40 8.6 0 40
69 36 8.6 0 36
70 41 8.6 0 41
71 18 8.6 0 18
72 9 8.6 0 9
73 12 8.6 0 12
74 12 8.6 0 12
75 14 8.6 0 14
76 13 8.6 0 13
77 15 8.6 0 15
78 11 8.6 0 11
79 14 8.6 0 14
80 14 8.6 0 14
81 10 8.6 0 10
82 12 8.6 0 12
83 13 8.6 0 13
84 13 8.6 0 13
85 22 8.6 0 22
86 395 8.6 0 395
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 11420 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.8%
C: 22.3%
G: 19.4%
T: 22.4%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
3 8209 8757.1 0 8209
4 2002 2189.3 0 2002
5 394 547.3 0 394
6 34 136.8 0 34
7 1 34.2 0 1
8 2 34.2 0 2
9 8 34.2 0 8
10 6 34.2 0 6
11 12 34.2 0 12
12 2 34.2 0 2
13 6 34.2 0 6
14 15 34.2 0 15
15 2 34.2 0 2
16 11 34.2 0 11
17 2 34.2 0 2
18 7 34.2 0 7
19 7 34.2 0 7
20 10 34.2 0 10
22 1 34.2 0 1
23 3 34.2 0 3
24 11 34.2 0 11
25 2 34.2 0 2
26 7 34.2 0 7
27 1 34.2 0 1
28 15 34.2 0 15
29 32 34.2 0 32
30 10 34.2 0 10
31 9 34.2 0 9
32 32 34.2 0 32
33 8 34.2 0 8
34 7 34.2 0 7
35 15 34.2 0 15
36 6 34.2 0 6
37 7 34.2 0 7
38 11 34.2 0 11
39 5 34.2 0 5
40 12 34.2 0 12
41 17 34.2 0 17
42 6 34.2 0 6
43 15 34.2 0 15
44 2 34.2 0 2
45 6 34.2 0 6
46 11 34.2 0 11
47 5 34.2 0 5
48 8 34.2 0 8
49 6 34.2 0 6
50 3 34.2 0 3
51 16 34.2 0 16
52 1 34.2 0 1
53 54 34.2 0 54
54 8 34.2 0 8
55 2 34.2 0 2
56 6 34.2 0 6
57 3 34.2 0 3
58 8 34.2 0 8
59 17 34.2 0 17
60 8 34.2 0 8
61 14 34.2 0 14
62 19 34.2 0 19
63 7 34.2 0 7
64 6 34.2 0 6
65 8 34.2 0 8
66 3 34.2 0 3
67 10 34.2 0 10
68 2 34.2 0 2
69 12 34.2 0 12
70 11 34.2 0 11
71 5 34.2 0 5
72 16 34.2 0 16
73 2 34.2 0 2
74 1 34.2 0 1
75 7 34.2 0 7
76 7 34.2 0 7
77 76 34.2 0 76
78 22 34.2 0 22
79 11 34.2 0 11
80 4 34.2 0 4
81 12 34.2 0 12
82 21 34.2 0 21
83 4 34.2 0 4
84 8 34.2 0 8
85 2 34.2 0 2
86 4 34.2 0 4
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X45_S159_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X45_S159_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.71 s (10 µs/read; 6.07 M reads/minute).
=== Summary ===
Total reads processed: 2,904,302
Reads with adapters: 1,006,606 (34.7%)
== Read fate breakdown ==
Reads that were too short: 284,950 (9.8%)
Reads written (passing filters): 2,619,352 (90.2%)
Total basepairs processed: 293,334,502 bp
Total written (filtered): 205,521,881 bp (70.1%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 912106 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.0%
G: 27.1%
T: 29.7%
none/other: 13.2%
Overview of removed sequences
length count expect max.err error counts
3 66119 45379.7 0 66119
4 29718 11344.9 0 29718
5 16051 2836.2 0 16051
6 11191 709.1 0 11191
7 9145 177.3 0 9145
8 8071 44.3 0 8071
9 8348 44.3 0 8348
10 8290 44.3 0 8290
11 8024 44.3 0 8024
12 8163 44.3 0 8163
13 8218 44.3 0 8218
14 8355 44.3 0 8355
15 8399 44.3 0 8399
16 8464 44.3 0 8464
17 8650 44.3 0 8650
18 8615 44.3 0 8615
19 8193 44.3 0 8193
20 8385 44.3 0 8385
21 8500 44.3 0 8500
22 8127 44.3 0 8127
23 7862 44.3 0 7862
24 8026 44.3 0 8026
25 7885 44.3 0 7885
26 7806 44.3 0 7806
27 8024 44.3 0 8024
28 8378 44.3 0 8378
29 8468 44.3 0 8468
30 8175 44.3 0 8175
31 8751 44.3 0 8751
32 8585 44.3 0 8585
33 8361 44.3 0 8361
34 8231 44.3 0 8231
35 8872 44.3 0 8872
36 8018 44.3 0 8018
37 8157 44.3 0 8157
38 7727 44.3 0 7727
39 8089 44.3 0 8089
40 8073 44.3 0 8073
41 8251 44.3 0 8251
42 8444 44.3 0 8444
43 8702 44.3 0 8702
44 7904 44.3 0 7904
45 8464 44.3 0 8464
46 8464 44.3 0 8464
47 8490 44.3 0 8490
48 8188 44.3 0 8188
49 12209 44.3 0 12209
50 14150 44.3 0 14150
51 8556 44.3 0 8556
52 8863 44.3 0 8863
53 8937 44.3 0 8937
54 7730 44.3 0 7730
55 8253 44.3 0 8253
56 8345 44.3 0 8345
57 7872 44.3 0 7872
58 8590 44.3 0 8590
59 8290 44.3 0 8290
60 8293 44.3 0 8293
61 8355 44.3 0 8355
62 8313 44.3 0 8313
63 7784 44.3 0 7784
64 8100 44.3 0 8100
65 7933 44.3 0 7933
66 7693 44.3 0 7693
67 7699 44.3 0 7699
68 7924 44.3 0 7924
69 7338 44.3 0 7338
70 6943 44.3 0 6943
71 7609 44.3 0 7609
72 7489 44.3 0 7489
73 6791 44.3 0 6791
74 6679 44.3 0 6679
75 6847 44.3 0 6847
76 6678 44.3 0 6678
77 6888 44.3 0 6888
78 7134 44.3 0 7134
79 8289 44.3 0 8289
80 8022 44.3 0 8022
81 9365 44.3 0 9365
82 11281 44.3 0 11281
83 11992 44.3 0 11992
84 13348 44.3 0 13348
85 14067 44.3 0 14067
86 120036 44.3 0 120036
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 32692 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.5%
C: 33.5%
G: 0.0%
T: 35.3%
none/other: 2.7%
Overview of removed sequences
length count expect max.err error counts
3 15042 45379.7 0 15042
4 3459 11344.9 0 3459
5 830 2836.2 0 830
6 384 709.1 0 384
7 291 177.3 0 291
8 314 44.3 0 314
9 255 44.3 0 255
10 260 44.3 0 260
11 249 44.3 0 249
12 213 44.3 0 213
13 205 44.3 0 205
14 199 44.3 0 199
15 199 44.3 0 199
16 202 44.3 0 202
17 234 44.3 0 234
18 209 44.3 0 209
19 219 44.3 0 219
20 221 44.3 0 221
21 207 44.3 0 207
22 188 44.3 0 188
23 204 44.3 0 204
24 195 44.3 0 195
25 213 44.3 0 213
26 210 44.3 0 210
27 201 44.3 0 201
28 220 44.3 0 220
29 192 44.3 0 192
30 189 44.3 0 189
31 168 44.3 0 168
32 194 44.3 0 194
33 207 44.3 0 207
34 194 44.3 0 194
35 198 44.3 0 198
36 177 44.3 0 177
37 179 44.3 0 179
38 184 44.3 0 184
39 169 44.3 0 169
40 173 44.3 0 173
41 189 44.3 0 189
42 185 44.3 0 185
43 175 44.3 0 175
44 175 44.3 0 175
45 180 44.3 0 180
46 172 44.3 0 172
47 165 44.3 0 165
48 168 44.3 0 168
49 166 44.3 0 166
50 172 44.3 0 172
51 138 44.3 0 138
52 159 44.3 0 159
53 151 44.3 0 151
54 143 44.3 0 143
55 160 44.3 0 160
56 147 44.3 0 147
57 145 44.3 0 145
58 170 44.3 0 170
59 162 44.3 0 162
60 137 44.3 0 137
61 158 44.3 0 158
62 129 44.3 0 129
63 149 44.3 0 149
64 105 44.3 0 105
65 107 44.3 0 107
66 103 44.3 0 103
67 91 44.3 0 91
68 79 44.3 0 79
69 71 44.3 0 71
70 72 44.3 0 72
71 65 44.3 0 65
72 66 44.3 0 66
73 73 44.3 0 73
74 54 44.3 0 54
75 31 44.3 0 31
76 41 44.3 0 41
77 16 44.3 0 16
78 33 44.3 0 33
79 37 44.3 0 37
80 29 44.3 0 29
81 30 44.3 0 30
82 34 44.3 0 34
83 48 44.3 0 48
84 47 44.3 0 47
85 40 44.3 0 40
86 878 44.3 0 878
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61808 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 36.0%
C: 23.0%
G: 21.0%
T: 20.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 46163 45379.7 0 46163
4 10302 11344.9 0 10302
5 2317 2836.2 0 2317
6 341 709.1 0 341
7 24 177.3 0 24
8 33 177.3 0 33
9 26 177.3 0 26
10 34 177.3 0 34
11 32 177.3 0 32
12 25 177.3 0 25
13 34 177.3 0 34
14 35 177.3 0 35
15 30 177.3 0 30
16 40 177.3 0 40
17 35 177.3 0 35
18 30 177.3 0 30
19 36 177.3 0 36
20 28 177.3 0 28
21 35 177.3 0 35
22 23 177.3 0 23
23 23 177.3 0 23
24 40 177.3 0 40
25 39 177.3 0 39
26 30 177.3 0 30
27 34 177.3 0 34
28 41 177.3 0 41
29 28 177.3 0 28
30 44 177.3 0 44
31 26 177.3 0 26
32 41 177.3 0 41
33 28 177.3 0 28
34 30 177.3 0 30
35 21 177.3 0 21
36 44 177.3 0 44
37 33 177.3 0 33
38 30 177.3 0 30
39 28 177.3 0 28
40 22 177.3 0 22
41 44 177.3 0 44
42 29 177.3 0 29
43 32 177.3 0 32
44 36 177.3 0 36
45 29 177.3 0 29
46 25 177.3 0 25
47 36 177.3 0 36
48 46 177.3 0 46
49 35 177.3 0 35
50 35 177.3 0 35
51 35 177.3 0 35
52 34 177.3 0 34
53 37 177.3 0 37
54 28 177.3 0 28
55 30 177.3 0 30
56 17 177.3 0 17
57 32 177.3 0 32
58 47 177.3 0 47
59 35 177.3 0 35
60 29 177.3 0 29
61 32 177.3 0 32
62 45 177.3 0 45
63 21 177.3 0 21
64 40 177.3 0 40
65 46 177.3 0 46
66 52 177.3 0 52
67 36 177.3 0 36
68 26 177.3 0 26
69 35 177.3 0 35
70 36 177.3 0 36
71 41 177.3 0 41
72 24 177.3 0 24
73 25 177.3 0 25
74 21 177.3 0 21
75 30 177.3 0 30
76 22 177.3 0 22
77 56 177.3 0 56
78 43 177.3 0 43
79 26 177.3 0 26
80 29 177.3 0 29
81 28 177.3 0 28
82 39 177.3 0 39
83 52 177.3 0 52
84 31 177.3 0 31
85 33 177.3 0 33
86 63 177.3 0 63
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X45_S159_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X45_S159_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 28.20 s (10 µs/read; 6.30 M reads/minute).
=== Summary ===
Total reads processed: 2,959,192
Reads with adapters: 1,035,165 (35.0%)
== Read fate breakdown ==
Reads that were too short: 298,037 (10.1%)
Reads written (passing filters): 2,661,155 (89.9%)
Total basepairs processed: 298,878,392 bp
Total written (filtered): 208,621,265 bp (69.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 938689 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 29.9%
G: 27.0%
T: 29.6%
none/other: 13.5%
Overview of removed sequences
length count expect max.err error counts
3 67031 46237.4 0 67031
4 30146 11559.3 0 30146
5 16213 2889.8 0 16213
6 11205 722.5 0 11205
7 9341 180.6 0 9341
8 8488 45.2 0 8488
9 8352 45.2 0 8352
10 8410 45.2 0 8410
11 8360 45.2 0 8360
12 8454 45.2 0 8454
13 8346 45.2 0 8346
14 8589 45.2 0 8589
15 8674 45.2 0 8674
16 8616 45.2 0 8616
17 8513 45.2 0 8513
18 8714 45.2 0 8714
19 8308 45.2 0 8308
20 8521 45.2 0 8521
21 8569 45.2 0 8569
22 8119 45.2 0 8119
23 8132 45.2 0 8132
24 8038 45.2 0 8038
25 7933 45.2 0 7933
26 8153 45.2 0 8153
27 8072 45.2 0 8072
28 8410 45.2 0 8410
29 8659 45.2 0 8659
30 8338 45.2 0 8338
31 9087 45.2 0 9087
32 8801 45.2 0 8801
33 8586 45.2 0 8586
34 8588 45.2 0 8588
35 8870 45.2 0 8870
36 8134 45.2 0 8134
37 8078 45.2 0 8078
38 7789 45.2 0 7789
39 8355 45.2 0 8355
40 8221 45.2 0 8221
41 8326 45.2 0 8326
42 8706 45.2 0 8706
43 8953 45.2 0 8953
44 8341 45.2 0 8341
45 8598 45.2 0 8598
46 8894 45.2 0 8894
47 8674 45.2 0 8674
48 8405 45.2 0 8405
49 12464 45.2 0 12464
50 14424 45.2 0 14424
51 8629 45.2 0 8629
52 9481 45.2 0 9481
53 9200 45.2 0 9200
54 7939 45.2 0 7939
55 8467 45.2 0 8467
56 8638 45.2 0 8638
57 8236 45.2 0 8236
58 9017 45.2 0 9017
59 8596 45.2 0 8596
60 8554 45.2 0 8554
61 8681 45.2 0 8681
62 8452 45.2 0 8452
63 8099 45.2 0 8099
64 8275 45.2 0 8275
65 8118 45.2 0 8118
66 7785 45.2 0 7785
67 8105 45.2 0 8105
68 8101 45.2 0 8101
69 7741 45.2 0 7741
70 7285 45.2 0 7285
71 7566 45.2 0 7566
72 7752 45.2 0 7752
73 7394 45.2 0 7394
74 7038 45.2 0 7038
75 7167 45.2 0 7167
76 6955 45.2 0 6955
77 7026 45.2 0 7026
78 7476 45.2 0 7476
79 8681 45.2 0 8681
80 8310 45.2 0 8310
81 9906 45.2 0 9906
82 11822 45.2 0 11822
83 12697 45.2 0 12697
84 13722 45.2 0 13722
85 14541 45.2 0 14541
86 126239 45.2 0 126239
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 33345 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 28.6%
C: 33.6%
G: 0.0%
T: 35.2%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 15476 46237.4 0 15476
4 3403 11559.3 0 3403
5 856 2889.8 0 856
6 357 722.5 0 357
7 331 180.6 0 331
8 317 45.2 0 317
9 307 45.2 0 307
10 255 45.2 0 255
11 262 45.2 0 262
12 238 45.2 0 238
13 231 45.2 0 231
14 245 45.2 0 245
15 239 45.2 0 239
16 230 45.2 0 230
17 191 45.2 0 191
18 207 45.2 0 207
19 227 45.2 0 227
20 218 45.2 0 218
21 206 45.2 0 206
22 209 45.2 0 209
23 215 45.2 0 215
24 232 45.2 0 232
25 201 45.2 0 201
26 204 45.2 0 204
27 191 45.2 0 191
28 185 45.2 0 185
29 182 45.2 0 182
30 181 45.2 0 181
31 185 45.2 0 185
32 176 45.2 0 176
33 187 45.2 0 187
34 225 45.2 0 225
35 194 45.2 0 194
36 213 45.2 0 213
37 179 45.2 0 179
38 177 45.2 0 177
39 176 45.2 0 176
40 190 45.2 0 190
41 191 45.2 0 191
42 173 45.2 0 173
43 182 45.2 0 182
44 170 45.2 0 170
45 217 45.2 0 217
46 176 45.2 0 176
47 175 45.2 0 175
48 166 45.2 0 166
49 164 45.2 0 164
50 166 45.2 0 166
51 182 45.2 0 182
52 151 45.2 0 151
53 158 45.2 0 158
54 163 45.2 0 163
55 148 45.2 0 148
56 145 45.2 0 145
57 178 45.2 0 178
58 163 45.2 0 163
59 144 45.2 0 144
60 134 45.2 0 134
61 128 45.2 0 128
62 108 45.2 0 108
63 105 45.2 0 105
64 104 45.2 0 104
65 116 45.2 0 116
66 113 45.2 0 113
67 109 45.2 0 109
68 90 45.2 0 90
69 87 45.2 0 87
70 81 45.2 0 81
71 61 45.2 0 61
72 60 45.2 0 60
73 62 45.2 0 62
74 47 45.2 0 47
75 41 45.2 0 41
76 36 45.2 0 36
77 27 45.2 0 27
78 31 45.2 0 31
79 36 45.2 0 36
80 29 45.2 0 29
81 27 45.2 0 27
82 32 45.2 0 32
83 31 45.2 0 31
84 33 45.2 0 33
85 42 45.2 0 42
86 865 45.2 0 865
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 63131 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.6%
C: 23.1%
G: 21.1%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 47311 46237.4 0 47311
4 10477 11559.3 0 10477
5 2237 2889.8 0 2237
6 330 722.5 0 330
7 27 180.6 0 27
8 29 180.6 0 29
9 23 180.6 0 23
10 31 180.6 0 31
11 36 180.6 0 36
12 27 180.6 0 27
13 36 180.6 0 36
14 29 180.6 0 29
15 40 180.6 0 40
16 37 180.6 0 37
17 25 180.6 0 25
18 36 180.6 0 36
19 46 180.6 0 46
20 24 180.6 0 24
21 38 180.6 0 38
22 30 180.6 0 30
23 40 180.6 0 40
24 37 180.6 0 37
25 39 180.6 0 39
26 40 180.6 0 40
27 37 180.6 0 37
28 35 180.6 0 35
29 35 180.6 0 35
30 28 180.6 0 28
31 28 180.6 0 28
32 44 180.6 0 44
33 41 180.6 0 41
34 35 180.6 0 35
35 32 180.6 0 32
36 32 180.6 0 32
37 27 180.6 0 27
38 24 180.6 0 24
39 29 180.6 0 29
40 23 180.6 0 23
41 26 180.6 0 26
42 31 180.6 0 31
43 36 180.6 0 36
44 39 180.6 0 39
45 27 180.6 0 27
46 28 180.6 0 28
47 42 180.6 0 42
48 34 180.6 0 34
49 36 180.6 0 36
50 53 180.6 0 53
51 36 180.6 0 36
52 51 180.6 0 51
53 27 180.6 0 27
54 25 180.6 0 25
55 56 180.6 0 56
56 36 180.6 0 36
57 34 180.6 0 34
58 43 180.6 0 43
59 32 180.6 0 32
60 35 180.6 0 35
61 34 180.6 0 34
62 44 180.6 0 44
63 38 180.6 0 38
64 41 180.6 0 41
65 44 180.6 0 44
66 42 180.6 0 42
67 39 180.6 0 39
68 26 180.6 0 26
69 30 180.6 0 30
70 23 180.6 0 23
71 41 180.6 0 41
72 36 180.6 0 36
73 27 180.6 0 27
74 37 180.6 0 37
75 29 180.6 0 29
76 16 180.6 0 16
77 68 180.6 0 68
78 42 180.6 0 42
79 32 180.6 0 32
80 28 180.6 0 28
81 23 180.6 0 23
82 26 180.6 0 26
83 50 180.6 0 50
84 34 180.6 0 34
85 34 180.6 0 34
86 45 180.6 0 45
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X46_S153_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X46_S153_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 30.60 s (9 µs/read; 6.53 M reads/minute).
=== Summary ===
Total reads processed: 3,328,202
Reads with adapters: 1,189,428 (35.7%)
== Read fate breakdown ==
Reads that were too short: 324,437 (9.7%)
Reads written (passing filters): 3,003,765 (90.3%)
Total basepairs processed: 336,148,402 bp
Total written (filtered): 233,847,995 bp (69.6%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1071272 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.6%
G: 27.2%
T: 28.9%
none/other: 12.3%
Overview of removed sequences
length count expect max.err error counts
3 78544 52003.2 0 78544
4 34654 13000.8 0 34654
5 18083 3250.2 0 18083
6 12421 812.5 0 12421
7 10207 203.1 0 10207
8 8972 50.8 0 8972
9 9255 50.8 0 9255
10 9242 50.8 0 9242
11 9136 50.8 0 9136
12 8935 50.8 0 8935
13 9217 50.8 0 9217
14 9517 50.8 0 9517
15 9732 50.8 0 9732
16 9819 50.8 0 9819
17 9569 50.8 0 9569
18 10083 50.8 0 10083
19 9551 50.8 0 9551
20 9737 50.8 0 9737
21 9918 50.8 0 9918
22 9530 50.8 0 9530
23 9257 50.8 0 9257
24 9444 50.8 0 9444
25 9473 50.8 0 9473
26 9315 50.8 0 9315
27 9280 50.8 0 9280
28 9778 50.8 0 9778
29 9800 50.8 0 9800
30 9521 50.8 0 9521
31 9965 50.8 0 9965
32 9624 50.8 0 9624
33 9729 50.8 0 9729
34 9631 50.8 0 9631
35 9992 50.8 0 9992
36 9970 50.8 0 9970
37 9620 50.8 0 9620
38 9369 50.8 0 9369
39 9693 50.8 0 9693
40 10065 50.8 0 10065
41 9910 50.8 0 9910
42 10290 50.8 0 10290
43 10300 50.8 0 10300
44 9899 50.8 0 9899
45 10284 50.8 0 10284
46 10598 50.8 0 10598
47 10455 50.8 0 10455
48 10316 50.8 0 10316
49 14206 50.8 0 14206
50 16113 50.8 0 16113
51 10763 50.8 0 10763
52 11684 50.8 0 11684
53 10927 50.8 0 10927
54 9951 50.8 0 9951
55 10382 50.8 0 10382
56 10583 50.8 0 10583
57 10188 50.8 0 10188
58 10887 50.8 0 10887
59 10598 50.8 0 10598
60 10523 50.8 0 10523
61 10563 50.8 0 10563
62 10797 50.8 0 10797
63 10256 50.8 0 10256
64 10288 50.8 0 10288
65 10247 50.8 0 10247
66 10032 50.8 0 10032
67 9881 50.8 0 9881
68 9875 50.8 0 9875
69 9319 50.8 0 9319
70 9088 50.8 0 9088
71 9582 50.8 0 9582
72 9226 50.8 0 9226
73 8956 50.8 0 8956
74 8388 50.8 0 8388
75 8402 50.8 0 8402
76 8081 50.8 0 8081
77 8230 50.8 0 8230
78 8068 50.8 0 8068
79 9110 50.8 0 9110
80 8662 50.8 0 8662
81 9812 50.8 0 9812
82 11871 50.8 0 11871
83 13347 50.8 0 13347
84 14120 50.8 0 14120
85 14898 50.8 0 14898
86 131668 50.8 0 131668
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 49555 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.7%
C: 32.8%
G: 0.0%
T: 37.9%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 15796 52003.2 0 15796
4 3823 13000.8 0 3823
5 1137 3250.2 0 1137
6 668 812.5 0 668
7 613 203.1 0 613
8 568 50.8 0 568
9 544 50.8 0 544
10 565 50.8 0 565
11 492 50.8 0 492
12 510 50.8 0 510
13 489 50.8 0 489
14 462 50.8 0 462
15 465 50.8 0 465
16 438 50.8 0 438
17 438 50.8 0 438
18 474 50.8 0 474
19 455 50.8 0 455
20 395 50.8 0 395
21 446 50.8 0 446
22 464 50.8 0 464
23 451 50.8 0 451
24 493 50.8 0 493
25 477 50.8 0 477
26 475 50.8 0 475
27 439 50.8 0 439
28 405 50.8 0 405
29 390 50.8 0 390
30 418 50.8 0 418
31 422 50.8 0 422
32 406 50.8 0 406
33 437 50.8 0 437
34 441 50.8 0 441
35 448 50.8 0 448
36 415 50.8 0 415
37 443 50.8 0 443
38 396 50.8 0 396
39 401 50.8 0 401
40 408 50.8 0 408
41 388 50.8 0 388
42 423 50.8 0 423
43 442 50.8 0 442
44 383 50.8 0 383
45 404 50.8 0 404
46 443 50.8 0 443
47 434 50.8 0 434
48 379 50.8 0 379
49 426 50.8 0 426
50 425 50.8 0 425
51 406 50.8 0 406
52 360 50.8 0 360
53 409 50.8 0 409
54 397 50.8 0 397
55 372 50.8 0 372
56 368 50.8 0 368
57 348 50.8 0 348
58 347 50.8 0 347
59 341 50.8 0 341
60 376 50.8 0 376
61 322 50.8 0 322
62 290 50.8 0 290
63 303 50.8 0 303
64 253 50.8 0 253
65 252 50.8 0 252
66 227 50.8 0 227
67 213 50.8 0 213
68 188 50.8 0 188
69 185 50.8 0 185
70 159 50.8 0 159
71 112 50.8 0 112
72 116 50.8 0 116
73 110 50.8 0 110
74 102 50.8 0 102
75 89 50.8 0 89
76 82 50.8 0 82
77 51 50.8 0 51
78 54 50.8 0 54
79 54 50.8 0 54
80 32 50.8 0 32
81 31 50.8 0 31
82 29 50.8 0 29
83 48 50.8 0 48
84 46 50.8 0 46
85 59 50.8 0 59
86 1270 50.8 0 1270
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 68601 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.7%
C: 23.5%
G: 20.9%
T: 19.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 50762 52003.2 0 50762
4 11888 13000.8 0 11888
5 2268 3250.2 0 2268
6 331 812.5 0 331
7 35 203.1 0 35
8 43 203.1 0 43
9 34 203.1 0 34
10 34 203.1 0 34
11 37 203.1 0 37
12 38 203.1 0 38
13 34 203.1 0 34
14 40 203.1 0 40
15 63 203.1 0 63
16 36 203.1 0 36
17 42 203.1 0 42
18 58 203.1 0 58
19 39 203.1 0 39
20 49 203.1 0 49
21 53 203.1 0 53
22 47 203.1 0 47
23 44 203.1 0 44
24 30 203.1 0 30
25 46 203.1 0 46
26 42 203.1 0 42
27 41 203.1 0 41
28 43 203.1 0 43
29 43 203.1 0 43
30 57 203.1 0 57
31 49 203.1 0 49
32 46 203.1 0 46
33 56 203.1 0 56
34 35 203.1 0 35
35 46 203.1 0 46
36 59 203.1 0 59
37 56 203.1 0 56
38 58 203.1 0 58
39 42 203.1 0 42
40 29 203.1 0 29
41 44 203.1 0 44
42 51 203.1 0 51
43 48 203.1 0 48
44 38 203.1 0 38
45 26 203.1 0 26
46 34 203.1 0 34
47 32 203.1 0 32
48 47 203.1 0 47
49 40 203.1 0 40
50 36 203.1 0 36
51 44 203.1 0 44
52 46 203.1 0 46
53 44 203.1 0 44
54 39 203.1 0 39
55 39 203.1 0 39
56 39 203.1 0 39
57 36 203.1 0 36
58 32 203.1 0 32
59 44 203.1 0 44
60 36 203.1 0 36
61 36 203.1 0 36
62 44 203.1 0 44
63 34 203.1 0 34
64 25 203.1 0 25
65 54 203.1 0 54
66 37 203.1 0 37
67 36 203.1 0 36
68 49 203.1 0 49
69 35 203.1 0 35
70 43 203.1 0 43
71 45 203.1 0 45
72 31 203.1 0 31
73 38 203.1 0 38
74 27 203.1 0 27
75 37 203.1 0 37
76 30 203.1 0 30
77 79 203.1 0 79
78 52 203.1 0 52
79 39 203.1 0 39
80 30 203.1 0 30
81 39 203.1 0 39
82 39 203.1 0 39
83 37 203.1 0 37
84 39 203.1 0 39
85 40 203.1 0 40
86 58 203.1 0 58
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X46_S153_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X46_S153_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 30.74 s (9 µs/read; 6.63 M reads/minute).
=== Summary ===
Total reads processed: 3,396,024
Reads with adapters: 1,224,355 (36.1%)
== Read fate breakdown ==
Reads that were too short: 339,901 (10.0%)
Reads written (passing filters): 3,056,123 (90.0%)
Total basepairs processed: 342,998,424 bp
Total written (filtered): 237,647,359 bp (69.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1103233 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.5%
G: 27.2%
T: 28.6%
none/other: 12.7%
Overview of removed sequences
length count expect max.err error counts
3 79475 53062.9 0 79475
4 35050 13265.7 0 35050
5 18465 3316.4 0 18465
6 12352 829.1 0 12352
7 10399 207.3 0 10399
8 9125 51.8 0 9125
9 9252 51.8 0 9252
10 9592 51.8 0 9592
11 9064 51.8 0 9064
12 9302 51.8 0 9302
13 9365 51.8 0 9365
14 9658 51.8 0 9658
15 9705 51.8 0 9705
16 9715 51.8 0 9715
17 9949 51.8 0 9949
18 10101 51.8 0 10101
19 9855 51.8 0 9855
20 9759 51.8 0 9759
21 9898 51.8 0 9898
22 9660 51.8 0 9660
23 9567 51.8 0 9567
24 9419 51.8 0 9419
25 9573 51.8 0 9573
26 9433 51.8 0 9433
27 9375 51.8 0 9375
28 9746 51.8 0 9746
29 10022 51.8 0 10022
30 9801 51.8 0 9801
31 10268 51.8 0 10268
32 9936 51.8 0 9936
33 9857 51.8 0 9857
34 9792 51.8 0 9792
35 10252 51.8 0 10252
36 10184 51.8 0 10184
37 9735 51.8 0 9735
38 9592 51.8 0 9592
39 10068 51.8 0 10068
40 10139 51.8 0 10139
41 10105 51.8 0 10105
42 10671 51.8 0 10671
43 10511 51.8 0 10511
44 10139 51.8 0 10139
45 10627 51.8 0 10627
46 11040 51.8 0 11040
47 10839 51.8 0 10839
48 10711 51.8 0 10711
49 14580 51.8 0 14580
50 16866 51.8 0 16866
51 10918 51.8 0 10918
52 11869 51.8 0 11869
53 11461 51.8 0 11461
54 10563 51.8 0 10563
55 10917 51.8 0 10917
56 11027 51.8 0 11027
57 10549 51.8 0 10549
58 11323 51.8 0 11323
59 11047 51.8 0 11047
60 11015 51.8 0 11015
61 10982 51.8 0 10982
62 11048 51.8 0 11048
63 10597 51.8 0 10597
64 10411 51.8 0 10411
65 10605 51.8 0 10605
66 10358 51.8 0 10358
67 10230 51.8 0 10230
68 9950 51.8 0 9950
69 9902 51.8 0 9902
70 9394 51.8 0 9394
71 9974 51.8 0 9974
72 9877 51.8 0 9877
73 9286 51.8 0 9286
74 8860 51.8 0 8860
75 8857 51.8 0 8857
76 8193 51.8 0 8193
77 8699 51.8 0 8699
78 8470 51.8 0 8470
79 9304 51.8 0 9304
80 9212 51.8 0 9212
81 10295 51.8 0 10295
82 12396 51.8 0 12396
83 13698 51.8 0 13698
84 14593 51.8 0 14593
85 15112 51.8 0 15112
86 139652 51.8 0 139652
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 51172 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 26.6%
C: 32.9%
G: 0.0%
T: 38.0%
none/other: 2.5%
Overview of removed sequences
length count expect max.err error counts
3 16139 53062.9 0 16139
4 3976 13265.7 0 3976
5 1269 3316.4 0 1269
6 686 829.1 0 686
7 600 207.3 0 600
8 573 51.8 0 573
9 546 51.8 0 546
10 539 51.8 0 539
11 525 51.8 0 525
12 514 51.8 0 514
13 528 51.8 0 528
14 492 51.8 0 492
15 506 51.8 0 506
16 441 51.8 0 441
17 440 51.8 0 440
18 471 51.8 0 471
19 451 51.8 0 451
20 480 51.8 0 480
21 431 51.8 0 431
22 469 51.8 0 469
23 451 51.8 0 451
24 457 51.8 0 457
25 462 51.8 0 462
26 434 51.8 0 434
27 422 51.8 0 422
28 456 51.8 0 456
29 453 51.8 0 453
30 415 51.8 0 415
31 448 51.8 0 448
32 478 51.8 0 478
33 463 51.8 0 463
34 452 51.8 0 452
35 447 51.8 0 447
36 440 51.8 0 440
37 472 51.8 0 472
38 477 51.8 0 477
39 434 51.8 0 434
40 421 51.8 0 421
41 438 51.8 0 438
42 436 51.8 0 436
43 411 51.8 0 411
44 417 51.8 0 417
45 448 51.8 0 448
46 410 51.8 0 410
47 445 51.8 0 445
48 433 51.8 0 433
49 408 51.8 0 408
50 437 51.8 0 437
51 374 51.8 0 374
52 408 51.8 0 408
53 417 51.8 0 417
54 366 51.8 0 366
55 400 51.8 0 400
56 370 51.8 0 370
57 389 51.8 0 389
58 323 51.8 0 323
59 375 51.8 0 375
60 408 51.8 0 408
61 345 51.8 0 345
62 283 51.8 0 283
63 308 51.8 0 308
64 304 51.8 0 304
65 257 51.8 0 257
66 270 51.8 0 270
67 221 51.8 0 221
68 192 51.8 0 192
69 170 51.8 0 170
70 152 51.8 0 152
71 149 51.8 0 149
72 148 51.8 0 148
73 102 51.8 0 102
74 109 51.8 0 109
75 87 51.8 0 87
76 65 51.8 0 65
77 66 51.8 0 66
78 56 51.8 0 56
79 60 51.8 0 60
80 43 51.8 0 43
81 36 51.8 0 36
82 39 51.8 0 39
83 50 51.8 0 50
84 65 51.8 0 65
85 59 51.8 0 59
86 1265 51.8 0 1265
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69950 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.5%
C: 23.7%
G: 20.6%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51742 53062.9 0 51742
4 12105 13265.7 0 12105
5 2410 3316.4 0 2410
6 301 829.1 0 301
7 31 207.3 0 31
8 34 207.3 0 34
9 36 207.3 0 36
10 36 207.3 0 36
11 42 207.3 0 42
12 53 207.3 0 53
13 41 207.3 0 41
14 42 207.3 0 42
15 48 207.3 0 48
16 35 207.3 0 35
17 38 207.3 0 38
18 55 207.3 0 55
19 50 207.3 0 50
20 48 207.3 0 48
21 62 207.3 0 62
22 44 207.3 0 44
23 36 207.3 0 36
24 41 207.3 0 41
25 57 207.3 0 57
26 43 207.3 0 43
27 46 207.3 0 46
28 32 207.3 0 32
29 40 207.3 0 40
30 75 207.3 0 75
31 34 207.3 0 34
32 40 207.3 0 40
33 49 207.3 0 49
34 47 207.3 0 47
35 58 207.3 0 58
36 79 207.3 0 79
37 46 207.3 0 46
38 37 207.3 0 37
39 51 207.3 0 51
40 38 207.3 0 38
41 46 207.3 0 46
42 47 207.3 0 47
43 39 207.3 0 39
44 38 207.3 0 38
45 29 207.3 0 29
46 23 207.3 0 23
47 49 207.3 0 49
48 43 207.3 0 43
49 46 207.3 0 46
50 48 207.3 0 48
51 54 207.3 0 54
52 39 207.3 0 39
53 35 207.3 0 35
54 43 207.3 0 43
55 34 207.3 0 34
56 32 207.3 0 32
57 31 207.3 0 31
58 26 207.3 0 26
59 43 207.3 0 43
60 37 207.3 0 37
61 39 207.3 0 39
62 49 207.3 0 49
63 31 207.3 0 31
64 28 207.3 0 28
65 56 207.3 0 56
66 50 207.3 0 50
67 50 207.3 0 50
68 39 207.3 0 39
69 37 207.3 0 37
70 38 207.3 0 38
71 38 207.3 0 38
72 26 207.3 0 26
73 32 207.3 0 32
74 39 207.3 0 39
75 26 207.3 0 26
76 32 207.3 0 32
77 89 207.3 0 89
78 34 207.3 0 34
79 37 207.3 0 37
80 48 207.3 0 48
81 44 207.3 0 44
82 33 207.3 0 33
83 48 207.3 0 48
84 48 207.3 0 48
85 39 207.3 0 39
86 36 207.3 0 36
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X47_S150_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X47_S150_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 37.66 s (11 µs/read; 5.42 M reads/minute).
=== Summary ===
Total reads processed: 3,403,891
Reads with adapters: 1,300,494 (38.2%)
== Read fate breakdown ==
Reads that were too short: 381,305 (11.2%)
Reads written (passing filters): 3,022,586 (88.8%)
Total basepairs processed: 343,792,991 bp
Total written (filtered): 233,091,885 bp (67.8%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1162081 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.2%
G: 26.1%
T: 27.9%
none/other: 14.8%
Overview of removed sequences
length count expect max.err error counts
3 75030 53185.8 0 75030
4 34713 13296.4 0 34713
5 17938 3324.1 0 17938
6 12513 831.0 0 12513
7 10399 207.8 0 10399
8 9051 51.9 0 9051
9 9426 51.9 0 9426
10 9503 51.9 0 9503
11 9085 51.9 0 9085
12 9076 51.9 0 9076
13 9454 51.9 0 9454
14 9882 51.9 0 9882
15 10111 51.9 0 10111
16 10110 51.9 0 10110
17 10287 51.9 0 10287
18 10289 51.9 0 10289
19 10149 51.9 0 10149
20 9983 51.9 0 9983
21 10420 51.9 0 10420
22 10185 51.9 0 10185
23 10184 51.9 0 10184
24 9680 51.9 0 9680
25 9902 51.9 0 9902
26 9939 51.9 0 9939
27 9715 51.9 0 9715
28 10384 51.9 0 10384
29 10602 51.9 0 10602
30 10137 51.9 0 10137
31 10340 51.9 0 10340
32 10035 51.9 0 10035
33 10412 51.9 0 10412
34 10450 51.9 0 10450
35 10274 51.9 0 10274
36 10257 51.9 0 10257
37 10323 51.9 0 10323
38 9971 51.9 0 9971
39 10306 51.9 0 10306
40 10439 51.9 0 10439
41 10262 51.9 0 10262
42 10622 51.9 0 10622
43 10872 51.9 0 10872
44 10079 51.9 0 10079
45 10686 51.9 0 10686
46 10725 51.9 0 10725
47 10817 51.9 0 10817
48 10966 51.9 0 10966
49 13069 51.9 0 13069
50 14779 51.9 0 14779
51 11605 51.9 0 11605
52 11931 51.9 0 11931
53 11766 51.9 0 11766
54 11600 51.9 0 11600
55 11828 51.9 0 11828
56 11908 51.9 0 11908
57 11941 51.9 0 11941
58 12534 51.9 0 12534
59 12033 51.9 0 12033
60 12331 51.9 0 12331
61 12670 51.9 0 12670
62 12256 51.9 0 12256
63 12202 51.9 0 12202
64 12029 51.9 0 12029
65 11937 51.9 0 11937
66 11781 51.9 0 11781
67 11686 51.9 0 11686
68 11374 51.9 0 11374
69 10948 51.9 0 10948
70 10587 51.9 0 10587
71 11271 51.9 0 11271
72 10451 51.9 0 10451
73 10088 51.9 0 10088
74 9507 51.9 0 9507
75 8955 51.9 0 8955
76 8795 51.9 0 8795
77 9542 51.9 0 9542
78 8685 51.9 0 8685
79 9368 51.9 0 9368
80 8810 51.9 0 8810
81 10054 51.9 0 10054
82 11697 51.9 0 11697
83 13169 51.9 0 13169
84 14501 51.9 0 14501
85 14872 51.9 0 14872
86 171538 51.9 0 171538
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 69306 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 25.0%
C: 32.9%
G: 0.0%
T: 39.6%
none/other: 2.5%
Overview of removed sequences
length count expect max.err error counts
3 15066 53185.8 0 15066
4 4165 13296.4 0 4165
5 1650 3324.1 0 1650
6 1093 831.0 0 1093
7 1049 207.8 0 1049
8 1101 51.9 0 1101
9 937 51.9 0 937
10 963 51.9 0 963
11 933 51.9 0 933
12 939 51.9 0 939
13 841 51.9 0 841
14 887 51.9 0 887
15 833 51.9 0 833
16 806 51.9 0 806
17 826 51.9 0 826
18 818 51.9 0 818
19 815 51.9 0 815
20 834 51.9 0 834
21 794 51.9 0 794
22 795 51.9 0 795
23 789 51.9 0 789
24 824 51.9 0 824
25 797 51.9 0 797
26 705 51.9 0 705
27 763 51.9 0 763
28 735 51.9 0 735
29 696 51.9 0 696
30 754 51.9 0 754
31 717 51.9 0 717
32 738 51.9 0 738
33 806 51.9 0 806
34 711 51.9 0 711
35 714 51.9 0 714
36 708 51.9 0 708
37 700 51.9 0 700
38 662 51.9 0 662
39 652 51.9 0 652
40 682 51.9 0 682
41 686 51.9 0 686
42 701 51.9 0 701
43 684 51.9 0 684
44 691 51.9 0 691
45 727 51.9 0 727
46 782 51.9 0 782
47 707 51.9 0 707
48 706 51.9 0 706
49 623 51.9 0 623
50 598 51.9 0 598
51 607 51.9 0 607
52 620 51.9 0 620
53 632 51.9 0 632
54 559 51.9 0 559
55 606 51.9 0 606
56 613 51.9 0 613
57 571 51.9 0 571
58 592 51.9 0 592
59 601 51.9 0 601
60 505 51.9 0 505
61 517 51.9 0 517
62 505 51.9 0 505
63 500 51.9 0 500
64 423 51.9 0 423
65 399 51.9 0 399
66 371 51.9 0 371
67 336 51.9 0 336
68 328 51.9 0 328
69 274 51.9 0 274
70 250 51.9 0 250
71 200 51.9 0 200
72 210 51.9 0 210
73 168 51.9 0 168
74 147 51.9 0 147
75 116 51.9 0 116
76 105 51.9 0 105
77 89 51.9 0 89
78 99 51.9 0 99
79 68 51.9 0 68
80 76 51.9 0 76
81 56 51.9 0 56
82 52 51.9 0 52
83 60 51.9 0 60
84 54 51.9 0 54
85 72 51.9 0 72
86 1722 51.9 0 1722
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69107 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.4%
C: 22.6%
G: 21.3%
T: 20.6%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 51711 53185.8 0 51711
4 11667 13296.4 0 11667
5 2091 3324.1 0 2091
6 273 831.0 0 273
7 35 207.8 0 35
8 26 207.8 0 26
9 43 207.8 0 43
10 32 207.8 0 32
11 37 207.8 0 37
12 33 207.8 0 33
13 43 207.8 0 43
14 37 207.8 0 37
15 33 207.8 0 33
16 36 207.8 0 36
17 39 207.8 0 39
18 44 207.8 0 44
19 54 207.8 0 54
20 53 207.8 0 53
21 38 207.8 0 38
22 39 207.8 0 39
23 41 207.8 0 41
24 34 207.8 0 34
25 33 207.8 0 33
26 60 207.8 0 60
27 30 207.8 0 30
28 39 207.8 0 39
29 52 207.8 0 52
30 55 207.8 0 55
31 35 207.8 0 35
32 38 207.8 0 38
33 59 207.8 0 59
34 40 207.8 0 40
35 36 207.8 0 36
36 68 207.8 0 68
37 32 207.8 0 32
38 45 207.8 0 45
39 48 207.8 0 48
40 32 207.8 0 32
41 51 207.8 0 51
42 42 207.8 0 42
43 43 207.8 0 43
44 30 207.8 0 30
45 44 207.8 0 44
46 37 207.8 0 37
47 43 207.8 0 43
48 44 207.8 0 44
49 48 207.8 0 48
50 36 207.8 0 36
51 46 207.8 0 46
52 52 207.8 0 52
53 46 207.8 0 46
54 38 207.8 0 38
55 41 207.8 0 41
56 26 207.8 0 26
57 44 207.8 0 44
58 36 207.8 0 36
59 36 207.8 0 36
60 38 207.8 0 38
61 29 207.8 0 29
62 51 207.8 0 51
63 32 207.8 0 32
64 34 207.8 0 34
65 49 207.8 0 49
66 25 207.8 0 25
67 27 207.8 0 27
68 25 207.8 0 25
69 51 207.8 0 51
70 45 207.8 0 45
71 32 207.8 0 32
72 30 207.8 0 30
73 38 207.8 0 38
74 42 207.8 0 42
75 30 207.8 0 30
76 30 207.8 0 30
77 163 207.8 0 163
78 82 207.8 0 82
79 51 207.8 0 51
80 42 207.8 0 42
81 33 207.8 0 33
82 32 207.8 0 32
83 55 207.8 0 55
84 33 207.8 0 33
85 32 207.8 0 32
86 52 207.8 0 52
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X47_S150_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X47_S150_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 27.88 s (8 µs/read; 7.50 M reads/minute).
=== Summary ===
Total reads processed: 3,486,651
Reads with adapters: 1,344,728 (38.6%)
== Read fate breakdown ==
Reads that were too short: 401,395 (11.5%)
Reads written (passing filters): 3,085,256 (88.5%)
Total basepairs processed: 352,151,751 bp
Total written (filtered): 237,553,148 bp (67.5%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1203307 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 31.1%
G: 26.1%
T: 27.7%
none/other: 15.1%
Overview of removed sequences
length count expect max.err error counts
3 75792 54478.9 0 75792
4 35101 13619.7 0 35101
5 18205 3404.9 0 18205
6 12758 851.2 0 12758
7 10461 212.8 0 10461
8 9546 53.2 0 9546
9 9520 53.2 0 9520
10 9462 53.2 0 9462
11 9438 53.2 0 9438
12 9341 53.2 0 9341
13 9530 53.2 0 9530
14 9968 53.2 0 9968
15 10247 53.2 0 10247
16 10441 53.2 0 10441
17 10340 53.2 0 10340
18 10822 53.2 0 10822
19 10286 53.2 0 10286
20 10084 53.2 0 10084
21 10864 53.2 0 10864
22 10571 53.2 0 10571
23 10219 53.2 0 10219
24 9868 53.2 0 9868
25 10245 53.2 0 10245
26 10039 53.2 0 10039
27 10150 53.2 0 10150
28 10593 53.2 0 10593
29 10706 53.2 0 10706
30 10371 53.2 0 10371
31 10785 53.2 0 10785
32 10268 53.2 0 10268
33 10203 53.2 0 10203
34 10712 53.2 0 10712
35 10504 53.2 0 10504
36 10647 53.2 0 10647
37 10538 53.2 0 10538
38 10118 53.2 0 10118
39 10671 53.2 0 10671
40 10865 53.2 0 10865
41 10469 53.2 0 10469
42 11097 53.2 0 11097
43 11244 53.2 0 11244
44 10606 53.2 0 10606
45 11002 53.2 0 11002
46 11246 53.2 0 11246
47 11312 53.2 0 11312
48 11309 53.2 0 11309
49 13673 53.2 0 13673
50 15041 53.2 0 15041
51 11973 53.2 0 11973
52 12550 53.2 0 12550
53 12177 53.2 0 12177
54 11724 53.2 0 11724
55 12662 53.2 0 12662
56 12207 53.2 0 12207
57 12473 53.2 0 12473
58 13041 53.2 0 13041
59 12494 53.2 0 12494
60 12982 53.2 0 12982
61 13120 53.2 0 13120
62 12801 53.2 0 12801
63 12613 53.2 0 12613
64 12735 53.2 0 12735
65 12617 53.2 0 12617
66 12296 53.2 0 12296
67 12081 53.2 0 12081
68 12066 53.2 0 12066
69 11347 53.2 0 11347
70 11131 53.2 0 11131
71 11661 53.2 0 11661
72 10834 53.2 0 10834
73 10644 53.2 0 10644
74 10139 53.2 0 10139
75 9507 53.2 0 9507
76 9154 53.2 0 9154
77 10323 53.2 0 10323
78 8887 53.2 0 8887
79 9909 53.2 0 9909
80 9415 53.2 0 9415
81 10520 53.2 0 10520
82 12293 53.2 0 12293
83 13937 53.2 0 13937
84 14777 53.2 0 14777
85 15324 53.2 0 15324
86 181615 53.2 0 181615
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 71515 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 24.9%
C: 33.3%
G: 0.0%
T: 39.2%
none/other: 2.6%
Overview of removed sequences
length count expect max.err error counts
3 15355 54478.9 0 15355
4 4185 13619.7 0 4185
5 1568 3404.9 0 1568
6 1087 851.2 0 1087
7 1062 212.8 0 1062
8 1097 53.2 0 1097
9 1056 53.2 0 1056
10 1023 53.2 0 1023
11 955 53.2 0 955
12 986 53.2 0 986
13 916 53.2 0 916
14 796 53.2 0 796
15 878 53.2 0 878
16 817 53.2 0 817
17 762 53.2 0 762
18 837 53.2 0 837
19 811 53.2 0 811
20 781 53.2 0 781
21 795 53.2 0 795
22 808 53.2 0 808
23 791 53.2 0 791
24 805 53.2 0 805
25 898 53.2 0 898
26 786 53.2 0 786
27 710 53.2 0 710
28 810 53.2 0 810
29 763 53.2 0 763
30 761 53.2 0 761
31 716 53.2 0 716
32 775 53.2 0 775
33 848 53.2 0 848
34 783 53.2 0 783
35 761 53.2 0 761
36 742 53.2 0 742
37 711 53.2 0 711
38 665 53.2 0 665
39 674 53.2 0 674
40 734 53.2 0 734
41 686 53.2 0 686
42 726 53.2 0 726
43 749 53.2 0 749
44 715 53.2 0 715
45 702 53.2 0 702
46 724 53.2 0 724
47 763 53.2 0 763
48 722 53.2 0 722
49 676 53.2 0 676
50 729 53.2 0 729
51 668 53.2 0 668
52 687 53.2 0 687
53 668 53.2 0 668
54 603 53.2 0 603
55 639 53.2 0 639
56 656 53.2 0 656
57 644 53.2 0 644
58 638 53.2 0 638
59 597 53.2 0 597
60 612 53.2 0 612
61 578 53.2 0 578
62 497 53.2 0 497
63 453 53.2 0 453
64 470 53.2 0 470
65 423 53.2 0 423
66 358 53.2 0 358
67 377 53.2 0 377
68 317 53.2 0 317
69 296 53.2 0 296
70 261 53.2 0 261
71 245 53.2 0 245
72 216 53.2 0 216
73 198 53.2 0 198
74 148 53.2 0 148
75 140 53.2 0 140
76 114 53.2 0 114
77 85 53.2 0 85
78 87 53.2 0 87
79 84 53.2 0 84
80 74 53.2 0 74
81 53 53.2 0 53
82 68 53.2 0 68
83 66 53.2 0 66
84 55 53.2 0 55
85 69 53.2 0 69
86 1871 53.2 0 1871
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69906 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 35.5%
C: 22.8%
G: 21.0%
T: 20.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 52328 54478.9 0 52328
4 11826 13619.7 0 11826
5 2063 3404.9 0 2063
6 289 851.2 0 289
7 45 212.8 0 45
8 25 212.8 0 25
9 22 212.8 0 22
10 49 212.8 0 49
11 43 212.8 0 43
12 21 212.8 0 21
13 42 212.8 0 42
14 38 212.8 0 38
15 41 212.8 0 41
16 37 212.8 0 37
17 42 212.8 0 42
18 42 212.8 0 42
19 44 212.8 0 44
20 59 212.8 0 59
21 44 212.8 0 44
22 23 212.8 0 23
23 39 212.8 0 39
24 18 212.8 0 18
25 34 212.8 0 34
26 68 212.8 0 68
27 38 212.8 0 38
28 49 212.8 0 49
29 53 212.8 0 53
30 48 212.8 0 48
31 29 212.8 0 29
32 47 212.8 0 47
33 48 212.8 0 48
34 50 212.8 0 50
35 55 212.8 0 55
36 68 212.8 0 68
37 28 212.8 0 28
38 40 212.8 0 40
39 53 212.8 0 53
40 35 212.8 0 35
41 35 212.8 0 35
42 41 212.8 0 41
43 36 212.8 0 36
44 43 212.8 0 43
45 36 212.8 0 36
46 38 212.8 0 38
47 34 212.8 0 34
48 41 212.8 0 41
49 42 212.8 0 42
50 31 212.8 0 31
51 44 212.8 0 44
52 45 212.8 0 45
53 26 212.8 0 26
54 46 212.8 0 46
55 39 212.8 0 39
56 25 212.8 0 25
57 28 212.8 0 28
58 39 212.8 0 39
59 31 212.8 0 31
60 32 212.8 0 32
61 27 212.8 0 27
62 36 212.8 0 36
63 57 212.8 0 57
64 35 212.8 0 35
65 51 212.8 0 51
66 38 212.8 0 38
67 35 212.8 0 35
68 34 212.8 0 34
69 42 212.8 0 42
70 50 212.8 0 50
71 49 212.8 0 49
72 24 212.8 0 24
73 52 212.8 0 52
74 30 212.8 0 30
75 33 212.8 0 33
76 36 212.8 0 36
77 177 212.8 0 177
78 68 212.8 0 68
79 45 212.8 0 45
80 62 212.8 0 62
81 54 212.8 0 54
82 36 212.8 0 36
83 47 212.8 0 47
84 41 212.8 0 41
85 42 212.8 0 42
86 50 212.8 0 50
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X48_S154_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X48_S154_L001_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 25.05 s (10 µs/read; 6.08 M reads/minute).
=== Summary ===
Total reads processed: 2,537,235
Reads with adapters: 865,609 (34.1%)
== Read fate breakdown ==
Reads that were too short: 242,755 (9.6%)
Reads written (passing filters): 2,294,480 (90.4%)
Total basepairs processed: 256,260,735 bp
Total written (filtered): 180,026,860 bp (70.3%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 787224 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.8%
G: 27.2%
T: 30.2%
none/other: 11.9%
Overview of removed sequences
length count expect max.err error counts
3 56074 39644.3 0 56074
4 25707 9911.1 0 25707
5 13764 2477.8 0 13764
6 9404 619.4 0 9404
7 7748 154.9 0 7748
8 6939 38.7 0 6939
9 7005 38.7 0 7005
10 6933 38.7 0 6933
11 6778 38.7 0 6778
12 6750 38.7 0 6750
13 6909 38.7 0 6909
14 6857 38.7 0 6857
15 7237 38.7 0 7237
16 7282 38.7 0 7282
17 6925 38.7 0 6925
18 7417 38.7 0 7417
19 7100 38.7 0 7100
20 7058 38.7 0 7058
21 7347 38.7 0 7347
22 7175 38.7 0 7175
23 6590 38.7 0 6590
24 6884 38.7 0 6884
25 6607 38.7 0 6607
26 6691 38.7 0 6691
27 6517 38.7 0 6517
28 6928 38.7 0 6928
29 7178 38.7 0 7178
30 7166 38.7 0 7166
31 7230 38.7 0 7230
32 7132 38.7 0 7132
33 7239 38.7 0 7239
34 7103 38.7 0 7103
35 7099 38.7 0 7099
36 7197 38.7 0 7197
37 7074 38.7 0 7074
38 6776 38.7 0 6776
39 7092 38.7 0 7092
40 7072 38.7 0 7072
41 6966 38.7 0 6966
42 7586 38.7 0 7586
43 7637 38.7 0 7637
44 7145 38.7 0 7145
45 7133 38.7 0 7133
46 7860 38.7 0 7860
47 7535 38.7 0 7535
48 7533 38.7 0 7533
49 10568 38.7 0 10568
50 11718 38.7 0 11718
51 7597 38.7 0 7597
52 8490 38.7 0 8490
53 7864 38.7 0 7864
54 6871 38.7 0 6871
55 7421 38.7 0 7421
56 7658 38.7 0 7658
57 7186 38.7 0 7186
58 7985 38.7 0 7985
59 7519 38.7 0 7519
60 7507 38.7 0 7507
61 7761 38.7 0 7761
62 7535 38.7 0 7535
63 7352 38.7 0 7352
64 7639 38.7 0 7639
65 7237 38.7 0 7237
66 7185 38.7 0 7185
67 7306 38.7 0 7306
68 7516 38.7 0 7516
69 6871 38.7 0 6871
70 6642 38.7 0 6642
71 7077 38.7 0 7077
72 6816 38.7 0 6816
73 6649 38.7 0 6649
74 6302 38.7 0 6302
75 6430 38.7 0 6430
76 6593 38.7 0 6593
77 6387 38.7 0 6387
78 6974 38.7 0 6974
79 7864 38.7 0 7864
80 7296 38.7 0 7296
81 8232 38.7 0 8232
82 9497 38.7 0 9497
83 10391 38.7 0 10391
84 11040 38.7 0 11040
85 11630 38.7 0 11630
86 93239 38.7 0 93239
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 24508 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.2%
C: 32.5%
G: 0.0%
T: 33.0%
none/other: 3.3%
Overview of removed sequences
length count expect max.err error counts
3 13145 39644.3 0 13145
4 3119 9911.1 0 3119
5 785 2477.8 0 785
6 234 619.4 0 234
7 180 154.9 0 180
8 178 38.7 0 178
9 148 38.7 0 148
10 135 38.7 0 135
11 134 38.7 0 134
12 112 38.7 0 112
13 122 38.7 0 122
14 110 38.7 0 110
15 114 38.7 0 114
16 115 38.7 0 115
17 101 38.7 0 101
18 110 38.7 0 110
19 113 38.7 0 113
20 97 38.7 0 97
21 120 38.7 0 120
22 103 38.7 0 103
23 101 38.7 0 101
24 120 38.7 0 120
25 94 38.7 0 94
26 90 38.7 0 90
27 84 38.7 0 84
28 95 38.7 0 95
29 82 38.7 0 82
30 101 38.7 0 101
31 100 38.7 0 100
32 86 38.7 0 86
33 89 38.7 0 89
34 111 38.7 0 111
35 105 38.7 0 105
36 83 38.7 0 83
37 103 38.7 0 103
38 93 38.7 0 93
39 86 38.7 0 86
40 108 38.7 0 108
41 93 38.7 0 93
42 96 38.7 0 96
43 127 38.7 0 127
44 104 38.7 0 104
45 95 38.7 0 95
46 115 38.7 0 115
47 96 38.7 0 96
48 88 38.7 0 88
49 77 38.7 0 77
50 84 38.7 0 84
51 80 38.7 0 80
52 67 38.7 0 67
53 78 38.7 0 78
54 86 38.7 0 86
55 81 38.7 0 81
56 73 38.7 0 73
57 75 38.7 0 75
58 76 38.7 0 76
59 69 38.7 0 69
60 67 38.7 0 67
61 58 38.7 0 58
62 71 38.7 0 71
63 73 38.7 0 73
64 55 38.7 0 55
65 39 38.7 0 39
66 59 38.7 0 59
67 59 38.7 0 59
68 55 38.7 0 55
69 44 38.7 0 44
70 37 38.7 0 37
71 35 38.7 0 35
72 21 38.7 0 21
73 31 38.7 0 31
74 41 38.7 0 41
75 23 38.7 0 23
76 21 38.7 0 21
77 23 38.7 0 23
78 19 38.7 0 19
79 32 38.7 0 32
80 25 38.7 0 25
81 31 38.7 0 31
82 25 38.7 0 25
83 28 38.7 0 28
84 31 38.7 0 31
85 32 38.7 0 32
86 807 38.7 0 807
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 53877 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.7%
C: 24.2%
G: 21.1%
T: 20.0%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 40875 39644.3 0 40875
4 8490 9911.1 0 8490
5 1886 2477.8 0 1886
6 222 619.4 0 222
7 9 154.9 0 9
8 21 154.9 0 21
9 39 154.9 0 39
10 28 154.9 0 28
11 34 154.9 0 34
12 37 154.9 0 37
13 38 154.9 0 38
14 40 154.9 0 40
15 39 154.9 0 39
16 36 154.9 0 36
17 37 154.9 0 37
18 31 154.9 0 31
19 37 154.9 0 37
20 37 154.9 0 37
21 28 154.9 0 28
22 28 154.9 0 28
23 30 154.9 0 30
24 37 154.9 0 37
25 45 154.9 0 45
26 32 154.9 0 32
27 23 154.9 0 23
28 33 154.9 0 33
29 36 154.9 0 36
30 39 154.9 0 39
31 30 154.9 0 30
32 37 154.9 0 37
33 26 154.9 0 26
34 28 154.9 0 28
35 32 154.9 0 32
36 24 154.9 0 24
37 26 154.9 0 26
38 36 154.9 0 36
39 24 154.9 0 24
40 31 154.9 0 31
41 39 154.9 0 39
42 37 154.9 0 37
43 31 154.9 0 31
44 35 154.9 0 35
45 15 154.9 0 15
46 23 154.9 0 23
47 27 154.9 0 27
48 31 154.9 0 31
49 27 154.9 0 27
50 31 154.9 0 31
51 22 154.9 0 22
52 26 154.9 0 26
53 21 154.9 0 21
54 21 154.9 0 21
55 38 154.9 0 38
56 22 154.9 0 22
57 25 154.9 0 25
58 31 154.9 0 31
59 31 154.9 0 31
60 27 154.9 0 27
61 22 154.9 0 22
62 36 154.9 0 36
63 31 154.9 0 31
64 24 154.9 0 24
65 31 154.9 0 31
66 29 154.9 0 29
67 27 154.9 0 27
68 21 154.9 0 21
69 21 154.9 0 21
70 26 154.9 0 26
71 30 154.9 0 30
72 33 154.9 0 33
73 26 154.9 0 26
74 27 154.9 0 27
75 25 154.9 0 25
76 29 154.9 0 29
77 45 154.9 0 45
78 36 154.9 0 36
79 25 154.9 0 25
80 30 154.9 0 30
81 27 154.9 0 27
82 29 154.9 0 29
83 32 154.9 0 32
84 28 154.9 0 28
85 31 154.9 0 31
86 35 154.9 0 35
This is cutadapt 3.7 with Python 3.9.7
Command line parameters: X48_S154_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/X48_S154_L002_R1_001.fastq
Processing reads on 1 core in single-end mode ...
Finished in 23.90 s (9 µs/read; 6.49 M reads/minute).
=== Summary ===
Total reads processed: 2,585,567
Reads with adapters: 889,692 (34.4%)
== Read fate breakdown ==
Reads that were too short: 254,602 (9.8%)
Reads written (passing filters): 2,330,965 (90.2%)
Total basepairs processed: 261,142,267 bp
Total written (filtered): 182,731,503 bp (70.0%)
=== Adapter 1 ===
Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 810068 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 0.0%
C: 30.8%
G: 27.1%
T: 30.0%
none/other: 12.1%
Overview of removed sequences
length count expect max.err error counts
3 56337 40399.5 0 56337
4 26312 10099.9 0 26312
5 13715 2525.0 0 13715
6 9626 631.2 0 9626
7 8057 157.8 0 8057
8 6841 39.5 0 6841
9 7039 39.5 0 7039
10 7041 39.5 0 7041
11 6764 39.5 0 6764
12 6810 39.5 0 6810
13 7072 39.5 0 7072
14 7242 39.5 0 7242
15 7282 39.5 0 7282
16 7316 39.5 0 7316
17 7006 39.5 0 7006
18 7634 39.5 0 7634
19 7167 39.5 0 7167
20 7237 39.5 0 7237
21 7499 39.5 0 7499
22 7301 39.5 0 7301
23 6713 39.5 0 6713
24 6945 39.5 0 6945
25 6739 39.5 0 6739
26 6679 39.5 0 6679
27 6714 39.5 0 6714
28 7189 39.5 0 7189
29 7219 39.5 0 7219
30 7383 39.5 0 7383
31 7384 39.5 0 7384
32 7224 39.5 0 7224
33 7367 39.5 0 7367
34 7222 39.5 0 7222
35 7209 39.5 0 7209
36 7510 39.5 0 7510
37 7130 39.5 0 7130
38 6899 39.5 0 6899
39 7286 39.5 0 7286
40 7409 39.5 0 7409
41 7181 39.5 0 7181
42 7352 39.5 0 7352
43 7733 39.5 0 7733
44 7499 39.5 0 7499
45 7450 39.5 0 7450
46 7871 39.5 0 7871
47 7811 39.5 0 7811
48 7580 39.5 0 7580
49 10920 39.5 0 10920
50 12176 39.5 0 12176
51 7646 39.5 0 7646
52 8704 39.5 0 8704
53 8078 39.5 0 8078
54 7109 39.5 0 7109
55 7668 39.5 0 7668
56 7774 39.5 0 7774
57 7473 39.5 0 7473
58 8273 39.5 0 8273
59 7787 39.5 0 7787
60 7650 39.5 0 7650
61 8077 39.5 0 8077
62 7789 39.5 0 7789
63 7429 39.5 0 7429
64 7763 39.5 0 7763
65 7663 39.5 0 7663
66 7529 39.5 0 7529
67 7696 39.5 0 7696
68 7746 39.5 0 7746
69 7102 39.5 0 7102
70 7147 39.5 0 7147
71 7463 39.5 0 7463
72 7337 39.5 0 7337
73 6952 39.5 0 6952
74 6555 39.5 0 6555
75 6710 39.5 0 6710
76 6893 39.5 0 6893
77 6874 39.5 0 6874
78 7266 39.5 0 7266
79 8130 39.5 0 8130
80 7587 39.5 0 7587
81 8567 39.5 0 8567
82 10001 39.5 0 10001
83 10758 39.5 0 10758
84 11464 39.5 0 11464
85 12096 39.5 0 12096
86 98220 39.5 0 98220
=== Adapter 2 ===
Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 24790 times
Minimum overlap: 3
No. of allowed errors:
1-8 bp: 0
Bases preceding removed adapters:
A: 31.4%
C: 33.0%
G: 0.0%
T: 32.4%
none/other: 3.2%
Overview of removed sequences
length count expect max.err error counts
3 13448 40399.5 0 13448
4 3025 10099.9 0 3025
5 786 2525.0 0 786
6 249 631.2 0 249
7 159 157.8 0 159
8 160 39.5 0 160
9 146 39.5 0 146
10 130 39.5 0 130
11 132 39.5 0 132
12 125 39.5 0 125
13 126 39.5 0 126
14 106 39.5 0 106
15 110 39.5 0 110
16 125 39.5 0 125
17 95 39.5 0 95
18 101 39.5 0 101
19 100 39.5 0 100
20 108 39.5 0 108
21 119 39.5 0 119
22 97 39.5 0 97
23 113 39.5 0 113
24 88 39.5 0 88
25 107 39.5 0 107
26 108 39.5 0 108
27 100 39.5 0 100
28 105 39.5 0 105
29 100 39.5 0 100
30 118 39.5 0 118
31 79 39.5 0 79
32 95 39.5 0 95
33 109 39.5 0 109
34 87 39.5 0 87
35 94 39.5 0 94
36 81 39.5 0 81
37 101 39.5 0 101
38 89 39.5 0 89
39 90 39.5 0 90
40 115 39.5 0 115
41 112 39.5 0 112
42 97 39.5 0 97
43 111 39.5 0 111
44 138 39.5 0 138
45 88 39.5 0 88
46 114 39.5 0 114
47 104 39.5 0 104
48 78 39.5 0 78
49 69 39.5 0 69
50 77 39.5 0 77
51 88 39.5 0 88
52 83 39.5 0 83
53 73 39.5 0 73
54 97 39.5 0 97
55 68 39.5 0 68
56 83 39.5 0 83
57 79 39.5 0 79
58 72 39.5 0 72
59 55 39.5 0 55
60 66 39.5 0 66
61 64 39.5 0 64
62 53 39.5 0 53
63 80 39.5 0 80
64 69 39.5 0 69
65 69 39.5 0 69
66 63 39.5 0 63
67 46 39.5 0 46
68 52 39.5 0 52
69 40 39.5 0 40
70 30 39.5 0 30
71 52 39.5 0 52
72 44 39.5 0 44
73 34 39.5 0 34
74 29 39.5 0 29
75 29 39.5 0 29
76 26 39.5 0 26
77 24 39.5 0 24
78 23 39.5 0 23
79 19 39.5 0 19
80 21 39.5 0 21
81 31 39.5 0 31
82 26 39.5 0 26
83 19 39.5 0 19
84 38 39.5 0 38
85 40 39.5 0 40
86 791 39.5 0 791
=== Adapter 3 ===
Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 54834 times
Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0
Bases preceding removed adapters:
A: 34.6%
C: 23.9%
G: 21.4%
T: 20.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 41479 40399.5 0 41479
4 8610 10099.9 0 8610
5 1996 2525.0 0 1996
6 252 631.2 0 252
7 30 157.8 0 30
8 34 157.8 0 34
9 42 157.8 0 42
10 30 157.8 0 30
11 35 157.8 0 35
12 33 157.8 0 33
13 24 157.8 0 24
14 32 157.8 0 32
15 39 157.8 0 39
16 40 157.8 0 40
17 35 157.8 0 35
18 37 157.8 0 37
19 42 157.8 0 42
20 32 157.8 0 32
21 28 157.8 0 28
22 21 157.8 0 21
23 26 157.8 0 26
24 21 157.8 0 21
25 26 157.8 0 26
26 20 157.8 0 20
27 28 157.8 0 28
28 23 157.8 0 23
29 34 157.8 0 34
30 31 157.8 0 31
31 23 157.8 0 23
32 40 157.8 0 40
33 28 157.8 0 28
34 21 157.8 0 21
35 33 157.8 0 33
36 36 157.8 0 36
37 26 157.8 0 26
38 44 157.8 0 44
39 27 157.8 0 27
40 34 157.8 0 34
41 36 157.8 0 36
42 30 157.8 0 30
43 29 157.8 0 29
44 28 157.8 0 28
45 30 157.8 0 30
46 28 157.8 0 28
47 40 157.8 0 40
48 25 157.8 0 25
49 40 157.8 0 40
50 36 157.8 0 36
51 29 157.8 0 29
52 39 157.8 0 39
53 24 157.8 0 24
54 21 157.8 0 21
55 41 157.8 0 41
56 31 157.8 0 31
57 31 157.8 0 31
58 25 157.8 0 25
59 30 157.8 0 30
60 33 157.8 0 33
61 24 157.8 0 24
62 44 157.8 0 44
63 29 157.8 0 29
64 33 157.8 0 33
65 42 157.8 0 42
66 20 157.8 0 20
67 27 157.8 0 27
68 31 157.8 0 31
69 24 157.8 0 24
70 32 157.8 0 32
71 34 157.8 0 34
72 19 157.8 0 19
73 33 157.8 0 33
74 20 157.8 0 20
75 20 157.8 0 20
76 40 157.8 0 40
77 44 157.8 0 44
78 35 157.8 0 35
79 27 157.8 0 27
80 32 157.8 0 32
81 27 157.8 0 27
82 30 157.8 0 30
83 37 157.8 0 37
84 33 157.8 0 33
85 32 157.8 0 32
86 47 157.8 0 47
# concatenate fastq files by lane
cd trim-fastq/
printf '%s\n' *.fastq | sed 's/^\([^_]*_[^_]*\).*/\1/' | uniq |
while read prefix; do
cat "$prefix"*R1*.fastq >"${prefix}_R1.fastq"
# cat "$prefix"*R2*.fastq >"${prefix}_R2.fastq" # include if more than one run
done
# I moved files to merged-fastq
cat: '*.fastq_R1.fastq*R1*.fastq': No such file or directory
---
title: "Process tagseq data"
output: html_notebook
---


```{bash, engine.opts='-l'}
echo $PATH
```

# Download genome feature table
```{bash}

cd sequences/

wget -r \
--no-directories --no-parent \
-P . \
-A GCF_902806645.1_cgigas_uk_roslin_v1_feature_table.txt.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/902/806/645/GCF_902806645.1_cgigas_uk_roslin_v1/GCF_902806645.1_cgigas_uk_roslin_v1_feature_table.txt.gz \
--no-check-certificate

gunzip *.gz
awk -F "\t" '$1 == "mRNA" {print $15, "\t", $14}' GCF_902806645.1_cgigas_uk_roslin_v1_feature_table.txt

```

# Download Roslin genome files
```{bash}
#mkdir sequences/

cd sequences/

wget -r \
--no-directories --no-parent \
-P . \
-A cgigas_uk_roslin_v1_genomic-mito.fa https://gannet.fish.washington.edu/panopea/Cg-roslin/ \
--no-check-certificate

wget -r \
--no-directories --no-parent \
-P . \
-A GCF_902806645.1_cgigas_uk_roslin_v1_genomic-mito.gtf https://gannet.fish.washington.edu/panopea/Cg-roslin/ \
--no-check-certificate

wget -r \
--no-directories --no-parent \
-P . \
-A cgigas_uk_roslin_v1_mRNA.gff https://gannet.fish.washington.edu/panopea/Cg-roslin/ \
--no-check-certificate

```


```{bash}
# Download tag-seq data
mkdir raw-data/
cd raw-data/

wget -r -A .fastq.gz https://gannet.fish.washington.edu/panopea/NOPP-gigas-ploidy-temp/022022-tagseq/ \
--no-check-certificate
```

```{bash}
# unzip .fastq.gz files
cd raw-data/
gunzip *.fastq.gz

```

# Run fastqc on untrimmed files
```{bash}
mkdir fastqc/
mkdir fastqc/untrimmed/

/home/shared/FastQC/fastqc \
raw-data/*.fastq \
--outdir fastqc/untrimmed/ \
--quiet

```

# Run multiqc on untrimmed files
```{bash}
eval "$(/opt/anaconda/anaconda3/bin/conda shell.bash hook)"
conda activate

cd fastqc/untrimmed/

multiqc .
```

```{bash}
# trim adapter sequences

mkdir trim-fastq/
cd raw-data/

for F in *.fastq
do
#strip .fastq and directory structure from each file, then
# add suffice .trim to create output name for each file
results_file="$(basename -a $F)"

# run cutadapt on each file, hard trim first 15 bp, minimum length 20
/home/shared/8TB_HDD_02/mattgeorgephd/.local/bin/cutadapt $F -a A{8} -a G{8} -a AGATCGG -u 15 -m 20 -o \
/home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/$results_file
done

```

```{bash}
# concatenate fastq files by lane

cd trim-fastq/

printf '%s\n' *.fastq | sed 's/^\([^_]*_[^_]*\).*/\1/' | uniq |
while read prefix; do
    cat "$prefix"*R1*.fastq >"${prefix}_R1.fastq"
    # cat "$prefix"*R2*.fastq >"${prefix}_R2.fastq" # include if more than one run
done

# I moved files to trim-merge-fastq
```
# Run fastqc on trimmed files
```{bash}
# mkdir fastqc/
mkdir fastqc/trim-merge/

/home/shared/FastQC/fastqc \
trim-merge-fastq/*.fastq \
--outdir fastqc/trim-merge/ \
--quiet

```

# Run multiqc on trimmed files
```{bash}
mkdir fastqc/trim-merge/

eval "$(/opt/anaconda/anaconda3/bin/conda shell.bash hook)"
conda activate

cd fastqc/trim-merge/

multiqc .
```


# Run multiqc on trimmed files
```{bash}
cd trim-merge-fastq/

for i in *.fastq; do
cat $i | awk '{if(NR%4==2) print length($1)}' >  ${i}.readslength.txt
done
```

# RUN HISAT2 ----------------------------------------------------------------------------------------------------------------
# create hisat2 index for cgigas genome (took 9 min on Raven)
```{bash}
/home/shared/hisat2-2.2.1/hisat2-build \
-f /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_uk_roslin_v1_genomic-mito.fa  /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_uk_roslin_v1_hisat2.fa # called the reference genome (scaffolds)

```

# Run hisat2 on trimmed reads
```{bash}
mkdir hisat2_sam/
mkdir hisat2_bam/
cd trim-merge-fastq/

# This script exports alignments as bam files
# sorts the bam file because Stringtie takes a sorted file for input (--dta)
# removes the sam file because it is no longer needed
array=($(ls *.fastq)) # call the sequences - make an array to align
for i in ${array[@]}; do
       sample_name=`echo $i| awk -F [.] '{print $1}'`
	/home/shared/hisat2-2.2.1/hisat2 \
	  -p 16 \
	  --dta \
	  -x /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_uk_roslin_v1_hisat2.fa \
	  -U ${i} \
	  -S /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/hisat2_sam/${sample_name}.sam 
	  
	  /home/shared/samtools-1.12/samtools sort -@ 8 -o                /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/hisat2_bam/${sample_name}.bam /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/hisat2_sam/${sample_name}.sam
    		echo "${i} bam-ified!"
        # rm ${sample_name}.sam
done >> hisat2out.txt 2>&1

```

```{bash}
# check % alignment from Hisat2

grep "overall alignment rate" /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/hisat2out.txt

# 20220906 - average alignment rate = 72.98 +/- 3.07 sd

```


# Calculate chromosome lengths
```{bash}
head sequences/cgigas_uk_roslin_v1_genomic-mito.fa

awk '$0 ~ ">" {print c; c=0;printf substr($0,2,14) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' \
sequences/cgigas_uk_roslin_v1_genomic-mito.fa \
| sed 's/Cr//g' \
| awk '{print $1"\t"$2}' \
| tail -n +2 \
> sequences/GCF_902806645.1_cgigas_uk_roslin_v1_genomic-sequence-lengths.txt

head sequences/GCF_902806645.1_cgigas_uk_roslin_v1_genomic-sequence-lengths.txt
```

# Generate mRNA feature track from genomic_sequence
```{bash}
head sequences/GCF_902806645.1_cgigas_uk_roslin_v1_genomic-mito.gtf

grep -e "Gnomon	mRNA" -e "RefSeq	mRNA" -e "cmsearch	mRNA" -e "tRNAscan-SE	mRNA" \
sequences/GCF_902806645.1_cgigas_uk_roslin_v1_genomic-mito.gtf \
| /home/shared/bedtools2/bin/sortBed \
-faidx sequences/GCF_902806645.1_cgigas_uk_roslin_v1_genomic-sequence-lengths.txt \
> sequences/GCF_902806645.1_cgigas_uk_roslin_v1_mRNA.gff

head sequences/GCF_902806645.1_cgigas_uk_roslin_v1_mRNA.gff
```
```{bash}
head sequences/cgigas_uk_roslin_v1_mRNA.gff
```

# Assemble hisat2 alignments w/ stringtie2 using mRNA genome feature track (took 14 min on Raven)
```{bash}
array=($(ls /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/hisat2_bam/*.bam))

for i in ${array[@]}; do
        sample_name=`echo $i| awk -F [.] '{print $1}'`
	      /home/shared/stringtie-2.2.1.Linux_x86_64/stringtie \
	      -p 48 \
	      -e \
	      -B \
	      -G /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_uk_roslin_v1_mRNA.gff \
	      -A ${sample_name}.gene_abund.tab \
	      -o ${sample_name}.gtf ${i} \

        echo "StringTie assembly for seq file ${i}" $(date)
done

echo "StringTie assembly COMPLETE, starting assembly analysis" $(date)

# 20220607 - I could not figure out how to designate the output. All outputs ended up in hisat2_bam folder.

```

```{bash}

cd /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/hisat2_bam

# make gtf list file (needed for stringtie merge function)
for filename in *.gtf; do 
  echo $PWD/$filename; 
  done > gtf_list.txt

# make listGTF file (needed for count matrix), two columns w/ sample ID
for filename in *.gtf; do 
  echo $filename $PWD/$filename; 
  done > listGTF.txt

# merge GTFs into a single file
/home/shared/stringtie-2.2.1.Linux_x86_64/stringtie \
  --merge \
  -p 48 \
	-G /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_uk_roslin_v1_mRNA.gff \
	-o gigas_merged.gtf gtf_list.txt #Merge GTFs to form $

echo "Stringtie merge complete" $(date)

# Compute accuracy of gff
# gffcompare -r ../../../refs/Panopea-generosa-v1.0.a4.mRNA_SJG.gff3 -G -o merged Pgenerosa_merged.gtf #Compute the accuracy and pre$
# echo "GFFcompare complete, Starting gene count matrix assembly..." $(date)

# Compile gene count matrix from GTFs
/home/shared/stringtie-2.2.1.Linux_x86_64/prepDE.py \
  -g gigas_gene_count_matrix.csv \
  -i listGTF.txt #Compile the gene count matrix

echo "Gene count matrix compiled." $(date)

```


# RUN BOWTIE2 ----------------------------------------------------------------------------------------------------------------

```{bash}
# create bowtie2 index for cgigas genome (took 8 min on Raven)

/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2-build \
/home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_uk_roslin_v1_genomic-mito.fa \
/home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_roslin_v1.fa

```

```{bash}
# Run bowtie on trimmed reads, pre-set option= --sensitive-local

mkdir bowtie_sam/
cd bowtie_sam/

for file in /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/*.fastq
do
results_file="$(basename -a $file).sam"

# run Bowtie2 on each file
/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 \
--local \
-x /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_roslin_v1.fa \
--sensitive-local \
--threads 48 \
--no-unal \
-k 5 \
-U $file \
-S $results_file; \
done >> bowtieout.txt 2>&1


```

```{bash}
# check % alignment from Bowtie

grep "overall alignment rate" /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/bowtie_sam/bowtieout.txt

# average alignment rate = 87.8% +/- 1.3

```


```{bash}
# Convert .sam files to .bam files, create bam indices

mkdir bowtie_bam/
cd bowtie_bam/

for file in /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/bowtie_sam/*.sam
do
results_file="$(basename -a $file)_sorted.bam"
/home/shared/samtools-1.12/samtools view -b $file | /home/shared/samtools-1.12/samtools sort -o /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/bowtie_bam/$results_file
done

```

```{bash}
# check % alignment from bowtie2

grep "overall alignment rate" /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/bowtie_sam/bowtieout.txt

```


```{bash}

#mkdir fastqc/
#mkdir fastqc/trimmed/

/home/shared/FastQC/fastqc \
/home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/trim-fastq/*.fastq \
--outdir /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/fastqc/trimmed/ \
--quiet

```



```{bash}
# Assemble bowtie alignments w/ stringtie2 using mRNA genome feature track
array=($(ls /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/bowtie_bam/*.bam))

for i in ${array[@]}; do
        sample_name=`echo $i| awk -F [.] '{print $1}'`
	      /home/shared/stringtie-2.2.1.Linux_x86_64/stringtie \
	      -p 48 \
	      -e \
	      -B \
	      -G /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_uk_roslin_v1_mRNA.gff \
	      -A ${sample_name}.gene_abund.tab \
	      -o ${sample_name}.gtf ${i} \

        echo "StringTie assembly for seq file ${i}" $(date)
done

echo "StringTie assembly COMPLETE, starting assembly analysis" $(date)

# 20220607 - I could not figure out how to designate the output. All outputs ended up in bowtie output folder.

```

```{bash}

cd /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/bowtie_bam

# make gtf list file (needed for stringtie merge function)
for filename in *.gtf; do 
  echo $PWD/$filename; 
  done > gtf_list.txt

# make listGTF file (needed for count matrix), two columns w/ sample ID
for filename in *.gtf; do 
  echo $filename $PWD/$filename; 
  done > listGTF.txt

# merge GTFs into a single file
/home/shared/stringtie-2.2.1.Linux_x86_64/stringtie \
  --merge \
  -p 48 \
	-G /home/shared/8TB_HDD_02/mattgeorgephd/NOPP-gigas-ploidy-temp/sequences/cgigas_uk_roslin_v1_mRNA.gff \
	-o cgigas_merged.gtf gtf_list.txt #Merge GTFs to form $

echo "Stringtie merge complete" $(date)

# Compute accuracy of gff
# gffcompare -r ../../../refs/Panopea-generosa-v1.0.a4.mRNA_SJG.gff3 -G -o merged Pgenerosa_merged.gtf #Compute the accuracy and pre$
# echo "GFFcompare complete, Starting gene count matrix assembly..." $(date)

# Compile gene count matrix from GTFs
/home/shared/stringtie-2.2.1.Linux_x86_64/prepDE.py \
  -g cgigas_gene_count_matrix.csv \
  -i listGTF.txt #Compile the gene count matrix

echo "Gene count matrix compiled." $(date)

```

