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TI_Nugen_trim_reports
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login as: ubuntu
ubuntu@nectarbioinformatics-tas:/NGS_Data/Andrew/AGRF_Trimmed_samples/AGRF_TI_Trimmed$ bash cut.sh
This is cutadapt 1.15 with Python 3.5.2
Command line parameters: -j 60 -a GCATAGTC -o /NGS_Data/Andrew/Nugen_trimmed_samples/AGRF_TI_Nugen_Trimmed/154467_TG12_TI_CB8LUANXX_GCATAGTC_all_trimmed.fq 154467_TG12_TI_CB8LUANXX_GCATAGTC_all_trimmed.fq
Running on 60 cores
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 96.77 s (2 us/read; 25.66 M reads/minute).
=== Summary ===
Total reads processed: 41,379,490
Reads with adapters: 347,885 (0.8%)
Reads written (passing filters): 41,379,490 (100.0%)
Total basepairs processed: 2,045,243,289 bp
Total written (filtered): 2,043,617,929 bp (99.9%)
=== Adapter 1 ===
Sequence: GCATAGTC; Type: regular 3'; Length: 8; Trimmed: 347885 times.
No. of allowed errors:
0-8 bp: 0
Bases preceding removed adapters:
A: 19.4%
C: 4.6%
G: 46.9%
T: 28.9%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 196891 646554.5 0 196891
4 127858 161638.6 0 127858
5 3564 40409.7 0 3564
6 320 10102.4 0 320
7 1075 2525.6 0 1075
8 324 631.4 0 324
9 307 631.4 0 307
10 673 631.4 0 673
11 110 631.4 0 110
12 511 631.4 0 511
13 602 631.4 0 602
14 119 631.4 0 119
15 621 631.4 0 621
16 84 631.4 0 84
17 170 631.4 0 170
18 452 631.4 0 452
19 701 631.4 0 701
20 351 631.4 0 351
21 529 631.4 0 529
22 3032 631.4 0 3032
23 614 631.4 0 614
24 134 631.4 0 134
25 542 631.4 0 542
26 120 631.4 0 120
27 354 631.4 0 354
28 394 631.4 0 394
29 362 631.4 0 362
30 272 631.4 0 272
31 290 631.4 0 290
32 415 631.4 0 415
33 352 631.4 0 352
34 364 631.4 0 364
35 324 631.4 0 324
36 378 631.4 0 378
37 301 631.4 0 301
38 320 631.4 0 320
39 546 631.4 0 546
40 301 631.4 0 301
41 121 631.4 0 121
42 457 631.4 0 457
43 393 631.4 0 393
44 344 631.4 0 344
45 350 631.4 0 350
46 158 631.4 0 158
47 447 631.4 0 447
48 347 631.4 0 347
49 286 631.4 0 286
50 305 631.4 0 305
This is cutadapt 1.15 with Python 3.5.2
Command line parameters: -j 60 -a GCACACAA -o /NGS_Data/Andrew/Nugen_trimmed_samples/AGRF_TI_Nugen_Trimmed/155688_WT12_TI_CB8LUANXX_GCACACAA_all_trimmed.fq 155688_WT12_TI_CB8LUANXX_GCACACAA_all_trimmed.fq
Running on 60 cores
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 101.05 s (3 us/read; 22.96 M reads/minute).
=== Summary ===
Total reads processed: 38,664,263
Reads with adapters: 474,215 (1.2%)
Reads written (passing filters): 38,664,263 (100.0%)
Total basepairs processed: 1,912,177,160 bp
Total written (filtered): 1,909,722,251 bp (99.9%)
=== Adapter 1 ===
Sequence: GCACACAA; Type: regular 3'; Length: 8; Trimmed: 474215 times.
No. of allowed errors:
0-8 bp: 0
Bases preceding removed adapters:
A: 31.2%
C: 5.0%
G: 29.5%
T: 34.2%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 201319 604129.1 0 201319
4 199539 151032.3 0 199539
5 10060 37758.1 0 10060
6 34994 9439.5 0 34994
7 882 2359.9 0 882
8 421 590.0 0 421
9 420 590.0 0 420
10 620 590.0 0 620
11 627 590.0 0 627
12 768 590.0 0 768
13 634 590.0 0 634
14 690 590.0 0 690
15 684 590.0 0 684
16 655 590.0 0 655
17 578 590.0 0 578
18 737 590.0 0 737
19 666 590.0 0 666
20 704 590.0 0 704
21 791 590.0 0 791
22 721 590.0 0 721
23 571 590.0 0 571
24 659 590.0 0 659
25 708 590.0 0 708
26 696 590.0 0 696
27 690 590.0 0 690
28 678 590.0 0 678
29 681 590.0 0 681
30 667 590.0 0 667
31 661 590.0 0 661
32 718 590.0 0 718
33 627 590.0 0 627
34 673 590.0 0 673
35 615 590.0 0 615
36 644 590.0 0 644
37 592 590.0 0 592
38 765 590.0 0 765
39 623 590.0 0 623
40 613 590.0 0 613
41 657 590.0 0 657
42 721 590.0 0 721
43 601 590.0 0 601
44 661 590.0 0 661
45 635 590.0 0 635
46 636 590.0 0 636
47 559 590.0 0 559
48 567 590.0 0 567
49 518 590.0 0 518
50 269 590.0 0 269
This is cutadapt 1.15 with Python 3.5.2
Command line parameters: -j 60 -a TGTGGCTT -o /NGS_Data/Andrew/Nugen_trimmed_samples/AGRF_TI_Nugen_Trimmed/158027_WT24_TI_CB8LUANXX_TGTGGCTT_all_trimmed.fq 158027_WT24_TI_CB8LUANXX_TGTGGCTT_all_trimmed.fq
Running on 60 cores
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 83.16 s (2 us/read; 26.76 M reads/minute).
=== Summary ===
Total reads processed: 37,088,882
Reads with adapters: 1,405,150 (3.8%)
Reads written (passing filters): 37,088,882 (100.0%)
Total basepairs processed: 1,834,535,353 bp
Total written (filtered): 1,828,395,087 bp (99.7%)
=== Adapter 1 ===
Sequence: TGTGGCTT; Type: regular 3'; Length: 8; Trimmed: 1405150 times.
No. of allowed errors:
0-8 bp: 0
Bases preceding removed adapters:
A: 21.1%
C: 29.5%
G: 32.7%
T: 16.7%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 937798 579513.8 0 937798
4 328883 144878.4 0 328883
5 64326 36219.6 0 64326
6 14515 9054.9 0 14515
7 4900 2263.7 0 4900
8 1813 565.9 0 1813
9 1233 565.9 0 1233
10 1036 565.9 0 1036
11 1298 565.9 0 1298
12 1270 565.9 0 1270
13 1156 565.9 0 1156
14 1294 565.9 0 1294
15 1223 565.9 0 1223
16 1208 565.9 0 1208
17 1263 565.9 0 1263
18 1319 565.9 0 1319
19 1296 565.9 0 1296
20 1259 565.9 0 1259
21 1594 565.9 0 1594
22 1745 565.9 0 1745
23 1001 565.9 0 1001
24 1168 565.9 0 1168
25 1412 565.9 0 1412
26 1258 565.9 0 1258
27 1348 565.9 0 1348
28 1285 565.9 0 1285
29 1347 565.9 0 1347
30 1268 565.9 0 1268
31 1166 565.9 0 1166
32 1311 565.9 0 1311
33 1496 565.9 0 1496
34 978 565.9 0 978
35 1199 565.9 0 1199
36 1265 565.9 0 1265
37 1290 565.9 0 1290
38 1189 565.9 0 1189
39 1101 565.9 0 1101
40 1250 565.9 0 1250
41 1272 565.9 0 1272
42 1242 565.9 0 1242
43 1427 565.9 0 1427
44 1248 565.9 0 1248
45 1067 565.9 0 1067
46 1220 565.9 0 1220
47 1286 565.9 0 1286
48 1327 565.9 0 1327
49 1335 565.9 0 1335
50 965 565.9 0 965
This is cutadapt 1.15 with Python 3.5.2
Command line parameters: -j 60 -a AACACGCT -o /NGS_Data/Andrew/Nugen_trimmed_samples/AGRF_TI_Nugen_Trimmed/163734_WT6_TI_CB8LUANXX_AACACGCT_all_trimmed.fq 163734_WT6_TI_CB8LUANXX_AACACGCT_all_trimmed.fq
Running on 60 cores
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 67.55 s (2 us/read; 28.78 M reads/minute).
=== Summary ===
Total reads processed: 32,401,357
Reads with adapters: 826,646 (2.6%)
Reads written (passing filters): 32,401,357 (100.0%)
Total basepairs processed: 1,602,095,516 bp
Total written (filtered): 1,596,744,613 bp (99.7%)
=== Adapter 1 ===
Sequence: AACACGCT; Type: regular 3'; Length: 8; Trimmed: 826646 times.
No. of allowed errors:
0-8 bp: 0
Bases preceding removed adapters:
A: 30.4%
C: 36.4%
G: 21.1%
T: 12.1%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
3 576382 506271.2 0 576382
4 49378 126567.8 0 49378
5 47142 31642.0 0 47142
6 2524 7910.5 0 2524
7 509 1977.6 0 509
8 545 494.4 0 545
9 611 494.4 0 611
10 920 494.4 0 920
11 6127 494.4 0 6127
12 1605 494.4 0 1605
13 4879 494.4 0 4879
14 699 494.4 0 699
15 3683 494.4 0 3683
16 530 494.4 0 530
17 1409 494.4 0 1409
18 11259 494.4 0 11259
19 3942 494.4 0 3942
20 7630 494.4 0 7630
21 10333 494.4 0 10333
22 84364 494.4 0 84364
23 1878 494.4 0 1878
24 567 494.4 0 567
25 332 494.4 0 332
26 809 494.4 0 809
27 569 494.4 0 569
28 543 494.4 0 543
29 385 494.4 0 385
30 312 494.4 0 312
31 659 494.4 0 659
32 220 494.4 0 220
33 353 494.4 0 353
34 1230 494.4 0 1230
35 166 494.4 0 166
36 49 494.4 0 49
37 130 494.4 0 130
38 36 494.4 0 36
39 264 494.4 0 264
40 664 494.4 0 664
41 1430 494.4 0 1430
42 283 494.4 0 283
43 103 494.4 0 103
44 57 494.4 0 57
45 183 494.4 0 183
46 155 494.4 0 155
47 290 494.4 0 290
48 215 494.4 0 215
49 132 494.4 0 132
50 161 494.4 0 161
This is cutadapt 1.15 with Python 3.5.2
Command line parameters: -j 60 -a TTCACGGA -o /NGS_Data/Andrew/Nugen_trimmed_samples/AGRF_TI_Nugen_Trimmed/326_TG6_TI_CB8LUANXX_TTCACGGA_all_trimmed.fq 326_TG6_TI_CB8LUANXX_TTCACGGA_all_trimmed.fq
Running on 60 cores
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 64.31 s (2 us/read; 34.72 M reads/minute).
=== Summary ===
Total reads processed: 37,213,050
Reads with adapters: 1,555,462 (4.2%)
Reads written (passing filters): 37,213,050 (100.0%)
Total basepairs processed: 1,840,517,391 bp
Total written (filtered): 1,835,219,998 bp (99.7%)
=== Adapter 1 ===
Sequence: TTCACGGA; Type: regular 3'; Length: 8; Trimmed: 1555462 times.
No. of allowed errors:
0-8 bp: 0
Bases preceding removed adapters:
A: 12.8%
C: 18.8%
G: 9.9%
T: 58.4%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
3 1338632 581453.9 0 1338632
4 83190 145363.5 0 83190
5 83248 36340.9 0 83248
6 39139 9085.2 0 39139
7 932 2271.3 0 932
8 135 567.8 0 135
9 171 567.8 0 171
10 228 567.8 0 228
11 134 567.8 0 134
12 237 567.8 0 237
13 519 567.8 0 519
14 120 567.8 0 120
15 134 567.8 0 134
16 204 567.8 0 204
17 199 567.8 0 199
18 203 567.8 0 203
19 320 567.8 0 320
20 184 567.8 0 184
21 393 567.8 0 393
22 931 567.8 0 931
23 355 567.8 0 355
24 146 567.8 0 146
25 234 567.8 0 234
26 255 567.8 0 255
27 221 567.8 0 221
28 341 567.8 0 341
29 143 567.8 0 143
30 132 567.8 0 132
31 274 567.8 0 274
32 130 567.8 0 130
33 209 567.8 0 209
34 218 567.8 0 218
35 298 567.8 0 298
36 423 567.8 0 423
37 218 567.8 0 218
38 213 567.8 0 213
39 116 567.8 0 116
40 306 567.8 0 306
41 132 567.8 0 132
42 231 567.8 0 231
43 214 567.8 0 214
44 239 567.8 0 239
45 212 567.8 0 212
46 400 567.8 0 400
47 121 567.8 0 121
48 138 567.8 0 138
49 210 567.8 0 210
50 80 567.8 0 80
This is cutadapt 1.15 with Python 3.5.2
Command line parameters: -j 60 -a TGCTGTGA -o /NGS_Data/Andrew/Nugen_trimmed_samples/AGRF_TI_Nugen_Trimmed/512_WT3_TI_CB8LUANXX_TGCTGTGA_all_trimmed.fq 512_WT3_TI_CB8LUANXX_TGCTGTGA_all_trimmed.fq
Running on 60 cores
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 61.33 s (2 us/read; 34.36 M reads/minute).
=== Summary ===
Total reads processed: 35,118,941
Reads with adapters: 1,019,504 (2.9%)
Reads written (passing filters): 35,118,941 (100.0%)
Total basepairs processed: 1,736,852,985 bp
Total written (filtered): 1,732,118,776 bp (99.7%)
=== Adapter 1 ===
Sequence: TGCTGTGA; Type: regular 3'; Length: 8; Trimmed: 1019504 times.
No. of allowed errors:
0-8 bp: 0
Bases preceding removed adapters:
A: 23.1%
C: 32.3%
G: 22.4%
T: 22.1%
none/other: 0.1%
Overview of removed sequences
length count expect max.err error counts
3 693187 548733.5 0 693187
4 182541 137183.4 0 182541
5 69972 34295.8 0 69972
6 17197 8574.0 0 17197
7 7158 2143.5 0 7158
8 515 535.9 0 515
9 779 535.9 0 779
10 1429 535.9 0 1429
11 1019 535.9 0 1019
12 1017 535.9 0 1017
13 1036 535.9 0 1036
14 1249 535.9 0 1249
15 987 535.9 0 987
16 1116 535.9 0 1116
17 1291 535.9 0 1291
18 1238 535.9 0 1238
19 1205 535.9 0 1205
20 1464 535.9 0 1464
21 1181 535.9 0 1181
22 2578 535.9 0 2578
23 1374 535.9 0 1374
24 1184 535.9 0 1184
25 1011 535.9 0 1011
26 1013 535.9 0 1013
27 1110 535.9 0 1110
28 1279 535.9 0 1279
29 1162 535.9 0 1162
30 995 535.9 0 995
31 1079 535.9 0 1079
32 1246 535.9 0 1246
33 1193 535.9 0 1193
34 1163 535.9 0 1163
35 1240 535.9 0 1240
36 1107 535.9 0 1107
37 1315 535.9 0 1315
38 1228 535.9 0 1228
39 1101 535.9 0 1101
40 1066 535.9 0 1066
41 1219 535.9 0 1219
42 1081 535.9 0 1081
43 1202 535.9 0 1202
44 1054 535.9 0 1054
45 1065 535.9 0 1065
46 1042 535.9 0 1042
47 1156 535.9 0 1156
48 1033 535.9 0 1033
49 945 535.9 0 945
50 682 535.9 0 682
This is cutadapt 1.15 with Python 3.5.2
Command line parameters: -j 60 -a CCTCGAAT -o /NGS_Data/Andrew/Nugen_trimmed_samples/AGRF_TI_Nugen_Trimmed/525_TG3_TI_CB8LUANXX_CCTCGAAT_all_trimmed.fq 525_TG3_TI_CB8LUANXX_CCTCGAAT_all_trimmed.fq
Running on 60 cores
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 73.62 s (2 us/read; 29.40 M reads/minute).
=== Summary ===
Total reads processed: 36,068,228
Reads with adapters: 1,231,387 (3.4%)
Reads written (passing filters): 36,068,228 (100.0%)
Total basepairs processed: 1,783,660,721 bp
Total written (filtered): 1,779,468,162 bp (99.8%)
=== Adapter 1 ===
Sequence: CCTCGAAT; Type: regular 3'; Length: 8; Trimmed: 1231387 times.
No. of allowed errors:
0-8 bp: 0
Bases preceding removed adapters:
A: 19.1%
C: 23.5%
G: 22.4%
T: 35.0%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
3 914812 563566.1 0 914812
4 280662 140891.5 0 280662
5 27416 35222.9 0 27416
6 1895 8805.7 0 1895
7 166 2201.4 0 166
8 204 550.4 0 204
9 135 550.4 0 135
10 176 550.4 0 176
11 96 550.4 0 96
12 137 550.4 0 137
13 157 550.4 0 157
14 193 550.4 0 193
15 100 550.4 0 100
16 118 550.4 0 118
17 127 550.4 0 127
18 224 550.4 0 224
19 193 550.4 0 193
20 193 550.4 0 193
21 170 550.4 0 170
22 583 550.4 0 583
23 170 550.4 0 170
24 111 550.4 0 111
25 166 550.4 0 166
26 138 550.4 0 138
27 121 550.4 0 121
28 125 550.4 0 125
29 157 550.4 0 157
30 104 550.4 0 104
31 146 550.4 0 146
32 136 550.4 0 136
33 139 550.4 0 139
34 115 550.4 0 115
35 172 550.4 0 172
36 135 550.4 0 135
37 116 550.4 0 116
38 111 550.4 0 111
39 170 550.4 0 170
40 93 550.4 0 93
41 117 550.4 0 117
42 137 550.4 0 137
43 145 550.4 0 145
44 149 550.4 0 149
45 129 550.4 0 129
46 86 550.4 0 86
47 135 550.4 0 135
48 114 550.4 0 114
49 126 550.4 0 126
50 67 550.4 0 67
ubuntu@nectarbioinformatics-tas:/NGS_Data/Andrew/AGRF_Trimmed_samples/AGRF_TI_Trimmed$