This is cutadapt 2.10 with Python 3.6.7 Command line parameters: -j 2 -a AGATCGGAAGAGC -A AGATCGGAAGAGC -q 20 -m 36 -O 3 -o fastq/input.sampleB_1.fastq.gz -p fastq/input.sampleB_2.fastq.gz sampleB_1.fastq.gz sampleB_2.fastq.gz Processing reads on 2 cores in paired-end mode ... Finished in 19.82 s (14 us/read; 4.39 M reads/minute). === Summary === Total read pairs processed: 1,450,000 Read 1 with adapter: 59,612 (4.1%) Read 2 with adapter: 15,917 (1.1%) Pairs written (passing filters): 1,449,721 (100.0%) Total basepairs processed: 362,500,000 bp Read 1: 181,250,000 bp Read 2: 181,250,000 bp Quality-trimmed: 40,600,000 bp (11.2%) Read 1: 20,300,000 bp Read 2: 20,300,000 bp Total written (filtered): 321,113,079 bp (88.6%) Read 1: 160,484,535 bp Read 2: 160,628,544 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 59612 times No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.8% C: 0.3% G: 22.8% T: 40.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 33492 22656.2 0 33492 4 13704 5664.1 0 13704 5 603 1416.0 0 603 6 517 354.0 0 517 7 484 88.5 0 484 8 441 22.1 0 441 9 502 5.5 0 475 27 10 472 1.4 1 429 43 11 449 0.3 1 415 34 12 419 0.1 1 393 26 13 389 0.0 1 367 22 14 372 0.0 1 355 17 15 383 0.0 1 369 14 16 332 0.0 1 317 15 17 368 0.0 1 348 20 18 325 0.0 1 319 6 19 287 0.0 1 271 16 20 295 0.0 1 280 15 21 272 0.0 1 261 11 22 253 0.0 1 247 6 23 266 0.0 1 260 6 24 235 0.0 1 228 7 25 238 0.0 1 232 6 26 203 0.0 1 203 27 204 0.0 1 199 5 28 217 0.0 1 213 4 29 194 0.0 1 192 2 30 154 0.0 1 149 5 31 169 0.0 1 166 3 32 189 0.0 1 188 1 33 153 0.0 1 152 1 34 154 0.0 1 151 3 35 156 0.0 1 152 4 36 163 0.0 1 161 2 37 156 0.0 1 156 38 134 0.0 1 132 2 39 117 0.0 1 117 40 102 0.0 1 102 41 106 0.0 1 106 42 75 0.0 1 74 1 43 117 0.0 1 116 1 44 103 0.0 1 103 45 84 0.0 1 84 46 93 0.0 1 93 47 90 0.0 1 90 48 65 0.0 1 64 1 49 71 0.0 1 71 50 79 0.0 1 79 51 58 0.0 1 57 1 52 61 0.0 1 61 53 52 0.0 1 52 54 60 0.0 1 60 55 40 0.0 1 40 56 42 0.0 1 42 57 53 0.0 1 53 58 42 0.0 1 42 59 40 0.0 1 40 60 41 0.0 1 41 61 37 0.0 1 37 62 32 0.0 1 32 63 30 0.0 1 30 64 30 0.0 1 30 65 27 0.0 1 27 66 29 0.0 1 29 67 32 0.0 1 32 68 27 0.0 1 27 69 27 0.0 1 26 1 70 23 0.0 1 23 71 23 0.0 1 23 72 21 0.0 1 21 73 18 0.0 1 18 74 25 0.0 1 25 75 19 0.0 1 19 76 17 0.0 1 17 77 17 0.0 1 17 78 13 0.0 1 13 79 12 0.0 1 12 80 17 0.0 1 17 81 15 0.0 1 15 82 17 0.0 1 17 83 19 0.0 1 19 84 8 0.0 1 8 85 9 0.0 1 9 86 12 0.0 1 12 87 12 0.0 1 12 88 7 0.0 1 7 89 5 0.0 1 5 90 8 0.0 1 8 91 5 0.0 1 5 92 7 0.0 1 7 93 6 0.0 1 6 94 3 0.0 1 3 95 3 0.0 1 3 96 7 0.0 1 7 97 4 0.0 1 4 98 6 0.0 1 6 99 4 0.0 1 4 100 6 0.0 1 6 102 5 0.0 1 5 103 4 0.0 1 4 104 2 0.0 1 2 105 1 0.0 1 1 106 2 0.0 1 2 107 3 0.0 1 3 108 5 0.0 1 5 109 1 0.0 1 1 111 15 0.0 1 15 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15917 times No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.9% C: 18.1% G: 0.3% T: 30.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 2531 22656.2 0 2531 4 1006 5664.1 0 1006 5 612 1416.0 0 612 6 504 354.0 0 504 7 492 88.5 0 492 8 445 22.1 0 445 9 483 5.5 0 483 10 456 1.4 1 426 30 11 440 0.3 1 414 26 12 416 0.1 1 387 29 13 389 0.0 1 366 23 14 373 0.0 1 355 18 15 383 0.0 1 367 16 16 332 0.0 1 319 13 17 368 0.0 1 356 12 18 326 0.0 1 314 12 19 288 0.0 1 276 12 20 295 0.0 1 286 9 21 272 0.0 1 265 7 22 253 0.0 1 242 11 23 266 0.0 1 264 2 24 234 0.0 1 225 9 25 238 0.0 1 234 4 26 203 0.0 1 198 5 27 204 0.0 1 201 3 28 217 0.0 1 216 1 29 194 0.0 1 188 6 30 154 0.0 1 151 3 31 169 0.0 1 166 3 32 189 0.0 1 185 4 33 153 0.0 1 153 34 154 0.0 1 151 3 35 156 0.0 1 155 1 36 163 0.0 1 163 37 156 0.0 1 154 2 38 134 0.0 1 133 1 39 117 0.0 1 117 40 102 0.0 1 101 1 41 106 0.0 1 105 1 42 75 0.0 1 72 3 43 117 0.0 1 117 44 103 0.0 1 103 45 84 0.0 1 84 46 93 0.0 1 93 47 90 0.0 1 90 48 64 0.0 1 64 49 71 0.0 1 71 50 78 0.0 1 78 51 58 0.0 1 58 52 61 0.0 1 61 53 52 0.0 1 52 54 60 0.0 1 60 55 40 0.0 1 40 56 42 0.0 1 42 57 53 0.0 1 53 58 42 0.0 1 42 59 40 0.0 1 40 60 41 0.0 1 41 61 37 0.0 1 37 62 32 0.0 1 32 63 30 0.0 1 30 64 30 0.0 1 29 1 65 27 0.0 1 27 66 29 0.0 1 28 1 67 32 0.0 1 32 68 27 0.0 1 27 69 27 0.0 1 27 70 23 0.0 1 23 71 23 0.0 1 23 72 21 0.0 1 21 73 18 0.0 1 18 74 26 0.0 1 26 75 19 0.0 1 19 76 17 0.0 1 17 77 17 0.0 1 17 78 13 0.0 1 13 79 12 0.0 1 12 80 17 0.0 1 17 81 15 0.0 1 15 82 17 0.0 1 17 83 19 0.0 1 19 84 8 0.0 1 8 85 10 0.0 1 10 86 12 0.0 1 12 87 12 0.0 1 12 88 7 0.0 1 7 89 5 0.0 1 5 90 8 0.0 1 8 91 5 0.0 1 5 92 7 0.0 1 7 93 6 0.0 1 6 94 3 0.0 1 3 95 3 0.0 1 3 96 7 0.0 1 7 97 4 0.0 1 4 98 6 0.0 1 6 99 4 0.0 1 4 100 6 0.0 1 6 102 5 0.0 1 5 103 4 0.0 1 4 104 2 0.0 1 2 105 1 0.0 1 1 106 2 0.0 1 2 107 3 0.0 1 3 108 5 0.0 1 5 109 1 0.0 1 1 111 16 0.0 1 16