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.sampleA_1.fastq.gz -p fastq/input.sampleA_2.fastq.gz sampleA_1.fastq.gz sampleA_2.fastq.gz Processing reads on 2 cores in paired-end mode ... Finished in 19.86 s (14 us/read; 4.38 M reads/minute). === Summary === Total read pairs processed: 1,450,000 Read 1 with adapter: 60,228 (4.2%) Read 2 with adapter: 16,003 (1.1%) Pairs written (passing filters): 1,449,757 (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): 321,106,240 bp (88.6%) Read 1: 160,480,240 bp Read 2: 160,626,000 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 60228 times No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.5% C: 0.4% G: 23.0% T: 40.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 33983 22656.2 0 33983 4 13641 5664.1 0 13641 5 652 1416.0 0 652 6 518 354.0 0 518 7 485 88.5 0 485 8 425 22.1 0 425 9 430 5.5 0 411 19 10 485 1.4 1 441 44 11 436 0.3 1 397 39 12 449 0.1 1 418 31 13 399 0.0 1 373 26 14 398 0.0 1 361 37 15 377 0.0 1 361 16 16 319 0.0 1 310 9 17 320 0.0 1 307 13 18 278 0.0 1 265 13 19 340 0.0 1 326 14 20 285 0.0 1 277 8 21 280 0.0 1 277 3 22 288 0.0 1 278 10 23 253 0.0 1 246 7 24 262 0.0 1 257 5 25 255 0.0 1 252 3 26 229 0.0 1 224 5 27 268 0.0 1 265 3 28 204 0.0 1 201 3 29 210 0.0 1 208 2 30 198 0.0 1 197 1 31 193 0.0 1 189 4 32 173 0.0 1 173 33 154 0.0 1 152 2 34 152 0.0 1 150 2 35 155 0.0 1 154 1 36 145 0.0 1 144 1 37 136 0.0 1 135 1 38 143 0.0 1 143 39 125 0.0 1 123 2 40 110 0.0 1 109 1 41 101 0.0 1 100 1 42 97 0.0 1 95 2 43 100 0.0 1 99 1 44 107 0.0 1 107 45 94 0.0 1 94 46 96 0.0 1 96 47 78 0.0 1 78 48 94 0.0 1 94 49 82 0.0 1 82 50 71 0.0 1 68 3 51 71 0.0 1 71 52 61 0.0 1 61 53 64 0.0 1 62 2 54 48 0.0 1 48 55 61 0.0 1 60 1 56 48 0.0 1 48 57 44 0.0 1 44 58 42 0.0 1 42 59 41 0.0 1 41 60 54 0.0 1 54 61 42 0.0 1 42 62 41 0.0 1 41 63 34 0.0 1 34 64 33 0.0 1 33 65 24 0.0 1 23 1 66 19 0.0 1 19 67 30 0.0 1 30 68 16 0.0 1 16 69 24 0.0 1 24 70 19 0.0 1 19 71 18 0.0 1 18 72 20 0.0 1 20 73 22 0.0 1 22 74 18 0.0 1 18 75 18 0.0 1 18 76 17 0.0 1 17 77 10 0.0 1 10 78 14 0.0 1 14 79 15 0.0 1 15 80 12 0.0 1 12 81 11 0.0 1 11 82 6 0.0 1 6 83 9 0.0 1 9 84 9 0.0 1 9 85 7 0.0 1 7 86 8 0.0 1 8 87 4 0.0 1 4 88 8 0.0 1 8 89 13 0.0 1 13 90 11 0.0 1 11 91 4 0.0 1 4 92 6 0.0 1 6 93 2 0.0 1 2 94 8 0.0 1 8 95 6 0.0 1 6 96 3 0.0 1 3 97 5 0.0 1 5 98 4 0.0 1 4 99 3 0.0 1 3 100 2 0.0 1 2 101 2 0.0 1 2 102 4 0.0 1 4 103 4 0.0 1 4 104 3 0.0 1 3 105 2 0.0 1 2 106 2 0.0 1 2 107 3 0.0 1 3 108 4 0.0 1 4 110 1 0.0 1 1 111 21 0.0 1 21 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16003 times No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.8% C: 18.0% G: 0.3% T: 30.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 2461 22656.2 0 2461 4 990 5664.1 0 990 5 661 1416.0 0 661 6 507 354.0 0 507 7 490 88.5 0 490 8 418 22.1 0 418 9 417 5.5 0 416 1 10 464 1.4 1 439 25 11 426 0.3 1 400 26 12 448 0.1 1 423 25 13 399 0.0 1 376 23 14 398 0.0 1 378 20 15 377 0.0 1 359 18 16 319 0.0 1 311 8 17 320 0.0 1 304 16 18 277 0.0 1 266 11 19 340 0.0 1 326 14 20 285 0.0 1 273 12 21 280 0.0 1 273 7 22 288 0.0 1 282 6 23 253 0.0 1 246 7 24 262 0.0 1 259 3 25 255 0.0 1 251 4 26 229 0.0 1 221 8 27 268 0.0 1 263 5 28 204 0.0 1 204 29 210 0.0 1 209 1 30 198 0.0 1 195 3 31 193 0.0 1 190 3 32 173 0.0 1 170 3 33 154 0.0 1 152 2 34 152 0.0 1 151 1 35 155 0.0 1 153 2 36 145 0.0 1 144 1 37 136 0.0 1 134 2 38 143 0.0 1 142 1 39 124 0.0 1 123 1 40 110 0.0 1 109 1 41 101 0.0 1 100 1 42 96 0.0 1 96 43 100 0.0 1 100 44 107 0.0 1 106 1 45 94 0.0 1 94 46 96 0.0 1 94 2 47 78 0.0 1 78 48 94 0.0 1 94 49 82 0.0 1 82 50 71 0.0 1 70 1 51 71 0.0 1 70 1 52 61 0.0 1 61 53 64 0.0 1 64 54 48 0.0 1 48 55 61 0.0 1 61 56 48 0.0 1 48 57 44 0.0 1 44 58 42 0.0 1 42 59 41 0.0 1 41 60 54 0.0 1 53 1 61 42 0.0 1 42 62 41 0.0 1 41 63 34 0.0 1 34 64 33 0.0 1 32 1 65 24 0.0 1 24 66 19 0.0 1 19 67 30 0.0 1 30 68 16 0.0 1 16 69 24 0.0 1 24 70 19 0.0 1 19 71 18 0.0 1 18 72 20 0.0 1 20 73 22 0.0 1 22 74 18 0.0 1 18 75 18 0.0 1 18 76 17 0.0 1 17 77 10 0.0 1 10 78 14 0.0 1 14 79 15 0.0 1 15 80 12 0.0 1 12 81 11 0.0 1 11 82 6 0.0 1 6 83 9 0.0 1 9 84 9 0.0 1 9 85 7 0.0 1 7 86 8 0.0 1 8 87 4 0.0 1 4 88 8 0.0 1 8 89 13 0.0 1 13 90 11 0.0 1 11 91 4 0.0 1 4 92 6 0.0 1 6 93 2 0.0 1 2 94 8 0.0 1 8 95 6 0.0 1 6 96 3 0.0 1 3 97 5 0.0 1 5 98 4 0.0 1 4 99 3 0.0 1 3 100 2 0.0 1 2 101 2 0.0 1 2 102 4 0.0 1 4 103 4 0.0 1 4 104 3 0.0 1 3 105 2 0.0 1 2 106 2 0.0 1 2 107 3 0.0 1 3 108 4 0.0 1 4 110 1 0.0 1 1 111 21 0.0 1 21