This is cutadapt 1.18 with Python 3.4.2 Command line parameters: -j 16 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT -o KOIL4_2_R1_trm.fastq.gz -p KOIL4_2_R2_trm.fastq.gz /mnt/max/b/genomics_facility/DKlab/mr/rnaseq/RNA_Seq/HI.1370.005.Index_1.KOIL4_2_R1.fastq.gz /mnt/max/b/genomics_facility/DKlab/mr/rnaseq/RNA_Seq/HI.1370.005.Index_1.KOIL4_2_R2.fastq.gz Processing reads on 16 cores in paired-end mode ... Finished in 343.30 s (6 us/read; 10.62 M reads/minute). === Summary === Total read pairs processed: 60,779,853 Read 1 with adapter: 3,196,589 (5.3%) Read 2 with adapter: 3,357,275 (5.5%) Pairs written (passing filters): 60,779,853 (100.0%) Total basepairs processed: 12,155,970,600 bp Read 1: 6,077,985,300 bp Read 2: 6,077,985,300 bp Total written (filtered): 12,108,317,387 bp (99.6%) Read 1: 6,054,368,509 bp Read 2: 6,053,948,878 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; Type: regular 3'; Length: 34; Trimmed: 3196589 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-34 bp: 3 Bases preceding removed adapters: A: 19.2% C: 31.9% G: 32.6% T: 16.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 1399282 949685.2 0 1399282 4 384286 237421.3 0 384286 5 191028 59355.3 0 191028 6 131368 14838.8 0 131368 7 105072 3709.7 0 105072 8 102821 927.4 0 102821 9 93778 231.9 0 92478 1300 10 86893 58.0 1 81748 5145 11 78259 14.5 1 74516 3743 12 71412 3.6 1 63654 7758 13 64051 0.9 1 60551 3500 14 57592 0.2 1 54713 2879 15 52362 0.1 1 50069 2293 16 45758 0.0 1 42714 3044 17 39998 0.0 1 38321 1677 18 35337 0.0 1 33230 1926 181 19 30716 0.0 1 27347 3161 208 20 27334 0.0 2 25578 1507 249 21 24731 0.0 2 23256 1218 257 22 21467 0.0 2 18894 2309 264 23 19330 0.0 2 18265 907 158 24 17192 0.0 2 14896 2063 233 25 15173 0.0 2 14178 838 157 26 13299 0.0 2 11897 1243 159 27 11460 0.0 2 10778 585 93 4 28 9812 0.0 2 8901 769 115 27 29 8713 0.0 2 8067 531 79 36 30 7343 0.0 3 6634 521 137 51 31 6570 0.0 3 5484 879 167 40 32 5570 0.0 3 4252 1178 106 34 33 5037 0.0 3 4629 347 47 14 34 4315 0.0 3 3898 327 65 25 35 3886 0.0 3 3606 241 34 5 36 3375 0.0 3 3140 191 33 11 37 2809 0.0 3 2577 176 33 23 38 2536 0.0 3 2373 128 20 15 39 2274 0.0 3 2098 140 13 23 40 1914 0.0 3 1772 115 12 15 41 1636 0.0 3 1502 110 12 12 42 1374 0.0 3 1271 87 7 9 43 1191 0.0 3 1114 69 7 1 44 1046 0.0 3 981 44 11 10 45 958 0.0 3 900 48 6 4 46 783 0.0 3 720 48 8 7 47 753 0.0 3 703 45 3 2 48 665 0.0 3 625 32 5 3 49 597 0.0 3 560 29 5 3 50 500 0.0 3 465 26 5 4 51 416 0.0 3 389 18 3 6 52 356 0.0 3 322 26 3 5 53 276 0.0 3 249 22 3 2 54 235 0.0 3 219 14 1 1 55 238 0.0 3 220 15 3 56 174 0.0 3 165 8 0 1 57 172 0.0 3 164 5 3 58 140 0.0 3 127 10 3 59 123 0.0 3 118 3 2 60 99 0.0 3 92 4 2 1 61 81 0.0 3 71 9 1 62 82 0.0 3 79 2 0 1 63 51 0.0 3 51 64 41 0.0 3 40 1 65 32 0.0 3 28 4 66 27 0.0 3 23 4 67 25 0.0 3 22 2 0 1 68 24 0.0 3 23 1 69 23 0.0 3 22 1 70 9 0.0 3 8 0 0 1 71 6 0.0 3 5 1 72 4 0.0 3 4 73 3 0.0 3 3 74 2 0.0 3 1 1 75 2 0.0 3 1 1 76 2 0.0 3 2 77 2 0.0 3 1 1 78 6 0.0 3 6 79 3 0.0 3 2 0 0 1 80 6 0.0 3 4 0 0 2 81 6 0.0 3 4 1 0 1 82 3 0.0 3 3 83 2 0.0 3 2 84 5 0.0 3 5 85 9 0.0 3 9 86 9 0.0 3 8 0 1 87 5 0.0 3 5 88 2 0.0 3 2 89 4 0.0 3 4 90 8 0.0 3 8 91 7 0.0 3 5 1 0 1 92 4 0.0 3 4 93 8 0.0 3 8 94 10 0.0 3 8 1 0 1 95 10 0.0 3 8 2 96 5 0.0 3 5 97 15 0.0 3 13 2 98 7 0.0 3 7 100 154 0.0 3 6 142 4 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT; Type: regular 3'; Length: 54; Trimmed: 3357275 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50-54 bp: 5 Bases preceding removed adapters: A: 20.9% C: 33.6% G: 34.8% T: 10.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 1524306 949685.2 0 1524306 4 414718 237421.3 0 414718 5 198176 59355.3 0 198176 6 132832 14838.8 0 132832 7 112152 3709.7 0 112152 8 101627 927.4 0 101627 9 91966 231.9 0 89685 2281 10 87248 58.0 1 80570 6678 11 77467 14.5 1 69916 7551 12 71094 3.6 1 67540 3554 13 63165 0.9 1 58863 4302 14 57044 0.2 1 54411 2633 15 51271 0.1 1 43244 8027 16 45272 0.0 1 42043 3229 17 39591 0.0 1 37689 1902 18 34752 0.0 1 29600 5147 5 19 30338 0.0 1 28572 1682 84 20 27029 0.0 2 23230 2536 1263 21 24425 0.0 2 19582 4351 492 22 21334 0.0 2 19849 1214 271 23 19143 0.0 2 17731 1147 265 24 17038 0.0 2 15553 1256 229 25 15013 0.0 2 13836 1014 163 26 13188 0.0 2 11245 1672 271 27 11333 0.0 2 9515 1536 278 4 28 9700 0.0 2 8123 1326 246 5 29 8607 0.0 2 6936 1359 267 45 30 7266 0.0 3 6098 929 163 76 31 6505 0.0 3 3961 2053 382 109 32 5527 0.0 3 4559 645 184 139 33 4997 0.0 3 3795 908 200 94 34 4271 0.0 3 3516 586 127 42 35 3846 0.0 3 3222 497 83 44 36 3340 0.0 3 2793 417 96 34 37 2766 0.0 3 2370 320 58 18 38 2500 0.0 3 2081 311 77 29 2 39 2253 0.0 3 1939 239 50 17 8 40 1892 0.0 4 1536 267 62 18 9 41 1623 0.0 4 1407 166 35 10 5 42 1372 0.0 4 1175 144 43 8 2 43 1184 0.0 4 783 324 51 17 9 44 1039 0.0 4 888 115 18 9 9 45 950 0.0 4 823 92 21 10 4 46 773 0.0 4 562 142 48 13 8 47 750 0.0 4 643 76 20 6 5 48 662 0.0 4 547 78 25 6 5 1 49 600 0.0 4 513 61 19 4 3 50 497 0.0 5 424 52 10 7 3 1 51 417 0.0 5 348 48 8 7 5 1 52 356 0.0 5 296 37 13 4 4 2 53 278 0.0 5 230 35 11 1 1 54 232 0.0 5 202 20 2 6 0 2 55 235 0.0 5 199 26 3 3 3 1 56 175 0.0 5 147 17 6 2 2 1 57 171 0.0 5 152 11 1 5 1 1 58 144 0.0 5 113 16 3 5 5 2 59 123 0.0 5 107 8 2 3 2 1 60 99 0.0 5 80 11 2 4 0 2 61 80 0.0 5 70 9 0 1 62 84 0.0 5 72 7 0 2 2 1 63 54 0.0 5 45 2 0 6 1 64 43 0.0 5 37 3 0 1 2 65 32 0.0 5 28 2 0 2 66 27 0.0 5 22 4 1 67 24 0.0 5 16 6 1 0 1 68 24 0.0 5 20 1 0 2 0 1 69 23 0.0 5 20 0 2 1 70 9 0.0 5 7 1 0 1 71 6 0.0 5 4 1 0 1 72 4 0.0 5 3 0 0 1 73 3 0.0 5 3 74 1 0.0 5 1 75 2 0.0 5 1 1 76 2 0.0 5 2 77 3 0.0 5 3 78 6 0.0 5 4 2 79 2 0.0 5 2 80 9 0.0 5 5 2 1 1 81 8 0.0 5 8 82 4 0.0 5 4 83 2 0.0 5 2 84 5 0.0 5 4 0 0 1 85 9 0.0 5 9 86 8 0.0 5 8 87 6 0.0 5 5 0 0 1 88 2 0.0 5 2 89 4 0.0 5 4 90 9 0.0 5 8 1 91 6 0.0 5 4 2 92 4 0.0 5 3 1 93 9 0.0 5 8 0 0 0 1 94 9 0.0 5 7 1 0 1 95 10 0.0 5 7 3 96 5 0.0 5 4 1 97 12 0.0 5 11 1 98 7 0.0 5 5 2 100 46 0.0 5 11 8 4 6 10 7