This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH01-38.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH01-38.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH01-38_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH01-38_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 208.493 s (6.258 µs/read; 9.59 M reads/minute). === Summary === Total read pairs processed: 33,314,749 Read 1 with adapter: 6,415,707 (19.3%) Read 2 with adapter: 6,368,151 (19.1%) == Read fate breakdown == Pairs that were too short: 244,892 (0.7%) Pairs written (passing filters): 33,069,857 (99.3%) Total basepairs processed: 9,994,424,700 bp Read 1: 4,997,212,350 bp Read 2: 4,997,212,350 bp Quality-trimmed: 1,349,165 bp (0.0%) Read 1: 615,732 bp Read 2: 733,433 bp Total written (filtered): 9,606,073,727 bp (96.1%) Read 1: 4,805,791,236 bp Read 2: 4,800,282,491 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 6415707 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-33 bp: 3 Bases preceding removed adapters: A: 25.6% C: 20.5% G: 30.7% T: 19.7% none/other: 3.5% Overview of removed sequences length count expect max.err error counts 3 749966 520543.0 0 749966 4 233254 130135.7 0 233254 5 134884 32533.9 0 134884 6 115916 8133.5 0 115916 7 126970 2033.4 0 126970 8 112871 508.3 0 112871 9 116265 127.1 0 115699 566 10 115414 31.8 1 101862 13552 11 116133 7.9 1 102936 13197 12 115316 2.0 1 102647 12669 13 138150 0.5 1 123070 15080 14 132762 0.1 1 118079 14683 15 140095 0.0 1 125463 14632 16 130146 0.0 1 116489 13657 17 124588 0.0 1 111701 12887 18 113327 0.0 1 101505 11771 51 19 104683 0.0 1 93224 11205 254 20 114779 0.0 2 97643 11563 5573 21 110541 0.0 2 94439 10837 5265 22 110515 0.0 2 94388 10935 5192 23 115585 0.0 2 98952 11221 5412 24 111779 0.0 2 95404 11189 5186 25 117577 0.0 2 100343 11710 5524 26 120361 0.0 2 102923 11887 5551 27 113046 0.0 2 96929 11001 5110 6 28 109862 0.0 2 93789 11111 4938 24 29 94874 0.0 2 80593 9773 4454 54 30 90871 0.0 3 74861 9104 4044 2862 31 93012 0.0 3 77038 9102 4058 2814 32 91180 0.0 3 75693 8914 3878 2695 33 97915 0.0 3 81071 9700 4206 2938 34 93795 0.0 3 78024 9134 3951 2686 35 89507 0.0 3 73919 9116 3865 2607 36 86256 0.0 3 71909 8315 3566 2466 37 87848 0.0 3 73087 8494 3698 2569 38 81312 0.0 3 67693 7896 3363 2360 39 80098 0.0 3 66995 7537 3274 2292 40 74555 0.0 3 62375 7086 3068 2026 41 71619 0.0 3 59706 7009 2893 2011 42 66317 0.0 3 55371 6311 2685 1950 43 63186 0.0 3 52719 6094 2612 1761 44 64251 0.0 3 53585 6262 2603 1801 45 60323 0.0 3 50463 5803 2397 1660 46 61112 0.0 3 51299 5751 2459 1603 47 57392 0.0 3 48131 5410 2275 1576 48 57592 0.0 3 48636 5285 2188 1483 49 51555 0.0 3 43133 5003 2067 1352 50 56195 0.0 3 47532 5146 2116 1401 51 45971 0.0 3 38814 4218 1782 1157 52 45041 0.0 3 38031 4144 1674 1192 53 45686 0.0 3 38815 4191 1597 1083 54 41309 0.0 3 35078 3748 1500 983 55 41840 0.0 3 35587 3806 1466 981 56 35184 0.0 3 29830 3156 1325 873 57 44315 0.0 3 38138 3781 1451 945 58 33901 0.0 3 28894 3080 1146 781 59 32039 0.0 3 27252 2976 1135 676 60 26657 0.0 3 22706 2392 967 592 61 22215 0.0 3 18952 2007 762 494 62 20353 0.0 3 17426 1709 733 485 63 20818 0.0 3 17752 1914 706 446 64 20380 0.0 3 17521 1747 668 444 65 16878 0.0 3 14385 1497 593 403 66 16314 0.0 3 13916 1425 563 410 67 15836 0.0 3 13519 1439 515 363 68 13966 0.0 3 12007 1159 466 334 69 11350 0.0 3 9643 1053 393 261 70 9856 0.0 3 8420 875 320 241 71 9116 0.0 3 7745 824 305 242 72 7492 0.0 3 6429 645 237 181 73 7190 0.0 3 6158 593 261 178 74 6259 0.0 3 5304 582 218 155 75 6218 0.0 3 5273 559 221 165 76 5256 0.0 3 4419 491 210 136 77 5035 0.0 3 4325 420 181 109 78 4455 0.0 3 3802 377 156 120 79 4287 0.0 3 3640 397 148 102 80 4181 0.0 3 3531 370 168 112 81 3485 0.0 3 2963 304 116 102 82 2833 0.0 3 2401 231 122 79 83 2933 0.0 3 2512 257 86 78 84 2113 0.0 3 1759 183 97 74 85 1732 0.0 3 1419 180 75 58 86 1673 0.0 3 1387 162 68 56 87 1630 0.0 3 1336 154 72 68 88 1715 0.0 3 1447 154 61 53 89 1881 0.0 3 1547 185 86 63 90 1571 0.0 3 1275 148 71 77 91 1511 0.0 3 1233 160 68 50 92 1309 0.0 3 1066 134 58 51 93 1076 0.0 3 863 102 56 55 94 858 0.0 3 680 99 39 40 95 781 0.0 3 588 101 50 42 96 714 0.0 3 528 98 40 48 97 734 0.0 3 557 78 51 48 98 781 0.0 3 597 95 52 37 99 759 0.0 3 571 89 52 47 100 716 0.0 3 528 104 52 32 101 682 0.0 3 520 76 44 42 102 603 0.0 3 439 76 48 40 103 602 0.0 3 464 62 42 34 104 2394 0.0 3 2056 195 90 53 105 431 0.0 3 303 61 28 39 106 445 0.0 3 300 68 44 33 107 365 0.0 3 257 47 34 27 108 386 0.0 3 267 54 38 27 109 384 0.0 3 264 51 35 34 110 349 0.0 3 239 43 41 26 111 321 0.0 3 202 48 28 43 112 332 0.0 3 221 56 32 23 113 279 0.0 3 182 46 28 23 114 398 0.0 3 282 55 31 30 115 249 0.0 3 164 48 20 17 116 281 0.0 3 190 36 31 24 117 209 0.0 3 137 39 18 15 118 277 0.0 3 181 48 27 21 119 225 0.0 3 148 35 26 16 120 244 0.0 3 154 39 23 28 121 209 0.0 3 144 29 21 15 122 223 0.0 3 148 31 23 21 123 177 0.0 3 114 40 12 11 124 465 0.0 3 391 46 17 11 125 170 0.0 3 111 25 20 14 126 200 0.0 3 132 22 24 22 127 143 0.0 3 94 26 12 11 128 217 0.0 3 165 32 11 9 129 193 0.0 3 157 17 11 8 130 260 0.0 3 206 31 11 12 131 1109 0.0 3 982 105 13 9 132 160 0.0 3 132 21 4 3 133 105 0.0 3 95 7 3 134 218 0.0 3 185 18 10 5 135 131 0.0 3 112 11 6 2 136 63 0.0 3 58 4 0 1 137 85 0.0 3 73 8 3 1 138 184 0.0 3 168 13 1 2 139 45 0.0 3 32 9 1 3 140 46 0.0 3 37 4 5 141 67 0.0 3 54 6 5 2 142 54 0.0 3 47 5 1 1 143 44 0.0 3 39 4 0 1 144 19 0.0 3 13 1 1 4 145 26 0.0 3 19 3 3 1 146 52 0.0 3 47 2 1 2 147 31 0.0 3 26 2 0 3 148 141 0.0 3 41 31 9 60 149 18030 0.0 3 42 12222 5344 422 150 217631 0.0 3 2763 202118 12100 650 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 6368151 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-33 bp: 3 Bases preceding removed adapters: A: 26.5% C: 21.5% G: 30.8% T: 21.1% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 720325 520543.0 0 720325 4 243469 130135.7 0 243469 5 138753 32533.9 0 138753 6 121723 8133.5 0 121723 7 133326 2033.4 0 133326 8 120081 508.3 0 120081 9 123020 127.1 0 122524 496 10 121507 31.8 1 108231 13276 11 121654 7.9 1 108321 13333 12 120278 2.0 1 108026 12252 13 145096 0.5 1 130841 14255 14 139077 0.1 1 124958 14119 15 146872 0.0 1 131951 14921 16 135257 0.0 1 121395 13862 17 129774 0.0 1 116723 13051 18 118155 0.0 1 105968 12163 24 19 111072 0.0 1 99086 11730 256 20 121383 0.0 2 104190 12081 5112 21 115406 0.0 2 98538 11702 5166 22 114281 0.0 2 96843 11936 5502 23 119505 0.0 2 101108 12757 5640 24 115530 0.0 2 97719 12133 5678 25 121998 0.0 2 103374 12753 5871 26 125356 0.0 2 102604 16441 6311 27 117370 0.0 2 94968 16245 6148 9 28 113982 0.0 2 91753 16249 5963 17 29 98397 0.0 2 79578 13512 5204 103 30 94005 0.0 3 73847 12215 4796 3147 31 96356 0.0 3 75800 12497 4876 3183 32 94481 0.0 3 74628 12185 4723 2945 33 101439 0.0 3 79763 13289 5106 3281 34 97010 0.0 3 76285 12536 4876 3313 35 92595 0.0 3 72951 11983 4645 3016 36 89225 0.0 3 70471 11368 4517 2869 37 90818 0.0 3 72053 11384 4520 2861 38 84248 0.0 3 66973 10509 4082 2684 39 82733 0.0 3 66285 9911 4034 2503 40 76799 0.0 3 61416 9301 3722 2360 41 73722 0.0 3 59462 8733 3346 2181 42 68273 0.0 3 54799 8179 3196 2099 43 65385 0.0 3 52557 7790 3011 2027 44 66176 0.0 3 53311 7744 3105 2016 45 62179 0.0 3 50058 7311 2918 1892 46 63033 0.0 3 51039 7285 2830 1879 47 58970 0.0 3 47596 6849 2752 1773 48 59026 0.0 3 47918 6845 2680 1583 49 52896 0.0 3 42665 6234 2453 1544 50 57538 0.0 3 46662 6729 2606 1541 51 47324 0.0 3 38408 5382 2138 1396 52 46143 0.0 3 37703 5102 2009 1329 53 46862 0.0 3 38468 5207 1962 1225 54 42522 0.0 3 34703 4894 1801 1124 55 43168 0.0 3 35415 4745 1883 1125 56 36069 0.0 3 29576 4009 1485 999 57 45042 0.0 3 37561 4654 1764 1063 58 34695 0.0 3 28934 3535 1352 874 59 32413 0.0 3 26833 3360 1375 845 60 27386 0.0 3 22541 2987 1130 728 61 22888 0.0 3 18887 2465 940 596 62 20900 0.0 3 17047 2308 932 613 63 21304 0.0 3 17686 2223 881 514 64 20776 0.0 3 17403 2090 797 486 65 17345 0.0 3 14336 1854 722 433 66 16720 0.0 3 13863 1762 692 403 67 16263 0.0 3 13571 1618 661 413 68 14350 0.0 3 11892 1470 589 399 69 11654 0.0 3 9642 1218 489 305 70 10154 0.0 3 8389 1026 455 284 71 9346 0.0 3 7736 942 391 277 72 7798 0.0 3 6430 814 349 205 73 7438 0.0 3 6121 783 333 201 74 6485 0.0 3 5391 651 260 183 75 6425 0.0 3 5291 642 288 204 76 5481 0.0 3 4458 598 260 165 77 5249 0.0 3 4290 539 245 175 78 4705 0.0 3 3787 547 214 157 79 4505 0.0 3 3686 500 194 125 80 4385 0.0 3 3550 479 200 156 81 3673 0.0 3 2970 401 185 117 82 3011 0.0 3 2448 315 135 113 83 3129 0.0 3 2542 321 149 117 84 2295 0.0 3 1777 281 135 102 85 1931 0.0 3 1505 217 129 80 86 1831 0.0 3 1416 202 122 91 87 1766 0.0 3 1352 217 105 92 88 1852 0.0 3 1454 198 113 87 89 2021 0.0 3 1594 233 113 81 90 1690 0.0 3 1311 189 103 87 91 1691 0.0 3 1273 219 112 87 92 1475 0.0 3 1122 169 110 74 93 1184 0.0 3 894 152 73 65 94 1020 0.0 3 723 145 89 63 95 901 0.0 3 661 109 74 57 96 847 0.0 3 579 126 75 67 97 850 0.0 3 600 120 80 50 98 922 0.0 3 626 148 74 74 99 874 0.0 3 625 114 80 55 100 869 0.0 3 588 136 81 64 101 790 0.0 3 542 136 61 51 102 711 0.0 3 498 96 74 43 103 708 0.0 3 500 100 53 55 104 2540 0.0 3 2164 213 98 65 105 547 0.0 3 348 94 55 50 106 560 0.0 3 346 111 47 56 107 449 0.0 3 294 71 38 46 108 476 0.0 3 294 79 55 48 109 485 0.0 3 297 83 50 55 110 414 0.0 3 261 85 37 31 111 389 0.0 3 236 63 44 46 112 414 0.0 3 259 65 41 49 113 344 0.0 3 195 63 49 37 114 462 0.0 3 306 70 49 37 115 334 0.0 3 198 59 38 39 116 340 0.0 3 212 55 38 35 117 254 0.0 3 161 44 30 19 118 333 0.0 3 189 50 48 46 119 282 0.0 3 167 56 25 34 120 284 0.0 3 169 49 38 28 121 244 0.0 3 149 37 33 25 122 278 0.0 3 151 57 38 32 123 222 0.0 3 127 38 26 31 124 494 0.0 3 386 51 39 18 125 216 0.0 3 109 57 21 29 126 231 0.0 3 134 38 37 22 127 160 0.0 3 86 35 25 14 128 232 0.0 3 175 32 14 11 129 198 0.0 3 146 25 18 9 130 244 0.0 3 183 36 12 13 131 863 0.0 3 626 154 58 25 132 139 0.0 3 110 16 12 1 133 105 0.0 3 87 13 3 2 134 204 0.0 3 185 12 4 3 135 128 0.0 3 114 9 2 3 136 59 0.0 3 50 5 4 137 83 0.0 3 72 6 3 2 138 181 0.0 3 155 18 5 3 139 36 0.0 3 31 3 1 1 140 41 0.0 3 40 0 0 1 141 59 0.0 3 46 12 1 142 52 0.0 3 42 9 0 1 143 40 0.0 3 40 144 14 0.0 3 14 145 21 0.0 3 13 6 1 1 146 47 0.0 3 45 0 2 147 26 0.0 3 25 1 148 44 0.0 3 32 10 0 2 149 80 0.0 3 41 19 8 12 150 3113 0.0 3 2731 172 119 91