This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH03-15.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH03-15.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH03-15_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH03-15_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 127.665 s (5.883 µs/read; 10.20 M reads/minute). === Summary === Total read pairs processed: 21,700,534 Read 1 with adapter: 4,087,694 (18.8%) Read 2 with adapter: 4,079,040 (18.8%) == Read fate breakdown == Pairs that were too short: 151,130 (0.7%) Pairs written (passing filters): 21,549,404 (99.3%) Total basepairs processed: 6,510,160,200 bp Read 1: 3,255,080,100 bp Read 2: 3,255,080,100 bp Quality-trimmed: 818,839 bp (0.0%) Read 1: 393,678 bp Read 2: 425,161 bp Total written (filtered): 6,258,543,834 bp (96.1%) Read 1: 3,130,922,479 bp Read 2: 3,127,621,355 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4087694 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: 28.1% C: 19.8% G: 28.5% T: 20.4% none/other: 3.3% Overview of removed sequences length count expect max.err error counts 3 404605 339070.8 0 404605 4 142704 84767.7 0 142704 5 79333 21191.9 0 79333 6 69277 5298.0 0 69277 7 80873 1324.5 0 80873 8 72292 331.1 0 72292 9 76802 82.8 0 76456 346 10 76061 20.7 1 67453 8608 11 74905 5.2 1 66649 8256 12 75231 1.3 1 67290 7941 13 90909 0.3 1 81453 9456 14 88054 0.1 1 78778 9276 15 95289 0.0 1 85462 9827 16 88990 0.0 1 80101 8889 17 86039 0.0 1 77557 8482 18 77794 0.0 1 69996 7777 21 19 69835 0.0 1 62498 7193 144 20 79172 0.0 2 67994 7574 3604 21 75570 0.0 2 64994 7209 3367 22 71413 0.0 2 61348 6800 3265 23 74852 0.0 2 64269 7164 3419 24 70986 0.0 2 60801 6959 3226 25 73918 0.0 2 63502 7132 3284 26 74114 0.0 2 63805 7055 3254 27 75793 0.0 2 65708 7043 3034 8 28 73548 0.0 2 63208 7191 3137 12 29 63217 0.0 2 53887 6420 2879 31 30 60148 0.0 3 49924 5994 2533 1697 31 60781 0.0 3 50712 5824 2530 1715 32 60479 0.0 3 50517 5734 2512 1716 33 64583 0.0 3 53933 6208 2590 1852 34 60414 0.0 3 50611 5565 2547 1691 35 55270 0.0 3 46091 5332 2281 1566 36 52132 0.0 3 43807 4790 2088 1447 37 55812 0.0 3 46858 5231 2204 1519 38 52015 0.0 3 43782 4909 2016 1308 39 52286 0.0 3 44021 4795 2058 1412 40 47338 0.0 3 39863 4373 1827 1275 41 44641 0.0 3 37581 4205 1709 1146 42 40928 0.0 3 34305 3906 1610 1107 43 38941 0.0 3 32509 3764 1646 1022 44 41157 0.0 3 34678 3753 1637 1089 45 36993 0.0 3 31235 3353 1444 961 46 37883 0.0 3 32042 3463 1429 949 47 34416 0.0 3 28834 3369 1317 896 48 34521 0.0 3 29409 3063 1218 831 49 31555 0.0 3 26781 2829 1191 754 50 36670 0.0 3 31168 3332 1289 881 51 29947 0.0 3 25461 2703 1052 731 52 29717 0.0 3 25291 2625 1119 682 53 31114 0.0 3 26608 2725 1094 687 54 27994 0.0 3 24017 2330 999 648 55 28828 0.0 3 24750 2441 1006 631 56 23286 0.0 3 19830 2071 829 556 57 28119 0.0 3 24305 2295 927 592 58 23118 0.0 3 19891 1957 757 513 59 23487 0.0 3 20232 2037 726 492 60 20105 0.0 3 17159 1765 728 453 61 16068 0.0 3 13820 1367 533 348 62 15033 0.0 3 12948 1294 478 313 63 15607 0.0 3 13525 1264 506 312 64 14612 0.0 3 12752 1189 408 263 65 12035 0.0 3 10339 1055 391 250 66 12156 0.0 3 10469 1038 402 247 67 12632 0.0 3 11006 989 397 240 68 10283 0.0 3 8899 855 328 201 69 8051 0.0 3 6896 743 286 126 70 7014 0.0 3 6036 571 245 162 71 6225 0.0 3 5369 524 207 125 72 5437 0.0 3 4733 425 148 131 73 5427 0.0 3 4751 425 141 110 74 4583 0.0 3 4002 375 127 79 75 4484 0.0 3 3918 365 122 79 76 3558 0.0 3 3065 273 129 91 77 3477 0.0 3 2982 300 124 71 78 2932 0.0 3 2530 239 98 65 79 2804 0.0 3 2418 225 91 70 80 2779 0.0 3 2404 231 89 55 81 2081 0.0 3 1779 167 80 55 82 1996 0.0 3 1719 157 65 55 83 2038 0.0 3 1805 138 56 39 84 1523 0.0 3 1340 108 47 28 85 1284 0.0 3 1107 91 55 31 86 1320 0.0 3 1122 106 50 42 87 1130 0.0 3 953 89 46 42 88 1094 0.0 3 933 100 32 29 89 1036 0.0 3 867 88 37 44 90 893 0.0 3 747 83 34 29 91 866 0.0 3 719 86 33 28 92 811 0.0 3 672 84 32 23 93 682 0.0 3 562 66 30 24 94 644 0.0 3 525 77 17 25 95 601 0.0 3 498 52 21 30 96 498 0.0 3 419 34 22 23 97 517 0.0 3 424 34 32 27 98 505 0.0 3 414 39 27 25 99 440 0.0 3 338 52 27 23 100 466 0.0 3 356 63 22 25 101 480 0.0 3 392 51 20 17 102 390 0.0 3 314 40 17 19 103 430 0.0 3 344 37 22 27 104 2772 0.0 3 2443 218 75 36 105 320 0.0 3 248 39 17 16 106 282 0.0 3 218 33 14 17 107 228 0.0 3 174 26 14 14 108 256 0.0 3 199 24 15 18 109 218 0.0 3 168 22 16 12 110 175 0.0 3 128 25 15 7 111 201 0.0 3 138 33 20 10 112 199 0.0 3 146 22 12 19 113 138 0.0 3 99 14 16 9 114 176 0.0 3 131 25 9 11 115 141 0.0 3 107 15 15 4 116 147 0.0 3 105 19 16 7 117 147 0.0 3 108 19 7 13 118 166 0.0 3 117 26 11 12 119 113 0.0 3 87 10 10 6 120 147 0.0 3 98 20 12 17 121 124 0.0 3 93 17 7 7 122 111 0.0 3 79 9 9 14 123 127 0.0 3 86 19 12 10 124 3793 0.0 3 3521 215 35 22 125 210 0.0 3 177 21 4 8 126 136 0.0 3 87 21 13 15 127 104 0.0 3 81 13 4 6 128 123 0.0 3 97 14 5 7 129 161 0.0 3 140 18 3 130 271 0.0 3 237 18 9 7 131 868 0.0 3 798 61 8 1 132 108 0.0 3 85 11 4 8 133 65 0.0 3 56 5 3 1 134 189 0.0 3 177 9 1 2 135 54 0.0 3 46 5 2 1 136 47 0.0 3 42 4 1 137 51 0.0 3 50 0 1 138 110 0.0 3 97 13 139 49 0.0 3 44 3 2 140 27 0.0 3 25 2 141 53 0.0 3 49 3 0 1 142 81 0.0 3 69 11 1 143 12 0.0 3 11 0 1 144 22 0.0 3 19 2 1 145 14 0.0 3 10 2 0 2 146 32 0.0 3 26 2 0 4 147 12 0.0 3 8 2 0 2 148 94 0.0 3 34 10 12 38 149 11829 0.0 3 35 8291 3236 267 150 129815 0.0 3 1849 120583 7015 368 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4079040 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: 29.0% C: 20.6% G: 28.7% T: 21.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 396055 339070.8 0 396055 4 149226 84767.7 0 149226 5 82493 21191.9 0 82493 6 73772 5298.0 0 73772 7 86106 1324.5 0 86106 8 77725 331.1 0 77725 9 81508 82.8 0 81198 310 10 80720 20.7 1 71581 9139 11 78951 5.2 1 69928 9023 12 78869 1.3 1 70525 8344 13 96134 0.3 1 86503 9631 14 92911 0.1 1 83388 9523 15 100937 0.0 1 90410 10527 16 93090 0.0 1 83379 9711 17 90389 0.0 1 81060 9329 18 80798 0.0 1 71067 9720 11 19 74020 0.0 1 64495 9392 133 20 83096 0.0 2 68143 10992 3961 21 78271 0.0 2 64119 9994 4158 22 73593 0.0 2 59799 9715 4079 23 76948 0.0 2 62680 10134 4134 24 72824 0.0 2 59707 9360 3757 25 76580 0.0 2 62829 9804 3947 26 76870 0.0 2 61657 10932 4281 27 78396 0.0 2 62943 11202 4250 1 28 75758 0.0 2 60569 10976 4205 8 29 65151 0.0 2 51895 9480 3725 51 30 62131 0.0 3 47943 8589 3500 2099 31 62747 0.0 3 48630 8683 3412 2022 32 62591 0.0 3 48603 8796 3305 1887 33 66498 0.0 3 51929 9026 3459 2084 34 62487 0.0 3 48648 8604 3249 1986 35 57067 0.0 3 44794 7482 3024 1767 36 53960 0.0 3 42097 7468 2772 1623 37 57530 0.0 3 45113 7720 2869 1828 38 53645 0.0 3 42328 6961 2642 1714 39 53860 0.0 3 42455 7008 2693 1704 40 48628 0.0 3 38177 6561 2422 1468 41 45836 0.0 3 36341 5881 2281 1333 42 42089 0.0 3 33246 5316 2269 1258 43 40013 0.0 3 31449 5422 1938 1204 44 42374 0.0 3 33448 5514 2122 1290 45 37987 0.0 3 30040 4956 1846 1145 46 38850 0.0 3 31016 4881 1826 1127 47 35435 0.0 3 28023 4542 1813 1057 48 35155 0.0 3 27943 4469 1701 1042 49 32351 0.0 3 25341 4349 1631 1030 50 37303 0.0 3 29866 4636 1746 1055 51 30655 0.0 3 24651 3813 1388 803 52 30353 0.0 3 24606 3664 1288 795 53 31722 0.0 3 25830 3746 1301 845 54 28709 0.0 3 23260 3459 1279 711 55 29448 0.0 3 24015 3403 1318 712 56 23884 0.0 3 19359 2828 1054 643 57 28689 0.0 3 23694 3147 1147 701 58 23651 0.0 3 19364 2648 1022 617 59 23810 0.0 3 19591 2647 1007 565 60 20521 0.0 3 16739 2381 886 515 61 16422 0.0 3 13335 1901 764 422 62 15367 0.0 3 12537 1800 659 371 63 15916 0.0 3 13072 1859 647 338 64 14882 0.0 3 12326 1659 564 333 65 12296 0.0 3 10187 1348 490 271 66 12395 0.0 3 10231 1365 520 279 67 12982 0.0 3 10683 1483 537 279 68 10477 0.0 3 8640 1168 454 215 69 8200 0.0 3 6729 913 347 211 70 7129 0.0 3 5863 753 299 214 71 6394 0.0 3 5261 685 286 162 72 5593 0.0 3 4574 672 206 141 73 5508 0.0 3 4589 575 231 113 74 4715 0.0 3 3887 538 190 100 75 4632 0.0 3 3829 494 183 126 76 3657 0.0 3 2968 388 185 116 77 3575 0.0 3 2935 401 147 92 78 3030 0.0 3 2434 346 166 84 79 2919 0.0 3 2377 340 123 79 80 2865 0.0 3 2330 336 117 82 81 2169 0.0 3 1754 238 122 55 82 2080 0.0 3 1689 228 100 63 83 2124 0.0 3 1741 218 100 65 84 1599 0.0 3 1299 170 87 43 85 1375 0.0 3 1098 154 76 47 86 1384 0.0 3 1107 165 74 38 87 1206 0.0 3 947 155 69 35 88 1158 0.0 3 918 143 57 40 89 1082 0.0 3 861 127 53 41 90 955 0.0 3 738 113 65 39 91 944 0.0 3 730 116 55 43 92 880 0.0 3 659 114 61 46 93 756 0.0 3 566 94 55 41 94 705 0.0 3 535 90 46 34 95 668 0.0 3 495 100 42 31 96 557 0.0 3 418 61 37 41 97 583 0.0 3 409 86 47 41 98 569 0.0 3 402 82 41 44 99 518 0.0 3 379 75 36 28 100 553 0.0 3 392 71 58 32 101 529 0.0 3 400 73 33 23 102 436 0.0 3 312 59 38 27 103 480 0.0 3 361 64 38 17 104 2876 0.0 3 2465 264 90 57 105 382 0.0 3 263 54 39 26 106 341 0.0 3 238 44 31 28 107 273 0.0 3 193 35 23 22 108 297 0.0 3 199 55 22 21 109 266 0.0 3 175 48 27 16 110 211 0.0 3 148 34 16 13 111 226 0.0 3 138 44 26 18 112 251 0.0 3 151 45 30 25 113 184 0.0 3 114 27 19 24 114 213 0.0 3 135 36 25 17 115 161 0.0 3 112 28 15 6 116 186 0.0 3 109 40 23 14 117 175 0.0 3 114 24 21 16 118 194 0.0 3 118 33 20 23 119 132 0.0 3 82 23 14 13 120 168 0.0 3 105 29 16 18 121 141 0.0 3 92 21 14 14 122 145 0.0 3 82 27 16 20 123 149 0.0 3 100 16 18 15 124 3757 0.0 3 3324 323 79 31 125 216 0.0 3 172 24 13 7 126 145 0.0 3 92 26 19 8 127 118 0.0 3 72 24 16 6 128 123 0.0 3 80 29 9 5 129 158 0.0 3 118 22 12 6 130 271 0.0 3 215 41 9 6 131 763 0.0 3 543 139 52 29 132 96 0.0 3 62 18 12 4 133 57 0.0 3 46 5 4 2 134 189 0.0 3 164 16 5 4 135 52 0.0 3 41 8 1 2 136 46 0.0 3 35 7 3 1 137 51 0.0 3 43 8 138 110 0.0 3 98 11 1 139 46 0.0 3 42 4 140 28 0.0 3 26 1 1 141 49 0.0 3 45 3 1 142 77 0.0 3 70 6 1 143 11 0.0 3 8 3 144 20 0.0 3 15 4 1 145 11 0.0 3 9 2 146 28 0.0 3 26 1 0 1 147 8 0.0 3 7 1 148 37 0.0 3 29 7 1 149 61 0.0 3 31 16 10 4 150 2107 0.0 3 1758 206 68 75