This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-08.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-08.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-08_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-08_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 223.477 s (6.393 µs/read; 9.39 M reads/minute). === Summary === Total read pairs processed: 34,955,662 Read 1 with adapter: 6,302,305 (18.0%) Read 2 with adapter: 6,421,322 (18.4%) == Read fate breakdown == Pairs that were too short: 99,473 (0.3%) Pairs written (passing filters): 34,856,189 (99.7%) Total basepairs processed: 10,486,698,600 bp Read 1: 5,243,349,300 bp Read 2: 5,243,349,300 bp Quality-trimmed: 1,363,832 bp (0.0%) Read 1: 633,134 bp Read 2: 730,698 bp Total written (filtered): 10,135,082,944 bp (96.6%) Read 1: 5,070,293,493 bp Read 2: 5,064,789,451 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 6302305 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: 25.9% C: 19.6% G: 32.4% T: 20.9% none/other: 1.3% Overview of removed sequences length count expect max.err error counts 3 738045 546182.2 0 738045 4 241329 136545.6 0 241329 5 129041 34136.4 0 129041 6 113233 8534.1 0 113233 7 126799 2133.5 0 126799 8 113267 533.4 0 113267 9 117584 133.3 0 117029 555 10 118501 33.3 1 105346 13155 11 115591 8.3 1 103019 12572 12 116717 2.1 1 104672 12045 13 133770 0.5 1 120217 13553 14 127117 0.1 1 113675 13442 15 132851 0.0 1 119017 13834 16 124488 0.0 1 111875 12613 17 122804 0.0 1 110530 12274 18 112930 0.0 1 101429 11466 35 19 106974 0.0 1 94944 11796 234 20 115252 0.0 2 97737 11931 5584 21 113305 0.0 2 96636 11545 5124 22 112490 0.0 2 95819 11398 5273 23 115445 0.0 2 98287 11709 5449 24 110991 0.0 2 94427 11404 5160 25 114349 0.0 2 97134 11858 5357 26 114901 0.0 2 98456 11415 5030 27 110508 0.0 2 94651 11002 4843 12 28 111190 0.0 2 94729 11411 5030 20 29 96951 0.0 2 82225 10246 4431 49 30 94420 0.0 3 78127 9465 4089 2739 31 98918 0.0 3 82097 9885 4055 2881 32 93100 0.0 3 77467 9204 3847 2582 33 96106 0.0 3 79735 9495 4108 2768 34 95662 0.0 3 79483 9485 3983 2711 35 89293 0.0 3 74062 8868 3848 2515 36 88122 0.0 3 73239 8725 3676 2482 37 88174 0.0 3 73421 8687 3599 2467 38 81819 0.0 3 68186 8075 3298 2260 39 82458 0.0 3 69176 7848 3287 2147 40 77096 0.0 3 64724 7370 3035 1967 41 73645 0.0 3 61558 7228 2862 1997 42 70379 0.0 3 58696 6916 2861 1906 43 66546 0.0 3 55245 6697 2742 1862 44 66785 0.0 3 55876 6476 2605 1828 45 63311 0.0 3 52932 6242 2507 1630 46 62458 0.0 3 52472 5986 2379 1621 47 58928 0.0 3 49284 5732 2283 1629 48 59432 0.0 3 50123 5626 2225 1458 49 52682 0.0 3 44344 5021 2002 1315 50 56096 0.0 3 47472 5222 2134 1268 51 48514 0.0 3 40915 4566 1831 1202 52 46393 0.0 3 39143 4453 1727 1070 53 46215 0.0 3 39122 4323 1687 1083 54 42610 0.0 3 36076 3984 1555 995 55 41878 0.0 3 35561 3872 1499 946 56 35459 0.0 3 30052 3255 1323 829 57 40673 0.0 3 34814 3652 1347 860 58 33693 0.0 3 28818 2992 1160 723 59 31940 0.0 3 27269 2858 1148 665 60 27221 0.0 3 23176 2413 1014 618 61 22304 0.0 3 18997 2034 805 468 62 21696 0.0 3 18551 1983 707 455 63 21203 0.0 3 18052 1899 744 508 64 20382 0.0 3 17421 1875 682 404 65 17267 0.0 3 14776 1502 614 375 66 16219 0.0 3 14031 1297 546 345 67 16640 0.0 3 14313 1444 570 313 68 13685 0.0 3 11734 1214 454 283 69 11624 0.0 3 10003 1000 375 246 70 10248 0.0 3 8774 944 328 202 71 8897 0.0 3 7612 802 288 195 72 7783 0.0 3 6693 686 241 163 73 7405 0.0 3 6368 635 253 149 74 6125 0.0 3 5200 551 206 168 75 6006 0.0 3 5184 494 197 131 76 5072 0.0 3 4364 424 164 120 77 4922 0.0 3 4232 413 173 104 78 4606 0.0 3 3964 399 151 92 79 4502 0.0 3 3866 379 157 100 80 4359 0.0 3 3685 379 183 112 81 3899 0.0 3 3364 332 110 93 82 3051 0.0 3 2622 273 78 78 83 2854 0.0 3 2488 220 91 55 84 2216 0.0 3 1876 203 81 56 85 1907 0.0 3 1588 174 88 57 86 1840 0.0 3 1561 163 66 50 87 1726 0.0 3 1448 151 79 48 88 1726 0.0 3 1439 161 78 48 89 1807 0.0 3 1534 152 69 52 90 1606 0.0 3 1346 160 47 53 91 1561 0.0 3 1298 160 55 48 92 1312 0.0 3 1101 131 50 30 93 1100 0.0 3 907 96 62 35 94 861 0.0 3 687 101 46 27 95 696 0.0 3 564 73 25 34 96 709 0.0 3 573 70 42 24 97 590 0.0 3 460 67 35 28 98 693 0.0 3 551 73 36 33 99 681 0.0 3 557 61 36 27 100 717 0.0 3 586 69 38 24 101 582 0.0 3 467 58 29 28 102 596 0.0 3 471 62 35 28 103 1255 0.0 3 1064 115 48 28 104 20137 0.0 3 17990 1509 417 221 105 626 0.0 3 508 61 27 30 106 338 0.0 3 241 42 29 26 107 366 0.0 3 248 58 31 29 108 321 0.0 3 243 36 20 22 109 285 0.0 3 209 43 17 16 110 289 0.0 3 205 40 26 18 111 284 0.0 3 204 31 24 25 112 231 0.0 3 157 25 25 24 113 227 0.0 3 147 35 18 27 114 264 0.0 3 191 30 21 22 115 196 0.0 3 124 33 18 21 116 185 0.0 3 122 23 19 21 117 172 0.0 3 119 24 13 16 118 189 0.0 3 122 25 24 18 119 155 0.0 3 108 15 11 21 120 140 0.0 3 97 18 14 11 121 141 0.0 3 102 21 9 9 122 135 0.0 3 79 22 15 19 123 103 0.0 3 80 15 6 2 124 834 0.0 3 758 52 15 9 125 135 0.0 3 89 20 16 10 126 126 0.0 3 91 17 10 8 127 106 0.0 3 79 13 7 7 128 257 0.0 3 216 23 10 8 129 930 0.0 3 869 46 10 5 130 394 0.0 3 360 26 5 3 131 4071 0.0 3 3826 207 30 8 132 294 0.0 3 254 36 2 2 133 173 0.0 3 151 16 3 3 134 336 0.0 3 307 23 3 3 135 122 0.0 3 113 8 0 1 136 140 0.0 3 129 3 3 5 137 126 0.0 3 117 6 1 2 138 214 0.0 3 194 13 3 4 139 81 0.0 3 74 7 140 45 0.0 3 42 2 0 1 141 53 0.0 3 44 3 4 2 142 49 0.0 3 39 5 1 4 143 29 0.0 3 22 1 2 4 144 20 0.0 3 13 7 145 16 0.0 3 12 1 2 1 146 24 0.0 3 21 0 1 2 147 22 0.0 3 16 2 1 3 148 73 0.0 3 26 14 4 29 149 9582 0.0 3 31 7337 2016 198 150 77890 0.0 3 2466 70774 4350 300 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 6421322 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: 25.9% C: 20.2% G: 31.9% T: 21.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 723394 546182.2 0 723394 4 253385 136545.6 0 253385 5 134387 34136.4 0 134387 6 119494 8534.1 0 119494 7 133028 2133.5 0 133028 8 120618 533.4 0 120618 9 123849 133.3 0 123359 490 10 124822 33.3 1 111340 13482 11 121280 8.3 1 107997 13283 12 122001 2.1 1 109687 12314 13 140617 0.5 1 127110 13507 14 133684 0.1 1 120597 13087 15 139795 0.0 1 125790 14005 16 129989 0.0 1 116816 13173 17 128473 0.0 1 115692 12781 18 118042 0.0 1 105606 12416 20 19 113540 0.0 1 101022 12312 206 20 121469 0.0 2 104122 12530 4817 21 118129 0.0 2 100783 12164 5182 22 116519 0.0 2 98900 12250 5369 23 119147 0.0 2 100796 12760 5591 24 114835 0.0 2 97573 11955 5307 25 118847 0.0 2 100933 12485 5429 26 119495 0.0 2 98301 15406 5788 27 114509 0.0 2 92969 15878 5655 7 28 115031 0.0 2 93019 16247 5744 21 29 100071 0.0 2 81089 13765 5139 78 30 97766 0.0 3 77288 12553 4912 3013 31 102839 0.0 3 81315 13289 4974 3261 32 96414 0.0 3 76506 12448 4515 2945 33 99238 0.0 3 78778 12530 4868 3062 34 98940 0.0 3 78780 12538 4676 2946 35 92452 0.0 3 73885 11613 4312 2642 36 91265 0.0 3 73084 11208 4289 2684 37 91505 0.0 3 73486 11067 4253 2699 38 84702 0.0 3 68087 10379 3893 2343 39 84977 0.0 3 68696 10005 3844 2432 40 79308 0.0 3 64008 9541 3511 2248 41 75652 0.0 3 61450 8740 3329 2133 42 72559 0.0 3 58917 8247 3267 2128 43 68491 0.0 3 55856 7835 2941 1859 44 68725 0.0 3 55926 7826 3046 1927 45 65184 0.0 3 53055 7499 2859 1771 46 64194 0.0 3 52495 7190 2771 1738 47 60796 0.0 3 49599 6938 2525 1734 48 61086 0.0 3 50106 6908 2511 1561 49 54067 0.0 3 44178 6138 2241 1510 50 57521 0.0 3 47436 6349 2278 1458 51 49828 0.0 3 41070 5320 2109 1329 52 47550 0.0 3 39430 4931 1951 1238 53 47397 0.0 3 39198 5108 1909 1182 54 43854 0.0 3 36291 4702 1752 1109 55 42882 0.0 3 35624 4585 1655 1018 56 36396 0.0 3 30295 3836 1380 885 57 41491 0.0 3 34705 4286 1537 963 58 34518 0.0 3 29076 3464 1256 722 59 32458 0.0 3 27216 3164 1240 838 60 27945 0.0 3 23330 2917 1056 642 61 22990 0.0 3 19189 2277 934 590 62 22215 0.0 3 18533 2270 836 576 63 21775 0.0 3 18298 2129 846 502 64 20848 0.0 3 17541 2025 806 476 65 17652 0.0 3 15018 1688 594 352 66 16660 0.0 3 14100 1583 606 371 67 17121 0.0 3 14475 1620 614 412 68 14029 0.0 3 11873 1290 549 317 69 11952 0.0 3 10018 1198 432 304 70 10569 0.0 3 8857 1024 404 284 71 9217 0.0 3 7722 918 354 223 72 8055 0.0 3 6765 763 324 203 73 7632 0.0 3 6475 710 298 149 74 6336 0.0 3 5279 667 241 149 75 6147 0.0 3 5183 569 227 168 76 5277 0.0 3 4430 511 184 152 77 5066 0.0 3 4302 458 181 125 78 4806 0.0 3 4032 455 184 135 79 4646 0.0 3 3886 442 200 118 80 4535 0.0 3 3751 479 181 124 81 4026 0.0 3 3386 386 151 103 82 3214 0.0 3 2685 296 141 92 83 3011 0.0 3 2506 286 149 70 84 2356 0.0 3 1943 244 89 80 85 2023 0.0 3 1675 184 99 65 86 1979 0.0 3 1596 210 103 70 87 1871 0.0 3 1502 198 92 79 88 1841 0.0 3 1502 184 87 68 89 1927 0.0 3 1594 194 70 69 90 1739 0.0 3 1423 170 82 64 91 1684 0.0 3 1372 168 84 60 92 1435 0.0 3 1179 130 67 59 93 1195 0.0 3 948 129 69 49 94 968 0.0 3 719 142 61 46 95 762 0.0 3 577 96 47 42 96 815 0.0 3 617 103 52 43 97 664 0.0 3 493 89 42 40 98 798 0.0 3 578 103 61 56 99 765 0.0 3 588 90 53 34 100 793 0.0 3 624 85 55 29 101 665 0.0 3 508 76 43 38 102 694 0.0 3 511 87 53 43 103 1316 0.0 3 1099 127 49 41 104 20396 0.0 3 18557 1322 326 191 105 695 0.0 3 541 70 50 34 106 404 0.0 3 258 73 31 42 107 437 0.0 3 290 62 42 43 108 395 0.0 3 264 61 35 35 109 352 0.0 3 235 52 35 30 110 352 0.0 3 221 50 39 42 111 311 0.0 3 194 53 34 30 112 277 0.0 3 165 50 33 29 113 264 0.0 3 169 36 32 27 114 310 0.0 3 202 53 33 22 115 233 0.0 3 150 31 29 23 116 209 0.0 3 130 37 22 20 117 196 0.0 3 128 36 16 16 118 207 0.0 3 138 30 20 19 119 192 0.0 3 124 27 22 19 120 164 0.0 3 93 32 16 23 121 161 0.0 3 104 26 21 10 122 151 0.0 3 97 23 16 15 123 129 0.0 3 85 18 21 5 124 842 0.0 3 752 55 18 17 125 142 0.0 3 105 15 13 9 126 129 0.0 3 83 23 12 11 127 109 0.0 3 73 17 12 7 128 252 0.0 3 198 34 13 7 129 931 0.0 3 786 103 23 19 130 382 0.0 3 320 40 16 6 131 3747 0.0 3 2913 576 181 77 132 259 0.0 3 199 34 17 9 133 158 0.0 3 127 24 6 1 134 325 0.0 3 291 22 6 6 135 119 0.0 3 109 7 2 1 136 136 0.0 3 121 9 4 2 137 123 0.0 3 109 10 3 1 138 203 0.0 3 193 10 139 79 0.0 3 75 3 1 140 44 0.0 3 38 4 1 1 141 48 0.0 3 44 4 142 44 0.0 3 39 4 1 143 24 0.0 3 23 1 144 14 0.0 3 10 3 1 145 13 0.0 3 12 1 146 21 0.0 3 18 1 2 147 18 0.0 3 17 1 148 34 0.0 3 23 6 4 1 149 61 0.0 3 32 12 6 11 150 2711 0.0 3 2433 147 81 50