This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-04.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-04.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-04_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-04_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 209.770 s (7.424 µs/read; 8.08 M reads/minute). === Summary === Total read pairs processed: 28,254,607 Read 1 with adapter: 4,281,705 (15.2%) Read 2 with adapter: 4,320,066 (15.3%) == Read fate breakdown == Pairs that were too short: 49,030 (0.2%) Pairs written (passing filters): 28,205,577 (99.8%) Total basepairs processed: 8,476,382,100 bp Read 1: 4,238,191,050 bp Read 2: 4,238,191,050 bp Quality-trimmed: 1,338,511 bp (0.0%) Read 1: 600,204 bp Read 2: 738,307 bp Total written (filtered): 8,263,763,636 bp (97.5%) Read 1: 4,133,739,487 bp Read 2: 4,130,024,149 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4281705 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: 25.1% C: 21.6% G: 33.2% T: 19.2% none/other: 0.8% Overview of removed sequences length count expect max.err error counts 3 783882 441478.2 0 783882 4 181774 110369.6 0 181774 5 92414 27592.4 0 92414 6 78208 6898.1 0 78208 7 78552 1724.5 0 78552 8 73698 431.1 0 73698 9 73271 107.8 0 72785 486 10 80108 26.9 1 67799 12309 11 79819 6.7 1 68111 11708 12 78778 1.7 1 67800 10978 13 83941 0.4 1 72687 11254 14 82186 0.1 1 70445 11741 15 83889 0.0 1 72337 11552 16 81092 0.0 1 70285 10807 17 78983 0.0 1 68438 10545 18 74775 0.0 1 64673 10062 40 19 69784 0.0 1 59597 9985 202 20 75248 0.0 2 60259 9808 5181 21 72903 0.0 2 58634 9333 4936 22 72365 0.0 2 58165 9338 4862 23 73468 0.0 2 59188 9470 4810 24 72099 0.0 2 58117 9377 4605 25 72920 0.0 2 58993 9296 4631 26 71799 0.0 2 58296 8979 4524 27 69492 0.0 2 56600 8509 4379 4 28 67385 0.0 2 54828 8323 4217 17 29 62221 0.0 2 50327 7932 3917 45 30 61317 0.0 3 47824 7441 3603 2449 31 60666 0.0 3 47383 7212 3521 2550 32 59218 0.0 3 46298 7051 3484 2385 33 60222 0.0 3 47130 7179 3459 2454 34 59219 0.0 3 46466 7069 3371 2313 35 57318 0.0 3 44777 6960 3293 2288 36 56814 0.0 3 44642 6773 3178 2221 37 55045 0.0 3 43268 6680 2960 2137 38 52581 0.0 3 41261 6261 2942 2117 39 50243 0.0 3 39705 5829 2796 1913 40 47018 0.0 3 37398 5295 2568 1757 41 45205 0.0 3 35704 5257 2516 1728 42 42937 0.0 3 33890 5017 2412 1618 43 40670 0.0 3 32164 4759 2177 1570 44 40405 0.0 3 32150 4646 2080 1529 45 38632 0.0 3 30665 4442 2037 1488 46 37780 0.0 3 30101 4351 1980 1348 47 35637 0.0 3 28504 4017 1863 1253 48 34124 0.0 3 27208 3908 1792 1216 49 31497 0.0 3 25103 3595 1668 1131 50 29851 0.0 3 23931 3364 1498 1058 51 26694 0.0 3 21456 3008 1332 898 52 25421 0.0 3 20428 2880 1247 866 53 24129 0.0 3 19398 2698 1194 839 54 23045 0.0 3 18731 2391 1164 759 55 22247 0.0 3 17925 2438 1080 804 56 20113 0.0 3 16296 2194 934 689 57 20165 0.0 3 16446 2124 972 623 58 17827 0.0 3 14423 1957 845 602 59 16456 0.0 3 13406 1736 783 531 60 14534 0.0 3 11740 1612 679 503 61 12833 0.0 3 10314 1414 650 455 62 11854 0.0 3 9677 1247 567 363 63 11184 0.0 3 9153 1144 513 374 64 10443 0.0 3 8595 1035 488 325 65 9816 0.0 3 8012 1018 466 320 66 8919 0.0 3 7238 960 410 311 67 8490 0.0 3 6904 899 399 288 68 7608 0.0 3 6224 787 348 249 69 6603 0.0 3 5303 724 318 258 70 5968 0.0 3 4815 676 293 184 71 5352 0.0 3 4362 558 239 193 72 4505 0.0 3 3638 478 217 172 73 4498 0.0 3 3663 448 220 167 74 3943 0.0 3 3186 430 188 139 75 3657 0.0 3 2953 393 188 123 76 3486 0.0 3 2797 399 163 127 77 3124 0.0 3 2500 347 160 117 78 3043 0.0 3 2414 346 169 114 79 2813 0.0 3 2220 317 160 116 80 2643 0.0 3 2079 305 146 113 81 2389 0.0 3 1892 242 145 110 82 2080 0.0 3 1669 218 108 85 83 1927 0.0 3 1517 216 119 75 84 1651 0.0 3 1297 172 105 77 85 1479 0.0 3 1137 161 98 83 86 1442 0.0 3 1086 156 106 94 87 1389 0.0 3 1048 171 100 70 88 1356 0.0 3 1033 156 97 70 89 1378 0.0 3 1057 157 83 81 90 1282 0.0 3 970 149 87 76 91 1231 0.0 3 929 135 98 69 92 1159 0.0 3 856 143 82 78 93 988 0.0 3 716 125 86 61 94 841 0.0 3 596 105 76 64 95 777 0.0 3 537 97 72 71 96 776 0.0 3 533 107 68 68 97 696 0.0 3 474 113 56 53 98 814 0.0 3 521 133 89 71 99 647 0.0 3 468 68 58 53 100 734 0.0 3 510 109 56 59 101 658 0.0 3 471 93 50 44 102 647 0.0 3 446 95 51 55 103 634 0.0 3 433 91 62 48 104 2070 0.0 3 1685 208 87 90 105 568 0.0 3 371 85 59 53 106 532 0.0 3 326 100 57 49 107 472 0.0 3 303 64 61 44 108 560 0.0 3 359 99 52 50 109 480 0.0 3 316 82 42 40 110 522 0.0 3 319 79 58 66 111 468 0.0 3 305 67 57 39 112 482 0.0 3 300 73 57 52 113 405 0.0 3 250 67 49 39 114 443 0.0 3 292 57 40 54 115 338 0.0 3 209 55 34 40 116 383 0.0 3 241 57 54 31 117 381 0.0 3 262 57 29 33 118 435 0.0 3 267 73 50 45 119 318 0.0 3 200 56 32 30 120 385 0.0 3 235 61 51 38 121 297 0.0 3 191 42 34 30 122 312 0.0 3 200 52 29 31 123 276 0.0 3 191 34 22 29 124 349 0.0 3 235 44 35 35 125 232 0.0 3 150 41 23 18 126 259 0.0 3 165 49 25 20 127 176 0.0 3 120 29 20 7 128 219 0.0 3 167 27 17 8 129 204 0.0 3 146 30 14 14 130 192 0.0 3 137 38 12 5 131 669 0.0 3 595 52 15 7 132 136 0.0 3 108 19 6 3 133 77 0.0 3 55 14 7 1 134 128 0.0 3 108 9 4 7 135 49 0.0 3 40 5 2 2 136 77 0.0 3 66 4 4 3 137 48 0.0 3 42 3 2 1 138 54 0.0 3 43 9 1 1 139 24 0.0 3 17 4 1 2 140 24 0.0 3 24 141 21 0.0 3 18 0 2 1 142 13 0.0 3 11 2 143 14 0.0 3 11 2 1 144 9 0.0 3 8 0 1 145 15 0.0 3 10 1 2 2 146 10 0.0 3 8 1 1 147 28 0.0 3 19 2 3 4 148 33 0.0 3 16 1 3 13 149 3539 0.0 3 20 2509 920 90 150 35138 0.0 3 928 32034 2016 160 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4320066 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: 24.9% C: 22.3% G: 32.5% T: 20.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 731264 441478.2 0 731264 4 187917 110369.6 0 187917 5 94698 27592.4 0 94698 6 82016 6898.1 0 82016 7 81868 1724.5 0 81868 8 77867 431.1 0 77867 9 76752 107.8 0 76237 515 10 84106 26.9 1 71649 12457 11 83118 6.7 1 70881 12237 12 82112 1.7 1 70643 11469 13 87461 0.4 1 76128 11333 14 86092 0.1 1 74591 11501 15 87407 0.0 1 75777 11630 16 83482 0.0 1 72380 11102 17 81999 0.0 1 71388 10611 18 76791 0.0 1 65836 10944 11 19 73722 0.0 1 62263 11220 239 20 78613 0.0 2 60961 11978 5674 21 74771 0.0 2 57212 11851 5708 22 73852 0.0 2 56080 12011 5761 23 74909 0.0 2 57733 11577 5599 24 73583 0.0 2 56755 11373 5455 25 74808 0.0 2 58275 11245 5288 26 74059 0.0 2 56418 12199 5442 27 71582 0.0 2 54360 11732 5486 4 28 69313 0.0 2 52755 11196 5354 8 29 63971 0.0 2 48539 10508 4882 42 30 63458 0.0 3 45998 9895 4590 2975 31 62878 0.0 3 45492 9842 4538 3006 32 61051 0.0 3 44588 9315 4246 2902 33 62128 0.0 3 45279 9668 4326 2855 34 60913 0.0 3 44513 9394 4167 2839 35 59361 0.0 3 43615 8956 4031 2759 36 58529 0.0 3 42978 8750 4094 2707 37 56742 0.0 3 42005 8432 3814 2491 38 54084 0.0 3 40165 7702 3675 2542 39 51710 0.0 3 38406 7473 3561 2270 40 48500 0.0 3 35917 7236 3194 2153 41 46595 0.0 3 34785 6743 3107 1960 42 44024 0.0 3 32667 6520 2938 1899 43 41913 0.0 3 31445 6149 2645 1674 44 41691 0.0 3 31197 5975 2685 1834 45 39711 0.0 3 29701 5778 2574 1658 46 38946 0.0 3 29628 5363 2416 1539 47 36849 0.0 3 27816 5214 2335 1484 48 34969 0.0 3 26353 4874 2234 1508 49 32462 0.0 3 24346 4666 2038 1412 50 30938 0.0 3 23354 4368 2005 1211 51 27728 0.0 3 21068 3837 1677 1146 52 26156 0.0 3 20059 3528 1555 1014 53 25003 0.0 3 19184 3283 1488 1048 54 23803 0.0 3 18388 3135 1364 916 55 23102 0.0 3 17882 3026 1342 852 56 20906 0.0 3 16059 2821 1234 792 57 20953 0.0 3 16301 2698 1176 778 58 18445 0.0 3 14351 2306 1096 692 59 16989 0.0 3 13262 2155 928 644 60 15121 0.0 3 11637 2029 853 602 61 13307 0.0 3 10214 1849 732 512 62 12335 0.0 3 9346 1710 755 524 63 11622 0.0 3 8983 1578 606 455 64 10844 0.0 3 8395 1487 593 369 65 10251 0.0 3 7936 1329 568 418 66 9349 0.0 3 7189 1218 552 390 67 8809 0.0 3 6817 1148 524 320 68 7971 0.0 3 6149 1073 452 297 69 6933 0.0 3 5337 904 407 285 70 6259 0.0 3 4795 787 411 266 71 5651 0.0 3 4362 721 344 224 72 4834 0.0 3 3630 644 321 239 73 4800 0.0 3 3597 667 306 230 74 4247 0.0 3 3195 567 278 207 75 3912 0.0 3 2938 538 261 175 76 3785 0.0 3 2780 502 291 212 77 3402 0.0 3 2535 440 257 170 78 3278 0.0 3 2422 452 233 171 79 3057 0.0 3 2225 464 202 166 80 2870 0.0 3 2094 424 209 143 81 2658 0.0 3 1909 396 200 153 82 2312 0.0 3 1702 311 163 136 83 2187 0.0 3 1589 294 165 139 84 1924 0.0 3 1353 298 140 133 85 1687 0.0 3 1163 262 133 129 86 1669 0.0 3 1136 262 150 121 87 1623 0.0 3 1089 254 150 130 88 1610 0.0 3 1079 254 147 130 89 1573 0.0 3 1111 224 131 107 90 1508 0.0 3 1021 220 157 110 91 1443 0.0 3 988 217 131 107 92 1338 0.0 3 836 247 147 108 93 1214 0.0 3 791 204 114 105 94 1051 0.0 3 640 171 131 109 95 946 0.0 3 575 173 116 82 96 970 0.0 3 604 158 101 107 97 885 0.0 3 548 152 100 85 98 1042 0.0 3 615 192 131 104 99 874 0.0 3 519 159 100 96 100 918 0.0 3 561 167 103 87 101 894 0.0 3 518 174 105 97 102 818 0.0 3 462 178 99 79 103 802 0.0 3 480 163 90 69 104 2287 0.0 3 1784 275 143 85 105 767 0.0 3 436 142 105 84 106 690 0.0 3 411 130 89 60 107 621 0.0 3 340 130 74 77 108 746 0.0 3 409 152 112 73 109 623 0.0 3 345 123 83 72 110 678 0.0 3 360 153 98 67 111 591 0.0 3 329 117 80 65 112 618 0.0 3 328 120 88 82 113 518 0.0 3 291 97 78 52 114 536 0.0 3 311 109 64 52 115 432 0.0 3 241 84 58 49 116 506 0.0 3 273 96 74 63 117 495 0.0 3 258 113 72 52 118 519 0.0 3 285 96 76 62 119 394 0.0 3 228 64 58 44 120 469 0.0 3 258 99 61 51 121 373 0.0 3 206 82 49 36 122 406 0.0 3 200 90 64 52 123 351 0.0 3 190 74 47 40 124 408 0.0 3 257 74 46 31 125 301 0.0 3 174 51 47 29 126 298 0.0 3 171 57 40 30 127 209 0.0 3 121 47 19 22 128 246 0.0 3 147 46 27 26 129 219 0.0 3 146 30 26 17 130 190 0.0 3 131 38 14 7 131 535 0.0 3 370 99 46 20 132 131 0.0 3 89 21 14 7 133 78 0.0 3 57 13 7 1 134 128 0.0 3 102 16 6 4 135 45 0.0 3 33 11 1 136 77 0.0 3 62 9 4 2 137 45 0.0 3 34 8 3 138 54 0.0 3 46 4 2 2 139 23 0.0 3 15 5 3 140 24 0.0 3 20 3 0 1 141 18 0.0 3 16 2 142 13 0.0 3 10 3 143 11 0.0 3 9 1 1 144 8 0.0 3 6 2 145 11 0.0 3 10 1 146 8 0.0 3 6 2 147 23 0.0 3 20 2 1 148 16 0.0 3 14 2 149 31 0.0 3 18 8 4 1 150 1043 0.0 3 912 83 35 13