This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH03-04.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH03-04.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH03-04_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH03-04_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 122.819 s (6.361 µs/read; 9.43 M reads/minute). === Summary === Total read pairs processed: 19,309,158 Read 1 with adapter: 3,789,407 (19.6%) Read 2 with adapter: 3,726,944 (19.3%) == Read fate breakdown == Pairs that were too short: 154,292 (0.8%) Pairs written (passing filters): 19,154,866 (99.2%) Total basepairs processed: 5,792,747,400 bp Read 1: 2,896,373,700 bp Read 2: 2,896,373,700 bp Quality-trimmed: 761,344 bp (0.0%) Read 1: 356,106 bp Read 2: 405,238 bp Total written (filtered): 5,557,792,214 bp (95.9%) Read 1: 2,780,181,720 bp Read 2: 2,777,610,494 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 3789407 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: 25.3% C: 20.9% G: 30.9% T: 19.2% none/other: 3.8% Overview of removed sequences length count expect max.err error counts 3 461170 301705.6 0 461170 4 132792 75426.4 0 132792 5 74557 18856.6 0 74557 6 64129 4714.1 0 64129 7 71181 1178.5 0 71181 8 63456 294.6 0 63456 9 66281 73.7 0 66019 262 10 66564 18.4 1 58293 8271 11 66915 4.6 1 58836 8079 12 66404 1.2 1 58509 7895 13 75344 0.3 1 67066 8278 14 72786 0.1 1 64350 8436 15 77029 0.0 1 68368 8661 16 71769 0.0 1 64068 7701 17 70754 0.0 1 63061 7693 18 65682 0.0 1 58407 7258 17 19 60879 0.0 1 53695 7015 169 20 66060 0.0 2 55572 6921 3567 21 64788 0.0 2 54788 6754 3246 22 63713 0.0 2 53931 6531 3251 23 65781 0.0 2 55628 6820 3333 24 63815 0.0 2 53828 6734 3253 25 65954 0.0 2 55504 6989 3461 26 66932 0.0 2 56717 6910 3305 27 64673 0.0 2 54982 6584 3103 4 28 63113 0.0 2 53205 6643 3255 10 29 56599 0.0 2 47767 6013 2794 25 30 55157 0.0 3 44681 5824 2727 1925 31 56043 0.0 3 45955 5673 2584 1831 32 53954 0.0 3 44056 5690 2519 1689 33 55866 0.0 3 45886 5652 2562 1766 34 55395 0.0 3 45385 5586 2542 1882 35 52406 0.0 3 42792 5439 2473 1702 36 51076 0.0 3 41885 5200 2318 1673 37 52195 0.0 3 42780 5462 2233 1720 38 48486 0.0 3 39893 4855 2193 1545 39 47670 0.0 3 39264 4770 2127 1509 40 45923 0.0 3 38038 4556 1951 1378 41 44692 0.0 3 36890 4420 1975 1407 42 40863 0.0 3 33573 4235 1827 1228 43 38798 0.0 3 31819 3899 1781 1299 44 39302 0.0 3 32458 4018 1628 1198 45 37522 0.0 3 30926 3802 1639 1155 46 37440 0.0 3 31043 3666 1632 1099 47 36163 0.0 3 29938 3616 1551 1058 48 36214 0.0 3 30067 3605 1552 990 49 31630 0.0 3 26344 3049 1344 893 50 34784 0.0 3 29147 3324 1342 971 51 28915 0.0 3 24182 2691 1234 808 52 28805 0.0 3 24065 2816 1159 765 53 27927 0.0 3 23422 2650 1102 753 54 25798 0.0 3 21624 2459 1009 706 55 25546 0.0 3 21532 2326 973 715 56 21877 0.0 3 18403 1999 857 618 57 26928 0.0 3 22810 2426 1003 689 58 20906 0.0 3 17626 1922 842 516 59 20364 0.0 3 17164 1915 760 525 60 16743 0.0 3 14033 1612 633 465 61 14279 0.0 3 12021 1296 608 354 62 13393 0.0 3 11321 1228 482 362 63 13262 0.0 3 11201 1238 493 330 64 12473 0.0 3 10659 1073 437 304 65 11012 0.0 3 9297 967 421 327 66 10345 0.0 3 8817 882 383 263 67 10290 0.0 3 8760 906 363 261 68 8583 0.0 3 7283 725 362 213 69 7170 0.0 3 6019 672 275 204 70 6475 0.0 3 5507 571 242 155 71 5602 0.0 3 4724 528 196 154 72 4914 0.0 3 4140 464 173 137 73 4674 0.0 3 3937 443 161 133 74 3886 0.0 3 3263 357 145 121 75 4040 0.0 3 3420 386 139 95 76 3448 0.0 3 2892 299 153 104 77 3090 0.0 3 2605 286 128 71 78 2948 0.0 3 2480 272 118 78 79 2714 0.0 3 2251 269 126 68 80 2684 0.0 3 2275 230 97 82 81 2211 0.0 3 1837 210 84 80 82 1936 0.0 3 1621 185 78 52 83 1712 0.0 3 1455 135 70 52 84 1380 0.0 3 1127 150 62 41 85 1140 0.0 3 934 100 59 47 86 1086 0.0 3 892 110 49 35 87 1055 0.0 3 863 101 53 38 88 1055 0.0 3 852 105 56 42 89 1175 0.0 3 974 101 64 36 90 1005 0.0 3 828 96 49 32 91 961 0.0 3 780 101 46 34 92 805 0.0 3 641 82 51 31 93 707 0.0 3 562 71 32 42 94 626 0.0 3 478 89 30 29 95 515 0.0 3 400 45 40 30 96 486 0.0 3 368 69 24 25 97 427 0.0 3 327 52 21 27 98 456 0.0 3 330 54 38 34 99 441 0.0 3 312 62 32 35 100 435 0.0 3 319 51 33 32 101 382 0.0 3 290 45 26 21 102 405 0.0 3 304 45 36 20 103 458 0.0 3 351 55 26 26 104 3789 0.0 3 3325 300 101 63 105 348 0.0 3 244 44 37 23 106 284 0.0 3 177 41 31 35 107 245 0.0 3 156 39 30 20 108 226 0.0 3 145 27 23 31 109 242 0.0 3 168 30 19 25 110 228 0.0 3 135 45 26 22 111 183 0.0 3 108 38 22 15 112 214 0.0 3 130 41 24 19 113 162 0.0 3 96 30 18 18 114 165 0.0 3 102 34 16 13 115 174 0.0 3 118 22 18 16 116 188 0.0 3 125 30 18 15 117 151 0.0 3 93 20 21 17 118 149 0.0 3 100 16 15 18 119 153 0.0 3 103 20 10 20 120 134 0.0 3 89 23 13 9 121 122 0.0 3 79 19 14 10 122 133 0.0 3 77 24 16 16 123 96 0.0 3 59 17 8 12 124 451 0.0 3 378 37 20 16 125 110 0.0 3 66 22 12 10 126 113 0.0 3 80 9 17 7 127 82 0.0 3 52 15 8 7 128 163 0.0 3 120 21 14 8 129 167 0.0 3 144 16 3 4 130 186 0.0 3 154 17 9 6 131 704 0.0 3 645 46 11 2 132 106 0.0 3 85 13 2 6 133 75 0.0 3 65 7 3 134 130 0.0 3 112 13 4 1 135 75 0.0 3 67 5 2 1 136 74 0.0 3 59 9 4 2 137 76 0.0 3 68 7 1 138 107 0.0 3 101 5 1 139 56 0.0 3 54 1 0 1 140 98 0.0 3 89 8 0 1 141 74 0.0 3 62 6 3 3 142 141 0.0 3 120 20 1 143 27 0.0 3 20 6 1 144 15 0.0 3 9 3 2 1 145 29 0.0 3 16 2 10 1 146 19 0.0 3 16 0 2 1 147 19 0.0 3 15 1 1 2 148 51 0.0 3 16 3 3 29 149 9141 0.0 3 23 5524 3292 302 150 139083 0.0 3 1070 130691 6957 365 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 3726944 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: 26.3% C: 21.9% G: 31.0% T: 20.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 437470 301705.6 0 437470 4 140024 75426.4 0 140024 5 77491 18856.6 0 77491 6 67616 4714.1 0 67616 7 74534 1178.5 0 74534 8 67597 294.6 0 67597 9 70437 73.7 0 70178 259 10 70247 18.4 1 61676 8571 11 70000 4.6 1 61471 8529 12 69219 1.2 1 61258 7961 13 79277 0.3 1 70716 8561 14 76477 0.1 1 67933 8544 15 80835 0.0 1 71869 8966 16 74001 0.0 1 65808 8193 17 73568 0.0 1 65592 7976 18 67939 0.0 1 59665 8256 18 19 64253 0.0 1 55839 8230 184 20 69496 0.0 2 57193 8633 3670 21 67082 0.0 2 55106 8207 3769 22 65690 0.0 2 53746 8081 3863 23 67435 0.0 2 54998 8437 4000 24 65191 0.0 2 53332 8107 3752 25 67561 0.0 2 54980 8587 3994 26 68892 0.0 2 53637 10915 4340 27 66288 0.0 2 50866 11103 4311 8 28 64402 0.0 2 49157 11053 4180 12 29 57906 0.0 2 44593 9463 3774 76 30 56476 0.0 3 42129 8510 3543 2294 31 57575 0.0 3 42751 8890 3537 2397 32 55290 0.0 3 40801 8700 3517 2272 33 57345 0.0 3 42688 8713 3634 2310 34 56722 0.0 3 42207 8670 3535 2310 35 53921 0.0 3 40141 8278 3370 2132 36 52438 0.0 3 38892 8096 3325 2125 37 53638 0.0 3 40116 7996 3387 2139 38 49720 0.0 3 37451 7222 3052 1995 39 48814 0.0 3 36922 7020 2903 1969 40 46852 0.0 3 35438 6885 2786 1743 41 45681 0.0 3 34798 6577 2663 1643 42 41617 0.0 3 31584 5924 2482 1627 43 39665 0.0 3 30166 5668 2316 1515 44 40042 0.0 3 30491 5565 2449 1537 45 38255 0.0 3 29160 5410 2216 1469 46 38386 0.0 3 29433 5440 2187 1326 47 36812 0.0 3 28245 5054 2069 1444 48 36791 0.0 3 28084 5269 2085 1353 49 32255 0.0 3 24588 4581 1863 1223 50 35407 0.0 3 27431 4887 1897 1192 51 29541 0.0 3 22873 3923 1660 1085 52 29351 0.0 3 22861 4012 1492 986 53 28452 0.0 3 22074 3900 1556 922 54 26444 0.0 3 20471 3647 1429 897 55 26041 0.0 3 20477 3380 1328 856 56 22338 0.0 3 17508 2930 1177 723 57 27353 0.0 3 21841 3357 1331 824 58 21325 0.0 3 16784 2738 1141 662 59 20518 0.0 3 16206 2527 1068 717 60 17100 0.0 3 13484 2153 903 560 61 14674 0.0 3 11409 1976 794 495 62 13621 0.0 3 10730 1706 740 445 63 13471 0.0 3 10650 1671 712 438 64 12738 0.0 3 10209 1541 598 390 65 11235 0.0 3 9030 1277 573 355 66 10582 0.0 3 8390 1287 535 370 67 10462 0.0 3 8383 1240 517 322 68 8823 0.0 3 6941 1106 465 311 69 7285 0.0 3 5772 891 388 234 70 6561 0.0 3 5217 793 323 228 71 5784 0.0 3 4552 745 305 182 72 5090 0.0 3 3944 638 306 202 73 4759 0.0 3 3722 595 259 183 74 4045 0.0 3 3139 516 238 152 75 4154 0.0 3 3270 500 214 170 76 3610 0.0 3 2821 454 213 122 77 3200 0.0 3 2495 404 188 113 78 3031 0.0 3 2367 377 167 120 79 2822 0.0 3 2126 403 185 108 80 2752 0.0 3 2123 353 179 97 81 2316 0.0 3 1812 271 149 84 82 2034 0.0 3 1602 243 108 81 83 1812 0.0 3 1390 221 120 81 84 1472 0.0 3 1100 205 101 66 85 1236 0.0 3 909 171 83 73 86 1205 0.0 3 888 179 71 67 87 1129 0.0 3 841 157 80 51 88 1137 0.0 3 839 150 84 64 89 1254 0.0 3 960 170 61 63 90 1107 0.0 3 819 162 71 55 91 1031 0.0 3 765 146 70 50 92 858 0.0 3 636 118 50 54 93 778 0.0 3 543 130 55 50 94 682 0.0 3 470 119 50 43 95 616 0.0 3 404 100 62 50 96 573 0.0 3 362 95 52 64 97 496 0.0 3 319 83 49 45 98 513 0.0 3 345 81 54 33 99 488 0.0 3 316 81 56 35 100 512 0.0 3 348 67 58 39 101 441 0.0 3 315 59 37 30 102 477 0.0 3 312 81 47 37 103 533 0.0 3 370 82 36 45 104 3865 0.0 3 3315 346 144 60 105 406 0.0 3 276 54 39 37 106 349 0.0 3 208 71 38 32 107 291 0.0 3 177 56 32 26 108 301 0.0 3 164 59 42 36 109 286 0.0 3 174 55 30 27 110 274 0.0 3 158 49 35 32 111 206 0.0 3 123 38 30 15 112 255 0.0 3 133 56 35 31 113 185 0.0 3 110 37 16 22 114 215 0.0 3 119 45 24 27 115 205 0.0 3 120 41 24 20 116 246 0.0 3 130 57 30 29 117 185 0.0 3 100 38 18 29 118 173 0.0 3 95 38 26 14 119 190 0.0 3 105 28 33 24 120 169 0.0 3 91 31 25 22 121 140 0.0 3 74 24 26 16 122 156 0.0 3 80 34 22 20 123 109 0.0 3 66 15 16 12 124 456 0.0 3 371 53 17 15 125 124 0.0 3 64 27 21 12 126 121 0.0 3 69 20 19 13 127 88 0.0 3 49 15 12 12 128 157 0.0 3 108 25 10 14 129 161 0.0 3 117 31 7 6 130 181 0.0 3 144 24 10 3 131 600 0.0 3 400 114 49 37 132 88 0.0 3 60 14 8 6 133 74 0.0 3 55 13 6 134 125 0.0 3 101 16 4 4 135 71 0.0 3 60 7 4 136 65 0.0 3 49 7 6 3 137 76 0.0 3 69 4 1 2 138 105 0.0 3 89 12 3 1 139 52 0.0 3 48 2 2 140 94 0.0 3 79 10 4 1 141 65 0.0 3 57 8 142 128 0.0 3 112 12 3 1 143 21 0.0 3 20 0 0 1 144 10 0.0 3 9 1 145 18 0.0 3 14 4 146 16 0.0 3 15 1 147 16 0.0 3 15 1 148 18 0.0 3 16 2 149 38 0.0 3 23 5 4 6 150 1278 0.0 3 1033 93 57 95