This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-29.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-29.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-29_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-29_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 214.581 s (7.199 µs/read; 8.33 M reads/minute). === Summary === Total read pairs processed: 29,807,164 Read 1 with adapter: 2,099,514 (7.0%) Read 2 with adapter: 2,081,133 (7.0%) == Read fate breakdown == Pairs that were too short: 91,275 (0.3%) Pairs written (passing filters): 29,715,889 (99.7%) Total basepairs processed: 8,942,149,200 bp Read 1: 4,471,074,600 bp Read 2: 4,471,074,600 bp Quality-trimmed: 1,355,133 bp (0.0%) Read 1: 565,649 bp Read 2: 789,484 bp Total written (filtered): 8,834,453,591 bp (98.8%) Read 1: 4,418,361,849 bp Read 2: 4,416,091,742 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 2099514 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: 26.2% C: 20.3% G: 33.3% T: 16.4% none/other: 3.8% Overview of removed sequences length count expect max.err error counts 3 569244 465736.9 0 569244 4 149834 116434.2 0 149834 5 45394 29108.6 0 45394 6 36607 7277.1 0 36607 7 37746 1819.3 0 37746 8 33703 454.8 0 33703 9 34170 113.7 0 33849 321 10 35531 28.4 1 31527 4004 11 34975 7.1 1 31104 3871 12 33462 1.8 1 30056 3406 13 35113 0.4 1 31427 3686 14 34692 0.1 1 31020 3672 15 34109 0.0 1 30518 3591 16 31920 0.0 1 28424 3496 17 30941 0.0 1 27809 3132 18 29411 0.0 1 26371 3028 12 19 28101 0.0 1 24882 3127 92 20 29199 0.0 2 24755 3052 1392 21 28468 0.0 2 24141 2974 1353 22 27479 0.0 2 23241 2871 1367 23 27642 0.0 2 23540 2819 1283 24 27351 0.0 2 23226 2815 1310 25 27235 0.0 2 23051 2863 1321 26 26551 0.0 2 22534 2766 1251 27 25992 0.0 2 22155 2602 1234 1 28 24791 0.0 2 20969 2689 1126 7 29 22743 0.0 2 19310 2344 1068 21 30 22029 0.0 3 18079 2312 976 662 31 22257 0.0 3 18356 2264 964 673 32 21515 0.0 3 17785 2161 941 628 33 22001 0.0 3 18108 2278 989 626 34 20962 0.0 3 17362 2079 886 635 35 20218 0.0 3 16642 2104 866 606 36 19804 0.0 3 16414 1957 829 604 37 18920 0.0 3 15599 1967 788 566 38 18048 0.0 3 14907 1845 758 538 39 18047 0.0 3 15046 1776 715 510 40 16826 0.0 3 14079 1617 680 450 41 15716 0.0 3 13023 1595 650 448 42 14809 0.0 3 12213 1550 621 425 43 14608 0.0 3 12136 1475 601 396 44 14906 0.0 3 12362 1457 662 425 45 13743 0.0 3 11366 1392 596 389 46 13166 0.0 3 11026 1280 490 370 47 12136 0.0 3 10064 1245 475 352 48 12108 0.0 3 10166 1148 475 319 49 11376 0.0 3 9560 1075 440 301 50 11530 0.0 3 9586 1148 494 302 51 9832 0.0 3 8142 985 442 263 52 9459 0.0 3 7836 955 376 292 53 8874 0.0 3 7438 867 334 235 54 8763 0.0 3 7293 872 364 234 55 8303 0.0 3 6967 841 301 194 56 7608 0.0 3 6344 779 303 182 57 7788 0.0 3 6471 824 301 192 58 6697 0.0 3 5605 615 289 188 59 6317 0.0 3 5276 649 240 152 60 5555 0.0 3 4616 551 245 143 61 4708 0.0 3 3911 472 193 132 62 4719 0.0 3 3944 445 201 129 63 4381 0.0 3 3659 430 168 124 64 4137 0.0 3 3461 385 175 116 65 3772 0.0 3 3112 366 167 127 66 3559 0.0 3 2915 356 174 114 67 3466 0.0 3 2885 336 151 94 68 3020 0.0 3 2449 330 148 93 69 2610 0.0 3 2103 299 114 94 70 2415 0.0 3 1933 272 115 95 71 2181 0.0 3 1740 247 99 95 72 1882 0.0 3 1511 201 91 79 73 1701 0.0 3 1342 186 95 78 74 1545 0.0 3 1240 162 74 69 75 1589 0.0 3 1256 179 87 67 76 1432 0.0 3 1160 167 58 47 77 1381 0.0 3 1074 157 75 75 78 1394 0.0 3 1105 164 74 51 79 1305 0.0 3 1002 163 83 57 80 1166 0.0 3 889 137 85 55 81 1097 0.0 3 844 113 88 52 82 979 0.0 3 714 129 77 59 83 946 0.0 3 721 104 66 55 84 776 0.0 3 547 97 71 61 85 776 0.0 3 563 111 48 54 86 711 0.0 3 499 98 63 51 87 674 0.0 3 485 87 54 48 88 761 0.0 3 566 99 50 46 89 740 0.0 3 529 94 62 55 90 698 0.0 3 511 94 48 45 91 683 0.0 3 493 98 45 47 92 653 0.0 3 458 90 52 53 93 533 0.0 3 348 84 61 40 94 517 0.0 3 336 84 54 43 95 419 0.0 3 266 58 47 48 96 419 0.0 3 268 66 46 39 97 450 0.0 3 294 74 39 43 98 448 0.0 3 288 66 53 41 99 452 0.0 3 286 76 44 46 100 456 0.0 3 276 86 44 50 101 422 0.0 3 271 73 39 39 102 424 0.0 3 258 77 42 47 103 583 0.0 3 406 77 67 33 104 4666 0.0 3 4049 403 133 81 105 395 0.0 3 243 68 48 36 106 368 0.0 3 209 70 48 41 107 351 0.0 3 206 53 46 46 108 362 0.0 3 223 48 50 41 109 319 0.0 3 192 64 29 34 110 299 0.0 3 186 48 30 35 111 303 0.0 3 182 54 34 33 112 331 0.0 3 180 55 54 42 113 245 0.0 3 147 36 34 28 114 296 0.0 3 173 58 41 24 115 237 0.0 3 131 48 36 22 116 245 0.0 3 158 42 26 19 117 232 0.0 3 131 48 20 33 118 240 0.0 3 142 42 31 25 119 209 0.0 3 114 50 19 26 120 243 0.0 3 147 37 38 21 121 205 0.0 3 121 32 28 24 122 208 0.0 3 117 43 27 21 123 191 0.0 3 117 32 25 17 124 223 0.0 3 153 30 25 15 125 167 0.0 3 107 32 15 13 126 182 0.0 3 120 31 19 12 127 151 0.0 3 88 30 22 11 128 139 0.0 3 97 17 17 8 129 194 0.0 3 158 21 11 4 130 159 0.0 3 124 22 10 3 131 323 0.0 3 276 22 13 12 132 117 0.0 3 89 16 9 3 133 75 0.0 3 62 5 1 7 134 132 0.0 3 114 8 7 3 135 44 0.0 3 37 3 2 2 136 74 0.0 3 56 6 10 2 137 58 0.0 3 42 6 10 138 101 0.0 3 92 5 4 139 33 0.0 3 23 6 4 140 22 0.0 3 18 1 2 1 141 47 0.0 3 36 7 2 2 142 26 0.0 3 22 2 2 143 25 0.0 3 17 6 1 1 144 24 0.0 3 21 1 1 1 145 17 0.0 3 15 0 0 2 146 26 0.0 3 19 4 1 2 147 34 0.0 3 27 2 1 4 148 70 0.0 3 37 9 5 19 149 6415 0.0 3 24 4255 1929 207 150 77386 0.0 3 1104 71625 4350 307 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 2081133 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: 27.2% C: 21.7% G: 33.5% T: 17.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 558036 465736.9 0 558036 4 158075 116434.2 0 158075 5 48012 29108.6 0 48012 6 38692 7277.1 0 38692 7 40012 1819.3 0 40012 8 36387 454.8 0 36387 9 36092 113.7 0 35799 293 10 37548 28.4 1 33377 4171 11 37040 7.1 1 32919 4121 12 35167 1.8 1 31743 3424 13 37031 0.4 1 33418 3613 14 36791 0.1 1 33194 3597 15 36041 0.0 1 32324 3717 16 33250 0.0 1 29879 3371 17 32524 0.0 1 29179 3345 18 30762 0.0 1 27314 3444 4 19 30018 0.0 1 26407 3541 70 20 30667 0.0 2 25613 3566 1488 21 29856 0.0 2 24662 3612 1582 22 28590 0.0 2 23713 3395 1482 23 28680 0.0 2 23881 3304 1495 24 28285 0.0 2 23617 3326 1342 25 28406 0.0 2 23702 3224 1480 26 27695 0.0 2 21965 4200 1530 27 26908 0.0 2 21159 4195 1554 28 25721 0.0 2 20142 4031 1547 1 29 23542 0.0 2 18506 3644 1375 17 30 22799 0.0 3 17418 3268 1312 801 31 23191 0.0 3 17661 3465 1264 801 32 22396 0.0 3 17047 3401 1203 745 33 22802 0.0 3 17403 3318 1276 805 34 21676 0.0 3 16549 3228 1149 750 35 20999 0.0 3 16226 2905 1140 728 36 20478 0.0 3 15692 2952 1109 725 37 19711 0.0 3 15213 2730 1085 683 38 18752 0.0 3 14465 2695 1013 579 39 18585 0.0 3 14525 2506 978 576 40 17405 0.0 3 13517 2433 911 544 41 16300 0.0 3 12682 2209 879 530 42 15373 0.0 3 11957 2019 831 566 43 15163 0.0 3 11934 1966 740 523 44 15411 0.0 3 12125 1978 796 512 45 14293 0.0 3 11180 1884 761 468 46 13692 0.0 3 10676 1796 778 442 47 12638 0.0 3 9769 1769 694 406 48 12428 0.0 3 9838 1624 583 383 49 11730 0.0 3 9151 1611 574 394 50 12000 0.0 3 9445 1568 611 376 51 10182 0.0 3 8001 1351 537 293 52 9836 0.0 3 7763 1290 474 309 53 9254 0.0 3 7320 1145 491 298 54 9097 0.0 3 7135 1178 453 331 55 8666 0.0 3 6839 1102 433 292 56 7907 0.0 3 6267 1000 416 224 57 8051 0.0 3 6550 934 336 231 58 6980 0.0 3 5552 877 347 204 59 6591 0.0 3 5223 810 337 221 60 5838 0.0 3 4647 702 293 196 61 5037 0.0 3 3858 668 302 209 62 5004 0.0 3 3908 626 282 188 63 4666 0.0 3 3682 571 224 189 64 4424 0.0 3 3412 593 227 192 65 4010 0.0 3 3148 502 210 150 66 3827 0.0 3 3000 481 221 125 67 3717 0.0 3 2898 482 196 141 68 3232 0.0 3 2495 429 198 110 69 2804 0.0 3 2143 359 190 112 70 2664 0.0 3 2044 361 158 101 71 2411 0.0 3 1811 310 165 125 72 2098 0.0 3 1578 282 132 106 73 1855 0.0 3 1353 262 136 104 74 1759 0.0 3 1270 268 128 93 75 1749 0.0 3 1297 224 124 104 76 1648 0.0 3 1178 247 131 92 77 1577 0.0 3 1149 209 129 90 78 1592 0.0 3 1152 242 115 83 79 1522 0.0 3 1078 217 126 101 80 1384 0.0 3 954 204 135 91 81 1290 0.0 3 897 206 117 70 82 1156 0.0 3 788 175 104 89 83 1145 0.0 3 759 184 105 97 84 969 0.0 3 617 175 95 82 85 959 0.0 3 608 160 104 87 86 901 0.0 3 567 152 107 75 87 828 0.0 3 505 155 91 77 88 973 0.0 3 612 185 92 84 89 909 0.0 3 580 151 93 85 90 909 0.0 3 549 163 96 101 91 867 0.0 3 561 140 85 81 92 860 0.0 3 547 139 90 84 93 694 0.0 3 431 110 79 74 94 679 0.0 3 411 118 81 69 95 577 0.0 3 319 114 78 66 96 586 0.0 3 324 120 83 59 97 597 0.0 3 328 123 79 67 98 606 0.0 3 359 113 72 62 99 605 0.0 3 352 125 71 57 100 596 0.0 3 332 110 87 67 101 573 0.0 3 330 113 69 61 102 590 0.0 3 296 133 78 83 103 717 0.0 3 469 102 68 78 104 4898 0.0 3 4144 453 196 105 105 522 0.0 3 286 108 70 58 106 483 0.0 3 253 93 78 59 107 463 0.0 3 247 107 72 37 108 500 0.0 3 261 109 64 66 109 442 0.0 3 235 92 57 58 110 401 0.0 3 200 84 66 51 111 384 0.0 3 204 95 55 30 112 451 0.0 3 241 86 70 54 113 317 0.0 3 166 58 59 34 114 397 0.0 3 194 87 59 57 115 294 0.0 3 138 66 46 44 116 347 0.0 3 187 76 46 38 117 304 0.0 3 147 86 45 26 118 289 0.0 3 159 56 45 29 119 280 0.0 3 128 69 49 34 120 302 0.0 3 157 66 44 35 121 231 0.0 3 126 45 43 17 122 270 0.0 3 145 59 37 29 123 230 0.0 3 118 65 27 20 124 262 0.0 3 150 57 36 19 125 205 0.0 3 125 38 26 16 126 212 0.0 3 110 41 32 29 127 169 0.0 3 82 43 25 19 128 153 0.0 3 97 25 15 16 129 206 0.0 3 146 26 18 16 130 157 0.0 3 116 24 9 8 131 296 0.0 3 211 46 30 9 132 104 0.0 3 76 17 9 2 133 75 0.0 3 50 16 2 7 134 125 0.0 3 99 19 4 3 135 43 0.0 3 34 6 2 1 136 60 0.0 3 57 2 0 1 137 45 0.0 3 38 3 3 1 138 96 0.0 3 80 10 4 2 139 27 0.0 3 19 4 2 2 140 19 0.0 3 14 2 3 141 38 0.0 3 32 3 1 2 142 23 0.0 3 20 3 143 22 0.0 3 21 1 144 22 0.0 3 19 2 0 1 145 15 0.0 3 13 2 146 21 0.0 3 20 1 147 27 0.0 3 26 1 148 38 0.0 3 34 4 149 31 0.0 3 25 1 3 2 150 1219 0.0 3 1095 68 29 27