This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-21.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-21.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-21_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-21_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 149.412 s (5.868 µs/read; 10.22 M reads/minute). === Summary === Total read pairs processed: 25,461,703 Read 1 with adapter: 3,857,153 (15.1%) Read 2 with adapter: 3,945,790 (15.5%) == Read fate breakdown == Pairs that were too short: 43,354 (0.2%) Pairs written (passing filters): 25,418,349 (99.8%) Total basepairs processed: 7,638,510,900 bp Read 1: 3,819,255,450 bp Read 2: 3,819,255,450 bp Quality-trimmed: 919,246 bp (0.0%) Read 1: 432,951 bp Read 2: 486,295 bp Total written (filtered): 7,440,919,711 bp (97.4%) Read 1: 3,721,957,624 bp Read 2: 3,718,962,087 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 3857153 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: 28.9% C: 19.3% G: 29.7% T: 21.1% none/other: 0.9% Overview of removed sequences length count expect max.err error counts 3 450059 397839.1 0 450059 4 163087 99459.8 0 163087 5 87671 24864.9 0 87671 6 73163 6216.2 0 73163 7 88012 1554.1 0 88012 8 76470 388.5 0 76470 9 79935 97.1 0 79574 361 10 78689 24.3 1 70632 8057 11 76931 6.1 1 69233 7698 12 75858 1.5 1 68469 7389 13 89243 0.4 1 80778 8465 14 87652 0.1 1 78987 8665 15 90102 0.0 1 81503 8599 16 85219 0.0 1 77219 8000 17 85601 0.0 1 77922 7679 18 76675 0.0 1 69426 7223 26 19 70290 0.0 1 63191 6927 172 20 74919 0.0 2 64894 6731 3294 21 73028 0.0 2 63544 6509 2975 22 71429 0.0 2 61894 6430 3105 23 74612 0.0 2 64818 6776 3018 24 70943 0.0 2 61646 6404 2893 25 73058 0.0 2 63576 6576 2906 26 73030 0.0 2 63624 6490 2916 27 72976 0.0 2 63778 6425 2767 6 28 75793 0.0 2 65748 7026 2999 20 29 63670 0.0 2 55095 6020 2521 34 30 56727 0.0 3 47785 5165 2269 1508 31 59912 0.0 3 50958 5190 2218 1546 32 57017 0.0 3 48420 5098 2060 1439 33 62572 0.0 3 52970 5653 2374 1575 34 60470 0.0 3 51304 5445 2198 1523 35 55293 0.0 3 46864 5045 1979 1405 36 51673 0.0 3 44020 4516 1832 1305 37 50847 0.0 3 43149 4605 1835 1258 38 47195 0.0 3 40228 4191 1663 1113 39 48682 0.0 3 41618 4200 1672 1192 40 44467 0.0 3 38026 3870 1533 1038 41 40229 0.0 3 34377 3523 1441 888 42 37988 0.0 3 32219 3418 1390 961 43 35689 0.0 3 30443 3094 1298 854 44 35292 0.0 3 30073 3118 1267 834 45 34076 0.0 3 29174 2925 1263 714 46 32944 0.0 3 28199 2877 1152 716 47 29438 0.0 3 25172 2538 1058 670 48 28802 0.0 3 24811 2459 921 611 49 25665 0.0 3 21930 2226 917 592 50 28351 0.0 3 24394 2433 904 620 51 23178 0.0 3 19969 1938 789 482 52 22990 0.0 3 19841 1894 758 497 53 22784 0.0 3 19624 1882 788 490 54 20921 0.0 3 18044 1799 682 396 55 20705 0.0 3 17842 1754 661 448 56 17615 0.0 3 15243 1414 587 371 57 20931 0.0 3 18246 1675 625 385 58 17003 0.0 3 14733 1445 498 327 59 15885 0.0 3 13720 1379 467 319 60 14860 0.0 3 12860 1257 460 283 61 11520 0.0 3 9941 972 368 239 62 10375 0.0 3 8997 819 331 228 63 10363 0.0 3 8935 896 312 220 64 10344 0.0 3 9086 758 322 178 65 8489 0.0 3 7461 651 224 153 66 8241 0.0 3 7242 614 237 148 67 8810 0.0 3 7691 677 272 170 68 7017 0.0 3 6094 595 204 124 69 5404 0.0 3 4724 434 149 97 70 4999 0.0 3 4369 390 154 86 71 4571 0.0 3 3997 346 144 84 72 3701 0.0 3 3216 283 137 65 73 3681 0.0 3 3238 285 100 58 74 3220 0.0 3 2833 236 104 47 75 3129 0.0 3 2736 267 68 58 76 2655 0.0 3 2312 231 63 49 77 2505 0.0 3 2173 212 63 57 78 2139 0.0 3 1859 161 76 43 79 1983 0.0 3 1719 172 54 38 80 1863 0.0 3 1633 151 43 36 81 1597 0.0 3 1390 125 50 32 82 1330 0.0 3 1146 110 41 33 83 1274 0.0 3 1099 108 34 33 84 1049 0.0 3 896 94 37 22 85 880 0.0 3 770 67 27 16 86 869 0.0 3 752 71 22 24 87 804 0.0 3 687 70 26 21 88 721 0.0 3 617 56 27 21 89 708 0.0 3 601 68 21 18 90 619 0.0 3 524 53 23 19 91 613 0.0 3 502 56 25 30 92 519 0.0 3 437 49 18 15 93 449 0.0 3 369 42 25 13 94 392 0.0 3 322 38 15 17 95 348 0.0 3 286 29 20 13 96 329 0.0 3 264 29 19 17 97 360 0.0 3 269 46 28 17 98 346 0.0 3 275 33 19 19 99 356 0.0 3 293 29 15 19 100 345 0.0 3 274 43 15 13 101 275 0.0 3 218 25 18 14 102 267 0.0 3 218 23 11 15 103 373 0.0 3 311 31 19 12 104 5040 0.0 3 4650 289 70 31 105 270 0.0 3 211 37 16 6 106 183 0.0 3 142 22 9 10 107 210 0.0 3 162 20 12 16 108 184 0.0 3 118 30 21 15 109 182 0.0 3 128 23 20 11 110 160 0.0 3 111 15 14 20 111 146 0.0 3 100 24 7 15 112 153 0.0 3 101 29 12 11 113 132 0.0 3 89 24 12 7 114 152 0.0 3 104 27 13 8 115 87 0.0 3 60 13 7 7 116 111 0.0 3 78 10 13 10 117 104 0.0 3 74 14 11 5 118 105 0.0 3 80 14 8 3 119 86 0.0 3 65 8 8 5 120 90 0.0 3 58 11 12 9 121 87 0.0 3 59 16 5 7 122 93 0.0 3 71 9 9 4 123 82 0.0 3 58 10 8 6 124 221 0.0 3 188 17 10 6 125 73 0.0 3 53 11 5 4 126 101 0.0 3 76 16 6 3 127 71 0.0 3 54 8 3 6 128 92 0.0 3 79 7 3 3 129 79 0.0 3 62 12 3 2 130 435 0.0 3 371 49 9 6 131 242 0.0 3 215 23 2 2 132 54 0.0 3 43 7 2 2 133 86 0.0 3 82 2 1 1 134 169 0.0 3 151 14 3 1 135 57 0.0 3 51 4 2 136 46 0.0 3 40 5 0 1 137 52 0.0 3 52 138 92 0.0 3 86 6 139 18 0.0 3 17 1 140 21 0.0 3 16 0 3 2 141 22 0.0 3 18 3 1 142 35 0.0 3 29 4 1 1 143 14 0.0 3 11 3 144 11 0.0 3 6 3 1 1 145 9 0.0 3 4 5 146 17 0.0 3 15 1 0 1 147 4 0.0 3 3 1 148 52 0.0 3 25 8 6 13 149 3673 0.0 3 12 2655 933 73 150 35602 0.0 3 995 32577 1924 106 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 3945790 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: 29.2% C: 19.6% G: 29.4% T: 21.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 447235 397839.1 0 447235 4 170510 99459.8 0 170510 5 91194 24864.9 0 91194 6 76941 6216.2 0 76941 7 92477 1554.1 0 92477 8 81778 388.5 0 81778 9 84799 97.1 0 84538 261 10 83027 24.3 1 75296 7731 11 80691 6.1 1 72983 7708 12 79373 1.5 1 72258 7115 13 93823 0.4 1 85881 7942 14 91832 0.1 1 83938 7894 15 94931 0.0 1 86549 8382 16 89012 0.0 1 81074 7938 17 89625 0.0 1 81674 7951 18 79737 0.0 1 71486 8239 12 19 74372 0.0 1 65942 8277 153 20 78489 0.0 2 66066 9125 3298 21 75481 0.0 2 63221 8740 3520 22 73414 0.0 2 60999 8810 3605 23 76627 0.0 2 63828 9028 3771 24 72741 0.0 2 61181 8253 3307 25 75539 0.0 2 63521 8685 3333 26 75903 0.0 2 62956 9469 3478 27 75594 0.0 2 62556 9510 3525 3 28 78220 0.0 2 64813 9705 3687 15 29 65467 0.0 2 54117 8274 3046 30 30 58495 0.0 3 47058 7075 2694 1668 31 61901 0.0 3 49938 7361 2888 1714 32 59005 0.0 3 47669 7100 2696 1540 33 64555 0.0 3 52111 7763 2913 1768 34 62322 0.0 3 50712 7131 2775 1704 35 57092 0.0 3 46774 6476 2416 1426 36 53328 0.0 3 43435 6206 2379 1308 37 52472 0.0 3 42564 6272 2260 1376 38 48595 0.0 3 39785 5500 2085 1225 39 49999 0.0 3 41118 5452 2128 1301 40 45563 0.0 3 37177 5379 1894 1113 41 41350 0.0 3 33783 4857 1714 996 42 38969 0.0 3 31741 4453 1729 1046 43 36670 0.0 3 29986 4255 1518 911 44 36246 0.0 3 29690 4142 1499 915 45 34977 0.0 3 28693 4031 1393 860 46 33996 0.0 3 27876 3819 1429 872 47 30202 0.0 3 24829 3379 1286 708 48 29434 0.0 3 24240 3288 1203 703 49 26348 0.0 3 21430 3103 1113 702 50 29009 0.0 3 23943 3208 1164 694 51 23783 0.0 3 19736 2549 916 582 52 23453 0.0 3 19555 2513 863 522 53 23301 0.0 3 19430 2450 908 513 54 21391 0.0 3 17832 2276 833 450 55 21213 0.0 3 17740 2206 770 497 56 18083 0.0 3 15038 1888 742 415 57 21285 0.0 3 18028 2068 785 404 58 17342 0.0 3 14637 1733 618 354 59 16138 0.0 3 13489 1680 603 366 60 15155 0.0 3 12733 1496 571 355 61 11758 0.0 3 9853 1209 432 264 62 10587 0.0 3 8829 1102 405 251 63 10616 0.0 3 8881 1136 368 231 64 10563 0.0 3 8910 1059 381 213 65 8701 0.0 3 7306 875 322 198 66 8492 0.0 3 7209 776 313 194 67 8959 0.0 3 7545 904 313 197 68 7147 0.0 3 6064 693 242 148 69 5560 0.0 3 4663 570 210 117 70 5116 0.0 3 4295 513 190 118 71 4700 0.0 3 3958 454 172 116 72 3831 0.0 3 3148 426 166 91 73 3774 0.0 3 3142 412 135 85 74 3289 0.0 3 2782 338 99 70 75 3227 0.0 3 2719 331 112 65 76 2751 0.0 3 2281 283 125 62 77 2568 0.0 3 2173 249 91 55 78 2209 0.0 3 1820 253 85 51 79 2081 0.0 3 1728 217 88 48 80 1941 0.0 3 1607 193 91 50 81 1658 0.0 3 1361 185 62 50 82 1403 0.0 3 1140 146 68 49 83 1329 0.0 3 1080 163 56 30 84 1111 0.0 3 911 106 46 48 85 951 0.0 3 768 107 44 32 86 921 0.0 3 735 114 40 32 87 877 0.0 3 690 111 46 30 88 782 0.0 3 615 86 47 34 89 771 0.0 3 610 93 39 29 90 691 0.0 3 533 83 40 35 91 655 0.0 3 513 84 35 23 92 584 0.0 3 445 71 31 37 93 502 0.0 3 387 65 33 17 94 448 0.0 3 340 52 32 24 95 392 0.0 3 293 53 29 17 96 392 0.0 3 286 49 31 26 97 399 0.0 3 287 59 32 21 98 380 0.0 3 275 65 29 11 99 395 0.0 3 301 52 24 18 100 398 0.0 3 281 56 30 31 101 318 0.0 3 229 40 26 23 102 309 0.0 3 213 47 31 18 103 414 0.0 3 322 52 22 18 104 5094 0.0 3 4615 333 90 56 105 309 0.0 3 220 42 28 19 106 205 0.0 3 146 31 20 8 107 257 0.0 3 182 39 18 18 108 236 0.0 3 135 49 30 22 109 221 0.0 3 140 39 24 18 110 192 0.0 3 126 31 18 17 111 189 0.0 3 106 38 29 16 112 191 0.0 3 113 36 22 20 113 166 0.0 3 101 28 21 16 114 171 0.0 3 108 39 10 14 115 108 0.0 3 67 23 8 10 116 146 0.0 3 98 15 19 14 117 123 0.0 3 69 27 14 13 118 121 0.0 3 73 22 16 10 119 99 0.0 3 65 16 12 6 120 96 0.0 3 62 17 10 7 121 97 0.0 3 67 16 9 5 122 102 0.0 3 70 15 8 9 123 88 0.0 3 63 10 8 7 124 236 0.0 3 187 27 17 5 125 83 0.0 3 57 12 8 6 126 111 0.0 3 76 14 14 7 127 81 0.0 3 50 14 10 7 128 100 0.0 3 75 12 7 6 129 80 0.0 3 61 14 2 3 130 435 0.0 3 374 46 10 5 131 195 0.0 3 149 29 12 5 132 48 0.0 3 37 9 1 1 133 78 0.0 3 66 7 1 4 134 165 0.0 3 145 13 4 3 135 59 0.0 3 53 4 0 2 136 45 0.0 3 40 4 1 137 52 0.0 3 41 11 138 92 0.0 3 83 6 1 2 139 18 0.0 3 17 1 140 19 0.0 3 14 3 2 141 22 0.0 3 21 1 142 32 0.0 3 26 3 3 143 12 0.0 3 11 1 144 6 0.0 3 5 1 145 9 0.0 3 5 4 146 16 0.0 3 16 147 3 0.0 3 3 148 30 0.0 3 20 10 149 21 0.0 3 11 5 2 3 150 1077 0.0 3 957 79 24 17