This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH01-06.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH01-06.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH01-06_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH01-06_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 115.150 s (6.593 µs/read; 9.10 M reads/minute). === Summary === Total read pairs processed: 17,466,320 Read 1 with adapter: 2,915,304 (16.7%) Read 2 with adapter: 2,945,561 (16.9%) == Read fate breakdown == Pairs that were too short: 55,543 (0.3%) Pairs written (passing filters): 17,410,777 (99.7%) Total basepairs processed: 5,239,896,000 bp Read 1: 2,619,948,000 bp Read 2: 2,619,948,000 bp Quality-trimmed: 693,305 bp (0.0%) Read 1: 333,698 bp Read 2: 359,607 bp Total written (filtered): 5,081,743,302 bp (97.0%) Read 1: 2,541,970,194 bp Read 2: 2,539,773,108 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 2915304 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: 25.8% C: 20.2% G: 32.6% T: 19.8% none/other: 1.6% Overview of removed sequences length count expect max.err error counts 3 400008 272911.2 0 400008 4 116347 68227.8 0 116347 5 61054 17057.0 0 61054 6 52232 4264.2 0 52232 7 57811 1066.1 0 57811 8 51382 266.5 0 51382 9 52569 66.6 0 52347 222 10 53068 16.7 1 46493 6575 11 52490 4.2 1 46120 6370 12 52659 1.0 1 46560 6099 13 61437 0.3 1 54667 6770 14 59633 0.1 1 52769 6864 15 62693 0.0 1 55648 7045 16 60332 0.0 1 53669 6663 17 58190 0.0 1 51921 6269 18 52668 0.0 1 47007 5639 22 19 48818 0.0 1 43108 5584 126 20 52285 0.0 2 43918 5466 2901 21 50272 0.0 2 42366 5229 2677 22 50502 0.0 2 42716 5246 2540 23 52837 0.0 2 44861 5368 2608 24 50762 0.0 2 42814 5308 2640 25 53245 0.0 2 44969 5552 2724 26 53442 0.0 2 45381 5447 2614 27 51943 0.0 2 44093 5326 2519 5 28 51265 0.0 2 43273 5487 2497 8 29 43647 0.0 2 36814 4606 2210 17 30 42684 0.0 3 34782 4391 2022 1489 31 42540 0.0 3 34704 4385 2041 1410 32 42108 0.0 3 34431 4328 1996 1353 33 44719 0.0 3 36638 4598 2054 1429 34 43704 0.0 3 35770 4480 1972 1482 35 40272 0.0 3 32916 4155 1842 1359 36 40071 0.0 3 32860 4026 1846 1339 37 40652 0.0 3 33479 4059 1853 1261 38 37096 0.0 3 30414 3732 1721 1229 39 37015 0.0 3 30605 3590 1640 1180 40 33344 0.0 3 27474 3264 1550 1056 41 31924 0.0 3 26280 3165 1424 1055 42 29828 0.0 3 24535 3001 1323 969 43 28457 0.0 3 23377 2849 1296 935 44 29127 0.0 3 24024 2915 1265 923 45 28072 0.0 3 23033 2862 1278 899 46 27464 0.0 3 22538 2838 1277 811 47 25601 0.0 3 21072 2517 1197 815 48 24678 0.0 3 20404 2461 1071 742 49 22079 0.0 3 18133 2203 1014 729 50 23219 0.0 3 19295 2210 1011 703 51 19904 0.0 3 16552 1896 852 604 52 19028 0.0 3 15866 1784 832 546 53 18909 0.0 3 15803 1751 811 544 54 17589 0.0 3 14721 1654 732 482 55 17786 0.0 3 14904 1694 730 458 56 15460 0.0 3 12960 1425 627 448 57 17310 0.0 3 14622 1602 657 429 58 14449 0.0 3 12187 1302 546 414 59 13475 0.0 3 11256 1258 595 366 60 11510 0.0 3 9664 1071 428 347 61 9496 0.0 3 7947 850 391 308 62 8940 0.0 3 7527 814 375 224 63 8814 0.0 3 7381 839 360 234 64 8359 0.0 3 7074 727 330 228 65 7518 0.0 3 6254 736 323 205 66 7129 0.0 3 6038 649 262 180 67 7095 0.0 3 6001 653 266 175 68 6026 0.0 3 5101 529 225 171 69 4931 0.0 3 4124 474 194 139 70 4170 0.0 3 3471 394 200 105 71 3885 0.0 3 3276 348 168 93 72 3287 0.0 3 2780 292 130 85 73 3131 0.0 3 2653 270 119 89 74 2762 0.0 3 2319 266 103 74 75 2724 0.0 3 2267 277 108 72 76 2267 0.0 3 1882 205 114 66 77 2235 0.0 3 1876 197 93 69 78 1956 0.0 3 1590 219 92 55 79 1923 0.0 3 1608 195 62 58 80 1708 0.0 3 1435 154 69 50 81 1490 0.0 3 1220 135 83 52 82 1207 0.0 3 1018 99 58 32 83 1233 0.0 3 1028 119 52 34 84 919 0.0 3 766 69 49 35 85 823 0.0 3 656 80 41 46 86 766 0.0 3 610 80 40 36 87 758 0.0 3 614 80 38 26 88 791 0.0 3 642 72 43 34 89 775 0.0 3 632 78 35 30 90 717 0.0 3 565 81 33 38 91 650 0.0 3 523 62 42 23 92 603 0.0 3 478 68 31 26 93 491 0.0 3 376 56 39 20 94 409 0.0 3 299 55 29 26 95 420 0.0 3 308 59 30 23 96 327 0.0 3 240 43 19 25 97 340 0.0 3 258 35 24 23 98 347 0.0 3 257 40 28 22 99 367 0.0 3 272 45 23 27 100 333 0.0 3 254 35 20 24 101 287 0.0 3 203 42 24 18 102 292 0.0 3 216 39 20 17 103 345 0.0 3 262 34 27 22 104 2636 0.0 3 2305 219 74 38 105 235 0.0 3 151 32 27 25 106 216 0.0 3 128 44 22 22 107 180 0.0 3 115 26 27 12 108 206 0.0 3 129 30 23 24 109 164 0.0 3 123 19 13 9 110 178 0.0 3 120 24 16 18 111 156 0.0 3 100 26 14 16 112 167 0.0 3 109 21 17 20 113 154 0.0 3 93 29 11 21 114 153 0.0 3 97 21 18 17 115 124 0.0 3 81 23 15 5 116 148 0.0 3 91 28 17 12 117 122 0.0 3 71 24 9 18 118 146 0.0 3 97 25 13 11 119 104 0.0 3 66 14 11 13 120 134 0.0 3 80 26 14 14 121 100 0.0 3 59 16 12 13 122 131 0.0 3 93 9 15 14 123 79 0.0 3 50 13 8 8 124 301 0.0 3 254 33 6 8 125 77 0.0 3 48 13 8 8 126 102 0.0 3 58 21 13 10 127 86 0.0 3 60 14 10 2 128 169 0.0 3 143 12 7 7 129 220 0.0 3 194 15 10 1 130 419 0.0 3 376 31 7 5 131 916 0.0 3 835 60 14 7 132 208 0.0 3 187 13 3 5 133 122 0.0 3 107 10 5 134 133 0.0 3 118 12 1 2 135 80 0.0 3 72 4 3 1 136 67 0.0 3 57 7 1 2 137 53 0.0 3 49 3 0 1 138 114 0.0 3 106 8 139 46 0.0 3 42 4 140 45 0.0 3 41 4 141 35 0.0 3 30 3 1 1 142 47 0.0 3 43 4 143 30 0.0 3 27 2 0 1 144 22 0.0 3 15 4 3 145 14 0.0 3 12 0 1 1 146 21 0.0 3 19 2 147 22 0.0 3 15 2 3 2 148 42 0.0 3 15 9 4 14 149 5368 0.0 3 11 4102 1162 93 150 44301 0.0 3 1012 40971 2171 147 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 2945561 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: 26.0% C: 20.8% G: 32.3% T: 21.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 387831 272911.2 0 387831 4 122107 68227.8 0 122107 5 63576 17057.0 0 63576 6 55274 4264.2 0 55274 7 60938 1066.1 0 60938 8 54974 266.5 0 54974 9 55741 66.6 0 55560 181 10 55924 16.7 1 48979 6945 11 55308 4.2 1 48593 6715 12 55071 1.0 1 48852 6219 13 64942 0.3 1 57900 7042 14 62867 0.1 1 55751 7116 15 66124 0.0 1 58667 7457 16 62620 0.0 1 55563 7057 17 60869 0.0 1 54204 6665 18 54651 0.0 1 47695 6946 10 19 51489 0.0 1 44248 7136 105 20 54647 0.0 2 43387 7996 3264 21 51892 0.0 2 40755 7720 3417 22 51966 0.0 2 40362 8050 3554 23 53978 0.0 2 42444 8071 3463 24 51778 0.0 2 40953 7528 3297 25 54700 0.0 2 43098 8093 3509 26 54670 0.0 2 41361 9413 3896 27 52946 0.0 2 39569 9431 3945 1 28 52277 0.0 2 39355 9117 3802 3 29 44481 0.0 2 33607 7596 3247 31 30 43819 0.0 3 31751 7171 3026 1871 31 43838 0.0 3 31700 7241 3057 1840 32 43416 0.0 3 31520 7089 2968 1839 33 46026 0.0 3 33443 7630 3074 1879 34 44962 0.0 3 32621 7450 3044 1847 35 41521 0.0 3 30594 6504 2767 1656 36 41189 0.0 3 29953 6839 2658 1739 37 41800 0.0 3 30725 6724 2683 1668 38 38035 0.0 3 28098 5822 2547 1568 39 38070 0.0 3 28027 6056 2440 1547 40 34241 0.0 3 25207 5490 2231 1313 41 32785 0.0 3 24333 5032 2128 1292 42 30464 0.0 3 22556 4654 1981 1273 43 29292 0.0 3 21605 4570 1889 1228 44 29684 0.0 3 22019 4594 1845 1226 45 28712 0.0 3 21264 4440 1822 1186 46 28195 0.0 3 21014 4268 1841 1072 47 26361 0.0 3 19426 4133 1713 1089 48 25211 0.0 3 18734 3796 1614 1067 49 22535 0.0 3 16541 3595 1475 924 50 23786 0.0 3 17795 3546 1504 941 51 20357 0.0 3 15332 2983 1274 768 52 19484 0.0 3 14835 2825 1136 688 53 19282 0.0 3 14582 2861 1143 696 54 18086 0.0 3 13768 2614 1065 639 55 18287 0.0 3 14015 2559 1079 634 56 15911 0.0 3 12186 2256 918 551 57 17740 0.0 3 13761 2395 1005 579 58 14814 0.0 3 11453 2038 835 488 59 13732 0.0 3 10485 1893 841 513 60 11837 0.0 3 9027 1729 650 431 61 9848 0.0 3 7465 1377 627 379 62 9209 0.0 3 7036 1317 522 334 63 8996 0.0 3 6886 1199 572 339 64 8538 0.0 3 6621 1170 449 298 65 7652 0.0 3 5856 1073 465 258 66 7400 0.0 3 5735 1017 384 264 67 7305 0.0 3 5635 990 441 239 68 6200 0.0 3 4779 850 362 209 69 5077 0.0 3 3926 688 279 184 70 4337 0.0 3 3271 599 282 185 71 4031 0.0 3 3072 545 240 174 72 3408 0.0 3 2603 448 207 150 73 3190 0.0 3 2447 418 211 114 74 2891 0.0 3 2190 405 170 126 75 2828 0.0 3 2174 368 166 120 76 2377 0.0 3 1768 337 148 124 77 2349 0.0 3 1789 321 149 90 78 2044 0.0 3 1524 269 147 104 79 2016 0.0 3 1498 290 144 84 80 1770 0.0 3 1363 240 99 68 81 1602 0.0 3 1161 234 121 86 82 1292 0.0 3 983 178 74 57 83 1301 0.0 3 976 166 103 56 84 1029 0.0 3 717 181 75 56 85 885 0.0 3 649 130 60 46 86 865 0.0 3 601 136 75 53 87 828 0.0 3 596 124 66 42 88 870 0.0 3 618 139 75 38 89 830 0.0 3 585 123 76 46 90 789 0.0 3 545 114 82 48 91 718 0.0 3 527 90 54 47 92 680 0.0 3 466 97 68 49 93 562 0.0 3 358 107 60 37 94 479 0.0 3 306 91 36 46 95 474 0.0 3 305 80 48 41 96 394 0.0 3 261 61 42 30 97 389 0.0 3 239 74 42 34 98 445 0.0 3 278 72 53 42 99 423 0.0 3 275 75 43 30 100 405 0.0 3 247 79 48 31 101 349 0.0 3 198 82 39 30 102 337 0.0 3 215 60 33 29 103 391 0.0 3 275 51 39 26 104 2718 0.0 3 2321 253 87 57 105 281 0.0 3 154 54 34 39 106 283 0.0 3 136 68 47 32 107 228 0.0 3 132 36 36 24 108 260 0.0 3 139 49 43 29 109 211 0.0 3 103 57 25 26 110 223 0.0 3 121 45 32 25 111 188 0.0 3 98 39 33 18 112 209 0.0 3 104 48 33 24 113 194 0.0 3 111 38 27 18 114 165 0.0 3 89 43 18 15 115 140 0.0 3 78 25 15 22 116 182 0.0 3 99 30 29 24 117 154 0.0 3 74 32 25 23 118 163 0.0 3 86 31 30 16 119 121 0.0 3 60 26 23 12 120 150 0.0 3 84 28 16 22 121 115 0.0 3 66 23 14 12 122 155 0.0 3 82 36 23 14 123 91 0.0 3 49 21 8 13 124 314 0.0 3 239 36 22 17 125 80 0.0 3 43 16 11 10 126 124 0.0 3 59 37 15 13 127 101 0.0 3 60 20 10 11 128 166 0.0 3 126 26 8 6 129 214 0.0 3 155 37 12 10 130 411 0.0 3 274 82 34 21 131 819 0.0 3 499 199 77 44 132 193 0.0 3 145 31 11 6 133 116 0.0 3 80 18 10 8 134 125 0.0 3 98 15 8 4 135 78 0.0 3 69 7 1 1 136 64 0.0 3 51 10 2 1 137 51 0.0 3 50 1 138 110 0.0 3 101 6 2 1 139 46 0.0 3 41 2 3 140 41 0.0 3 33 5 3 141 32 0.0 3 31 1 142 43 0.0 3 39 2 2 143 26 0.0 3 20 5 1 144 16 0.0 3 13 2 1 145 13 0.0 3 11 0 1 1 146 21 0.0 3 15 6 147 17 0.0 3 15 2 148 16 0.0 3 11 3 2 149 23 0.0 3 11 5 4 3 150 1154 0.0 3 953 115 56 30