This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH09-28.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH09-28.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH09-28_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH09-28_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 127.496 s (6.544 µs/read; 9.17 M reads/minute). === Summary === Total read pairs processed: 19,482,911 Read 1 with adapter: 4,923,844 (25.3%) Read 2 with adapter: 4,950,021 (25.4%) == Read fate breakdown == Pairs that were too short: 129,033 (0.7%) Pairs written (passing filters): 19,353,878 (99.3%) Total basepairs processed: 5,844,873,300 bp Read 1: 2,922,436,650 bp Read 2: 2,922,436,650 bp Quality-trimmed: 827,647 bp (0.0%) Read 1: 401,014 bp Read 2: 426,633 bp Total written (filtered): 5,535,359,442 bp (94.7%) Read 1: 2,770,024,828 bp Read 2: 2,765,334,614 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4923844 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: 26.1% C: 21.3% G: 31.1% T: 19.4% none/other: 2.2% Overview of removed sequences length count expect max.err error counts 3 476743 304420.5 0 476743 4 149924 76105.1 0 149924 5 92937 19026.3 0 92937 6 85646 4756.6 0 85646 7 87106 1189.1 0 87106 8 81584 297.3 0 81584 9 84554 74.3 0 84117 437 10 86781 18.6 1 75559 11222 11 87024 4.6 1 76070 10954 12 86160 1.2 1 75652 10508 13 101346 0.3 1 89686 11660 14 97107 0.1 1 85362 11745 15 102649 0.0 1 90957 11692 16 98676 0.0 1 87405 11271 17 91336 0.0 1 81130 10206 18 86972 0.0 1 77041 9896 35 19 81614 0.0 1 71970 9433 211 20 88349 0.0 2 73874 9550 4925 21 83663 0.0 2 69970 9165 4528 22 81841 0.0 2 68376 8976 4489 23 86453 0.0 2 72418 9444 4591 24 85483 0.0 2 71739 9176 4568 25 89804 0.0 2 75394 9698 4712 26 89745 0.0 2 75602 9511 4632 27 86702 0.0 2 73155 9110 4424 13 28 82466 0.0 2 69313 8941 4196 16 29 75971 0.0 2 63675 8316 3930 50 30 75681 0.0 3 61210 7981 3765 2725 31 74238 0.0 3 60212 7853 3633 2540 32 73101 0.0 3 59458 7707 3410 2526 33 76062 0.0 3 62205 7744 3628 2485 34 72940 0.0 3 59460 7569 3541 2370 35 72426 0.0 3 59105 7575 3364 2382 36 72121 0.0 3 58832 7479 3385 2425 37 71050 0.0 3 58029 7434 3215 2372 38 68349 0.0 3 55958 7030 3149 2212 39 64863 0.0 3 53225 6652 2939 2047 40 60781 0.0 3 49821 6196 2805 1959 41 60401 0.0 3 49484 6214 2750 1953 42 55393 0.0 3 45316 5706 2537 1834 43 54911 0.0 3 45010 5672 2484 1745 44 56932 0.0 3 47073 5597 2528 1734 45 53389 0.0 3 44072 5285 2374 1658 46 53570 0.0 3 44424 5281 2271 1594 47 50335 0.0 3 41513 5147 2195 1480 48 48833 0.0 3 40476 4862 2046 1449 49 44751 0.0 3 37150 4322 1964 1315 50 46636 0.0 3 38990 4444 1890 1312 51 41470 0.0 3 34629 3986 1679 1176 52 39809 0.0 3 33224 3874 1567 1144 53 39082 0.0 3 32733 3739 1515 1095 54 36384 0.0 3 30496 3445 1462 981 55 35290 0.0 3 29576 3307 1479 928 56 32960 0.0 3 27721 3021 1286 932 57 33799 0.0 3 28643 3049 1253 854 58 30354 0.0 3 25581 2856 1151 766 59 29780 0.0 3 25248 2652 1148 732 60 24457 0.0 3 20683 2184 956 634 61 22021 0.0 3 18648 1938 867 568 62 20914 0.0 3 17630 1935 805 544 63 19460 0.0 3 16466 1772 712 510 64 19268 0.0 3 16385 1745 679 459 65 16685 0.0 3 14240 1438 589 418 66 16402 0.0 3 14015 1448 583 356 67 15926 0.0 3 13601 1357 549 419 68 14235 0.0 3 12153 1231 508 343 69 12334 0.0 3 10466 1122 440 306 70 11133 0.0 3 9536 963 379 255 71 10087 0.0 3 8707 827 321 232 72 8406 0.0 3 7153 732 299 222 73 8157 0.0 3 6951 717 304 185 74 7265 0.0 3 6243 638 231 153 75 7068 0.0 3 6047 584 248 189 76 6263 0.0 3 5401 523 192 147 77 6002 0.0 3 5158 499 212 133 78 5694 0.0 3 4921 456 181 136 79 5555 0.0 3 4803 427 193 132 80 5548 0.0 3 4823 441 184 100 81 4710 0.0 3 4053 409 136 112 82 4085 0.0 3 3557 306 135 87 83 4070 0.0 3 3545 321 121 83 84 3209 0.0 3 2757 267 93 92 85 2808 0.0 3 2430 217 105 56 86 2648 0.0 3 2297 210 77 64 87 2543 0.0 3 2167 221 95 60 88 2644 0.0 3 2294 218 82 50 89 2732 0.0 3 2381 208 85 58 90 2502 0.0 3 2165 194 84 59 91 2246 0.0 3 1919 191 78 58 92 2056 0.0 3 1783 152 70 51 93 1615 0.0 3 1377 136 60 42 94 1428 0.0 3 1235 109 48 36 95 1265 0.0 3 1069 117 42 37 96 1132 0.0 3 958 94 42 38 97 1155 0.0 3 978 97 43 37 98 1138 0.0 3 1012 64 37 25 99 1095 0.0 3 923 97 40 35 100 1050 0.0 3 892 88 43 27 101 951 0.0 3 815 72 35 29 102 872 0.0 3 724 77 44 27 103 1435 0.0 3 1257 111 47 20 104 25478 0.0 3 23263 1594 391 230 105 942 0.0 3 792 98 31 21 106 604 0.0 3 483 66 34 21 107 520 0.0 3 415 53 29 23 108 525 0.0 3 418 46 35 26 109 517 0.0 3 405 59 25 28 110 454 0.0 3 354 39 30 31 111 369 0.0 3 305 34 12 18 112 361 0.0 3 272 52 20 17 113 359 0.0 3 293 42 17 7 114 338 0.0 3 268 40 20 10 115 270 0.0 3 221 20 18 11 116 329 0.0 3 261 32 25 11 117 284 0.0 3 223 33 13 15 118 287 0.0 3 206 39 23 19 119 244 0.0 3 194 14 17 19 120 250 0.0 3 197 23 19 11 121 209 0.0 3 163 21 12 13 122 199 0.0 3 147 16 17 19 123 206 0.0 3 163 21 16 6 124 985 0.0 3 901 47 24 13 125 154 0.0 3 109 23 13 9 126 132 0.0 3 100 12 11 9 127 115 0.0 3 83 18 4 10 128 151 0.0 3 121 17 6 7 129 243 0.0 3 209 22 4 8 130 1556 0.0 3 1308 148 56 44 131 1434 0.0 3 1322 88 15 9 132 152 0.0 3 127 21 1 3 133 108 0.0 3 98 4 4 2 134 142 0.0 3 131 8 2 1 135 98 0.0 3 86 8 3 1 136 103 0.0 3 92 5 2 4 137 75 0.0 3 71 1 1 2 138 63 0.0 3 59 4 139 76 0.0 3 70 3 3 140 47 0.0 3 46 0 0 1 141 55 0.0 3 50 2 0 3 142 69 0.0 3 56 11 0 2 143 29 0.0 3 24 4 1 144 25 0.0 3 24 0 1 145 11 0.0 3 11 146 23 0.0 3 23 147 16 0.0 3 14 2 148 66 0.0 3 17 10 6 33 149 10671 0.0 3 37 7826 2609 199 150 107904 0.0 3 2899 99425 5290 290 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4950021 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: 22.2% G: 30.5% T: 21.1% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 451836 304420.5 0 451836 4 153875 76105.1 0 153875 5 95047 19026.3 0 95047 6 89610 4756.6 0 89610 7 90693 1189.1 0 90693 8 85904 297.3 0 85904 9 88618 74.3 0 88222 396 10 91072 18.6 1 79526 11546 11 91187 4.6 1 79923 11264 12 90068 1.2 1 79500 10568 13 106115 0.3 1 94418 11697 14 101283 0.1 1 89661 11622 15 107647 0.0 1 95286 12361 16 102088 0.0 1 90498 11590 17 94867 0.0 1 84061 10806 18 90428 0.0 1 79576 10830 22 19 86809 0.0 1 75749 10818 242 20 93427 0.0 2 77784 10785 4858 21 87418 0.0 2 72672 9967 4779 22 84931 0.0 2 70026 10092 4813 23 89380 0.0 2 73477 10747 5156 24 88354 0.0 2 72990 10429 4935 25 93353 0.0 2 77154 11213 4986 26 93819 0.0 2 74721 13430 5668 27 90252 0.0 2 71250 13553 5446 3 28 85747 0.0 2 67313 13199 5220 15 29 78460 0.0 2 62095 11548 4739 78 30 78193 0.0 3 60103 10647 4412 3031 31 77071 0.0 3 59013 10727 4456 2875 32 76013 0.0 3 58500 10523 4230 2760 33 79352 0.0 3 61444 10746 4304 2858 34 75525 0.0 3 58234 10333 4174 2784 35 75401 0.0 3 58546 9966 4186 2703 36 74988 0.0 3 58176 10060 4130 2622 37 73982 0.0 3 57398 9802 4076 2706 38 70858 0.0 3 55381 9227 3752 2498 39 67305 0.0 3 52815 8592 3622 2276 40 62987 0.0 3 49282 8112 3380 2213 41 62565 0.0 3 49634 7609 3206 2116 42 57172 0.0 3 45066 7089 3033 1984 43 56965 0.0 3 45273 6946 2927 1819 44 58796 0.0 3 46896 7051 2946 1903 45 55227 0.0 3 43926 6783 2762 1756 46 55219 0.0 3 44266 6609 2623 1721 47 52010 0.0 3 41436 6379 2534 1661 48 50354 0.0 3 40197 6129 2470 1558 49 46078 0.0 3 36721 5530 2323 1504 50 48051 0.0 3 38671 5633 2229 1518 51 42785 0.0 3 34519 4985 1993 1288 52 40916 0.0 3 33213 4671 1815 1217 53 40192 0.0 3 32611 4568 1863 1150 54 37660 0.0 3 30512 4393 1651 1104 55 36330 0.0 3 29571 4137 1580 1042 56 34162 0.0 3 27817 3890 1493 962 57 34814 0.0 3 28694 3682 1517 921 58 31134 0.0 3 25737 3222 1350 825 59 30406 0.0 3 25185 3130 1219 872 60 25202 0.0 3 20624 2755 1118 705 61 22744 0.0 3 18678 2446 1005 615 62 21546 0.0 3 17587 2335 985 639 63 19930 0.0 3 16402 2039 907 582 64 19851 0.0 3 16546 1966 788 551 65 17232 0.0 3 14308 1751 699 474 66 16984 0.0 3 14114 1785 662 423 67 16387 0.0 3 13537 1784 666 400 68 14630 0.0 3 12218 1459 567 386 69 12727 0.0 3 10592 1290 534 311 70 11531 0.0 3 9535 1204 501 291 71 10449 0.0 3 8714 999 435 301 72 8675 0.0 3 7140 877 397 261 73 8410 0.0 3 7008 833 355 214 74 7484 0.0 3 6219 753 299 213 75 7286 0.0 3 6093 704 303 186 76 6440 0.0 3 5348 662 290 140 77 6168 0.0 3 5148 617 244 159 78 5884 0.0 3 4919 582 224 159 79 5715 0.0 3 4792 526 251 146 80 5732 0.0 3 4813 544 222 153 81 4925 0.0 3 4128 460 218 119 82 4227 0.0 3 3552 386 159 130 83 4214 0.0 3 3547 386 155 126 84 3325 0.0 3 2753 335 150 87 85 2915 0.0 3 2428 270 128 89 86 2782 0.0 3 2326 261 109 86 87 2671 0.0 3 2207 268 115 81 88 2781 0.0 3 2323 262 117 79 89 2830 0.0 3 2383 261 110 76 90 2605 0.0 3 2168 245 114 78 91 2336 0.0 3 1888 259 109 80 92 2138 0.0 3 1778 202 83 75 93 1710 0.0 3 1391 173 102 44 94 1516 0.0 3 1236 161 60 59 95 1373 0.0 3 1095 154 81 43 96 1181 0.0 3 948 130 70 33 97 1228 0.0 3 975 142 64 47 98 1223 0.0 3 978 127 58 60 99 1170 0.0 3 920 135 55 60 100 1103 0.0 3 889 115 58 41 101 1011 0.0 3 826 106 51 28 102 941 0.0 3 744 100 51 46 103 1523 0.0 3 1277 142 65 39 104 25722 0.0 3 23496 1583 443 200 105 979 0.0 3 821 81 51 26 106 645 0.0 3 491 86 37 31 107 574 0.0 3 432 78 36 28 108 580 0.0 3 442 62 37 39 109 562 0.0 3 433 65 39 25 110 484 0.0 3 368 66 29 21 111 399 0.0 3 309 46 22 22 112 395 0.0 3 285 51 30 29 113 396 0.0 3 299 41 35 21 114 375 0.0 3 282 43 31 19 115 301 0.0 3 225 37 20 19 116 357 0.0 3 266 47 20 24 117 308 0.0 3 228 40 24 16 118 296 0.0 3 211 40 22 23 119 252 0.0 3 179 41 16 16 120 254 0.0 3 192 30 16 16 121 231 0.0 3 162 30 22 17 122 228 0.0 3 145 46 23 14 123 215 0.0 3 175 13 14 13 124 979 0.0 3 859 72 32 16 125 166 0.0 3 121 22 17 6 126 140 0.0 3 96 24 7 13 127 116 0.0 3 85 15 8 8 128 157 0.0 3 115 24 9 9 129 240 0.0 3 202 26 6 6 130 1557 0.0 3 1416 108 21 12 131 1259 0.0 3 923 209 92 35 132 143 0.0 3 119 15 8 1 133 99 0.0 3 83 12 2 2 134 135 0.0 3 113 19 2 1 135 93 0.0 3 83 7 1 2 136 102 0.0 3 87 10 5 137 71 0.0 3 64 7 138 65 0.0 3 60 1 2 2 139 75 0.0 3 65 6 3 1 140 46 0.0 3 41 3 2 141 52 0.0 3 50 2 142 57 0.0 3 52 5 143 27 0.0 3 26 1 144 24 0.0 3 23 0 1 145 11 0.0 3 11 146 23 0.0 3 22 1 147 16 0.0 3 15 1 148 20 0.0 3 14 5 1 149 59 0.0 3 36 13 5 5 150 3202 0.0 3 2834 187 98 83