This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-06.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-06.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-06_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-06_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 130.633 s (6.515 µs/read; 9.21 M reads/minute). === Summary === Total read pairs processed: 20,050,303 Read 1 with adapter: 3,057,902 (15.3%) Read 2 with adapter: 3,077,076 (15.3%) == Read fate breakdown == Pairs that were too short: 62,434 (0.3%) Pairs written (passing filters): 19,987,869 (99.7%) Total basepairs processed: 6,015,090,900 bp Read 1: 3,007,545,450 bp Read 2: 3,007,545,450 bp Quality-trimmed: 788,815 bp (0.0%) Read 1: 368,891 bp Read 2: 419,924 bp Total written (filtered): 5,852,662,347 bp (97.3%) Read 1: 2,927,396,678 bp Read 2: 2,925,265,669 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 3057902 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: 27.0% C: 19.8% G: 31.2% T: 20.2% none/other: 1.7% Overview of removed sequences length count expect max.err error counts 3 449650 313286.0 0 449650 4 130238 78321.5 0 130238 5 64733 19580.4 0 64733 6 55993 4895.1 0 55993 7 63106 1223.8 0 63106 8 56034 305.9 0 56034 9 57145 76.5 0 56845 300 10 57152 19.1 1 50150 7002 11 56989 4.8 1 50219 6770 12 55993 1.2 1 49649 6344 13 65394 0.3 1 58379 7015 14 63761 0.1 1 56502 7259 15 66280 0.0 1 59092 7188 16 63134 0.0 1 56309 6825 17 61394 0.0 1 54888 6506 18 55641 0.0 1 49727 5898 16 19 50580 0.0 1 44815 5631 134 20 55533 0.0 2 47010 5632 2891 21 53777 0.0 2 45558 5527 2692 22 53420 0.0 2 45410 5338 2672 23 54667 0.0 2 46400 5549 2718 24 52728 0.0 2 44916 5277 2535 25 54798 0.0 2 46667 5478 2653 26 55951 0.0 2 47724 5603 2624 27 53786 0.0 2 45925 5329 2530 2 28 54423 0.0 2 46172 5608 2637 6 29 45576 0.0 2 38620 4771 2162 23 30 44016 0.0 3 36129 4392 2061 1434 31 43968 0.0 3 36392 4216 1966 1394 32 43304 0.0 3 35649 4301 1993 1361 33 45537 0.0 3 37644 4541 1943 1409 34 44323 0.0 3 36607 4373 1963 1380 35 42068 0.0 3 34686 4184 1865 1333 36 39780 0.0 3 32938 3798 1758 1286 37 40211 0.0 3 33355 3869 1768 1219 38 36495 0.0 3 30242 3503 1598 1152 39 36810 0.0 3 30661 3423 1613 1113 40 33912 0.0 3 28205 3230 1483 994 41 31574 0.0 3 26128 3118 1371 957 42 29861 0.0 3 24718 2915 1272 956 43 28136 0.0 3 23327 2700 1250 859 44 28086 0.0 3 23357 2722 1167 840 45 26775 0.0 3 22319 2502 1169 785 46 26053 0.0 3 21751 2461 1088 753 47 24636 0.0 3 20601 2209 1082 744 48 24074 0.0 3 20156 2268 1004 646 49 21524 0.0 3 17978 2015 906 625 50 22629 0.0 3 18962 2115 955 597 51 19126 0.0 3 16080 1721 790 535 52 18815 0.0 3 15793 1770 727 525 53 17931 0.0 3 15062 1670 752 447 54 16660 0.0 3 14081 1499 640 440 55 16712 0.0 3 14143 1515 624 430 56 14238 0.0 3 12019 1305 539 375 57 16435 0.0 3 14080 1402 559 394 58 13493 0.0 3 11440 1208 534 311 59 12973 0.0 3 11047 1149 447 330 60 10833 0.0 3 9156 991 409 277 61 9228 0.0 3 7853 760 352 263 62 8365 0.0 3 7078 754 310 223 63 8287 0.0 3 7106 677 292 212 64 8240 0.0 3 7041 737 288 174 65 6815 0.0 3 5816 587 261 151 66 6586 0.0 3 5608 589 215 174 67 6496 0.0 3 5569 535 255 137 68 5613 0.0 3 4780 494 202 137 69 4605 0.0 3 3873 421 194 117 70 4224 0.0 3 3574 365 152 133 71 3646 0.0 3 3112 318 131 85 72 3021 0.0 3 2551 276 103 91 73 2939 0.0 3 2471 259 109 100 74 2627 0.0 3 2225 246 101 55 75 2522 0.0 3 2138 224 96 64 76 2164 0.0 3 1823 183 75 83 77 2071 0.0 3 1750 176 86 59 78 1927 0.0 3 1622 182 64 59 79 1808 0.0 3 1514 168 78 48 80 1657 0.0 3 1370 152 69 66 81 1496 0.0 3 1274 126 62 34 82 1375 0.0 3 1159 122 59 35 83 1173 0.0 3 991 100 44 38 84 857 0.0 3 707 67 50 33 85 819 0.0 3 648 82 50 39 86 761 0.0 3 608 90 42 21 87 775 0.0 3 619 90 39 27 88 721 0.0 3 582 74 33 32 89 737 0.0 3 604 68 41 24 90 687 0.0 3 560 61 34 32 91 635 0.0 3 531 48 30 26 92 542 0.0 3 436 58 26 22 93 436 0.0 3 359 34 19 24 94 441 0.0 3 339 51 35 16 95 350 0.0 3 271 36 19 24 96 352 0.0 3 261 42 27 22 97 313 0.0 3 237 33 19 24 98 343 0.0 3 265 35 25 18 99 350 0.0 3 261 41 22 26 100 331 0.0 3 244 45 22 20 101 319 0.0 3 237 36 23 23 102 303 0.0 3 222 35 23 23 103 432 0.0 3 355 36 26 15 104 8608 0.0 3 7986 435 111 76 105 280 0.0 3 218 33 17 12 106 287 0.0 3 197 41 25 24 107 216 0.0 3 148 26 14 28 108 218 0.0 3 141 31 28 18 109 178 0.0 3 125 25 16 12 110 185 0.0 3 123 26 20 16 111 172 0.0 3 114 30 14 14 112 176 0.0 3 114 28 20 14 113 145 0.0 3 91 20 17 17 114 158 0.0 3 97 36 11 14 115 138 0.0 3 90 14 20 14 116 135 0.0 3 83 25 16 11 117 130 0.0 3 93 19 10 8 118 148 0.0 3 99 22 12 15 119 105 0.0 3 74 13 9 9 120 131 0.0 3 86 23 11 11 121 122 0.0 3 71 20 13 18 122 116 0.0 3 72 18 17 9 123 94 0.0 3 61 15 14 4 124 262 0.0 3 219 20 10 13 125 96 0.0 3 60 17 11 8 126 84 0.0 3 56 12 9 7 127 68 0.0 3 48 11 3 6 128 160 0.0 3 126 13 11 10 129 156 0.0 3 141 11 2 2 130 439 0.0 3 393 29 10 7 131 664 0.0 3 621 30 8 5 132 175 0.0 3 149 18 4 4 133 85 0.0 3 78 4 3 134 149 0.0 3 140 7 2 135 96 0.0 3 88 7 1 136 50 0.0 3 41 3 4 2 137 73 0.0 3 68 4 0 1 138 88 0.0 3 79 7 1 1 139 66 0.0 3 58 5 3 140 41 0.0 3 39 1 1 141 36 0.0 3 31 5 142 42 0.0 3 40 0 0 2 143 27 0.0 3 23 1 3 144 9 0.0 3 9 145 12 0.0 3 10 1 1 146 26 0.0 3 21 3 0 2 147 13 0.0 3 10 1 0 2 148 42 0.0 3 14 8 3 17 149 5213 0.0 3 13 3806 1279 115 150 51735 0.0 3 1501 47492 2603 139 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 3077076 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: 27.6% C: 20.3% G: 30.8% T: 21.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 434214 313286.0 0 434214 4 136568 78321.5 0 136568 5 66866 19580.4 0 66866 6 58992 4895.1 0 58992 7 66213 1223.8 0 66213 8 59809 305.9 0 59809 9 60080 76.5 0 59869 211 10 60220 19.1 1 53099 7121 11 59543 4.8 1 52516 7027 12 58642 1.2 1 52230 6412 13 68930 0.3 1 61653 7277 14 67147 0.1 1 60027 7120 15 69540 0.0 1 62177 7363 16 65412 0.0 1 58288 7124 17 64016 0.0 1 57214 6802 18 57518 0.0 1 50376 7135 7 19 53223 0.0 1 46174 6925 124 20 58177 0.0 2 46690 8144 3343 21 55106 0.0 2 43928 7784 3394 22 54837 0.0 2 43229 8136 3472 23 55711 0.0 2 44291 7976 3444 24 54056 0.0 2 43218 7734 3104 25 56151 0.0 2 44649 8081 3421 26 57538 0.0 2 44166 9432 3940 27 54983 0.0 2 41793 9320 3870 28 55451 0.0 2 42424 9348 3678 1 29 46468 0.0 2 35536 7714 3192 26 30 45068 0.0 3 33165 7143 2947 1813 31 45295 0.0 3 33474 7006 2943 1872 32 44401 0.0 3 32927 6965 2803 1706 33 46865 0.0 3 34734 7399 2958 1774 34 45459 0.0 3 33768 7163 2721 1807 35 43449 0.0 3 32484 6624 2740 1601 36 41012 0.0 3 30426 6437 2500 1649 37 41291 0.0 3 30891 6191 2597 1612 38 37659 0.0 3 28362 5542 2336 1419 39 37746 0.0 3 28538 5537 2277 1394 40 34657 0.0 3 25809 5439 2079 1330 41 32292 0.0 3 24253 4858 1987 1194 42 30544 0.0 3 23013 4470 1930 1131 43 28851 0.0 3 21737 4305 1803 1006 44 28868 0.0 3 21682 4218 1813 1155 45 27388 0.0 3 20737 4034 1640 977 46 26542 0.0 3 20161 3855 1565 961 47 25205 0.0 3 19041 3651 1622 891 48 24466 0.0 3 18535 3550 1521 860 49 21939 0.0 3 16506 3365 1242 826 50 22986 0.0 3 17573 3305 1303 805 51 19598 0.0 3 15091 2723 1095 689 52 19196 0.0 3 14792 2714 1063 627 53 18404 0.0 3 14213 2527 1055 609 54 17159 0.0 3 13447 2226 929 557 55 17089 0.0 3 13338 2347 870 534 56 14617 0.0 3 11419 1953 765 480 57 16794 0.0 3 13299 2151 868 476 58 13814 0.0 3 10888 1772 724 430 59 13128 0.0 3 10356 1699 661 412 60 11103 0.0 3 8607 1532 589 375 61 9485 0.0 3 7345 1294 547 299 62 8572 0.0 3 6658 1110 508 296 63 8505 0.0 3 6724 1083 428 270 64 8418 0.0 3 6630 1085 434 269 65 7037 0.0 3 5563 919 318 237 66 6803 0.0 3 5362 857 369 215 67 6671 0.0 3 5175 947 331 218 68 5757 0.0 3 4544 729 309 175 69 4755 0.0 3 3720 625 244 166 70 4325 0.0 3 3399 569 224 133 71 3780 0.0 3 2957 463 226 134 72 3126 0.0 3 2397 422 194 113 73 3013 0.0 3 2286 441 175 111 74 2741 0.0 3 2100 378 154 109 75 2597 0.0 3 2014 359 161 63 76 2263 0.0 3 1761 300 111 91 77 2156 0.0 3 1640 284 144 88 78 2017 0.0 3 1519 269 138 91 79 1890 0.0 3 1447 247 111 85 80 1738 0.0 3 1302 242 121 73 81 1574 0.0 3 1183 225 117 49 82 1431 0.0 3 1081 198 90 62 83 1253 0.0 3 966 154 79 54 84 950 0.0 3 684 124 78 64 85 903 0.0 3 636 137 66 64 86 834 0.0 3 596 112 66 60 87 850 0.0 3 627 110 68 45 88 802 0.0 3 578 107 70 47 89 790 0.0 3 580 105 67 38 90 769 0.0 3 544 121 66 38 91 717 0.0 3 501 110 62 44 92 615 0.0 3 434 93 53 35 93 523 0.0 3 346 85 57 35 94 508 0.0 3 332 84 57 35 95 417 0.0 3 278 60 51 28 96 423 0.0 3 272 80 37 34 97 353 0.0 3 239 54 35 25 98 407 0.0 3 280 55 38 34 99 435 0.0 3 281 70 43 41 100 395 0.0 3 255 60 37 43 101 386 0.0 3 237 65 42 42 102 366 0.0 3 230 59 53 24 103 500 0.0 3 344 73 51 32 104 8691 0.0 3 7686 701 207 97 105 323 0.0 3 226 45 32 20 106 345 0.0 3 229 48 38 30 107 260 0.0 3 149 50 37 24 108 248 0.0 3 150 42 35 21 109 229 0.0 3 124 51 39 15 110 241 0.0 3 126 48 34 33 111 189 0.0 3 105 44 22 18 112 220 0.0 3 117 48 20 35 113 168 0.0 3 88 33 22 25 114 191 0.0 3 105 41 29 16 115 164 0.0 3 94 29 17 24 116 157 0.0 3 81 36 28 12 117 159 0.0 3 82 30 24 23 118 168 0.0 3 90 43 20 15 119 113 0.0 3 67 25 7 14 120 152 0.0 3 78 31 27 16 121 133 0.0 3 69 31 24 9 122 136 0.0 3 71 21 24 20 123 105 0.0 3 64 20 8 13 124 272 0.0 3 197 37 25 13 125 106 0.0 3 61 26 10 9 126 95 0.0 3 48 27 5 15 127 69 0.0 3 39 13 13 4 128 161 0.0 3 110 25 10 16 129 154 0.0 3 115 19 12 8 130 428 0.0 3 336 63 23 6 131 591 0.0 3 383 131 47 30 132 157 0.0 3 105 38 10 4 133 84 0.0 3 64 11 6 3 134 148 0.0 3 125 19 3 1 135 92 0.0 3 72 13 4 3 136 48 0.0 3 37 6 5 137 72 0.0 3 63 4 3 2 138 83 0.0 3 71 9 3 139 63 0.0 3 54 5 2 2 140 41 0.0 3 38 2 1 141 35 0.0 3 30 4 1 142 40 0.0 3 31 7 2 143 24 0.0 3 22 1 1 144 9 0.0 3 9 145 10 0.0 3 8 2 146 23 0.0 3 21 1 1 147 10 0.0 3 9 1 148 15 0.0 3 12 3 149 22 0.0 3 13 4 3 2 150 1686 0.0 3 1433 166 47 40