This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-07.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-07.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-07_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-07_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 246.766 s (7.281 µs/read; 8.24 M reads/minute). === Summary === Total read pairs processed: 33,893,404 Read 1 with adapter: 5,966,793 (17.6%) Read 2 with adapter: 5,909,946 (17.4%) == Read fate breakdown == Pairs that were too short: 177,315 (0.5%) Pairs written (passing filters): 33,716,089 (99.5%) Total basepairs processed: 10,168,021,200 bp Read 1: 5,084,010,600 bp Read 2: 5,084,010,600 bp Quality-trimmed: 1,492,046 bp (0.0%) Read 1: 682,138 bp Read 2: 809,908 bp Total written (filtered): 9,834,358,213 bp (96.7%) Read 1: 4,919,356,070 bp Read 2: 4,915,002,143 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 5966793 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: 24.9% C: 20.6% G: 32.5% T: 19.3% none/other: 2.7% Overview of removed sequences length count expect max.err error counts 3 942475 529584.4 0 942475 4 225003 132396.1 0 225003 5 121598 33099.0 0 121598 6 107768 8274.8 0 107768 7 112017 2068.7 0 112017 8 101383 517.2 0 101383 9 102403 129.3 0 101698 705 10 107349 32.3 1 91913 15436 11 107006 8.1 1 91857 15149 12 106300 2.0 1 92098 14202 13 121348 0.5 1 106050 15298 14 115658 0.1 1 100064 15594 15 120794 0.0 1 105498 15296 16 117523 0.0 1 102514 15009 17 110963 0.0 1 96941 14022 18 105056 0.0 1 91660 13354 42 19 95787 0.0 1 82654 12866 267 20 104997 0.0 2 85263 12918 6816 21 100237 0.0 2 81728 12401 6108 22 99694 0.0 2 81408 12070 6216 23 102259 0.0 2 83486 12473 6300 24 100733 0.0 2 82161 12315 6257 25 105070 0.0 2 86023 12660 6387 26 103600 0.0 2 85146 12307 6147 27 98231 0.0 2 80624 11899 5692 16 28 96901 0.0 2 79529 11655 5694 23 29 86402 0.0 2 70388 10768 5192 54 30 84866 0.0 3 66567 10078 4862 3359 31 83546 0.0 3 66277 9584 4519 3166 32 82817 0.0 3 65558 9561 4478 3220 33 86488 0.0 3 68664 9860 4659 3305 34 85121 0.0 3 67550 9751 4555 3265 35 81454 0.0 3 64627 9288 4467 3072 36 79513 0.0 3 63054 9204 4327 2928 37 80438 0.0 3 64131 9135 4143 3029 38 74381 0.0 3 59182 8388 4016 2795 39 72071 0.0 3 57774 8024 3719 2554 40 66601 0.0 3 53489 7384 3390 2338 41 63484 0.0 3 50660 7254 3320 2250 42 59214 0.0 3 47210 6733 3070 2201 43 57359 0.0 3 45479 6672 3137 2071 44 57895 0.0 3 46512 6422 2917 2044 45 55461 0.0 3 44568 6122 2822 1949 46 54913 0.0 3 44112 6129 2785 1887 47 51307 0.0 3 41212 5779 2572 1744 48 48756 0.0 3 39391 5338 2472 1555 49 44825 0.0 3 36109 5001 2197 1518 50 44496 0.0 3 36056 4768 2183 1489 51 39583 0.0 3 32135 4226 1932 1290 52 37140 0.0 3 30101 3934 1854 1251 53 36705 0.0 3 29920 3938 1671 1176 54 34351 0.0 3 28183 3633 1530 1005 55 33305 0.0 3 27228 3440 1605 1032 56 30334 0.0 3 24724 3273 1364 973 57 33070 0.0 3 27375 3358 1426 911 58 27771 0.0 3 22835 2829 1241 866 59 26406 0.0 3 21766 2711 1124 805 60 22218 0.0 3 18092 2335 1075 716 61 18882 0.0 3 15375 2018 907 582 62 17678 0.0 3 14466 1881 812 519 63 17107 0.0 3 14131 1756 751 469 64 16546 0.0 3 13685 1668 706 487 65 14652 0.0 3 12058 1518 664 412 66 13970 0.0 3 11551 1384 610 425 67 13462 0.0 3 11199 1322 549 392 68 11911 0.0 3 9943 1116 517 335 69 9744 0.0 3 8042 963 450 289 70 8566 0.0 3 7107 834 391 234 71 8212 0.0 3 6804 813 348 247 72 6968 0.0 3 5770 671 310 217 73 6654 0.0 3 5449 715 278 212 74 5506 0.0 3 4517 578 242 169 75 5400 0.0 3 4510 508 211 171 76 4836 0.0 3 3933 507 234 162 77 4671 0.0 3 3818 506 208 139 78 4412 0.0 3 3660 437 196 119 79 3862 0.0 3 3089 441 180 152 80 3695 0.0 3 3029 359 171 136 81 3036 0.0 3 2462 307 153 114 82 2721 0.0 3 2176 296 141 108 83 2690 0.0 3 2222 254 119 95 84 2177 0.0 3 1724 215 124 114 85 1792 0.0 3 1399 178 123 92 86 1741 0.0 3 1362 196 104 79 87 1679 0.0 3 1338 176 101 64 88 1620 0.0 3 1245 188 86 101 89 1777 0.0 3 1399 173 110 95 90 1697 0.0 3 1328 183 89 97 91 1475 0.0 3 1167 148 81 79 92 1318 0.0 3 983 159 96 80 93 1094 0.0 3 821 142 70 61 94 935 0.0 3 654 129 78 74 95 877 0.0 3 637 119 60 61 96 715 0.0 3 504 109 44 58 97 728 0.0 3 488 111 74 55 98 782 0.0 3 529 105 74 74 99 810 0.0 3 567 120 64 59 100 782 0.0 3 564 94 70 54 101 734 0.0 3 510 106 63 55 102 694 0.0 3 472 98 61 63 103 758 0.0 3 531 97 68 62 104 4897 0.0 3 4292 376 130 99 105 609 0.0 3 400 110 47 52 106 540 0.0 3 334 94 48 64 107 430 0.0 3 266 78 41 45 108 440 0.0 3 275 70 56 39 109 433 0.0 3 269 74 48 42 110 442 0.0 3 268 86 48 40 111 396 0.0 3 245 65 42 44 112 427 0.0 3 243 76 59 49 113 369 0.0 3 215 74 40 40 114 378 0.0 3 235 69 27 47 115 318 0.0 3 190 59 34 35 116 363 0.0 3 200 62 56 45 117 284 0.0 3 174 51 36 23 118 374 0.0 3 220 72 33 49 119 272 0.0 3 166 40 38 28 120 344 0.0 3 197 60 40 47 121 251 0.0 3 138 46 31 36 122 277 0.0 3 161 47 49 20 123 208 0.0 3 139 36 18 15 124 437 0.0 3 329 49 24 35 125 196 0.0 3 106 42 27 21 126 257 0.0 3 157 37 35 28 127 174 0.0 3 113 21 25 15 128 248 0.0 3 177 32 21 18 129 527 0.0 3 479 32 13 3 130 298 0.0 3 252 26 11 9 131 2060 0.0 3 1897 125 30 8 132 222 0.0 3 176 31 12 3 133 141 0.0 3 123 11 5 2 134 224 0.0 3 198 18 2 6 135 97 0.0 3 83 8 3 3 136 106 0.0 3 90 9 6 1 137 70 0.0 3 66 4 138 106 0.0 3 92 11 2 1 139 79 0.0 3 68 7 3 1 140 47 0.0 3 42 4 0 1 141 62 0.0 3 57 4 0 1 142 42 0.0 3 37 2 1 2 143 27 0.0 3 20 4 1 2 144 7 0.0 3 7 145 25 0.0 3 21 2 0 2 146 69 0.0 3 64 2 1 2 147 27 0.0 3 25 0 1 1 148 91 0.0 3 39 12 6 34 149 10747 0.0 3 40 6729 3630 348 150 154545 0.0 3 5066 140718 8179 582 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 5909946 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: 25.2% C: 21.6% G: 32.4% T: 20.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 876998 529584.4 0 876998 4 235168 132396.1 0 235168 5 125224 33099.0 0 125224 6 113477 8274.8 0 113477 7 117381 2068.7 0 117381 8 107560 517.2 0 107560 9 107353 129.3 0 106799 554 10 112729 32.3 1 96762 15967 11 111730 8.1 1 95751 15979 12 110255 2.0 1 95626 14629 13 127339 0.5 1 111574 15765 14 121453 0.1 1 106065 15388 15 126298 0.0 1 110190 16108 16 121473 0.0 1 106131 15342 17 115049 0.0 1 100463 14586 18 107639 0.0 1 91999 15617 23 19 100721 0.0 1 85098 15323 300 20 109549 0.0 2 85057 16821 7671 21 102898 0.0 2 79455 15824 7619 22 101825 0.0 2 78008 16252 7565 23 104257 0.0 2 80383 16234 7640 24 102486 0.0 2 79682 15425 7379 25 107658 0.0 2 83765 16471 7422 26 106830 0.0 2 80970 17962 7898 27 100673 0.0 2 76070 16974 7624 5 28 99119 0.0 2 75078 16561 7467 13 29 88208 0.0 2 66535 14792 6794 87 30 86971 0.0 3 62991 13686 6289 4005 31 86389 0.0 3 62510 13798 6043 4038 32 85207 0.0 3 61854 13517 6025 3811 33 88699 0.0 3 64497 14124 6158 3920 34 87287 0.0 3 63805 13612 5954 3916 35 83909 0.0 3 61602 12916 5732 3659 36 81763 0.0 3 59789 12784 5556 3634 37 82582 0.0 3 60992 12480 5533 3577 38 76696 0.0 3 56621 11525 5192 3358 39 74095 0.0 3 55207 10717 4851 3320 40 68535 0.0 3 50597 10433 4615 2890 41 65087 0.0 3 48607 9662 4090 2728 42 60497 0.0 3 44847 9070 3908 2672 43 58716 0.0 3 43754 8732 3715 2515 44 59495 0.0 3 44484 8594 3941 2476 45 57021 0.0 3 42460 8595 3581 2385 46 56269 0.0 3 42329 8071 3541 2328 47 52662 0.0 3 39644 7534 3343 2141 48 49949 0.0 3 37598 7194 3156 2001 49 45835 0.0 3 34181 6799 3024 1831 50 45720 0.0 3 34663 6578 2758 1721 51 40637 0.0 3 31028 5739 2372 1498 52 37984 0.0 3 29142 5176 2218 1448 53 37659 0.0 3 29002 5084 2147 1426 54 35238 0.0 3 27175 4760 2005 1298 55 34299 0.0 3 26485 4613 1973 1228 56 31261 0.0 3 24111 4198 1783 1169 57 34010 0.0 3 26742 4349 1774 1145 58 28438 0.0 3 22269 3651 1538 980 59 26943 0.0 3 21060 3435 1482 966 60 22911 0.0 3 17771 3017 1267 856 61 19434 0.0 3 14863 2665 1165 741 62 18196 0.0 3 13985 2454 1036 721 63 17565 0.0 3 13573 2323 1031 638 64 17016 0.0 3 13318 2228 925 545 65 15110 0.0 3 11763 1919 843 585 66 14420 0.0 3 11234 1914 774 498 67 13879 0.0 3 10917 1760 716 486 68 12313 0.0 3 9588 1573 697 455 69 10129 0.0 3 7870 1317 541 401 70 8862 0.0 3 6912 1073 496 381 71 8541 0.0 3 6682 1073 468 318 72 7293 0.0 3 5586 990 441 276 73 6893 0.0 3 5261 900 445 287 74 5817 0.0 3 4441 737 370 269 75 5642 0.0 3 4381 709 323 229 76 5082 0.0 3 3910 679 292 201 77 4968 0.0 3 3824 604 325 215 78 4647 0.0 3 3516 639 300 192 79 4126 0.0 3 3077 571 287 191 80 3958 0.0 3 2925 586 274 173 81 3198 0.0 3 2409 428 209 152 82 2937 0.0 3 2155 426 197 159 83 2906 0.0 3 2151 403 200 152 84 2372 0.0 3 1724 351 189 108 85 1976 0.0 3 1428 302 126 120 86 1993 0.0 3 1425 284 163 121 87 1881 0.0 3 1350 295 137 99 88 1845 0.0 3 1297 273 150 125 89 1958 0.0 3 1414 276 152 116 90 1904 0.0 3 1353 280 149 122 91 1695 0.0 3 1188 253 135 119 92 1490 0.0 3 1014 234 137 105 93 1309 0.0 3 893 208 125 83 94 1124 0.0 3 703 189 131 101 95 1038 0.0 3 673 162 106 97 96 884 0.0 3 542 164 87 91 97 920 0.0 3 544 159 108 109 98 1000 0.0 3 577 185 129 109 99 963 0.0 3 620 150 105 88 100 911 0.0 3 593 131 102 85 101 873 0.0 3 544 160 90 79 102 833 0.0 3 486 149 117 81 103 888 0.0 3 571 145 110 62 104 5103 0.0 3 4298 507 175 123 105 717 0.0 3 448 126 82 61 106 674 0.0 3 355 150 96 73 107 574 0.0 3 304 113 90 67 108 564 0.0 3 285 121 76 82 109 550 0.0 3 314 101 74 61 110 572 0.0 3 290 112 102 68 111 509 0.0 3 249 109 71 80 112 491 0.0 3 260 101 72 58 113 468 0.0 3 246 99 61 62 114 483 0.0 3 246 94 77 66 115 412 0.0 3 210 81 56 65 116 463 0.0 3 203 125 73 62 117 359 0.0 3 185 69 52 53 118 470 0.0 3 235 104 77 54 119 337 0.0 3 174 65 55 43 120 409 0.0 3 209 90 63 47 121 305 0.0 3 136 80 43 46 122 342 0.0 3 162 82 53 45 123 273 0.0 3 141 62 39 31 124 486 0.0 3 324 72 52 38 125 224 0.0 3 115 45 40 24 126 281 0.0 3 157 59 37 28 127 204 0.0 3 118 34 27 25 128 262 0.0 3 162 54 28 18 129 550 0.0 3 387 103 33 27 130 302 0.0 3 210 57 24 11 131 1754 0.0 3 1232 355 116 51 132 186 0.0 3 146 27 8 5 133 136 0.0 3 102 20 5 9 134 216 0.0 3 177 29 7 3 135 94 0.0 3 69 12 12 1 136 105 0.0 3 80 16 4 5 137 71 0.0 3 63 4 3 1 138 98 0.0 3 92 5 0 1 139 72 0.0 3 65 3 2 2 140 44 0.0 3 39 4 1 141 59 0.0 3 52 3 4 142 40 0.0 3 35 5 143 21 0.0 3 17 2 1 1 144 7 0.0 3 7 145 23 0.0 3 17 6 146 65 0.0 3 61 3 1 147 25 0.0 3 21 4 148 40 0.0 3 36 3 1 149 76 0.0 3 40 20 8 8 150 5527 0.0 3 4887 428 136 76