This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-24.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-24.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-24_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-24_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 176.170 s (6.852 µs/read; 8.76 M reads/minute). === Summary === Total read pairs processed: 25,712,602 Read 1 with adapter: 4,529,881 (17.6%) Read 2 with adapter: 4,590,640 (17.9%) == Read fate breakdown == Pairs that were too short: 69,230 (0.3%) Pairs written (passing filters): 25,643,372 (99.7%) Total basepairs processed: 7,713,780,600 bp Read 1: 3,856,890,300 bp Read 2: 3,856,890,300 bp Quality-trimmed: 1,016,638 bp (0.0%) Read 1: 471,265 bp Read 2: 545,373 bp Total written (filtered): 7,475,066,429 bp (96.9%) Read 1: 3,739,181,519 bp Read 2: 3,735,884,910 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4529881 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: 26.5% C: 20.8% G: 31.8% T: 19.6% none/other: 1.3% Overview of removed sequences length count expect max.err error counts 3 567248 401759.4 0 567248 4 185272 100439.9 0 185272 5 102437 25110.0 0 102437 6 88433 6277.5 0 88433 7 95888 1569.4 0 95888 8 86972 392.3 0 86972 9 89388 98.1 0 88960 428 10 89595 24.5 1 79275 10320 11 89614 6.1 1 79683 9931 12 87867 1.5 1 78430 9437 13 99867 0.4 1 89412 10455 14 96472 0.1 1 86004 10468 15 99683 0.0 1 89031 10652 16 93861 0.0 1 84202 9659 17 91983 0.0 1 82546 9437 18 86298 0.0 1 77426 8842 30 19 79450 0.0 1 70519 8676 255 20 85085 0.0 2 72507 8382 4196 21 82200 0.0 2 70316 8069 3815 22 81954 0.0 2 70120 7958 3876 23 84046 0.0 2 71899 8110 4037 24 82486 0.0 2 70388 8334 3764 25 84272 0.0 2 72116 8148 4008 26 85103 0.0 2 73004 8233 3866 27 81230 0.0 2 69744 7831 3644 11 28 80795 0.0 2 68980 8121 3678 16 29 70258 0.0 2 59798 7243 3176 41 30 67334 0.0 3 55791 6626 2951 1966 31 68733 0.0 3 57117 6697 2863 2056 32 66027 0.0 3 54510 6573 2903 2041 33 68813 0.0 3 57051 6882 2826 2054 34 66915 0.0 3 55753 6416 2741 2005 35 65158 0.0 3 54111 6454 2717 1876 36 63548 0.0 3 53221 5820 2691 1816 37 61037 0.0 3 50969 5882 2467 1719 38 57605 0.0 3 48207 5478 2291 1629 39 55180 0.0 3 46161 5194 2296 1529 40 51724 0.0 3 43173 4990 2086 1475 41 49595 0.0 3 41520 4747 1992 1336 42 46072 0.0 3 38473 4405 1924 1270 43 44523 0.0 3 37138 4275 1879 1231 44 44122 0.0 3 37022 4178 1738 1184 45 41939 0.0 3 35158 3913 1676 1192 46 41586 0.0 3 35129 3826 1590 1041 47 38129 0.0 3 32060 3578 1453 1038 48 38035 0.0 3 32042 3586 1447 960 49 34281 0.0 3 28882 3182 1338 879 50 35196 0.0 3 29835 3277 1217 867 51 29939 0.0 3 25339 2693 1136 771 52 28403 0.0 3 24106 2610 998 689 53 27863 0.0 3 23561 2562 1042 698 54 25662 0.0 3 21849 2319 898 596 55 25844 0.0 3 21926 2388 936 594 56 22471 0.0 3 19122 1959 828 562 57 24772 0.0 3 21312 2106 836 518 58 20312 0.0 3 17447 1692 707 466 59 19576 0.0 3 16710 1687 721 458 60 16142 0.0 3 13806 1410 544 382 61 13840 0.0 3 11864 1190 470 316 62 12719 0.0 3 10929 1072 426 292 63 12246 0.0 3 10530 1081 372 263 64 12114 0.0 3 10494 984 384 252 65 10315 0.0 3 8825 935 339 216 66 9726 0.0 3 8350 856 308 212 67 9730 0.0 3 8355 858 330 187 68 8395 0.0 3 7200 742 267 186 69 6850 0.0 3 5845 619 224 162 70 6175 0.0 3 5314 523 187 151 71 5409 0.0 3 4635 434 202 138 72 4611 0.0 3 3922 397 168 124 73 4316 0.0 3 3704 368 126 118 74 3556 0.0 3 2991 355 116 94 75 3749 0.0 3 3213 332 132 72 76 3300 0.0 3 2802 304 116 78 77 2899 0.0 3 2481 245 110 63 78 2810 0.0 3 2410 231 91 78 79 2552 0.0 3 2157 241 91 63 80 2395 0.0 3 2060 207 83 45 81 2147 0.0 3 1836 175 78 58 82 1873 0.0 3 1581 161 81 50 83 1661 0.0 3 1430 124 60 47 84 1189 0.0 3 990 115 52 32 85 1077 0.0 3 903 93 44 37 86 1084 0.0 3 909 96 45 34 87 1012 0.0 3 838 101 38 35 88 1087 0.0 3 890 106 50 41 89 1090 0.0 3 923 97 46 24 90 964 0.0 3 800 85 49 30 91 898 0.0 3 733 84 44 37 92 757 0.0 3 586 94 40 37 93 669 0.0 3 535 64 38 32 94 605 0.0 3 472 65 39 29 95 478 0.0 3 371 47 30 30 96 484 0.0 3 349 74 35 26 97 397 0.0 3 304 48 30 15 98 453 0.0 3 357 51 19 26 99 493 0.0 3 377 46 35 35 100 418 0.0 3 319 41 33 25 101 385 0.0 3 286 40 33 26 102 339 0.0 3 254 37 29 19 103 502 0.0 3 390 52 34 26 104 7942 0.0 3 7289 483 106 64 105 341 0.0 3 269 33 18 21 106 277 0.0 3 194 28 26 29 107 231 0.0 3 151 35 28 17 108 215 0.0 3 147 27 26 15 109 217 0.0 3 141 39 20 17 110 213 0.0 3 136 35 23 19 111 209 0.0 3 147 37 15 10 112 213 0.0 3 150 26 19 18 113 148 0.0 3 107 18 17 6 114 186 0.0 3 128 25 17 16 115 169 0.0 3 110 22 19 18 116 180 0.0 3 112 24 25 19 117 126 0.0 3 84 18 11 13 118 146 0.0 3 88 31 16 11 119 141 0.0 3 101 17 12 11 120 148 0.0 3 92 16 21 19 121 140 0.0 3 83 32 14 11 122 133 0.0 3 93 16 16 8 123 91 0.0 3 57 17 15 2 124 270 0.0 3 220 28 11 11 125 104 0.0 3 67 22 9 6 126 122 0.0 3 91 17 11 3 127 93 0.0 3 55 18 10 10 128 159 0.0 3 117 18 10 14 129 107 0.0 3 88 8 3 8 130 486 0.0 3 402 51 19 14 131 471 0.0 3 427 34 4 6 132 77 0.0 3 63 8 3 3 133 76 0.0 3 65 4 3 4 134 160 0.0 3 140 13 5 2 135 62 0.0 3 56 4 2 136 68 0.0 3 60 6 2 137 50 0.0 3 47 2 1 138 91 0.0 3 83 6 1 1 139 39 0.0 3 32 3 3 1 140 14 0.0 3 12 1 0 1 141 30 0.0 3 26 2 1 1 142 42 0.0 3 31 10 0 1 143 19 0.0 3 18 1 144 13 0.0 3 12 1 145 9 0.0 3 5 0 2 2 146 17 0.0 3 12 0 3 2 147 8 0.0 3 5 0 1 2 148 74 0.0 3 42 11 4 17 149 6548 0.0 3 16 4909 1497 126 150 57144 0.0 3 1152 52786 3052 154 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4590640 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: 26.7% C: 21.4% G: 31.3% T: 20.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 553492 401759.4 0 553492 4 192744 100439.9 0 192744 5 106353 25110.0 0 106353 6 92369 6277.5 0 92369 7 100269 1569.4 0 100269 8 92186 392.3 0 92186 9 94025 98.1 0 93674 351 10 93887 24.5 1 83487 10400 11 93625 6.1 1 83330 10295 12 91422 1.5 1 82118 9304 13 104411 0.4 1 94125 10286 14 101103 0.1 1 90809 10294 15 104317 0.0 1 93576 10741 16 97192 0.0 1 87294 9898 17 95777 0.0 1 86264 9513 18 89607 0.0 1 79664 9926 17 19 83697 0.0 1 73733 9774 190 20 89257 0.0 2 75046 10075 4136 21 85190 0.0 2 71224 9650 4316 22 84434 0.0 2 70351 9690 4393 23 86323 0.0 2 71803 10103 4417 24 84594 0.0 2 70638 9704 4252 25 86961 0.0 2 72612 9972 4377 26 87806 0.0 2 70007 12818 4981 27 83660 0.0 2 65732 13016 4908 4 28 82959 0.0 2 65150 13052 4742 15 29 72081 0.0 2 56870 10948 4181 82 30 69301 0.0 3 53293 9853 3730 2425 31 71175 0.0 3 54470 10325 3942 2438 32 67970 0.0 3 52086 9870 3731 2283 33 70844 0.0 3 54196 10242 3937 2469 34 68598 0.0 3 52647 9644 3900 2407 35 67117 0.0 3 51669 9471 3692 2285 36 65383 0.0 3 50431 9080 3655 2217 37 62849 0.0 3 48668 8745 3365 2071 38 59136 0.0 3 46072 8016 3064 1984 39 56619 0.0 3 44291 7472 3012 1844 40 52987 0.0 3 41279 7150 2857 1701 41 50955 0.0 3 39927 6783 2554 1691 42 47169 0.0 3 36830 6233 2503 1603 43 45711 0.0 3 35744 6060 2409 1498 44 45231 0.0 3 35695 5723 2331 1482 45 43028 0.0 3 33696 5716 2239 1377 46 42631 0.0 3 33822 5389 2102 1318 47 39096 0.0 3 30823 5046 1978 1249 48 38805 0.0 3 30522 5108 1946 1229 49 34959 0.0 3 27636 4497 1727 1099 50 35905 0.0 3 28443 4557 1814 1091 51 30569 0.0 3 24428 3738 1498 905 52 28965 0.0 3 23176 3608 1359 822 53 28483 0.0 3 22877 3438 1344 824 54 26390 0.0 3 21099 3364 1161 766 55 26336 0.0 3 21205 3285 1144 702 56 23018 0.0 3 18554 2762 1030 672 57 25226 0.0 3 20575 2886 1120 645 58 20808 0.0 3 16924 2406 909 569 59 19767 0.0 3 16137 2250 862 518 60 16533 0.0 3 13480 1931 675 447 61 14145 0.0 3 11438 1656 633 418 62 12993 0.0 3 10532 1489 606 366 63 12530 0.0 3 10214 1472 532 312 64 12377 0.0 3 10174 1371 529 303 65 10564 0.0 3 8649 1183 453 279 66 9998 0.0 3 8163 1138 429 268 67 9988 0.0 3 8168 1126 442 252 68 8630 0.0 3 7086 911 390 243 69 7061 0.0 3 5719 816 318 208 70 6288 0.0 3 5162 670 293 163 71 5551 0.0 3 4509 605 261 176 72 4688 0.0 3 3795 571 199 123 73 4411 0.0 3 3590 488 212 121 74 3701 0.0 3 3008 408 165 120 75 3875 0.0 3 3128 456 173 118 76 3412 0.0 3 2782 351 163 116 77 2996 0.0 3 2407 343 159 87 78 2909 0.0 3 2342 339 144 84 79 2657 0.0 3 2133 299 133 92 80 2514 0.0 3 2040 251 144 79 81 2248 0.0 3 1780 269 116 83 82 2004 0.0 3 1607 219 111 67 83 1747 0.0 3 1400 199 90 58 84 1292 0.0 3 987 165 73 67 85 1155 0.0 3 883 147 83 42 86 1169 0.0 3 922 132 61 54 87 1095 0.0 3 849 130 66 50 88 1164 0.0 3 870 164 70 60 89 1186 0.0 3 917 143 74 52 90 1029 0.0 3 804 114 60 51 91 984 0.0 3 736 129 70 49 92 835 0.0 3 610 109 67 49 93 735 0.0 3 552 98 48 37 94 672 0.0 3 476 100 48 48 95 556 0.0 3 381 96 45 34 96 538 0.0 3 381 80 34 43 97 494 0.0 3 311 85 55 43 98 533 0.0 3 373 83 43 34 99 552 0.0 3 387 91 41 33 100 495 0.0 3 325 84 44 42 101 469 0.0 3 312 67 48 42 102 397 0.0 3 269 64 37 27 103 550 0.0 3 403 71 48 28 104 8041 0.0 3 7150 617 164 110 105 409 0.0 3 271 63 52 23 106 347 0.0 3 219 53 34 41 107 318 0.0 3 168 69 43 38 108 291 0.0 3 156 46 43 46 109 261 0.0 3 155 48 30 28 110 267 0.0 3 154 51 33 29 111 246 0.0 3 133 47 42 24 112 258 0.0 3 143 48 37 30 113 178 0.0 3 109 34 15 20 114 230 0.0 3 143 36 30 21 115 196 0.0 3 117 42 17 20 116 210 0.0 3 121 42 24 23 117 167 0.0 3 88 30 22 27 118 160 0.0 3 91 37 18 14 119 166 0.0 3 106 23 22 15 120 170 0.0 3 94 28 26 22 121 148 0.0 3 74 37 24 13 122 165 0.0 3 106 24 14 21 123 107 0.0 3 60 14 15 18 124 278 0.0 3 209 29 23 17 125 105 0.0 3 61 25 9 10 126 129 0.0 3 82 14 24 9 127 97 0.0 3 53 27 7 10 128 161 0.0 3 111 20 20 10 129 106 0.0 3 79 14 5 8 130 488 0.0 3 404 55 16 13 131 385 0.0 3 273 67 34 11 132 68 0.0 3 50 11 5 2 133 72 0.0 3 53 11 7 1 134 149 0.0 3 128 15 4 2 135 60 0.0 3 52 4 4 136 68 0.0 3 54 9 5 137 48 0.0 3 44 3 1 138 89 0.0 3 80 8 1 139 32 0.0 3 25 3 2 2 140 14 0.0 3 12 0 2 141 26 0.0 3 22 2 1 1 142 34 0.0 3 27 5 2 143 19 0.0 3 17 2 144 12 0.0 3 11 1 145 5 0.0 3 4 1 146 12 0.0 3 12 147 5 0.0 3 4 1 148 48 0.0 3 36 12 149 39 0.0 3 16 5 9 9 150 1264 0.0 3 1117 100 30 17