This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH01-14.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH01-14.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH01-14_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH01-14_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 239.795 s (6.844 µs/read; 8.77 M reads/minute). === Summary === Total read pairs processed: 35,039,602 Read 1 with adapter: 5,758,011 (16.4%) Read 2 with adapter: 5,807,490 (16.6%) == Read fate breakdown == Pairs that were too short: 109,105 (0.3%) Pairs written (passing filters): 34,930,497 (99.7%) Total basepairs processed: 10,511,880,600 bp Read 1: 5,255,940,300 bp Read 2: 5,255,940,300 bp Quality-trimmed: 1,449,574 bp (0.0%) Read 1: 654,317 bp Read 2: 795,257 bp Total written (filtered): 10,207,079,049 bp (97.1%) Read 1: 5,105,852,506 bp Read 2: 5,101,226,543 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 5758011 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: 25.7% C: 21.2% G: 32.5% T: 18.9% none/other: 1.6% Overview of removed sequences length count expect max.err error counts 3 849905 547493.8 0 849905 4 233990 136873.4 0 233990 5 125695 34218.4 0 125695 6 107449 8554.6 0 107449 7 117748 2138.6 0 117748 8 104900 534.7 0 104900 9 106851 133.7 0 106294 557 10 108429 33.4 1 94889 13540 11 108763 8.4 1 95483 13280 12 107842 2.1 1 95391 12451 13 122773 0.5 1 109118 13655 14 119036 0.1 1 105077 13959 15 123009 0.0 1 109390 13619 16 116670 0.0 1 103867 12803 17 113011 0.0 1 100629 12382 18 102909 0.0 1 91427 11444 38 19 98045 0.0 1 86315 11444 286 20 104287 0.0 2 87685 10922 5680 21 101127 0.0 2 85453 10596 5078 22 99818 0.0 2 84398 10338 5082 23 102591 0.0 2 86904 10504 5183 24 99705 0.0 2 84356 10480 4869 25 102466 0.0 2 86734 10570 5162 26 103590 0.0 2 88016 10510 5064 27 99890 0.0 2 85046 10022 4812 10 28 97197 0.0 2 82369 10024 4784 20 29 85917 0.0 2 72608 9085 4191 33 30 82970 0.0 3 67812 8618 3836 2704 31 83729 0.0 3 68923 8401 3765 2640 32 80706 0.0 3 66308 8077 3685 2636 33 84512 0.0 3 69470 8652 3738 2652 34 82652 0.0 3 68153 8196 3708 2595 35 78686 0.0 3 64772 7960 3455 2499 36 75983 0.0 3 62817 7415 3350 2401 37 76138 0.0 3 62875 7481 3407 2375 38 70663 0.0 3 58553 6851 3102 2157 39 69942 0.0 3 58119 6793 2976 2054 40 64639 0.0 3 53709 6283 2766 1881 41 61079 0.0 3 50647 5981 2630 1821 42 56843 0.0 3 47213 5579 2453 1598 43 55068 0.0 3 45212 5673 2446 1737 44 54824 0.0 3 45520 5251 2323 1730 45 51807 0.0 3 43122 5046 2190 1449 46 51057 0.0 3 42719 4826 2068 1444 47 48382 0.0 3 40251 4739 2027 1365 48 46755 0.0 3 39058 4498 1949 1250 49 42019 0.0 3 34993 4084 1748 1194 50 43182 0.0 3 36265 3942 1771 1204 51 37232 0.0 3 31279 3486 1486 981 52 35843 0.0 3 29918 3490 1431 1004 53 35460 0.0 3 29825 3309 1357 969 54 32589 0.0 3 27371 3085 1266 867 55 32440 0.0 3 27506 2921 1172 841 56 27825 0.0 3 23443 2573 1080 729 57 32999 0.0 3 28224 2882 1104 789 58 26518 0.0 3 22457 2366 1026 669 59 24671 0.0 3 20910 2197 929 635 60 21131 0.0 3 17891 1878 807 555 61 17730 0.0 3 15062 1603 617 448 62 16472 0.0 3 13910 1539 586 437 63 16391 0.0 3 13890 1477 600 424 64 15646 0.0 3 13391 1326 544 385 65 13762 0.0 3 11728 1215 492 327 66 13026 0.0 3 11137 1108 471 310 67 12988 0.0 3 11078 1140 453 317 68 11048 0.0 3 9395 953 442 258 69 9063 0.0 3 7688 837 326 212 70 8268 0.0 3 6947 756 326 239 71 7510 0.0 3 6321 676 309 204 72 6197 0.0 3 5214 558 261 164 73 6155 0.0 3 5189 569 237 160 74 5032 0.0 3 4230 468 196 138 75 4932 0.0 3 4193 453 148 138 76 4414 0.0 3 3697 408 193 116 77 4215 0.0 3 3586 368 160 101 78 3922 0.0 3 3327 335 151 109 79 3635 0.0 3 3021 355 147 112 80 3445 0.0 3 2876 314 132 123 81 3020 0.0 3 2517 275 121 107 82 2625 0.0 3 2182 240 97 106 83 2389 0.0 3 1970 223 118 78 84 1929 0.0 3 1570 192 87 80 85 1648 0.0 3 1304 187 92 65 86 1654 0.0 3 1329 168 93 64 87 1635 0.0 3 1316 150 91 78 88 1639 0.0 3 1321 148 95 75 89 1644 0.0 3 1334 173 81 56 90 1418 0.0 3 1110 149 93 66 91 1333 0.0 3 1043 137 89 64 92 1131 0.0 3 883 110 80 58 93 965 0.0 3 752 107 55 51 94 921 0.0 3 688 101 73 59 95 814 0.0 3 593 105 53 63 96 775 0.0 3 544 113 53 65 97 641 0.0 3 463 90 41 47 98 741 0.0 3 527 101 42 71 99 693 0.0 3 500 81 64 48 100 742 0.0 3 524 102 64 52 101 669 0.0 3 470 84 69 46 102 649 0.0 3 445 98 56 50 103 627 0.0 3 438 73 73 43 104 2336 0.0 3 1974 196 104 62 105 483 0.0 3 279 107 49 48 106 474 0.0 3 294 76 62 42 107 408 0.0 3 266 64 44 34 108 455 0.0 3 292 62 59 42 109 393 0.0 3 263 64 33 33 110 419 0.0 3 246 79 43 51 111 331 0.0 3 210 50 38 33 112 379 0.0 3 252 54 37 36 113 346 0.0 3 209 67 37 33 114 398 0.0 3 241 61 53 43 115 335 0.0 3 209 59 36 31 116 348 0.0 3 217 52 45 34 117 258 0.0 3 160 40 27 31 118 328 0.0 3 212 56 33 27 119 288 0.0 3 174 56 28 30 120 317 0.0 3 186 59 40 32 121 246 0.0 3 159 42 25 20 122 281 0.0 3 186 45 25 25 123 214 0.0 3 135 36 21 22 124 576 0.0 3 477 53 27 19 125 198 0.0 3 127 33 22 16 126 222 0.0 3 135 44 23 20 127 149 0.0 3 89 30 20 10 128 238 0.0 3 167 36 21 14 129 145 0.0 3 106 22 10 7 130 201 0.0 3 152 28 13 8 131 424 0.0 3 370 37 14 3 132 104 0.0 3 81 12 6 5 133 106 0.0 3 86 12 2 6 134 135 0.0 3 114 15 3 3 135 84 0.0 3 64 12 4 4 136 71 0.0 3 55 8 7 1 137 72 0.0 3 61 4 2 5 138 92 0.0 3 83 7 1 1 139 37 0.0 3 35 1 1 140 29 0.0 3 26 2 1 141 31 0.0 3 24 3 3 1 142 37 0.0 3 32 5 143 18 0.0 3 18 144 15 0.0 3 7 2 2 4 145 19 0.0 3 16 0 2 1 146 24 0.0 3 19 3 0 2 147 19 0.0 3 16 1 1 1 148 86 0.0 3 25 18 5 38 149 8355 0.0 3 24 5811 2359 161 150 91377 0.0 3 1934 84406 4786 251 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 5807490 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: 21.9% G: 32.0% T: 19.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 813897 547493.8 0 813897 4 242792 136873.4 0 242792 5 130139 34218.4 0 130139 6 113662 8554.6 0 113662 7 124324 2138.6 0 124324 8 112015 534.7 0 112015 9 113508 133.7 0 113008 500 10 114601 33.4 1 101144 13457 11 114130 8.4 1 100653 13477 12 113147 2.1 1 100895 12252 13 129069 0.5 1 115730 13339 14 124972 0.1 1 111759 13213 15 128987 0.0 1 115238 13749 16 120882 0.0 1 107770 13112 17 117806 0.0 1 105294 12512 18 106378 0.0 1 93228 13135 15 19 103364 0.0 1 89513 13601 250 20 108948 0.0 2 88063 14774 6111 21 104173 0.0 2 83817 14136 6220 22 102396 0.0 2 81625 14403 6368 23 105034 0.0 2 84298 14183 6553 24 102353 0.0 2 82594 13742 6017 25 105455 0.0 2 85611 13903 5941 26 107169 0.0 2 85403 15384 6382 27 103289 0.0 2 82137 14933 6216 3 28 99997 0.0 2 79631 14319 6043 4 29 88195 0.0 2 69954 12801 5393 47 30 85506 0.0 3 65402 11912 5050 3142 31 86700 0.0 3 66569 11938 5016 3177 32 83511 0.0 3 64158 11497 4803 3053 33 87107 0.0 3 67357 11811 4808 3131 34 85059 0.0 3 65953 11364 4685 3057 35 81363 0.0 3 63404 10655 4408 2896 36 78324 0.0 3 61037 10353 4229 2705 37 78513 0.0 3 61050 10415 4330 2718 38 72676 0.0 3 56962 9325 3882 2507 39 71727 0.0 3 56344 9102 3868 2413 40 66257 0.0 3 51541 8836 3619 2261 41 62785 0.0 3 48983 8350 3382 2070 42 58353 0.0 3 45460 7544 3303 2046 43 56526 0.0 3 44297 7418 2927 1884 44 56401 0.0 3 44249 7212 3044 1896 45 53320 0.0 3 41949 6918 2765 1688 46 52264 0.0 3 41422 6496 2654 1692 47 49537 0.0 3 38978 6309 2653 1597 48 47766 0.0 3 37780 5934 2479 1573 49 42913 0.0 3 33596 5611 2299 1407 50 44259 0.0 3 34995 5571 2312 1381 51 38175 0.0 3 30389 4744 1831 1211 52 36827 0.0 3 29415 4412 1864 1136 53 36332 0.0 3 29304 4181 1745 1102 54 33653 0.0 3 27051 3965 1584 1053 55 33276 0.0 3 26853 3901 1552 970 56 28551 0.0 3 22877 3424 1385 865 57 33729 0.0 3 27704 3666 1482 877 58 27268 0.0 3 22132 3115 1248 773 59 25153 0.0 3 20397 2830 1164 762 60 21611 0.0 3 17478 2493 991 649 61 18246 0.0 3 14738 2084 886 538 62 16920 0.0 3 13583 1998 799 540 63 16935 0.0 3 13673 1995 770 497 64 16049 0.0 3 13132 1765 713 439 65 14190 0.0 3 11526 1629 626 409 66 13423 0.0 3 10947 1467 606 403 67 13390 0.0 3 10893 1555 582 360 68 11381 0.0 3 9173 1380 501 327 69 9304 0.0 3 7505 1069 446 284 70 8555 0.0 3 6882 980 413 280 71 7749 0.0 3 6236 876 406 231 72 6485 0.0 3 5104 811 336 234 73 6441 0.0 3 5125 766 303 247 74 5267 0.0 3 4163 663 270 171 75 5208 0.0 3 4193 574 268 173 76 4620 0.0 3 3668 555 236 161 77 4461 0.0 3 3501 528 257 175 78 4152 0.0 3 3287 489 222 154 79 3826 0.0 3 3014 441 228 143 80 3679 0.0 3 2824 512 224 119 81 3266 0.0 3 2538 394 203 131 82 2798 0.0 3 2180 334 150 134 83 2595 0.0 3 1987 317 185 106 84 2168 0.0 3 1611 272 149 136 85 1847 0.0 3 1382 246 120 99 86 1862 0.0 3 1377 248 138 99 87 1838 0.0 3 1345 277 114 102 88 1821 0.0 3 1326 249 147 99 89 1849 0.0 3 1356 248 138 107 90 1596 0.0 3 1173 219 122 82 91 1527 0.0 3 1083 233 122 89 92 1299 0.0 3 933 177 100 89 93 1151 0.0 3 785 175 106 85 94 1114 0.0 3 721 190 112 91 95 969 0.0 3 644 162 97 66 96 976 0.0 3 637 140 111 88 97 803 0.0 3 513 125 94 71 98 912 0.0 3 573 151 102 86 99 874 0.0 3 561 147 91 75 100 923 0.0 3 595 147 109 72 101 813 0.0 3 523 137 86 67 102 792 0.0 3 515 131 77 69 103 794 0.0 3 491 135 91 77 104 2526 0.0 3 2053 259 131 83 105 613 0.0 3 361 114 81 57 106 636 0.0 3 365 114 88 69 107 520 0.0 3 293 102 72 53 108 583 0.0 3 334 105 73 71 109 506 0.0 3 278 104 69 55 110 547 0.0 3 309 115 72 51 111 438 0.0 3 248 85 58 47 112 488 0.0 3 258 100 70 60 113 436 0.0 3 237 84 62 53 114 502 0.0 3 290 92 72 48 115 431 0.0 3 247 85 40 59 116 470 0.0 3 248 109 61 52 117 344 0.0 3 187 58 51 48 118 418 0.0 3 225 86 56 51 119 365 0.0 3 184 84 57 40 120 402 0.0 3 206 80 64 52 121 329 0.0 3 182 62 41 44 122 360 0.0 3 183 82 61 34 123 283 0.0 3 160 60 33 30 124 623 0.0 3 456 88 45 34 125 235 0.0 3 144 42 29 20 126 261 0.0 3 152 54 31 24 127 173 0.0 3 91 42 24 16 128 238 0.0 3 159 44 18 17 129 154 0.0 3 104 24 12 14 130 210 0.0 3 151 38 13 8 131 364 0.0 3 257 69 29 9 132 98 0.0 3 72 14 6 6 133 94 0.0 3 75 15 2 2 134 131 0.0 3 108 11 9 3 135 77 0.0 3 62 13 0 2 136 71 0.0 3 55 8 5 3 137 67 0.0 3 55 8 2 2 138 90 0.0 3 77 11 2 139 35 0.0 3 31 4 140 27 0.0 3 26 1 141 26 0.0 3 25 1 142 36 0.0 3 27 6 3 143 18 0.0 3 15 2 1 144 7 0.0 3 7 145 16 0.0 3 13 2 1 146 20 0.0 3 18 2 147 16 0.0 3 15 1 148 28 0.0 3 24 4 149 48 0.0 3 24 14 4 6 150 2138 0.0 3 1865 165 66 42