This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH09-02.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH09-02.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH09-02_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH09-02_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 151.480 s (6.149 µs/read; 9.76 M reads/minute). === Summary === Total read pairs processed: 24,635,656 Read 1 with adapter: 4,239,069 (17.2%) Read 2 with adapter: 4,273,053 (17.3%) == Read fate breakdown == Pairs that were too short: 101,983 (0.4%) Pairs written (passing filters): 24,533,673 (99.6%) Total basepairs processed: 7,390,696,800 bp Read 1: 3,695,348,400 bp Read 2: 3,695,348,400 bp Quality-trimmed: 987,724 bp (0.0%) Read 1: 455,638 bp Read 2: 532,086 bp Total written (filtered): 7,150,733,284 bp (96.8%) Read 1: 3,576,990,734 bp Read 2: 3,573,742,550 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4239069 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: 27.3% C: 19.7% G: 29.6% T: 21.5% none/other: 1.9% Overview of removed sequences length count expect max.err error counts 3 511001 384932.1 0 511001 4 165368 96233.0 0 165368 5 86918 24058.3 0 86918 6 73833 6014.6 0 73833 7 93061 1503.6 0 93061 8 79706 375.9 0 79706 9 79100 94.0 0 78706 394 10 78641 23.5 1 69630 9011 11 76461 5.9 1 67887 8574 12 76467 1.5 1 68356 8111 13 90291 0.4 1 81005 9286 14 85937 0.1 1 76732 9205 15 87661 0.0 1 78628 9033 16 80864 0.0 1 72651 8213 17 84759 0.0 1 76256 8503 18 75733 0.0 1 67913 7788 32 19 70411 0.0 1 62760 7468 183 20 76126 0.0 2 65009 7441 3676 21 72391 0.0 2 61946 7063 3382 22 74031 0.0 2 63548 7078 3405 23 77939 0.0 2 66931 7535 3473 24 74745 0.0 2 64150 7318 3277 25 80246 0.0 2 68873 7716 3657 26 82195 0.0 2 70908 7822 3465 27 78393 0.0 2 67545 7461 3381 6 28 80010 0.0 2 68670 7858 3462 20 29 67220 0.0 2 57399 6846 2939 36 30 64515 0.0 3 53712 6214 2795 1794 31 63251 0.0 3 52854 6074 2576 1747 32 59900 0.0 3 50067 5724 2423 1686 33 64490 0.0 3 53774 6240 2643 1833 34 63317 0.0 3 52984 6040 2609 1684 35 62231 0.0 3 52090 5968 2440 1733 36 64080 0.0 3 54020 5806 2517 1737 37 60748 0.0 3 50906 5751 2419 1672 38 52814 0.0 3 44288 5010 2124 1392 39 55359 0.0 3 46704 5102 2147 1406 40 50338 0.0 3 42430 4710 1901 1297 41 46969 0.0 3 39454 4463 1809 1243 42 43763 0.0 3 36637 4175 1796 1155 43 41022 0.0 3 34361 3896 1647 1118 44 40595 0.0 3 34212 3787 1554 1042 45 38834 0.0 3 32831 3595 1440 968 46 38718 0.0 3 32776 3574 1441 927 47 37203 0.0 3 31378 3447 1433 945 48 36445 0.0 3 30860 3341 1396 848 49 33042 0.0 3 27985 2968 1246 843 50 36789 0.0 3 31417 3186 1332 854 51 29402 0.0 3 25011 2648 1083 660 52 29488 0.0 3 25221 2565 1014 688 53 28619 0.0 3 24484 2464 1001 670 54 27649 0.0 3 23620 2441 956 632 55 26984 0.0 3 23172 2285 954 573 56 21670 0.0 3 18476 1925 784 485 57 25694 0.0 3 22134 2157 848 555 58 20633 0.0 3 17812 1725 666 430 59 19699 0.0 3 16882 1694 675 448 60 18056 0.0 3 15514 1542 623 377 61 13659 0.0 3 11616 1200 514 329 62 13700 0.0 3 11718 1192 464 326 63 13427 0.0 3 11562 1151 449 265 64 13112 0.0 3 11396 1111 353 252 65 10938 0.0 3 9367 985 352 234 66 10368 0.0 3 8852 947 349 220 67 10187 0.0 3 8770 893 304 220 68 8954 0.0 3 7743 732 285 194 69 7007 0.0 3 6003 604 246 154 70 6289 0.0 3 5394 554 200 141 71 5299 0.0 3 4536 455 188 120 72 4612 0.0 3 3951 382 168 111 73 4909 0.0 3 4250 389 161 109 74 3969 0.0 3 3434 320 125 90 75 3976 0.0 3 3431 327 131 87 76 3429 0.0 3 2917 317 112 83 77 3234 0.0 3 2804 260 100 70 78 2823 0.0 3 2435 231 93 64 79 2710 0.0 3 2336 234 82 58 80 2674 0.0 3 2322 229 76 47 81 2256 0.0 3 1915 207 80 54 82 1990 0.0 3 1709 164 66 51 83 1776 0.0 3 1548 132 51 45 84 1322 0.0 3 1093 135 54 40 85 1006 0.0 3 842 90 48 26 86 1149 0.0 3 955 110 38 46 87 1114 0.0 3 944 106 33 31 88 1082 0.0 3 881 101 55 45 89 1125 0.0 3 947 100 43 35 90 989 0.0 3 837 72 44 36 91 927 0.0 3 782 88 30 27 92 797 0.0 3 642 81 46 28 93 728 0.0 3 592 63 41 32 94 619 0.0 3 499 62 29 29 95 522 0.0 3 405 58 27 32 96 458 0.0 3 364 46 24 24 97 480 0.0 3 382 56 21 21 98 518 0.0 3 411 46 40 21 99 482 0.0 3 374 51 29 28 100 438 0.0 3 346 39 29 24 101 459 0.0 3 375 41 24 19 102 381 0.0 3 290 43 27 21 103 483 0.0 3 381 54 27 21 104 8348 0.0 3 7727 441 105 75 105 406 0.0 3 315 47 23 21 106 283 0.0 3 219 25 18 21 107 240 0.0 3 187 23 15 15 108 250 0.0 3 188 30 21 11 109 183 0.0 3 137 22 11 13 110 222 0.0 3 148 41 18 15 111 207 0.0 3 152 22 18 15 112 203 0.0 3 138 23 25 17 113 178 0.0 3 115 30 18 15 114 229 0.0 3 167 33 15 14 115 163 0.0 3 102 20 25 16 116 183 0.0 3 117 32 18 16 117 167 0.0 3 109 28 14 16 118 153 0.0 3 100 23 18 12 119 154 0.0 3 95 30 14 15 120 159 0.0 3 103 25 17 14 121 152 0.0 3 96 28 14 14 122 129 0.0 3 88 24 13 4 123 142 0.0 3 109 15 10 8 124 1385 0.0 3 1257 90 23 15 125 145 0.0 3 106 20 9 10 126 142 0.0 3 102 20 10 10 127 96 0.0 3 67 18 8 3 128 212 0.0 3 174 18 10 10 129 346 0.0 3 281 39 18 8 130 3476 0.0 3 2902 370 121 83 131 3693 0.0 3 3373 242 49 29 132 301 0.0 3 229 52 11 9 133 163 0.0 3 142 10 6 5 134 315 0.0 3 284 17 13 1 135 97 0.0 3 86 4 3 4 136 114 0.0 3 103 4 5 2 137 73 0.0 3 69 3 0 1 138 175 0.0 3 163 10 1 1 139 46 0.0 3 44 1 0 1 140 18 0.0 3 14 3 1 141 25 0.0 3 20 4 1 142 40 0.0 3 25 11 0 4 143 16 0.0 3 13 1 0 2 144 14 0.0 3 13 1 145 28 0.0 3 19 3 3 3 146 17 0.0 3 16 1 147 21 0.0 3 11 4 3 3 148 63 0.0 3 18 8 9 28 149 8261 0.0 3 32 6107 1934 188 150 79434 0.0 3 1740 73229 4221 244 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4273053 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: 27.9% C: 20.3% G: 29.4% T: 22.4% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 500847 384932.1 0 500847 4 173555 96233.0 0 173555 5 89831 24058.3 0 89831 6 77768 6014.6 0 77768 7 97549 1503.6 0 97549 8 84862 375.9 0 84862 9 83276 94.0 0 82993 283 10 82822 23.5 1 73254 9568 11 80040 5.9 1 70917 9123 12 79781 1.5 1 71140 8641 13 94880 0.4 1 85301 9579 14 90470 0.1 1 80987 9483 15 91778 0.0 1 82149 9629 16 83966 0.0 1 74963 9003 17 88158 0.0 1 79155 9003 18 78556 0.0 1 69250 9291 15 19 74051 0.0 1 64773 9144 134 20 79586 0.0 2 65408 10252 3926 21 74476 0.0 2 60863 9632 3981 22 75961 0.0 2 61854 9947 4160 23 79718 0.0 2 65222 10131 4365 24 76431 0.0 2 62806 9644 3981 25 82812 0.0 2 68304 10336 4172 26 85017 0.0 2 68597 11883 4537 27 80717 0.0 2 64784 11412 4515 6 28 82353 0.0 2 66021 11764 4549 19 29 69010 0.0 2 55218 9890 3842 60 30 66311 0.0 3 51688 9029 3540 2054 31 65391 0.0 3 50864 8955 3452 2120 32 61648 0.0 3 48053 8427 3198 1970 33 66374 0.0 3 51746 9167 3349 2112 34 65121 0.0 3 51150 8568 3297 2106 35 64276 0.0 3 50704 8283 3329 1960 36 66070 0.0 3 51920 8725 3308 2117 37 62576 0.0 3 49056 8427 3147 1946 38 54430 0.0 3 42963 7180 2673 1614 39 56907 0.0 3 45271 7124 2777 1735 40 51750 0.0 3 40669 6903 2613 1565 41 48202 0.0 3 38028 6308 2448 1418 42 44851 0.0 3 35479 5683 2338 1351 43 42205 0.0 3 33439 5385 2094 1287 44 41825 0.0 3 33230 5219 2112 1264 45 39966 0.0 3 31820 5093 1905 1148 46 39802 0.0 3 31937 4824 1869 1172 47 38076 0.0 3 30480 4649 1824 1123 48 37301 0.0 3 29925 4543 1701 1132 49 33677 0.0 3 26754 4343 1582 998 50 37422 0.0 3 30163 4565 1690 1004 51 30018 0.0 3 24284 3548 1385 801 52 30085 0.0 3 24383 3591 1339 772 53 29339 0.0 3 23897 3393 1283 766 54 28249 0.0 3 23019 3236 1252 742 55 27512 0.0 3 22528 3098 1193 693 56 22200 0.0 3 17951 2707 967 575 57 26163 0.0 3 21545 2963 1065 590 58 21120 0.0 3 17449 2357 842 472 59 20112 0.0 3 16541 2183 835 553 60 18467 0.0 3 15090 2137 772 468 61 13936 0.0 3 11346 1628 612 350 62 13980 0.0 3 11441 1575 625 339 63 13677 0.0 3 11229 1575 552 321 64 13395 0.0 3 11109 1479 510 297 65 11239 0.0 3 9282 1235 440 282 66 10653 0.0 3 8871 1084 435 263 67 10431 0.0 3 8593 1181 394 263 68 9163 0.0 3 7583 1006 383 191 69 7141 0.0 3 5928 752 288 173 70 6500 0.0 3 5357 682 281 180 71 5492 0.0 3 4504 583 257 148 72 4771 0.0 3 3856 519 237 159 73 5029 0.0 3 4103 572 226 128 74 4103 0.0 3 3347 491 154 111 75 4111 0.0 3 3423 425 150 113 76 3560 0.0 3 2894 413 141 112 77 3341 0.0 3 2736 364 145 96 78 2945 0.0 3 2377 333 139 96 79 2804 0.0 3 2281 308 133 82 80 2822 0.0 3 2278 316 145 83 81 2348 0.0 3 1899 251 119 79 82 2108 0.0 3 1698 259 92 59 83 1878 0.0 3 1510 209 110 49 84 1446 0.0 3 1122 188 76 60 85 1138 0.0 3 877 149 71 41 86 1238 0.0 3 953 160 74 51 87 1204 0.0 3 947 143 60 54 88 1174 0.0 3 903 142 65 64 89 1215 0.0 3 949 153 72 41 90 1108 0.0 3 858 126 64 60 91 1001 0.0 3 787 119 60 35 92 891 0.0 3 650 135 47 59 93 816 0.0 3 597 103 75 41 94 731 0.0 3 540 106 51 34 95 624 0.0 3 450 96 50 28 96 546 0.0 3 398 78 41 29 97 575 0.0 3 410 80 37 48 98 587 0.0 3 425 78 47 37 99 589 0.0 3 426 79 52 32 100 516 0.0 3 356 77 45 38 101 550 0.0 3 397 75 46 32 102 463 0.0 3 318 72 37 36 103 544 0.0 3 414 71 39 20 104 8430 0.0 3 7582 613 158 77 105 471 0.0 3 338 75 31 27 106 361 0.0 3 239 50 37 35 107 304 0.0 3 200 49 32 23 108 313 0.0 3 209 52 22 30 109 227 0.0 3 142 45 20 20 110 281 0.0 3 165 44 42 30 111 251 0.0 3 167 41 23 20 112 246 0.0 3 142 42 34 28 113 232 0.0 3 130 47 32 23 114 258 0.0 3 160 48 26 24 115 194 0.0 3 105 46 24 19 116 219 0.0 3 118 43 37 21 117 197 0.0 3 119 42 20 16 118 179 0.0 3 112 47 7 13 119 188 0.0 3 113 33 26 16 120 179 0.0 3 123 28 22 6 121 170 0.0 3 115 23 13 19 122 155 0.0 3 96 28 14 17 123 168 0.0 3 111 26 16 15 124 1382 0.0 3 1186 127 42 27 125 166 0.0 3 119 24 9 14 126 152 0.0 3 105 19 18 10 127 107 0.0 3 72 17 13 5 128 214 0.0 3 158 28 19 9 129 349 0.0 3 303 29 11 6 130 3503 0.0 3 3079 315 75 34 131 2733 0.0 3 1843 579 198 113 132 222 0.0 3 174 34 11 3 133 138 0.0 3 116 11 8 3 134 275 0.0 3 226 35 11 3 135 92 0.0 3 82 8 2 136 104 0.0 3 88 14 1 1 137 72 0.0 3 65 6 1 138 168 0.0 3 154 9 5 139 45 0.0 3 42 1 2 140 15 0.0 3 15 141 23 0.0 3 19 4 142 26 0.0 3 25 1 143 13 0.0 3 12 1 144 14 0.0 3 12 2 145 24 0.0 3 19 3 1 1 146 17 0.0 3 15 2 147 12 0.0 3 12 148 25 0.0 3 18 7 149 55 0.0 3 33 10 6 6 150 1984 0.0 3 1658 179 81 66