This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-14.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-14.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-14_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-14_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 206.081 s (6.959 µs/read; 8.62 M reads/minute). === Summary === Total read pairs processed: 29,614,948 Read 1 with adapter: 4,995,722 (16.9%) Read 2 with adapter: 5,054,191 (17.1%) == Read fate breakdown == Pairs that were too short: 86,418 (0.3%) Pairs written (passing filters): 29,528,530 (99.7%) Total basepairs processed: 8,884,484,400 bp Read 1: 4,442,242,200 bp Read 2: 4,442,242,200 bp Quality-trimmed: 1,217,523 bp (0.0%) Read 1: 570,438 bp Read 2: 647,085 bp Total written (filtered): 8,612,517,060 bp (96.9%) Read 1: 4,308,179,346 bp Read 2: 4,304,337,714 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4995722 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: 25.8% C: 20.6% G: 32.0% T: 20.2% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 3 664134 462733.6 0 664134 4 202225 115683.4 0 202225 5 105058 28920.8 0 105058 6 89043 7230.2 0 89043 7 99647 1807.6 0 99647 8 89162 451.9 0 89162 9 91291 113.0 0 90859 432 10 92335 28.2 1 81486 10849 11 92253 7.1 1 81453 10800 12 92234 1.8 1 81763 10471 13 101848 0.4 1 90842 11006 14 100584 0.1 1 88927 11657 15 102496 0.0 1 91102 11394 16 97301 0.0 1 86607 10694 17 95798 0.0 1 85498 10300 18 88660 0.0 1 78890 9741 29 19 82071 0.0 1 72203 9661 207 20 89149 0.0 2 74717 9781 4651 21 87906 0.0 2 73838 9706 4362 22 88496 0.0 2 74458 9578 4460 23 90508 0.0 2 76018 9951 4539 24 87415 0.0 2 73444 9508 4463 25 89407 0.0 2 75155 9749 4503 26 90183 0.0 2 76316 9544 4323 27 86717 0.0 2 73311 9185 4215 6 28 87987 0.0 2 74173 9541 4261 12 29 76810 0.0 2 64508 8432 3827 43 30 73860 0.0 3 60309 7755 3508 2288 31 76972 0.0 3 63191 7904 3488 2389 32 72723 0.0 3 59591 7526 3342 2264 33 75461 0.0 3 61976 7690 3435 2360 34 74958 0.0 3 61513 7842 3368 2235 35 71737 0.0 3 58839 7536 3191 2171 36 69356 0.0 3 57240 6980 3058 2078 37 68233 0.0 3 56276 7014 2939 2004 38 63545 0.0 3 52343 6544 2794 1864 39 62587 0.0 3 51770 6249 2727 1841 40 59394 0.0 3 49087 6085 2554 1668 41 56506 0.0 3 46694 5712 2470 1630 42 53034 0.0 3 43854 5384 2293 1503 43 50599 0.0 3 41408 5364 2242 1585 44 50162 0.0 3 41375 5246 2106 1435 45 48454 0.0 3 40167 4943 1986 1358 46 47291 0.0 3 39188 4814 1980 1309 47 44539 0.0 3 36790 4562 1954 1233 48 43900 0.0 3 36550 4343 1821 1186 49 40225 0.0 3 33393 4044 1663 1125 50 41721 0.0 3 34786 4138 1679 1118 51 35804 0.0 3 29940 3519 1462 883 52 34888 0.0 3 29241 3399 1368 880 53 34550 0.0 3 29060 3315 1315 860 54 31694 0.0 3 26621 3102 1231 740 55 31539 0.0 3 26448 3105 1222 764 56 27021 0.0 3 22745 2618 977 681 57 31081 0.0 3 26483 2746 1125 727 58 25582 0.0 3 21716 2319 953 594 59 23386 0.0 3 19711 2212 896 567 60 20843 0.0 3 17533 2046 753 511 61 17474 0.0 3 14662 1710 661 441 62 16142 0.0 3 13700 1515 558 369 63 15882 0.0 3 13468 1425 630 359 64 15414 0.0 3 13185 1350 550 329 65 13154 0.0 3 11156 1206 480 312 66 11987 0.0 3 10158 1107 428 294 67 12369 0.0 3 10475 1151 454 289 68 10732 0.0 3 9218 937 347 230 69 8837 0.0 3 7477 825 340 195 70 7841 0.0 3 6672 727 261 181 71 6752 0.0 3 5781 594 211 166 72 5996 0.0 3 5064 554 230 148 73 5532 0.0 3 4739 480 179 134 74 4888 0.0 3 4153 450 186 99 75 4873 0.0 3 4177 401 184 111 76 4114 0.0 3 3470 381 154 109 77 3946 0.0 3 3380 334 134 98 78 3490 0.0 3 2923 356 135 76 79 3473 0.0 3 2935 343 123 72 80 3161 0.0 3 2675 256 139 91 81 2788 0.0 3 2359 239 114 76 82 2519 0.0 3 2089 265 113 52 83 2194 0.0 3 1883 184 75 52 84 1784 0.0 3 1458 187 82 57 85 1407 0.0 3 1152 137 79 39 86 1410 0.0 3 1119 142 84 65 87 1395 0.0 3 1124 139 75 57 88 1284 0.0 3 1040 139 65 40 89 1399 0.0 3 1164 131 59 45 90 1365 0.0 3 1102 155 64 44 91 1181 0.0 3 968 123 51 39 92 1063 0.0 3 856 114 42 51 93 829 0.0 3 644 88 61 36 94 742 0.0 3 564 76 60 42 95 643 0.0 3 509 67 35 32 96 635 0.0 3 482 72 47 34 97 563 0.0 3 418 65 49 31 98 622 0.0 3 470 79 44 29 99 573 0.0 3 417 85 39 32 100 575 0.0 3 440 72 41 22 101 586 0.0 3 451 63 40 32 102 510 0.0 3 364 72 38 36 103 565 0.0 3 429 74 35 27 104 3740 0.0 3 3254 312 106 68 105 380 0.0 3 263 57 32 28 106 306 0.0 3 205 40 34 27 107 312 0.0 3 214 46 26 26 108 314 0.0 3 203 55 34 22 109 309 0.0 3 202 43 32 32 110 289 0.0 3 174 47 37 31 111 252 0.0 3 166 31 27 28 112 263 0.0 3 170 35 39 19 113 225 0.0 3 145 33 24 23 114 259 0.0 3 163 55 19 22 115 210 0.0 3 135 40 20 15 116 244 0.0 3 170 34 21 19 117 178 0.0 3 117 25 20 16 118 219 0.0 3 143 33 29 14 119 177 0.0 3 117 25 21 14 120 206 0.0 3 117 44 23 22 121 161 0.0 3 100 33 15 13 122 194 0.0 3 121 33 22 18 123 158 0.0 3 95 32 18 13 124 2144 0.0 3 1967 123 33 21 125 187 0.0 3 134 26 17 10 126 137 0.0 3 103 17 9 8 127 119 0.0 3 83 15 13 8 128 198 0.0 3 158 26 8 6 129 470 0.0 3 415 35 12 8 130 251 0.0 3 221 19 8 3 131 2055 0.0 3 1883 126 27 19 132 172 0.0 3 136 25 5 6 133 131 0.0 3 107 12 9 3 134 229 0.0 3 199 17 12 1 135 80 0.0 3 72 5 3 136 68 0.0 3 55 9 3 1 137 73 0.0 3 67 3 2 1 138 138 0.0 3 125 8 3 2 139 30 0.0 3 25 2 1 2 140 31 0.0 3 29 0 0 2 141 35 0.0 3 30 3 0 2 142 44 0.0 3 39 1 1 3 143 20 0.0 3 20 144 12 0.0 3 11 1 145 16 0.0 3 14 0 1 1 146 22 0.0 3 19 2 0 1 147 31 0.0 3 26 4 0 1 148 84 0.0 3 33 16 8 27 149 7744 0.0 3 14 5916 1670 144 150 67753 0.0 3 2262 61336 3837 318 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 5054191 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: 25.9% C: 21.2% G: 31.8% T: 21.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 642147 462733.6 0 642147 4 211784 115683.4 0 211784 5 109711 28920.8 0 109711 6 93992 7230.2 0 93992 7 104918 1807.6 0 104918 8 95141 451.9 0 95141 9 95798 113.0 0 95351 447 10 97051 28.2 1 85233 11818 11 96448 7.1 1 84601 11847 12 96200 1.8 1 85244 10956 13 106808 0.4 1 95442 11366 14 105780 0.1 1 93991 11789 15 107619 0.0 1 95313 12306 16 100872 0.0 1 89421 11451 17 99932 0.0 1 88757 11175 18 91293 0.0 1 79577 11703 13 19 86701 0.0 1 74711 11774 216 20 93067 0.0 2 74755 13146 5166 21 90502 0.0 2 72547 12436 5519 22 90767 0.0 2 72183 12899 5685 23 92277 0.0 2 74105 12798 5374 24 89289 0.0 2 71958 12163 5168 25 92159 0.0 2 74552 12382 5225 26 93299 0.0 2 73663 14052 5584 27 88989 0.0 2 70266 13286 5436 1 28 90332 0.0 2 71362 13553 5401 16 29 78591 0.0 2 61838 11946 4751 56 30 75865 0.0 3 57727 10985 4509 2644 31 79399 0.0 3 60506 11395 4667 2831 32 74833 0.0 3 56971 10950 4315 2597 33 77791 0.0 3 59474 11161 4419 2737 34 77081 0.0 3 59439 10812 4277 2553 35 74122 0.0 3 57220 10097 4191 2614 36 71456 0.0 3 55069 10117 3804 2466 37 70334 0.0 3 54128 9956 3963 2287 38 65341 0.0 3 50728 8912 3568 2133 39 64308 0.0 3 50258 8559 3430 2061 40 60926 0.0 3 47018 8509 3325 2074 41 58198 0.0 3 45225 8009 3080 1884 42 54391 0.0 3 42173 7397 2995 1826 43 51845 0.0 3 40290 7075 2752 1728 44 51478 0.0 3 40139 6791 2795 1753 45 49823 0.0 3 38851 6743 2630 1599 46 48268 0.0 3 38071 6220 2462 1515 47 45653 0.0 3 35911 5965 2325 1452 48 44666 0.0 3 35284 5771 2270 1341 49 41120 0.0 3 32133 5549 2151 1287 50 42796 0.0 3 33775 5536 2150 1335 51 36844 0.0 3 29137 4844 1766 1097 52 35530 0.0 3 28421 4423 1692 994 53 35312 0.0 3 28372 4370 1640 930 54 32511 0.0 3 26087 3965 1522 937 55 32276 0.0 3 25950 3953 1467 906 56 27780 0.0 3 22347 3309 1313 811 57 31724 0.0 3 25873 3650 1347 854 58 26238 0.0 3 21332 3056 1125 725 59 23829 0.0 3 19371 2727 1091 640 60 21323 0.0 3 17231 2612 909 571 61 17896 0.0 3 14343 2150 873 530 62 16447 0.0 3 13276 1966 760 445 63 16277 0.0 3 13232 1921 673 451 64 15774 0.0 3 12913 1814 684 363 65 13502 0.0 3 11038 1507 603 354 66 12318 0.0 3 10052 1429 536 301 67 12723 0.0 3 10345 1502 571 305 68 11009 0.0 3 8888 1329 463 329 69 9112 0.0 3 7351 1078 417 266 70 8050 0.0 3 6513 928 374 235 71 7015 0.0 3 5675 827 307 206 72 6170 0.0 3 4966 691 304 209 73 5753 0.0 3 4640 675 267 171 74 5115 0.0 3 4125 601 230 159 75 5038 0.0 3 4104 546 242 146 76 4301 0.0 3 3437 535 201 128 77 4138 0.0 3 3321 482 207 128 78 3665 0.0 3 2864 455 223 123 79 3649 0.0 3 2915 415 201 118 80 3363 0.0 3 2646 461 155 101 81 2955 0.0 3 2311 396 152 96 82 2662 0.0 3 2112 326 145 79 83 2323 0.0 3 1881 248 116 78 84 1921 0.0 3 1482 237 122 80 85 1570 0.0 3 1188 205 99 78 86 1566 0.0 3 1133 216 119 98 87 1493 0.0 3 1152 198 81 62 88 1418 0.0 3 1064 191 88 75 89 1536 0.0 3 1156 211 97 72 90 1502 0.0 3 1103 222 98 79 91 1318 0.0 3 999 172 74 73 92 1181 0.0 3 900 158 77 46 93 959 0.0 3 658 152 73 76 94 874 0.0 3 612 132 73 57 95 763 0.0 3 547 103 58 55 96 765 0.0 3 532 119 68 46 97 693 0.0 3 470 119 59 45 98 765 0.0 3 515 115 61 74 99 696 0.0 3 459 117 61 59 100 721 0.0 3 479 105 73 64 101 679 0.0 3 471 103 54 51 102 645 0.0 3 419 107 64 55 103 673 0.0 3 460 95 55 63 104 3893 0.0 3 3329 330 135 99 105 463 0.0 3 274 89 55 45 106 405 0.0 3 226 73 69 37 107 391 0.0 3 256 70 40 25 108 372 0.0 3 222 72 42 36 109 390 0.0 3 236 71 43 40 110 356 0.0 3 198 78 48 32 111 322 0.0 3 195 58 37 32 112 315 0.0 3 175 58 44 38 113 289 0.0 3 156 63 38 32 114 320 0.0 3 175 70 37 38 115 283 0.0 3 157 58 37 31 116 303 0.0 3 184 52 34 33 117 235 0.0 3 118 56 27 34 118 288 0.0 3 152 64 34 38 119 224 0.0 3 121 60 24 19 120 241 0.0 3 147 44 22 28 121 206 0.0 3 117 42 29 18 122 240 0.0 3 129 44 40 27 123 185 0.0 3 113 40 18 14 124 2146 0.0 3 1900 155 49 42 125 205 0.0 3 139 27 20 19 126 164 0.0 3 108 31 12 13 127 145 0.0 3 78 31 16 20 128 214 0.0 3 164 30 16 4 129 472 0.0 3 374 63 29 6 130 245 0.0 3 188 42 9 6 131 1714 0.0 3 1197 344 106 67 132 139 0.0 3 109 22 2 6 133 118 0.0 3 100 13 4 1 134 220 0.0 3 179 29 6 6 135 79 0.0 3 68 6 3 2 136 59 0.0 3 48 6 4 1 137 67 0.0 3 57 7 3 138 132 0.0 3 121 10 1 139 28 0.0 3 21 7 140 29 0.0 3 24 4 1 141 33 0.0 3 30 3 142 40 0.0 3 35 5 143 21 0.0 3 19 2 144 11 0.0 3 9 2 145 15 0.0 3 13 1 0 1 146 21 0.0 3 21 147 29 0.0 3 25 4 148 35 0.0 3 31 4 149 41 0.0 3 15 14 8 4 150 2527 0.0 3 2165 215 89 58