This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH10-11.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH10-11.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH10-11_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH10-11_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 167.866 s (6.348 µs/read; 9.45 M reads/minute). === Summary === Total read pairs processed: 26,445,444 Read 1 with adapter: 4,903,114 (18.5%) Read 2 with adapter: 4,906,032 (18.6%) == Read fate breakdown == Pairs that were too short: 137,363 (0.5%) Pairs written (passing filters): 26,308,081 (99.5%) Total basepairs processed: 7,933,633,200 bp Read 1: 3,966,816,600 bp Read 2: 3,966,816,600 bp Quality-trimmed: 1,014,309 bp (0.0%) Read 1: 475,381 bp Read 2: 538,928 bp Total written (filtered): 7,650,612,631 bp (96.4%) Read 1: 3,827,138,596 bp Read 2: 3,823,474,035 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4903114 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: 20.5% G: 29.4% T: 20.4% none/other: 2.4% Overview of removed sequences length count expect max.err error counts 3 585904 413210.1 0 585904 4 175990 103302.5 0 175990 5 100043 25825.6 0 100043 6 88128 6456.4 0 88128 7 96969 1614.1 0 96969 8 85776 403.5 0 85776 9 90583 100.9 0 90142 441 10 89405 25.2 1 78161 11244 11 89636 6.3 1 78814 10822 12 90119 1.6 1 79661 10458 13 105946 0.4 1 94065 11881 14 103497 0.1 1 91372 12125 15 110114 0.0 1 97624 12490 16 104741 0.0 1 93074 11667 17 98599 0.0 1 87461 11138 18 90927 0.0 1 80377 10515 35 19 81186 0.0 1 70992 10035 159 20 90796 0.0 2 75601 10068 5127 21 85417 0.0 2 71359 9528 4530 22 84510 0.0 2 70555 9293 4662 23 88814 0.0 2 74386 9680 4748 24 87910 0.0 2 73516 9632 4762 25 92375 0.0 2 77209 10355 4811 26 91020 0.0 2 76731 9726 4563 27 89870 0.0 2 76044 9509 4304 13 28 87123 0.0 2 73196 9474 4436 17 29 75455 0.0 2 63014 8518 3874 49 30 72160 0.0 3 58595 7735 3461 2369 31 72521 0.0 3 58824 7866 3472 2359 32 71418 0.0 3 58064 7700 3331 2323 33 76406 0.0 3 62261 8081 3580 2484 34 74815 0.0 3 61110 7914 3439 2352 35 68865 0.0 3 55769 7474 3374 2248 36 66708 0.0 3 54566 6969 3056 2117 37 67844 0.0 3 55392 7163 3105 2184 38 62330 0.0 3 50876 6500 2937 2017 39 62368 0.0 3 51149 6417 2856 1946 40 55394 0.0 3 45390 5850 2427 1727 41 52890 0.0 3 43083 5662 2474 1671 42 49195 0.0 3 40220 5197 2207 1571 43 48095 0.0 3 39227 5019 2282 1567 44 48467 0.0 3 39786 5013 2188 1480 45 46778 0.0 3 38334 4947 2083 1414 46 45710 0.0 3 37577 4857 1937 1339 47 42620 0.0 3 34891 4490 1927 1312 48 42214 0.0 3 34798 4358 1815 1243 49 38139 0.0 3 31427 3932 1645 1135 50 40479 0.0 3 33365 4223 1706 1185 51 34256 0.0 3 28386 3481 1427 962 52 32552 0.0 3 26898 3322 1378 954 53 33214 0.0 3 27731 3282 1325 876 54 31170 0.0 3 26036 2958 1298 878 55 30367 0.0 3 25379 2942 1223 823 56 27166 0.0 3 22704 2660 1061 741 57 30836 0.0 3 26041 2863 1170 762 58 25327 0.0 3 21191 2486 965 685 59 24781 0.0 3 20869 2338 945 629 60 20857 0.0 3 17431 2006 876 544 61 17349 0.0 3 14551 1610 705 483 62 15652 0.0 3 13091 1516 654 391 63 15810 0.0 3 13324 1531 570 385 64 15650 0.0 3 13218 1520 542 370 65 13297 0.0 3 11201 1218 548 330 66 12580 0.0 3 10610 1186 476 308 67 13162 0.0 3 11147 1194 497 324 68 10961 0.0 3 9266 1042 388 265 69 9013 0.0 3 7568 870 344 231 70 7671 0.0 3 6382 744 310 235 71 7419 0.0 3 6227 706 277 209 72 6071 0.0 3 5143 541 216 171 73 5820 0.0 3 4902 526 216 176 74 5118 0.0 3 4354 455 171 138 75 4931 0.0 3 4150 475 180 126 76 4145 0.0 3 3479 398 144 124 77 4013 0.0 3 3349 381 164 119 78 3600 0.0 3 3027 339 132 102 79 3389 0.0 3 2840 325 137 87 80 3065 0.0 3 2578 301 115 71 81 2696 0.0 3 2243 275 108 70 82 2187 0.0 3 1801 211 104 71 83 2313 0.0 3 1963 205 83 62 84 1833 0.0 3 1485 192 92 64 85 1436 0.0 3 1159 149 67 61 86 1505 0.0 3 1248 141 55 61 87 1401 0.0 3 1172 115 68 46 88 1322 0.0 3 1062 144 59 57 89 1360 0.0 3 1135 120 58 47 90 1114 0.0 3 902 108 63 41 91 1100 0.0 3 888 110 62 40 92 955 0.0 3 779 88 49 39 93 883 0.0 3 740 75 34 34 94 775 0.0 3 604 92 41 38 95 697 0.0 3 549 76 45 27 96 663 0.0 3 509 72 48 34 97 622 0.0 3 482 71 38 31 98 601 0.0 3 456 63 45 37 99 553 0.0 3 448 47 33 25 100 600 0.0 3 460 71 33 36 101 527 0.0 3 397 60 33 37 102 452 0.0 3 349 47 25 31 103 593 0.0 3 467 63 40 23 104 3267 0.0 3 2879 254 79 55 105 369 0.0 3 272 54 25 18 106 334 0.0 3 247 35 20 32 107 291 0.0 3 218 24 26 23 108 353 0.0 3 242 59 30 22 109 279 0.0 3 191 36 27 25 110 284 0.0 3 183 42 42 17 111 226 0.0 3 150 38 19 19 112 238 0.0 3 166 35 10 27 113 226 0.0 3 157 26 25 18 114 269 0.0 3 182 39 26 22 115 216 0.0 3 139 41 19 17 116 210 0.0 3 141 38 13 18 117 174 0.0 3 114 30 13 17 118 210 0.0 3 138 35 19 18 119 179 0.0 3 110 28 24 17 120 212 0.0 3 133 44 15 20 121 166 0.0 3 112 21 23 10 122 165 0.0 3 110 22 19 14 123 138 0.0 3 95 21 11 11 124 560 0.0 3 468 55 16 21 125 106 0.0 3 64 16 16 10 126 136 0.0 3 97 19 9 11 127 98 0.0 3 65 14 12 7 128 169 0.0 3 137 21 6 5 129 452 0.0 3 407 31 7 7 130 336 0.0 3 295 24 12 5 131 1938 0.0 3 1801 115 18 4 132 232 0.0 3 185 38 7 2 133 258 0.0 3 235 15 6 2 134 359 0.0 3 322 27 4 6 135 100 0.0 3 94 4 1 1 136 135 0.0 3 122 8 4 1 137 102 0.0 3 88 7 4 3 138 159 0.0 3 143 14 1 1 139 59 0.0 3 55 4 140 75 0.0 3 69 2 1 3 141 49 0.0 3 41 6 0 2 142 49 0.0 3 45 2 1 1 143 30 0.0 3 22 6 2 144 16 0.0 3 15 1 145 26 0.0 3 23 3 146 50 0.0 3 45 3 1 1 147 37 0.0 3 24 0 8 5 148 96 0.0 3 25 11 19 41 149 10834 0.0 3 32 7648 2886 268 150 117148 0.0 3 4540 105815 6388 405 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4906032 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: 21.1% G: 29.4% T: 21.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 559969 413210.1 0 559969 4 184251 103302.5 0 184251 5 104043 25825.6 0 104043 6 93353 6456.4 0 93353 7 101808 1614.1 0 101808 8 91474 403.5 0 91474 9 95658 100.9 0 95292 366 10 94010 25.2 1 83190 10820 11 94006 6.3 1 83118 10888 12 94093 1.6 1 83577 10516 13 111479 0.4 1 99985 11494 14 108706 0.1 1 97139 11567 15 116012 0.0 1 103544 12468 16 109094 0.0 1 97134 11960 17 103061 0.0 1 91928 11133 18 93474 0.0 1 81810 11648 16 19 85743 0.0 1 74003 11533 207 20 94816 0.0 2 76465 12936 5415 21 87737 0.0 2 70382 11956 5399 22 86466 0.0 2 68982 12248 5236 23 90816 0.0 2 72731 12483 5602 24 89942 0.0 2 72382 12192 5368 25 95285 0.0 2 77004 12731 5550 26 94359 0.0 2 75262 13495 5602 27 92647 0.0 2 73983 13069 5584 11 28 89655 0.0 2 71791 12512 5335 17 29 77310 0.0 2 60995 11434 4816 65 30 74314 0.0 3 56824 10388 4290 2812 31 75287 0.0 3 57384 10537 4346 3020 32 73560 0.0 3 56562 10175 4220 2603 33 78728 0.0 3 60650 10956 4386 2736 34 76823 0.0 3 59609 10233 4181 2800 35 71175 0.0 3 55173 9471 3950 2581 36 68691 0.0 3 53275 9190 3750 2476 37 69740 0.0 3 54112 9460 3743 2425 38 64016 0.0 3 49934 8309 3461 2312 39 64222 0.0 3 50119 8343 3542 2218 40 56781 0.0 3 44051 7585 3111 2034 41 54324 0.0 3 42380 7259 2887 1798 42 50537 0.0 3 39227 6551 2935 1824 43 49360 0.0 3 38320 6594 2720 1726 44 49668 0.0 3 38786 6444 2691 1747 45 47989 0.0 3 37594 6278 2539 1578 46 46944 0.0 3 36932 5975 2483 1554 47 43499 0.0 3 34132 5540 2384 1443 48 42999 0.0 3 33768 5378 2361 1492 49 39031 0.0 3 30499 5133 2091 1308 50 41215 0.0 3 32599 5232 2124 1260 51 35275 0.0 3 28021 4507 1663 1084 52 33235 0.0 3 26581 4084 1567 1003 53 33994 0.0 3 27360 4058 1557 1019 54 31956 0.0 3 25844 3705 1491 916 55 31048 0.0 3 25057 3636 1494 861 56 27909 0.0 3 22295 3396 1354 864 57 31510 0.0 3 25842 3484 1363 821 58 25954 0.0 3 21017 2983 1181 773 59 25041 0.0 3 20254 2834 1207 746 60 21352 0.0 3 17199 2566 958 629 61 17761 0.0 3 14242 2074 909 536 62 15913 0.0 3 12744 1926 746 497 63 16130 0.0 3 12983 1924 741 482 64 15965 0.0 3 13038 1734 706 487 65 13629 0.0 3 11027 1579 585 438 66 12925 0.0 3 10461 1499 589 376 67 13466 0.0 3 11018 1506 577 365 68 11232 0.0 3 9086 1328 494 324 69 9254 0.0 3 7506 1047 460 241 70 7856 0.0 3 6317 896 386 257 71 7579 0.0 3 6021 927 372 259 72 6307 0.0 3 5066 710 317 214 73 6035 0.0 3 4802 739 287 207 74 5268 0.0 3 4235 614 255 164 75 5032 0.0 3 4050 582 257 143 76 4309 0.0 3 3457 492 204 156 77 4111 0.0 3 3276 491 201 143 78 3730 0.0 3 2981 438 176 135 79 3518 0.0 3 2789 438 181 110 80 3188 0.0 3 2525 385 167 111 81 2828 0.0 3 2243 341 137 107 82 2313 0.0 3 1794 312 129 78 83 2418 0.0 3 1924 265 137 92 84 1938 0.0 3 1492 240 112 94 85 1518 0.0 3 1148 207 89 74 86 1642 0.0 3 1271 206 93 72 87 1524 0.0 3 1179 179 94 72 88 1428 0.0 3 1089 174 89 76 89 1478 0.0 3 1143 173 101 61 90 1186 0.0 3 903 160 60 63 91 1203 0.0 3 903 142 92 66 92 1033 0.0 3 788 124 78 43 93 959 0.0 3 728 112 59 60 94 872 0.0 3 641 122 70 39 95 784 0.0 3 573 106 56 49 96 732 0.0 3 519 97 64 52 97 710 0.0 3 507 90 63 50 98 693 0.0 3 501 92 55 45 99 630 0.0 3 454 89 41 46 100 696 0.0 3 492 104 54 46 101 580 0.0 3 413 87 37 43 102 521 0.0 3 362 84 41 34 103 667 0.0 3 500 87 51 29 104 3387 0.0 3 2923 294 105 65 105 446 0.0 3 287 70 50 39 106 391 0.0 3 256 71 38 26 107 367 0.0 3 232 50 45 40 108 416 0.0 3 255 75 49 37 109 342 0.0 3 214 54 49 25 110 335 0.0 3 208 58 34 35 111 277 0.0 3 161 58 30 28 112 293 0.0 3 178 55 35 25 113 288 0.0 3 150 73 41 24 114 309 0.0 3 181 67 31 30 115 266 0.0 3 159 53 34 20 116 260 0.0 3 137 60 31 32 117 211 0.0 3 115 44 29 23 118 249 0.0 3 141 55 28 25 119 205 0.0 3 126 36 27 16 120 258 0.0 3 155 41 40 22 121 196 0.0 3 127 33 16 20 122 186 0.0 3 107 31 27 21 123 164 0.0 3 90 39 20 15 124 567 0.0 3 431 85 24 27 125 120 0.0 3 71 18 17 14 126 150 0.0 3 86 38 14 12 127 105 0.0 3 72 15 10 8 128 174 0.0 3 136 21 10 7 129 455 0.0 3 357 72 20 6 130 322 0.0 3 248 52 15 7 131 1689 0.0 3 1241 307 99 42 132 183 0.0 3 135 35 3 10 133 220 0.0 3 181 32 5 2 134 333 0.0 3 290 30 10 3 135 98 0.0 3 85 9 3 1 136 130 0.0 3 104 18 7 1 137 97 0.0 3 87 3 4 3 138 152 0.0 3 134 15 2 1 139 59 0.0 3 49 6 3 1 140 72 0.0 3 62 8 2 141 44 0.0 3 40 4 142 46 0.0 3 39 6 1 143 25 0.0 3 22 3 144 16 0.0 3 15 1 145 25 0.0 3 21 3 0 1 146 49 0.0 3 43 6 147 25 0.0 3 20 4 0 1 148 26 0.0 3 18 6 2 149 72 0.0 3 31 23 9 9 150 4927 0.0 3 4396 367 95 69