This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-11.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-11.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-11_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-11_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 244.588 s (6.485 µs/read; 9.25 M reads/minute). === Summary === Total read pairs processed: 37,715,877 Read 1 with adapter: 7,595,547 (20.1%) Read 2 with adapter: 7,659,849 (20.3%) == Read fate breakdown == Pairs that were too short: 149,909 (0.4%) Pairs written (passing filters): 37,565,968 (99.6%) Total basepairs processed: 11,314,763,100 bp Read 1: 5,657,381,550 bp Read 2: 5,657,381,550 bp Quality-trimmed: 1,476,965 bp (0.0%) Read 1: 711,222 bp Read 2: 765,743 bp Total written (filtered): 10,897,418,635 bp (96.3%) Read 1: 5,451,787,794 bp Read 2: 5,445,630,841 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 7595547 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: 26.4% C: 20.8% G: 31.1% T: 20.0% none/other: 1.7% Overview of removed sequences length count expect max.err error counts 3 855278 589310.6 0 855278 4 278293 147327.6 0 278293 5 168122 36831.9 0 168122 6 147978 9208.0 0 147978 7 159353 2302.0 0 159353 8 145800 575.5 0 145800 9 149475 143.9 0 148733 742 10 150662 36.0 1 132161 18501 11 150522 9.0 1 132369 18153 12 150833 2.2 1 133409 17424 13 169869 0.6 1 151007 18862 14 165486 0.1 1 146288 19198 15 172641 0.0 1 153311 19330 16 161842 0.0 1 144259 17583 17 157812 0.0 1 140778 17034 18 145506 0.0 1 129473 15991 42 19 136800 0.0 1 120601 15838 361 20 145905 0.0 2 122667 15423 7815 21 138752 0.0 2 116949 14584 7219 22 137323 0.0 2 116066 14159 7098 23 144490 0.0 2 122412 14918 7160 24 141447 0.0 2 119393 14954 7100 25 144960 0.0 2 122338 15380 7242 26 144423 0.0 2 122420 14848 7155 27 139068 0.0 2 117964 14342 6749 13 28 134257 0.0 2 113787 13956 6491 23 29 118464 0.0 2 99574 12965 5870 55 30 116260 0.0 3 95037 11933 5418 3872 31 115154 0.0 3 94337 11818 5232 3767 32 113410 0.0 3 92746 11773 5277 3614 33 116395 0.0 3 95299 11900 5348 3848 34 114045 0.0 3 93721 11720 5102 3502 35 108440 0.0 3 89005 11113 4931 3391 36 105804 0.0 3 87310 10507 4698 3289 37 105459 0.0 3 86984 10540 4722 3213 38 97037 0.0 3 80022 9646 4340 3029 39 93327 0.0 3 77365 9136 4013 2813 40 87317 0.0 3 72207 8655 3735 2720 41 83743 0.0 3 69220 8338 3672 2513 42 77248 0.0 3 63973 7565 3482 2228 43 74434 0.0 3 61250 7504 3335 2345 44 76109 0.0 3 63219 7446 3186 2258 45 72898 0.0 3 60675 7142 2925 2156 46 71386 0.0 3 59526 6913 2935 2012 47 68202 0.0 3 56718 6676 2854 1954 48 64396 0.0 3 53648 6270 2648 1830 49 58019 0.0 3 48488 5490 2426 1615 50 59669 0.0 3 50151 5496 2456 1566 51 51320 0.0 3 42958 4779 2150 1433 52 49091 0.0 3 41360 4601 1905 1225 53 48587 0.0 3 41007 4503 1886 1191 54 45083 0.0 3 37944 4230 1750 1159 55 43409 0.0 3 36732 3975 1601 1101 56 39408 0.0 3 33158 3620 1561 1069 57 44051 0.0 3 37643 3862 1532 1014 58 35810 0.0 3 30465 3191 1308 846 59 33239 0.0 3 28052 3230 1161 796 60 27633 0.0 3 23425 2493 1045 670 61 23980 0.0 3 20334 2203 868 575 62 22536 0.0 3 19089 2047 820 580 63 21415 0.0 3 18277 1840 806 492 64 20767 0.0 3 17653 1858 757 499 65 18291 0.0 3 15692 1549 624 426 66 17543 0.0 3 15018 1529 576 420 67 16757 0.0 3 14423 1425 553 356 68 14385 0.0 3 12437 1123 480 345 69 12299 0.0 3 10548 1060 402 289 70 10732 0.0 3 9246 840 368 278 71 9384 0.0 3 8004 815 327 238 72 8047 0.0 3 6838 722 310 177 73 7868 0.0 3 6728 687 270 183 74 6832 0.0 3 5871 564 223 174 75 6573 0.0 3 5665 524 222 162 76 5921 0.0 3 5090 506 209 116 77 5734 0.0 3 4941 455 193 145 78 5102 0.0 3 4347 460 172 123 79 4731 0.0 3 4051 402 164 114 80 4327 0.0 3 3737 362 128 100 81 3665 0.0 3 3144 290 142 89 82 3170 0.0 3 2695 264 126 85 83 3114 0.0 3 2654 273 117 70 84 2232 0.0 3 1885 189 88 70 85 1998 0.0 3 1690 171 75 62 86 1908 0.0 3 1609 165 84 50 87 1838 0.0 3 1570 148 80 40 88 1845 0.0 3 1556 153 63 73 89 1866 0.0 3 1578 153 78 57 90 1692 0.0 3 1434 145 63 50 91 1579 0.0 3 1338 141 59 41 92 1306 0.0 3 1116 107 47 36 93 1095 0.0 3 891 97 50 57 94 903 0.0 3 738 84 48 33 95 858 0.0 3 686 81 51 40 96 694 0.0 3 542 70 43 39 97 704 0.0 3 574 57 41 32 98 810 0.0 3 658 78 39 35 99 701 0.0 3 561 73 34 33 100 685 0.0 3 535 72 42 36 101 619 0.0 3 454 83 38 44 102 599 0.0 3 458 79 38 24 103 629 0.0 3 500 64 34 31 104 14798 0.0 3 13843 702 156 97 105 585 0.0 3 474 57 24 30 106 417 0.0 3 307 49 27 34 107 376 0.0 3 274 50 27 25 108 396 0.0 3 302 39 25 30 109 331 0.0 3 227 54 27 23 110 324 0.0 3 220 43 27 34 111 269 0.0 3 192 30 17 30 112 269 0.0 3 186 37 29 17 113 261 0.0 3 185 42 16 18 114 282 0.0 3 196 44 26 16 115 186 0.0 3 124 29 19 14 116 215 0.0 3 149 25 18 23 117 180 0.0 3 122 24 17 17 118 219 0.0 3 154 29 19 17 119 194 0.0 3 127 26 20 21 120 184 0.0 3 127 29 17 11 121 189 0.0 3 118 25 19 27 122 174 0.0 3 96 29 20 29 123 127 0.0 3 85 23 11 8 124 462 0.0 3 386 41 22 13 125 119 0.0 3 79 12 17 11 126 136 0.0 3 99 19 13 5 127 98 0.0 3 76 9 7 6 128 141 0.0 3 94 28 5 14 129 114 0.0 3 95 9 6 4 130 446 0.0 3 373 53 13 7 131 2665 0.0 3 2439 160 45 21 132 191 0.0 3 156 28 5 2 133 90 0.0 3 81 6 2 1 134 218 0.0 3 191 18 8 1 135 86 0.0 3 79 3 2 2 136 66 0.0 3 59 3 2 2 137 49 0.0 3 46 2 1 138 143 0.0 3 133 9 0 1 139 28 0.0 3 25 2 1 140 32 0.0 3 24 3 3 2 141 56 0.0 3 44 7 5 142 37 0.0 3 31 6 143 33 0.0 3 30 1 1 1 144 11 0.0 3 10 0 0 1 145 17 0.0 3 12 0 2 3 146 39 0.0 3 35 2 1 1 147 20 0.0 3 13 1 4 2 148 100 0.0 3 29 19 4 48 149 13312 0.0 3 39 9917 3107 249 150 127384 0.0 3 3751 117055 6240 338 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 7659849 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: 26.6% C: 21.5% G: 30.5% T: 21.4% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 819586 589310.6 0 819586 4 286195 147327.6 0 286195 5 171219 36831.9 0 171219 6 153463 9208.0 0 153463 7 164641 2302.0 0 164641 8 153341 575.5 0 153341 9 157027 143.9 0 156450 577 10 157575 36.0 1 138948 18627 11 156589 9.0 1 138123 18466 12 156867 2.2 1 139661 17206 13 177120 0.6 1 158629 18491 14 172046 0.1 1 153446 18600 15 179795 0.0 1 160332 19463 16 167110 0.0 1 148854 18256 17 163138 0.0 1 145543 17595 18 151133 0.0 1 134590 16523 20 19 144856 0.0 1 128230 16281 345 20 153819 0.0 2 130640 16153 7026 21 144395 0.0 2 122355 14964 7076 22 141835 0.0 2 119064 15328 7443 23 148855 0.0 2 124492 16596 7767 24 145298 0.0 2 121324 16260 7714 25 150540 0.0 2 126223 16735 7582 26 150361 0.0 2 122604 19789 7968 27 144652 0.0 2 116632 20020 7995 5 28 139284 0.0 2 112055 19602 7613 14 29 122418 0.0 2 98527 17017 6754 120 30 119967 0.0 3 93877 15479 6411 4200 31 119338 0.0 3 93418 15417 6335 4168 32 117198 0.0 3 91926 15154 6074 4044 33 120296 0.0 3 94036 15664 6296 4300 34 117825 0.0 3 92269 15312 6204 4040 35 112546 0.0 3 88305 14571 5910 3760 36 109770 0.0 3 86188 14077 5749 3756 37 109400 0.0 3 86485 13724 5546 3645 38 100407 0.0 3 79529 12336 5222 3320 39 96453 0.0 3 77009 11420 4867 3157 40 90030 0.0 3 71732 10932 4400 2966 41 86517 0.0 3 69463 10215 4178 2661 42 79563 0.0 3 63785 9238 3941 2599 43 77039 0.0 3 61883 8885 3793 2478 44 78525 0.0 3 63185 9078 3839 2423 45 75315 0.0 3 60502 8750 3673 2390 46 73596 0.0 3 59617 8290 3416 2273 47 70230 0.0 3 56709 8104 3229 2188 48 66063 0.0 3 53485 7559 3068 1951 49 59826 0.0 3 48137 6911 2836 1942 50 61177 0.0 3 49720 6955 2793 1709 51 52619 0.0 3 43051 5785 2304 1479 52 50404 0.0 3 41347 5436 2173 1448 53 49830 0.0 3 40893 5447 2172 1318 54 46289 0.0 3 37999 5043 1987 1260 55 44644 0.0 3 36666 4906 1875 1197 56 40359 0.0 3 33127 4346 1742 1144 57 45024 0.0 3 37442 4684 1785 1113 58 36830 0.0 3 30532 3854 1466 978 59 33924 0.0 3 28097 3429 1468 930 60 28291 0.0 3 23330 2975 1189 797 61 24697 0.0 3 20359 2587 1045 706 62 23031 0.0 3 18962 2381 1028 660 63 22029 0.0 3 18388 2208 851 582 64 21272 0.0 3 17729 2116 876 551 65 18817 0.0 3 15778 1851 733 455 66 18041 0.0 3 15126 1769 691 455 67 17216 0.0 3 14355 1710 701 450 68 14836 0.0 3 12466 1406 597 367 69 12665 0.0 3 10571 1281 498 315 70 11055 0.0 3 9146 1106 476 327 71 9653 0.0 3 8086 885 414 268 72 8217 0.0 3 6839 835 343 200 73 8185 0.0 3 6807 766 375 237 74 7026 0.0 3 5898 667 275 186 75 6748 0.0 3 5640 628 286 194 76 6115 0.0 3 5100 610 244 161 77 5974 0.0 3 4922 614 261 177 78 5317 0.0 3 4385 529 256 147 79 4935 0.0 3 4043 519 210 163 80 4514 0.0 3 3762 411 202 139 81 3824 0.0 3 3173 387 168 96 82 3335 0.0 3 2747 334 146 108 83 3268 0.0 3 2701 309 136 122 84 2362 0.0 3 1911 234 127 90 85 2160 0.0 3 1749 223 80 108 86 2062 0.0 3 1673 209 99 81 87 1982 0.0 3 1602 192 111 77 88 1955 0.0 3 1534 215 113 93 89 2022 0.0 3 1632 225 84 81 90 1840 0.0 3 1464 198 86 92 91 1727 0.0 3 1383 180 91 73 92 1450 0.0 3 1139 173 83 55 93 1221 0.0 3 926 165 65 65 94 1037 0.0 3 765 132 80 60 95 966 0.0 3 719 125 68 54 96 802 0.0 3 597 85 62 58 97 779 0.0 3 584 102 58 35 98 908 0.0 3 671 117 64 56 99 788 0.0 3 602 93 53 40 100 791 0.0 3 558 118 74 41 101 685 0.0 3 502 97 52 34 102 697 0.0 3 510 89 59 39 103 734 0.0 3 539 101 50 44 104 14909 0.0 3 13697 852 233 127 105 688 0.0 3 492 107 58 31 106 498 0.0 3 323 87 50 38 107 446 0.0 3 298 65 39 44 108 477 0.0 3 323 60 60 34 109 377 0.0 3 254 62 35 26 110 389 0.0 3 224 82 51 32 111 341 0.0 3 217 49 41 34 112 314 0.0 3 201 53 35 25 113 311 0.0 3 206 60 30 15 114 326 0.0 3 208 54 35 29 115 239 0.0 3 134 42 30 33 116 274 0.0 3 165 40 35 34 117 201 0.0 3 127 38 21 15 118 252 0.0 3 169 40 24 19 119 200 0.0 3 127 33 19 21 120 214 0.0 3 139 33 25 17 121 196 0.0 3 130 28 23 15 122 192 0.0 3 97 38 38 19 123 149 0.0 3 92 24 14 19 124 484 0.0 3 391 53 24 16 125 134 0.0 3 74 29 17 14 126 140 0.0 3 98 24 12 6 127 111 0.0 3 71 18 15 7 128 142 0.0 3 107 16 11 8 129 119 0.0 3 92 15 8 4 130 434 0.0 3 369 45 14 6 131 1955 0.0 3 1436 321 120 78 132 139 0.0 3 109 18 11 1 133 81 0.0 3 60 16 4 1 134 193 0.0 3 167 19 5 2 135 84 0.0 3 73 7 4 136 57 0.0 3 54 2 1 137 47 0.0 3 44 2 0 1 138 138 0.0 3 123 12 3 139 25 0.0 3 23 1 0 1 140 23 0.0 3 21 2 141 49 0.0 3 42 4 1 2 142 33 0.0 3 29 4 143 30 0.0 3 29 1 144 10 0.0 3 8 1 1 145 12 0.0 3 11 1 146 36 0.0 3 35 1 147 14 0.0 3 14 148 34 0.0 3 26 8 149 72 0.0 3 42 16 8 6 150 4069 0.0 3 3699 205 103 62