This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH01-22.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH01-22.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH01-22_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH01-22_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 158.661 s (6.669 µs/read; 9.00 M reads/minute). === Summary === Total read pairs processed: 23,792,119 Read 1 with adapter: 4,350,942 (18.3%) Read 2 with adapter: 4,316,054 (18.1%) == Read fate breakdown == Pairs that were too short: 151,746 (0.6%) Pairs written (passing filters): 23,640,373 (99.4%) Total basepairs processed: 7,137,635,700 bp Read 1: 3,568,817,850 bp Read 2: 3,568,817,850 bp Quality-trimmed: 1,024,337 bp (0.0%) Read 1: 468,523 bp Read 2: 555,814 bp Total written (filtered): 6,881,767,839 bp (96.4%) Read 1: 3,442,589,734 bp Read 2: 3,439,178,105 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4350942 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: 24.7% C: 20.8% G: 32.3% T: 19.1% none/other: 3.1% Overview of removed sequences length count expect max.err error counts 3 584256 371751.9 0 584256 4 159815 92938.0 0 159815 5 89804 23234.5 0 89804 6 80213 5808.6 0 80213 7 84766 1452.2 0 84766 8 77046 363.0 0 77046 9 77492 90.8 0 77119 373 10 79057 22.7 1 68824 10233 11 77925 5.7 1 68103 9822 12 78143 1.4 1 68754 9389 13 90470 0.4 1 80110 10360 14 88254 0.1 1 77718 10536 15 93536 0.0 1 82805 10731 16 87268 0.0 1 77576 9692 17 83975 0.0 1 74551 9424 18 76881 0.0 1 68401 8460 20 19 70692 0.0 1 62333 8178 181 20 76639 0.0 2 64059 8256 4324 21 73459 0.0 2 61681 7879 3899 22 72106 0.0 2 60661 7557 3888 23 76431 0.0 2 64276 8142 4013 24 74770 0.0 2 62958 7907 3905 25 78719 0.0 2 66194 8409 4116 26 77801 0.0 2 65839 8149 3813 27 75753 0.0 2 63936 7809 3994 14 28 71538 0.0 2 60377 7469 3681 11 29 62543 0.0 2 52247 6986 3279 31 30 61363 0.0 3 49731 6478 3048 2106 31 61583 0.0 3 50254 6272 3044 2013 32 60765 0.0 3 49474 6294 2914 2083 33 63292 0.0 3 51709 6488 2942 2153 34 62391 0.0 3 51083 6301 3002 2005 35 58429 0.0 3 47562 6139 2792 1936 36 57166 0.0 3 46712 5857 2733 1864 37 58696 0.0 3 48118 5984 2676 1918 38 54597 0.0 3 44704 5569 2563 1761 39 53045 0.0 3 43507 5270 2483 1785 40 47902 0.0 3 39301 4826 2181 1594 41 46187 0.0 3 37965 4693 2084 1445 42 43366 0.0 3 35652 4349 2022 1343 43 41549 0.0 3 33962 4321 1925 1341 44 42919 0.0 3 35373 4292 1966 1288 45 40084 0.0 3 33083 3937 1814 1250 46 40671 0.0 3 33601 4068 1787 1215 47 38741 0.0 3 31977 3892 1715 1157 48 37694 0.0 3 31367 3667 1527 1133 49 33709 0.0 3 28025 3354 1381 949 50 35581 0.0 3 29715 3418 1424 1024 51 30396 0.0 3 25309 2895 1320 872 52 29619 0.0 3 24736 2880 1207 796 53 29672 0.0 3 24820 2848 1201 803 54 27295 0.0 3 22784 2579 1164 768 55 27865 0.0 3 23480 2564 1070 751 56 23871 0.0 3 20112 2187 925 647 57 28352 0.0 3 24123 2473 1044 712 58 22193 0.0 3 18694 2114 807 578 59 20871 0.0 3 17592 1914 840 525 60 16952 0.0 3 14205 1591 685 471 61 14660 0.0 3 12272 1382 604 402 62 13782 0.0 3 11583 1299 528 372 63 13315 0.0 3 11185 1254 570 306 64 13013 0.0 3 11058 1146 475 334 65 11545 0.0 3 9830 997 456 262 66 10725 0.0 3 9049 1005 419 252 67 10761 0.0 3 9190 931 391 249 68 9488 0.0 3 8027 852 360 249 69 7697 0.0 3 6494 687 291 225 70 6703 0.0 3 5672 620 235 176 71 5845 0.0 3 4916 536 234 159 72 5394 0.0 3 4542 500 214 138 73 4980 0.0 3 4262 422 163 133 74 4137 0.0 3 3490 360 181 106 75 4320 0.0 3 3677 360 158 125 76 3620 0.0 3 3048 327 140 105 77 3575 0.0 3 3002 337 139 97 78 3266 0.0 3 2736 301 130 99 79 3197 0.0 3 2676 282 130 109 80 2600 0.0 3 2191 241 95 73 81 2402 0.0 3 2001 224 111 66 82 2032 0.0 3 1698 184 77 73 83 2154 0.0 3 1801 197 96 60 84 1644 0.0 3 1327 154 88 75 85 1487 0.0 3 1213 164 55 55 86 1368 0.0 3 1128 118 66 56 87 1331 0.0 3 1078 137 68 48 88 1306 0.0 3 1054 124 85 43 89 1430 0.0 3 1161 130 80 59 90 1219 0.0 3 977 125 72 45 91 1135 0.0 3 912 116 58 49 92 1043 0.0 3 847 92 63 41 93 870 0.0 3 684 93 54 39 94 791 0.0 3 614 73 63 41 95 739 0.0 3 541 88 62 48 96 579 0.0 3 433 66 44 36 97 599 0.0 3 460 78 34 27 98 607 0.0 3 453 65 48 41 99 679 0.0 3 512 97 21 49 100 637 0.0 3 473 72 45 47 101 614 0.0 3 442 71 52 49 102 534 0.0 3 401 64 43 26 103 683 0.0 3 535 74 44 30 104 3529 0.0 3 3063 301 94 71 105 432 0.0 3 309 51 36 36 106 419 0.0 3 295 62 27 35 107 374 0.0 3 259 58 36 21 108 415 0.0 3 296 53 37 29 109 376 0.0 3 267 50 33 26 110 348 0.0 3 248 42 32 26 111 337 0.0 3 214 65 34 24 112 325 0.0 3 209 60 31 25 113 323 0.0 3 201 54 42 26 114 320 0.0 3 222 49 24 25 115 293 0.0 3 175 54 37 27 116 297 0.0 3 191 52 37 17 117 231 0.0 3 156 37 19 19 118 247 0.0 3 173 39 17 18 119 234 0.0 3 156 30 23 25 120 225 0.0 3 150 38 22 15 121 230 0.0 3 154 32 25 19 122 229 0.0 3 156 33 26 14 123 182 0.0 3 129 25 17 11 124 697 0.0 3 607 55 16 19 125 178 0.0 3 119 20 24 15 126 177 0.0 3 114 27 19 17 127 123 0.0 3 85 19 10 9 128 185 0.0 3 141 22 15 7 129 247 0.0 3 208 22 9 8 130 342 0.0 3 288 33 14 7 131 958 0.0 3 879 63 11 5 132 141 0.0 3 115 13 4 9 133 123 0.0 3 88 23 8 4 134 154 0.0 3 130 16 4 4 135 85 0.0 3 71 10 2 2 136 59 0.0 3 50 6 2 1 137 54 0.0 3 50 3 0 1 138 101 0.0 3 93 7 0 1 139 53 0.0 3 43 7 1 2 140 37 0.0 3 33 4 141 37 0.0 3 31 5 1 142 105 0.0 3 96 5 1 3 143 32 0.0 3 25 3 2 2 144 14 0.0 3 10 4 145 18 0.0 3 16 0 0 2 146 48 0.0 3 41 3 2 2 147 19 0.0 3 17 2 148 93 0.0 3 25 7 10 51 149 12614 0.0 3 36 9193 3103 282 150 130208 0.0 3 2704 120356 6766 382 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4316054 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: 25.3% C: 21.8% G: 32.3% T: 20.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 553798 371751.9 0 553798 4 166053 92938.0 0 166053 5 92996 23234.5 0 92996 6 84578 5808.6 0 84578 7 88997 1452.2 0 88997 8 82180 363.0 0 82180 9 82188 90.8 0 81844 344 10 83545 22.7 1 73085 10460 11 81860 5.7 1 71365 10495 12 81684 1.4 1 71947 9737 13 95507 0.4 1 84877 10630 14 92787 0.1 1 82069 10718 15 98383 0.0 1 87197 11186 16 91063 0.0 1 80504 10559 17 87351 0.0 1 77335 10016 18 79719 0.0 1 69529 10170 20 19 74674 0.0 1 64367 10103 204 20 80347 0.0 2 64338 11260 4749 21 75649 0.0 2 60037 10900 4712 22 74195 0.0 2 58225 11090 4880 23 78622 0.0 2 62287 11222 5113 24 76668 0.0 2 60836 10980 4852 25 80990 0.0 2 64545 11505 4940 26 80179 0.0 2 61756 12961 5462 27 77619 0.0 2 59521 12799 5295 4 28 73605 0.0 2 56750 11857 4993 5 29 64062 0.0 2 49098 10557 4336 71 30 63321 0.0 3 46733 9842 4118 2628 31 63630 0.0 3 47082 9714 4187 2647 32 62678 0.0 3 46338 9689 4080 2571 33 65001 0.0 3 48405 9929 4039 2628 34 64121 0.0 3 47729 10006 3936 2450 35 60415 0.0 3 45190 9078 3803 2344 36 59115 0.0 3 44173 8873 3645 2424 37 60647 0.0 3 45388 9040 3859 2360 38 56329 0.0 3 42387 8228 3429 2285 39 54630 0.0 3 41287 7947 3330 2066 40 49232 0.0 3 36722 7555 2978 1977 41 47343 0.0 3 35937 6862 2757 1787 42 44510 0.0 3 33752 6309 2710 1739 43 42724 0.0 3 32278 6264 2516 1666 44 44149 0.0 3 33413 6408 2658 1670 45 41247 0.0 3 31384 5933 2407 1523 46 41692 0.0 3 31914 5776 2472 1530 47 39837 0.0 3 30189 5784 2324 1540 48 38389 0.0 3 29239 5449 2302 1399 49 34523 0.0 3 26218 4966 2022 1317 50 36432 0.0 3 28190 4958 2051 1233 51 31171 0.0 3 24049 4249 1772 1101 52 30253 0.0 3 23714 3922 1629 988 53 30400 0.0 3 23803 3970 1632 995 54 28133 0.0 3 21976 3736 1472 949 55 28604 0.0 3 22427 3784 1500 893 56 24562 0.0 3 19259 3197 1326 780 57 28937 0.0 3 23050 3616 1415 856 58 22767 0.0 3 17985 2876 1147 759 59 21106 0.0 3 16818 2586 1053 649 60 17335 0.0 3 13591 2319 875 550 61 15074 0.0 3 11788 1919 861 506 62 14163 0.0 3 11089 1855 757 462 63 13651 0.0 3 10815 1731 696 409 64 13339 0.0 3 10553 1716 655 415 65 11853 0.0 3 9471 1449 569 364 66 11050 0.0 3 8765 1409 538 338 67 11081 0.0 3 8855 1370 512 344 68 9740 0.0 3 7674 1213 525 328 69 7946 0.0 3 6303 961 401 281 70 6906 0.0 3 5459 847 363 237 71 6034 0.0 3 4772 750 314 198 72 5565 0.0 3 4317 754 290 204 73 5163 0.0 3 4069 647 270 177 74 4303 0.0 3 3336 558 247 162 75 4477 0.0 3 3507 562 244 164 76 3811 0.0 3 2963 499 202 147 77 3717 0.0 3 2885 504 194 134 78 3393 0.0 3 2589 464 197 143 79 3355 0.0 3 2528 458 230 139 80 2759 0.0 3 2105 384 151 119 81 2502 0.0 3 1910 349 140 103 82 2169 0.0 3 1627 297 135 110 83 2275 0.0 3 1739 293 143 100 84 1765 0.0 3 1335 234 110 86 85 1621 0.0 3 1221 229 110 61 86 1493 0.0 3 1164 169 90 70 87 1470 0.0 3 1077 202 106 85 88 1460 0.0 3 1044 209 127 80 89 1574 0.0 3 1167 211 113 83 90 1320 0.0 3 959 197 91 73 91 1293 0.0 3 939 181 100 73 92 1126 0.0 3 808 174 71 73 93 1004 0.0 3 705 145 85 69 94 900 0.0 3 632 138 77 53 95 867 0.0 3 576 134 89 68 96 698 0.0 3 455 120 54 69 97 663 0.0 3 464 99 48 52 98 718 0.0 3 467 111 78 62 99 788 0.0 3 529 139 59 61 100 719 0.0 3 468 119 71 61 101 714 0.0 3 446 114 80 74 102 622 0.0 3 398 113 66 45 103 778 0.0 3 570 96 63 49 104 3665 0.0 3 3057 377 157 74 105 521 0.0 3 331 86 55 49 106 520 0.0 3 313 84 68 55 107 443 0.0 3 257 88 52 46 108 510 0.0 3 301 106 54 49 109 459 0.0 3 281 74 59 45 110 431 0.0 3 233 86 61 51 111 396 0.0 3 242 76 47 31 112 392 0.0 3 221 77 61 33 113 361 0.0 3 215 73 43 30 114 399 0.0 3 226 80 53 40 115 369 0.0 3 208 62 56 43 116 346 0.0 3 189 74 51 32 117 285 0.0 3 164 54 37 30 118 290 0.0 3 149 63 42 36 119 263 0.0 3 161 50 28 24 120 269 0.0 3 163 41 35 30 121 275 0.0 3 152 59 36 28 122 263 0.0 3 145 55 36 27 123 203 0.0 3 119 45 27 12 124 694 0.0 3 570 73 26 25 125 190 0.0 3 113 38 23 16 126 189 0.0 3 114 29 27 19 127 130 0.0 3 77 29 10 14 128 191 0.0 3 129 36 12 14 129 248 0.0 3 160 46 25 17 130 331 0.0 3 256 44 20 11 131 808 0.0 3 510 196 69 33 132 123 0.0 3 91 16 13 3 133 107 0.0 3 75 17 7 8 134 143 0.0 3 118 19 3 3 135 83 0.0 3 66 9 5 3 136 55 0.0 3 43 7 4 1 137 53 0.0 3 47 3 2 1 138 96 0.0 3 91 4 0 1 139 47 0.0 3 40 5 1 1 140 36 0.0 3 34 1 0 1 141 31 0.0 3 28 3 142 100 0.0 3 88 10 2 143 26 0.0 3 23 1 1 1 144 10 0.0 3 10 145 16 0.0 3 14 2 146 42 0.0 3 37 4 1 147 19 0.0 3 18 1 148 26 0.0 3 17 8 1 149 62 0.0 3 34 12 8 8 150 3087 0.0 3 2588 280 129 90