This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH09-13.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH09-13.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH09-13_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH09-13_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 153.459 s (6.882 µs/read; 8.72 M reads/minute). === Summary === Total read pairs processed: 22,298,220 Read 1 with adapter: 3,915,838 (17.6%) Read 2 with adapter: 3,995,117 (17.9%) == Read fate breakdown == Pairs that were too short: 67,145 (0.3%) Pairs written (passing filters): 22,231,075 (99.7%) Total basepairs processed: 6,689,466,000 bp Read 1: 3,344,733,000 bp Read 2: 3,344,733,000 bp Quality-trimmed: 961,134 bp (0.0%) Read 1: 462,680 bp Read 2: 498,454 bp Total written (filtered): 6,448,052,146 bp (96.4%) Read 1: 3,225,939,980 bp Read 2: 3,222,112,166 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 3915838 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: 23.1% C: 22.9% G: 33.1% T: 19.7% none/other: 1.1% Overview of removed sequences length count expect max.err error counts 3 452419 348409.7 0 452419 4 140978 87102.4 0 140978 5 78947 21775.6 0 78947 6 68355 5443.9 0 68355 7 73561 1361.0 0 73561 8 65530 340.2 0 65530 9 67505 85.1 0 67102 403 10 68918 21.3 1 60663 8255 11 68462 5.3 1 60450 8012 12 68406 1.3 1 60860 7546 13 75839 0.3 1 67735 8104 14 75655 0.1 1 67203 8452 15 78402 0.0 1 70193 8209 16 74241 0.0 1 66529 7712 17 73709 0.0 1 66098 7611 18 66669 0.0 1 59599 7050 20 19 62577 0.0 1 55551 6852 174 20 67166 0.0 2 57110 6636 3420 21 64838 0.0 2 55393 6378 3067 22 63742 0.0 2 54302 6345 3095 23 65447 0.0 2 55800 6491 3156 24 63586 0.0 2 54068 6389 3129 25 64618 0.0 2 55114 6424 3080 26 65536 0.0 2 56074 6425 3037 27 64280 0.0 2 55187 6198 2891 4 28 63068 0.0 2 54020 6192 2846 10 29 56743 0.0 2 48312 5739 2668 24 30 54261 0.0 3 44942 5223 2423 1673 31 54928 0.0 3 45938 5179 2215 1596 32 53517 0.0 3 44452 5223 2297 1545 33 55126 0.0 3 45922 5365 2276 1563 34 54200 0.0 3 45152 5238 2208 1602 35 52006 0.0 3 43210 4941 2272 1583 36 50355 0.0 3 41973 4805 2088 1489 37 50101 0.0 3 41914 4769 1966 1452 38 47297 0.0 3 39782 4287 1879 1349 39 46528 0.0 3 38986 4259 1925 1358 40 44322 0.0 3 37262 4077 1769 1214 41 42705 0.0 3 35872 3951 1729 1153 42 40078 0.0 3 33489 3800 1664 1125 43 38701 0.0 3 32563 3566 1498 1074 44 38393 0.0 3 32338 3491 1498 1066 45 36984 0.0 3 31266 3310 1485 923 46 36885 0.0 3 31013 3409 1451 1012 47 35277 0.0 3 29782 3111 1399 985 48 34790 0.0 3 29548 3077 1270 895 49 32297 0.0 3 27649 2710 1135 803 50 33006 0.0 3 28228 2810 1152 816 51 29925 0.0 3 25542 2598 1103 682 52 28732 0.0 3 24643 2393 1005 691 53 28877 0.0 3 24714 2490 1007 666 54 27582 0.0 3 23626 2369 941 646 55 26836 0.0 3 23168 2251 826 591 56 24713 0.0 3 21340 2005 804 564 57 26497 0.0 3 22945 2175 810 567 58 23767 0.0 3 20612 1838 774 543 59 22797 0.0 3 19676 1888 752 481 60 20812 0.0 3 17954 1764 634 460 61 19041 0.0 3 16483 1552 602 404 62 18027 0.0 3 15596 1488 553 390 63 17758 0.0 3 15447 1438 515 358 64 16767 0.0 3 14628 1361 463 315 65 15675 0.0 3 13727 1158 438 352 66 15067 0.0 3 13149 1133 466 319 67 15273 0.0 3 13355 1187 436 295 68 14014 0.0 3 12302 1052 410 250 69 12490 0.0 3 10976 916 348 250 70 12010 0.0 3 10613 853 323 221 71 11384 0.0 3 9993 859 304 228 72 10019 0.0 3 8785 749 284 201 73 10280 0.0 3 9102 699 295 184 74 9460 0.0 3 8401 654 252 153 75 9260 0.0 3 8162 660 267 171 76 8647 0.0 3 7664 576 250 157 77 8415 0.0 3 7477 563 228 147 78 8094 0.0 3 7144 567 231 152 79 7488 0.0 3 6684 486 178 140 80 7280 0.0 3 6497 503 159 121 81 6773 0.0 3 6060 434 145 134 82 6225 0.0 3 5531 439 155 100 83 6201 0.0 3 5503 446 151 101 84 5719 0.0 3 5082 391 132 114 85 5482 0.0 3 4922 353 125 82 86 5171 0.0 3 4652 309 122 88 87 4898 0.0 3 4371 313 119 95 88 4616 0.0 3 4117 294 121 84 89 4578 0.0 3 4107 300 88 83 90 4373 0.0 3 3898 288 121 66 91 3955 0.0 3 3569 237 85 64 92 3963 0.0 3 3550 256 92 65 93 3536 0.0 3 3159 231 87 59 94 3449 0.0 3 3109 210 74 56 95 3349 0.0 3 3015 228 67 39 96 3007 0.0 3 2700 192 73 42 97 2933 0.0 3 2648 187 60 38 98 2814 0.0 3 2520 182 66 46 99 2864 0.0 3 2596 172 56 40 100 2554 0.0 3 2288 149 72 45 101 2510 0.0 3 2246 181 46 37 102 2342 0.0 3 2122 130 50 40 103 2307 0.0 3 2093 142 36 36 104 7330 0.0 3 6756 395 108 71 105 2107 0.0 3 1881 143 42 41 106 1933 0.0 3 1704 152 44 33 107 1901 0.0 3 1738 101 45 17 108 1795 0.0 3 1613 123 32 27 109 1645 0.0 3 1487 105 33 20 110 1641 0.0 3 1436 126 40 39 111 1613 0.0 3 1454 102 31 26 112 1493 0.0 3 1348 92 21 32 113 1506 0.0 3 1363 99 23 21 114 1455 0.0 3 1314 85 34 22 115 1315 0.0 3 1180 70 43 22 116 1244 0.0 3 1130 74 26 14 117 1162 0.0 3 1043 83 24 12 118 1181 0.0 3 1068 63 30 20 119 1152 0.0 3 1037 71 28 16 120 1065 0.0 3 960 66 22 17 121 1049 0.0 3 964 53 16 16 122 974 0.0 3 887 53 17 17 123 746 0.0 3 675 50 13 8 124 793 0.0 3 717 46 20 10 125 545 0.0 3 485 33 15 12 126 412 0.0 3 365 29 13 5 127 328 0.0 3 293 20 7 8 128 323 0.0 3 282 25 8 8 129 184 0.0 3 162 14 4 4 130 564 0.0 3 465 59 28 12 131 492 0.0 3 432 40 10 10 132 89 0.0 3 64 16 4 5 133 67 0.0 3 61 4 1 1 134 113 0.0 3 99 8 5 1 135 47 0.0 3 38 4 0 5 136 69 0.0 3 57 7 1 4 137 51 0.0 3 48 1 0 2 138 78 0.0 3 75 1 1 1 139 63 0.0 3 59 3 0 1 140 33 0.0 3 29 3 1 141 19 0.0 3 16 2 0 1 142 41 0.0 3 31 9 1 143 25 0.0 3 16 3 2 4 144 1 0.0 3 0 1 145 12 0.0 3 10 1 0 1 146 18 0.0 3 18 147 14 0.0 3 12 0 2 148 29 0.0 3 17 2 3 7 149 3899 0.0 3 10 2748 1055 86 150 41662 0.0 3 1493 37841 2171 157 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 3995117 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: 23.1% C: 23.3% G: 32.9% T: 20.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 434244 348409.7 0 434244 4 147217 87102.4 0 147217 5 82451 21775.6 0 82451 6 72316 5443.9 0 72316 7 77548 1361.0 0 77548 8 70048 340.2 0 70048 9 71903 85.1 0 71552 351 10 72986 21.3 1 64663 8323 11 72068 5.3 1 63999 8069 12 71727 1.3 1 64201 7526 13 80125 0.3 1 72096 8029 14 79797 0.1 1 71516 8281 15 82703 0.0 1 74339 8364 16 77433 0.0 1 69531 7902 17 77378 0.0 1 69527 7851 18 69437 0.0 1 61689 7733 15 19 66906 0.0 1 59112 7653 141 20 70785 0.0 2 58182 8954 3649 21 67235 0.0 2 54825 8709 3701 22 66021 0.0 2 53208 8951 3862 23 67619 0.0 2 54977 8798 3844 24 65549 0.0 2 53607 8373 3569 25 67104 0.0 2 54579 8738 3787 26 68084 0.0 2 54254 9875 3955 27 66670 0.0 2 53253 9524 3891 2 28 65377 0.0 2 52204 9392 3775 6 29 58635 0.0 2 46969 8302 3332 32 30 56243 0.0 3 43547 7692 3085 1919 31 57084 0.0 3 44116 7779 3205 1984 32 55813 0.0 3 43161 7583 3090 1979 33 57209 0.0 3 44258 7845 3175 1931 34 56162 0.0 3 43556 7646 3028 1932 35 54065 0.0 3 42341 7085 2857 1782 36 52361 0.0 3 40772 7000 2864 1725 37 52214 0.0 3 40764 6910 2767 1773 38 49207 0.0 3 38802 6276 2490 1639 39 48198 0.0 3 37827 6286 2546 1539 40 45818 0.0 3 35749 6213 2353 1503 41 44176 0.0 3 34713 5695 2314 1454 42 41453 0.0 3 32658 5264 2139 1392 43 40110 0.0 3 31621 5179 2047 1263 44 39616 0.0 3 31443 4952 1935 1286 45 38378 0.0 3 30577 4717 1894 1190 46 38103 0.0 3 30305 4697 1910 1191 47 36558 0.0 3 29023 4611 1837 1087 48 35757 0.0 3 28512 4385 1741 1119 49 33243 0.0 3 26426 4208 1601 1008 50 34105 0.0 3 27289 4226 1599 991 51 30832 0.0 3 24847 3703 1412 870 52 29784 0.0 3 24056 3515 1392 821 53 29840 0.0 3 24135 3471 1390 844 54 28461 0.0 3 23229 3263 1177 792 55 27674 0.0 3 22586 3209 1143 736 56 25534 0.0 3 20785 2945 1119 685 57 27357 0.0 3 22581 2919 1128 729 58 24408 0.0 3 20112 2706 1006 584 59 23421 0.0 3 19286 2554 981 600 60 21459 0.0 3 17571 2371 938 579 61 19722 0.0 3 16221 2182 823 496 62 18522 0.0 3 15064 2148 799 511 63 18312 0.0 3 15007 2051 778 476 64 17319 0.0 3 14211 1971 693 444 65 16207 0.0 3 13394 1773 654 386 66 15598 0.0 3 12827 1727 628 416 67 15778 0.0 3 12965 1807 625 381 68 14431 0.0 3 11865 1633 597 336 69 12834 0.0 3 10693 1316 500 325 70 12239 0.0 3 10122 1324 484 309 71 11686 0.0 3 9669 1219 490 308 72 10317 0.0 3 8479 1134 430 274 73 10580 0.0 3 8664 1216 420 280 74 9774 0.0 3 8081 1090 368 235 75 9510 0.0 3 7909 975 392 234 76 8864 0.0 3 7388 946 325 205 77 8665 0.0 3 7139 978 340 208 78 8232 0.0 3 6830 875 303 224 79 7722 0.0 3 6423 824 290 185 80 7457 0.0 3 6139 836 289 193 81 6949 0.0 3 5732 806 243 168 82 6360 0.0 3 5283 674 270 133 83 6394 0.0 3 5307 670 250 167 84 5827 0.0 3 4845 607 238 137 85 5615 0.0 3 4712 579 195 129 86 5352 0.0 3 4472 545 195 140 87 5102 0.0 3 4185 551 221 145 88 4744 0.0 3 3923 493 202 126 89 4709 0.0 3 3923 479 193 114 90 4451 0.0 3 3727 485 154 85 91 4048 0.0 3 3398 415 147 88 92 4083 0.0 3 3372 435 164 112 93 3623 0.0 3 2994 377 154 98 94 3516 0.0 3 2966 351 121 78 95 3450 0.0 3 2858 380 130 82 96 3117 0.0 3 2596 331 103 87 97 3028 0.0 3 2517 321 117 73 98 2921 0.0 3 2447 295 104 75 99 2954 0.0 3 2456 317 111 70 100 2660 0.0 3 2223 267 108 62 101 2587 0.0 3 2144 287 83 73 102 2428 0.0 3 2008 271 98 51 103 2375 0.0 3 2006 229 85 55 104 7384 0.0 3 6548 584 157 95 105 2177 0.0 3 1809 249 64 55 106 2004 0.0 3 1662 215 80 47 107 1950 0.0 3 1646 200 66 38 108 1868 0.0 3 1552 196 73 47 109 1717 0.0 3 1446 188 50 33 110 1701 0.0 3 1389 191 70 51 111 1630 0.0 3 1342 168 81 39 112 1520 0.0 3 1259 171 52 38 113 1541 0.0 3 1273 170 53 45 114 1461 0.0 3 1206 169 49 37 115 1343 0.0 3 1087 153 60 43 116 1288 0.0 3 1090 118 46 34 117 1192 0.0 3 995 127 46 24 118 1213 0.0 3 993 144 47 29 119 1180 0.0 3 969 131 50 30 120 1082 0.0 3 888 121 46 27 121 1069 0.0 3 878 116 44 31 122 983 0.0 3 816 97 44 26 123 767 0.0 3 642 84 19 22 124 815 0.0 3 671 93 35 16 125 562 0.0 3 460 65 22 15 126 434 0.0 3 355 43 22 14 127 344 0.0 3 277 43 12 12 128 321 0.0 3 258 42 15 6 129 187 0.0 3 148 26 7 6 130 563 0.0 3 474 62 19 8 131 393 0.0 3 261 90 34 8 132 80 0.0 3 55 10 11 4 133 68 0.0 3 49 10 8 1 134 109 0.0 3 95 9 3 2 135 44 0.0 3 36 6 2 136 67 0.0 3 49 10 4 4 137 50 0.0 3 45 3 2 138 81 0.0 3 71 4 3 3 139 60 0.0 3 49 7 3 1 140 32 0.0 3 30 1 1 141 17 0.0 3 15 2 142 34 0.0 3 32 1 1 143 16 0.0 3 13 2 0 1 144 1 0.0 3 1 145 11 0.0 3 9 1 0 1 146 18 0.0 3 15 3 147 12 0.0 3 11 0 1 148 19 0.0 3 13 5 0 1 149 25 0.0 3 10 8 3 4 150 1613 0.0 3 1431 118 42 22