This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-01.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-01.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-01_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-01_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 152.422 s (6.338 µs/read; 9.47 M reads/minute). === Summary === Total read pairs processed: 24,047,114 Read 1 with adapter: 4,322,518 (18.0%) Read 2 with adapter: 4,339,000 (18.0%) == Read fate breakdown == Pairs that were too short: 117,482 (0.5%) Pairs written (passing filters): 23,929,632 (99.5%) Total basepairs processed: 7,214,134,200 bp Read 1: 3,607,067,100 bp Read 2: 3,607,067,100 bp Quality-trimmed: 991,543 bp (0.0%) Read 1: 431,035 bp Read 2: 560,508 bp Total written (filtered): 6,966,321,065 bp (96.6%) Read 1: 3,484,921,124 bp Read 2: 3,481,399,941 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4322518 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: 20.9% G: 28.7% T: 20.1% none/other: 2.3% Overview of removed sequences length count expect max.err error counts 3 509495 375736.2 0 509495 4 162310 93934.0 0 162310 5 88903 23483.5 0 88903 6 79429 5870.9 0 79429 7 89312 1467.7 0 89312 8 82266 366.9 0 82266 9 84421 91.7 0 84033 388 10 84332 22.9 1 74350 9982 11 84158 5.7 1 74609 9549 12 82644 1.4 1 73516 9128 13 96061 0.4 1 85828 10233 14 92927 0.1 1 82647 10280 15 97986 0.0 1 87226 10760 16 89606 0.0 1 80296 9310 17 88325 0.0 1 79206 9119 18 81167 0.0 1 72748 8400 19 19 74259 0.0 1 66061 8044 154 20 82758 0.0 2 70359 8286 4113 21 79169 0.0 2 67442 7886 3841 22 76919 0.0 2 65646 7501 3772 23 79047 0.0 2 67495 7825 3727 24 74518 0.0 2 63554 7408 3556 25 78828 0.0 2 67338 7765 3725 26 79757 0.0 2 68375 7755 3627 27 78103 0.0 2 66991 7553 3548 11 28 74832 0.0 2 63910 7576 3333 13 29 65357 0.0 2 55559 6806 2953 39 30 64052 0.0 3 52829 6363 2809 2051 31 63587 0.0 3 52541 6364 2731 1951 32 61976 0.0 3 51108 6124 2781 1963 33 63797 0.0 3 52870 6276 2771 1880 34 61643 0.0 3 51181 6093 2537 1832 35 57838 0.0 3 47814 5731 2470 1823 36 55155 0.0 3 45784 5375 2357 1639 37 55822 0.0 3 46393 5321 2395 1713 38 52819 0.0 3 43847 5105 2285 1582 39 51567 0.0 3 42941 4968 2182 1476 40 48563 0.0 3 40551 4600 1997 1415 41 46962 0.0 3 39114 4550 1932 1366 42 43015 0.0 3 35848 4142 1811 1214 43 40265 0.0 3 33338 4008 1717 1202 44 40956 0.0 3 34232 3891 1692 1141 45 38328 0.0 3 32020 3600 1570 1138 46 38504 0.0 3 32218 3618 1563 1105 47 36139 0.0 3 30196 3413 1498 1032 48 36400 0.0 3 30660 3351 1466 923 49 32977 0.0 3 27719 3044 1298 916 50 36365 0.0 3 30807 3197 1390 971 51 30147 0.0 3 25559 2696 1131 761 52 29960 0.0 3 25378 2735 1086 761 53 30110 0.0 3 25558 2692 1138 722 54 27151 0.0 3 23014 2462 1013 662 55 27483 0.0 3 23436 2431 956 660 56 22499 0.0 3 19189 1949 849 512 57 26099 0.0 3 22310 2272 883 634 58 21551 0.0 3 18434 1873 757 487 59 21354 0.0 3 18242 1870 738 504 60 17684 0.0 3 15013 1609 645 417 61 14710 0.0 3 12536 1328 477 369 62 14020 0.0 3 11967 1201 531 321 63 13583 0.0 3 11620 1161 470 332 64 12893 0.0 3 11117 1057 430 289 65 10813 0.0 3 9255 912 407 239 66 10722 0.0 3 9202 899 395 226 67 10921 0.0 3 9327 971 367 256 68 9228 0.0 3 7777 862 362 227 69 7242 0.0 3 6186 639 238 179 70 6367 0.0 3 5417 578 213 159 71 5605 0.0 3 4790 482 196 137 72 4942 0.0 3 4155 468 199 120 73 4641 0.0 3 3946 401 178 116 74 4036 0.0 3 3455 337 135 109 75 3822 0.0 3 3249 345 130 98 76 3217 0.0 3 2702 302 125 88 77 3098 0.0 3 2655 266 100 77 78 2870 0.0 3 2419 267 100 84 79 2870 0.0 3 2384 260 131 95 80 2776 0.0 3 2338 257 102 79 81 2291 0.0 3 1939 194 91 67 82 1941 0.0 3 1609 195 85 52 83 1862 0.0 3 1589 156 79 38 84 1326 0.0 3 1101 122 63 40 85 1078 0.0 3 881 107 45 45 86 1069 0.0 3 865 124 44 36 87 997 0.0 3 807 100 42 48 88 1134 0.0 3 889 120 70 55 89 1180 0.0 3 990 96 49 45 90 1080 0.0 3 876 105 57 42 91 1047 0.0 3 863 89 56 39 92 894 0.0 3 726 83 47 38 93 752 0.0 3 586 91 38 37 94 615 0.0 3 450 82 41 42 95 541 0.0 3 392 77 41 31 96 500 0.0 3 374 50 30 46 97 514 0.0 3 379 66 43 26 98 526 0.0 3 397 67 33 29 99 474 0.0 3 368 51 32 23 100 498 0.0 3 378 55 37 28 101 455 0.0 3 349 50 28 28 102 441 0.0 3 322 55 33 31 103 965 0.0 3 793 96 43 33 104 16077 0.0 3 14340 1207 333 197 105 538 0.0 3 416 56 37 29 106 389 0.0 3 266 59 42 22 107 307 0.0 3 190 48 37 32 108 280 0.0 3 180 35 28 37 109 264 0.0 3 172 42 27 23 110 284 0.0 3 195 41 25 23 111 263 0.0 3 172 37 31 23 112 273 0.0 3 170 39 34 30 113 216 0.0 3 138 31 22 25 114 246 0.0 3 159 41 23 23 115 215 0.0 3 129 37 22 27 116 249 0.0 3 136 51 31 31 117 207 0.0 3 129 29 24 25 118 233 0.0 3 155 29 35 14 119 194 0.0 3 128 28 19 19 120 192 0.0 3 113 32 30 17 121 162 0.0 3 104 27 14 17 122 169 0.0 3 94 40 17 18 123 140 0.0 3 89 26 15 10 124 1164 0.0 3 1036 74 31 23 125 134 0.0 3 89 28 9 8 126 176 0.0 3 110 23 19 24 127 103 0.0 3 65 17 10 11 128 176 0.0 3 122 27 18 9 129 293 0.0 3 250 24 10 9 130 566 0.0 3 464 65 30 7 131 1664 0.0 3 1562 79 16 7 132 205 0.0 3 164 25 8 8 133 103 0.0 3 87 13 2 1 134 184 0.0 3 164 10 4 6 135 88 0.0 3 73 10 4 1 136 118 0.0 3 101 7 3 7 137 78 0.0 3 68 6 2 2 138 114 0.0 3 104 2 5 3 139 85 0.0 3 80 4 0 1 140 64 0.0 3 62 1 1 141 71 0.0 3 60 6 4 1 142 163 0.0 3 137 23 3 143 31 0.0 3 26 2 1 2 144 19 0.0 3 13 3 1 2 145 18 0.0 3 16 1 0 1 146 32 0.0 3 28 1 3 147 16 0.0 3 12 1 1 2 148 70 0.0 3 22 10 8 30 149 8835 0.0 3 18 6175 2450 192 150 98837 0.0 3 1546 91769 5211 311 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4339000 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: 28.5% C: 21.6% G: 28.7% T: 21.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 492026 375736.2 0 492026 4 169915 93934.0 0 169915 5 91882 23483.5 0 91882 6 83459 5870.9 0 83459 7 93634 1467.7 0 93634 8 87204 366.9 0 87204 9 88671 91.7 0 88306 365 10 88912 22.9 1 78472 10440 11 88080 5.7 1 77441 10639 12 86266 1.4 1 76720 9546 13 101040 0.4 1 90450 10590 14 97555 0.1 1 87024 10531 15 102967 0.0 1 91863 11104 16 93010 0.0 1 82841 10169 17 92137 0.0 1 82320 9817 18 84439 0.0 1 74979 9451 9 19 78799 0.0 1 69342 9261 196 20 87187 0.0 2 73651 9652 3884 21 82334 0.0 2 69342 8929 4063 22 79435 0.0 2 66391 8945 4099 23 81350 0.0 2 67696 9401 4253 24 76757 0.0 2 64210 8691 3856 25 81501 0.0 2 67835 9410 4256 26 82591 0.0 2 66129 11833 4629 27 80474 0.0 2 63640 12166 4667 1 28 76911 0.0 2 60824 11688 4388 11 29 67180 0.0 2 53360 9951 3801 68 30 65980 0.0 3 50763 9231 3659 2327 31 65905 0.0 3 50510 9431 3692 2272 32 63749 0.0 3 49396 8718 3439 2196 33 66007 0.0 3 51034 9217 3528 2228 34 63584 0.0 3 49300 8807 3295 2182 35 59625 0.0 3 46378 7988 3225 2034 36 57083 0.0 3 44349 7736 3036 1962 37 57487 0.0 3 44819 7675 3023 1970 38 54426 0.0 3 42410 7295 2873 1848 39 53212 0.0 3 41713 7078 2709 1712 40 49975 0.0 3 39210 6529 2562 1674 41 48340 0.0 3 38178 6124 2506 1532 42 44043 0.0 3 34960 5515 2143 1425 43 41476 0.0 3 32618 5381 2116 1361 44 42109 0.0 3 33352 5243 2141 1373 45 39496 0.0 3 31128 5083 1992 1293 46 39568 0.0 3 31519 4882 1883 1284 47 37024 0.0 3 29466 4498 1867 1193 48 37071 0.0 3 29471 4629 1784 1187 49 33673 0.0 3 26710 4226 1699 1038 50 37123 0.0 3 29781 4568 1650 1124 51 30795 0.0 3 24893 3572 1442 888 52 30600 0.0 3 24695 3605 1405 895 53 30759 0.0 3 24801 3681 1368 909 54 27918 0.0 3 22493 3343 1291 791 55 28135 0.0 3 22884 3242 1282 727 56 23151 0.0 3 18776 2738 1011 626 57 26557 0.0 3 21983 2848 1045 681 58 22004 0.0 3 18074 2411 942 577 59 21505 0.0 3 17634 2360 935 576 60 18185 0.0 3 14807 2043 810 525 61 15068 0.0 3 12315 1659 671 423 62 14345 0.0 3 11631 1668 627 419 63 13887 0.0 3 11436 1494 583 374 64 13138 0.0 3 10860 1381 535 362 65 11141 0.0 3 9179 1161 490 311 66 10986 0.0 3 9065 1155 462 304 67 11227 0.0 3 9239 1215 476 297 68 9449 0.0 3 7708 1072 411 258 69 7472 0.0 3 6106 850 311 205 70 6520 0.0 3 5431 686 241 162 71 5734 0.0 3 4713 585 274 162 72 5092 0.0 3 4137 540 243 172 73 4785 0.0 3 3885 514 224 162 74 4189 0.0 3 3402 442 208 137 75 3957 0.0 3 3240 385 202 130 76 3346 0.0 3 2699 382 167 98 77 3258 0.0 3 2591 393 156 118 78 2986 0.0 3 2412 323 149 102 79 2991 0.0 3 2407 338 137 109 80 2939 0.0 3 2332 359 174 74 81 2394 0.0 3 1916 260 134 84 82 2089 0.0 3 1637 251 127 74 83 1975 0.0 3 1552 233 111 79 84 1429 0.0 3 1095 190 79 65 85 1215 0.0 3 912 161 74 68 86 1196 0.0 3 893 149 87 67 87 1093 0.0 3 849 126 64 54 88 1261 0.0 3 919 174 92 76 89 1279 0.0 3 1001 154 73 51 90 1192 0.0 3 883 160 86 63 91 1145 0.0 3 898 127 72 48 92 1015 0.0 3 763 136 60 56 93 844 0.0 3 642 97 61 44 94 707 0.0 3 474 117 66 50 95 663 0.0 3 456 96 69 42 96 596 0.0 3 397 87 63 49 97 605 0.0 3 409 91 62 43 98 636 0.0 3 441 90 59 46 99 583 0.0 3 394 98 56 35 100 599 0.0 3 407 88 57 47 101 525 0.0 3 370 71 51 33 102 549 0.0 3 335 104 50 60 103 1078 0.0 3 851 105 57 65 104 16297 0.0 3 14585 1197 352 163 105 634 0.0 3 449 95 47 43 106 479 0.0 3 308 71 58 42 107 386 0.0 3 226 70 48 42 108 347 0.0 3 200 59 54 34 109 343 0.0 3 196 65 37 45 110 359 0.0 3 221 61 52 25 111 327 0.0 3 182 71 36 38 112 327 0.0 3 180 71 45 31 113 280 0.0 3 160 52 34 34 114 314 0.0 3 182 62 41 29 115 263 0.0 3 147 54 36 26 116 292 0.0 3 157 56 39 40 117 250 0.0 3 152 34 33 31 118 280 0.0 3 159 49 37 35 119 233 0.0 3 124 52 29 28 120 227 0.0 3 116 42 35 34 121 201 0.0 3 104 47 26 24 122 205 0.0 3 110 40 29 26 123 171 0.0 3 94 40 23 14 124 1181 0.0 3 1003 100 48 30 125 157 0.0 3 93 20 25 19 126 187 0.0 3 105 36 27 19 127 127 0.0 3 70 30 17 10 128 195 0.0 3 126 37 17 15 129 291 0.0 3 219 37 22 13 130 558 0.0 3 457 61 23 17 131 1515 0.0 3 1096 268 99 52 132 178 0.0 3 142 21 7 8 133 100 0.0 3 83 12 3 2 134 179 0.0 3 156 15 4 4 135 82 0.0 3 70 8 3 1 136 109 0.0 3 98 7 3 1 137 75 0.0 3 65 6 3 1 138 109 0.0 3 101 5 2 1 139 83 0.0 3 78 5 140 66 0.0 3 64 1 1 141 68 0.0 3 60 5 1 2 142 148 0.0 3 138 9 1 143 27 0.0 3 25 0 1 1 144 14 0.0 3 13 1 145 17 0.0 3 15 2 146 28 0.0 3 24 4 147 13 0.0 3 12 0 1 148 25 0.0 3 19 2 4 149 43 0.0 3 18 7 10 8 150 1751 0.0 3 1510 107 77 57