This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-06.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH07-06.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-06_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH07-06_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 157.536 s (6.580 µs/read; 9.12 M reads/minute). === Summary === Total read pairs processed: 23,940,579 Read 1 with adapter: 5,324,359 (22.2%) Read 2 with adapter: 5,380,280 (22.5%) == Read fate breakdown == Pairs that were too short: 113,916 (0.5%) Pairs written (passing filters): 23,826,663 (99.5%) Total basepairs processed: 7,182,173,700 bp Read 1: 3,591,086,850 bp Read 2: 3,591,086,850 bp Quality-trimmed: 1,004,354 bp (0.0%) Read 1: 494,146 bp Read 2: 510,208 bp Total written (filtered): 6,869,537,558 bp (95.6%) Read 1: 3,437,205,807 bp Read 2: 3,432,331,751 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 5324359 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: 20.3% G: 33.0% T: 19.7% none/other: 1.8% Overview of removed sequences length count expect max.err error counts 3 584320 374071.5 0 584320 4 176731 93517.9 0 176731 5 104959 23379.5 0 104959 6 92469 5844.9 0 92469 7 98778 1461.2 0 98778 8 89611 365.3 0 89611 9 90580 91.3 0 90087 493 10 95073 22.8 1 83296 11777 11 95565 5.7 1 83958 11607 12 95250 1.4 1 84244 11006 13 109364 0.4 1 97099 12265 14 105408 0.1 1 93120 12288 15 109280 0.0 1 97025 12255 16 106551 0.0 1 94576 11975 17 102892 0.0 1 91632 11260 18 97415 0.0 1 86616 10771 28 19 90592 0.0 1 79753 10578 261 20 96817 0.0 2 81048 10462 5307 21 94413 0.0 2 79425 9973 5015 22 94218 0.0 2 79385 9942 4891 23 96546 0.0 2 81296 10402 4848 24 96028 0.0 2 80511 10483 5034 25 99188 0.0 2 83718 10357 5113 26 97682 0.0 2 82669 10190 4823 27 95509 0.0 2 80535 10164 4806 4 28 92965 0.0 2 78520 9785 4640 20 29 83859 0.0 2 70034 9422 4351 52 30 82733 0.0 3 67196 8671 4088 2778 31 83759 0.0 3 68238 8744 3987 2790 32 81036 0.0 3 65958 8458 3817 2803 33 84475 0.0 3 68805 8856 3955 2859 34 83339 0.0 3 68050 8684 3799 2806 35 82276 0.0 3 67186 8532 3885 2673 36 79344 0.0 3 64985 8089 3721 2549 37 78447 0.0 3 64474 7876 3676 2421 38 72774 0.0 3 59528 7491 3371 2384 39 70682 0.0 3 58241 7002 3232 2207 40 66864 0.0 3 55134 6694 2991 2045 41 64272 0.0 3 52777 6566 2954 1975 42 60337 0.0 3 49536 6234 2720 1847 43 58875 0.0 3 48141 6101 2727 1906 44 59960 0.0 3 49346 6024 2688 1902 45 57533 0.0 3 47548 5684 2499 1802 46 56323 0.0 3 46667 5471 2451 1734 47 53655 0.0 3 44322 5387 2386 1560 48 50632 0.0 3 41949 5049 2191 1443 49 45490 0.0 3 37676 4462 1989 1363 50 47091 0.0 3 39192 4552 1979 1368 51 41241 0.0 3 34462 3995 1584 1200 52 39123 0.0 3 32578 3848 1643 1054 53 38583 0.0 3 32368 3603 1584 1028 54 36509 0.0 3 30588 3412 1497 1012 55 35729 0.0 3 30010 3327 1448 944 56 32875 0.0 3 27527 3075 1345 928 57 34218 0.0 3 28966 3179 1227 846 58 28911 0.0 3 24372 2703 1075 761 59 27209 0.0 3 22854 2519 1139 697 60 23467 0.0 3 19722 2270 877 598 61 20741 0.0 3 17493 1877 823 548 62 19356 0.0 3 16176 1899 765 516 63 17892 0.0 3 15122 1575 712 483 64 16862 0.0 3 14254 1540 637 431 65 15435 0.0 3 13017 1441 590 387 66 15037 0.0 3 12782 1345 523 387 67 14453 0.0 3 12255 1277 575 346 68 12821 0.0 3 10897 1109 500 315 69 10621 0.0 3 8974 960 431 256 70 9585 0.0 3 8121 852 359 253 71 8575 0.0 3 7275 732 354 214 72 7356 0.0 3 6246 626 273 211 73 6746 0.0 3 5765 566 235 180 74 6175 0.0 3 5228 549 234 164 75 5916 0.0 3 5050 513 201 152 76 5302 0.0 3 4523 444 186 149 77 5028 0.0 3 4280 428 202 118 78 4774 0.0 3 4057 438 172 107 79 4494 0.0 3 3857 357 158 122 80 4091 0.0 3 3453 378 164 96 81 3509 0.0 3 2947 321 129 112 82 2939 0.0 3 2492 254 106 87 83 2844 0.0 3 2415 233 109 87 84 2241 0.0 3 1898 178 97 68 85 1946 0.0 3 1608 194 78 66 86 1802 0.0 3 1513 156 73 60 87 1814 0.0 3 1568 148 58 40 88 1812 0.0 3 1524 162 74 52 89 1908 0.0 3 1613 151 92 52 90 1811 0.0 3 1558 112 85 56 91 1640 0.0 3 1350 153 70 67 92 1363 0.0 3 1153 107 46 57 93 1027 0.0 3 851 99 39 38 94 973 0.0 3 794 95 45 39 95 765 0.0 3 613 74 48 30 96 729 0.0 3 581 65 43 40 97 673 0.0 3 531 68 42 32 98 749 0.0 3 601 72 47 29 99 673 0.0 3 528 63 44 38 100 717 0.0 3 562 77 39 39 101 568 0.0 3 444 59 33 32 102 500 0.0 3 396 44 24 36 103 641 0.0 3 505 70 30 36 104 14385 0.0 3 13370 723 177 115 105 570 0.0 3 461 53 30 26 106 391 0.0 3 278 49 34 30 107 331 0.0 3 236 44 30 21 108 334 0.0 3 235 49 27 23 109 305 0.0 3 210 41 30 24 110 290 0.0 3 197 38 27 28 111 253 0.0 3 171 35 30 17 112 277 0.0 3 192 32 33 20 113 214 0.0 3 144 31 13 26 114 225 0.0 3 146 40 25 14 115 179 0.0 3 115 26 22 16 116 214 0.0 3 143 37 17 17 117 179 0.0 3 112 30 22 15 118 221 0.0 3 146 28 23 24 119 159 0.0 3 95 33 20 11 120 199 0.0 3 123 34 22 20 121 136 0.0 3 85 23 16 12 122 145 0.0 3 90 24 14 17 123 130 0.0 3 82 26 14 8 124 367 0.0 3 314 25 14 14 125 116 0.0 3 80 13 12 11 126 126 0.0 3 92 10 15 9 127 102 0.0 3 76 10 8 8 128 141 0.0 3 114 17 6 4 129 207 0.0 3 164 27 10 6 130 2452 0.0 3 2114 233 75 30 131 1315 0.0 3 1130 150 25 10 132 183 0.0 3 133 32 9 9 133 163 0.0 3 144 15 3 1 134 193 0.0 3 177 13 1 2 135 95 0.0 3 85 9 1 136 150 0.0 3 139 7 1 3 137 74 0.0 3 66 5 1 2 138 99 0.0 3 87 10 0 2 139 101 0.0 3 93 4 3 1 140 69 0.0 3 65 3 1 141 66 0.0 3 64 2 142 92 0.0 3 72 16 3 1 143 35 0.0 3 32 1 1 1 144 17 0.0 3 13 4 145 14 0.0 3 11 1 0 2 146 41 0.0 3 37 2 2 147 26 0.0 3 18 1 3 4 148 61 0.0 3 22 5 9 25 149 8881 0.0 3 26 6333 2314 208 150 95307 0.0 3 2389 87698 4928 292 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 5380280 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: 25.2% C: 21.1% G: 32.4% T: 21.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 560245 374071.5 0 560245 4 183175 93517.9 0 183175 5 108250 23379.5 0 108250 6 97361 5844.9 0 97361 7 103417 1461.2 0 103417 8 95123 365.3 0 95123 9 95599 91.3 0 95189 410 10 99868 22.8 1 88032 11836 11 100076 5.7 1 88187 11889 12 99516 1.4 1 88346 11170 13 114751 0.4 1 102495 12256 14 110536 0.1 1 98344 12192 15 114647 0.0 1 102112 12535 16 110803 0.0 1 98711 12092 17 107275 0.0 1 95635 11640 18 101195 0.0 1 89171 11999 25 19 96197 0.0 1 83608 12368 221 20 101698 0.0 2 82682 13535 5481 21 97733 0.0 2 78816 13116 5801 22 97550 0.0 2 78257 13363 5930 23 99394 0.0 2 80019 13497 5878 24 98884 0.0 2 80075 13081 5728 25 102631 0.0 2 83162 13609 5860 26 101354 0.0 2 79814 15319 6221 27 98808 0.0 2 77490 15148 6162 8 28 96348 0.0 2 75455 14888 5993 12 29 86357 0.0 2 67496 13236 5563 62 30 85544 0.0 3 64663 12432 5209 3240 31 87031 0.0 3 65815 12700 5243 3273 32 84140 0.0 3 63703 12231 5029 3177 33 87718 0.0 3 66575 12768 5102 3273 34 86342 0.0 3 65443 12540 5135 3224 35 85392 0.0 3 65606 11884 4958 2944 36 82686 0.0 3 63384 11474 4744 3084 37 81347 0.0 3 62390 11341 4638 2978 38 75389 0.0 3 58040 10230 4374 2745 39 73503 0.0 3 56939 9871 4070 2623 40 69297 0.0 3 53245 9741 3874 2437 41 66582 0.0 3 51621 9000 3744 2217 42 62229 0.0 3 48304 8102 3570 2253 43 60905 0.0 3 47194 8324 3279 2108 44 62037 0.0 3 48255 8163 3398 2221 45 59495 0.0 3 46302 7953 3220 2020 46 58203 0.0 3 45639 7639 2979 1946 47 55437 0.0 3 43287 7364 2958 1828 48 52151 0.0 3 40634 6992 2755 1770 49 47004 0.0 3 36573 6358 2526 1547 50 48397 0.0 3 38119 6231 2495 1552 51 42563 0.0 3 33555 5536 2119 1353 52 40245 0.0 3 32056 5037 1963 1189 53 39675 0.0 3 31515 4899 1987 1274 54 37750 0.0 3 30010 4730 1838 1172 55 37028 0.0 3 29621 4589 1779 1039 56 34124 0.0 3 27213 4225 1629 1057 57 35210 0.0 3 28421 4176 1609 1004 58 29773 0.0 3 24019 3488 1393 873 59 27848 0.0 3 22446 3177 1361 864 60 24132 0.0 3 19383 2870 1163 716 61 21324 0.0 3 17042 2615 1044 623 62 19797 0.0 3 15787 2411 997 602 63 18439 0.0 3 14886 2129 854 570 64 17349 0.0 3 14050 2016 799 484 65 15941 0.0 3 12820 1874 752 495 66 15485 0.0 3 12619 1759 687 420 67 14827 0.0 3 12013 1777 626 411 68 13177 0.0 3 10632 1582 575 388 69 10956 0.0 3 8779 1359 513 305 70 9896 0.0 3 8005 1127 446 318 71 8849 0.0 3 7200 998 381 270 72 7603 0.0 3 6109 895 376 223 73 6939 0.0 3 5581 855 302 201 74 6403 0.0 3 5180 729 284 210 75 6119 0.0 3 4969 676 271 203 76 5474 0.0 3 4435 602 268 169 77 5238 0.0 3 4206 601 263 168 78 4906 0.0 3 3926 578 224 178 79 4684 0.0 3 3764 547 223 150 80 4236 0.0 3 3365 504 236 131 81 3698 0.0 3 2934 464 184 116 82 3114 0.0 3 2483 355 162 114 83 2956 0.0 3 2371 343 151 91 84 2366 0.0 3 1852 302 121 91 85 2054 0.0 3 1583 260 135 76 86 1921 0.0 3 1447 246 133 95 87 1934 0.0 3 1544 238 94 58 88 1927 0.0 3 1515 230 100 82 89 2042 0.0 3 1628 234 97 83 90 1941 0.0 3 1514 250 87 90 91 1738 0.0 3 1329 246 101 62 92 1466 0.0 3 1151 166 87 62 93 1134 0.0 3 865 141 75 53 94 1068 0.0 3 781 150 79 58 95 836 0.0 3 621 108 50 57 96 824 0.0 3 600 114 65 45 97 751 0.0 3 527 105 63 56 98 838 0.0 3 629 100 70 39 99 755 0.0 3 533 114 61 47 100 808 0.0 3 560 126 71 51 101 643 0.0 3 454 90 57 42 102 554 0.0 3 376 84 53 41 103 712 0.0 3 513 104 55 40 104 14514 0.0 3 12956 1117 305 136 105 639 0.0 3 454 100 53 32 106 452 0.0 3 276 73 59 44 107 397 0.0 3 249 66 40 42 108 400 0.0 3 238 67 39 56 109 368 0.0 3 223 73 41 31 110 316 0.0 3 203 55 28 30 111 296 0.0 3 188 49 30 29 112 323 0.0 3 202 53 38 30 113 244 0.0 3 153 46 20 25 114 284 0.0 3 161 55 38 30 115 218 0.0 3 119 37 38 24 116 242 0.0 3 131 50 31 30 117 214 0.0 3 105 45 35 29 118 223 0.0 3 143 46 16 18 119 178 0.0 3 102 39 19 18 120 203 0.0 3 123 33 27 20 121 142 0.0 3 81 29 20 12 122 158 0.0 3 83 28 31 16 123 147 0.0 3 76 37 15 19 124 373 0.0 3 291 40 25 17 125 116 0.0 3 73 24 14 5 126 138 0.0 3 75 31 22 10 127 103 0.0 3 68 15 9 11 128 141 0.0 3 103 21 11 6 129 199 0.0 3 164 20 11 4 130 2452 0.0 3 2084 273 64 31 131 1064 0.0 3 712 222 88 42 132 142 0.0 3 103 31 5 3 133 156 0.0 3 116 27 9 4 134 185 0.0 3 149 23 7 6 135 92 0.0 3 74 14 2 2 136 147 0.0 3 121 21 3 2 137 71 0.0 3 59 9 2 1 138 95 0.0 3 84 9 2 139 96 0.0 3 85 9 2 140 66 0.0 3 55 9 2 141 64 0.0 3 59 4 1 142 77 0.0 3 67 7 3 143 32 0.0 3 31 1 144 13 0.0 3 13 145 12 0.0 3 10 2 146 40 0.0 3 32 6 1 1 147 19 0.0 3 15 4 148 23 0.0 3 19 4 149 48 0.0 3 23 16 4 5 150 2668 0.0 3 2286 231 87 64