This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH10-08.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH10-08.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH10-08_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH10-08_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 173.033 s (6.822 µs/read; 8.80 M reads/minute). === Summary === Total read pairs processed: 25,364,326 Read 1 with adapter: 3,406,159 (13.4%) Read 2 with adapter: 3,458,319 (13.6%) == Read fate breakdown == Pairs that were too short: 46,584 (0.2%) Pairs written (passing filters): 25,317,742 (99.8%) Total basepairs processed: 7,609,297,800 bp Read 1: 3,804,648,900 bp Read 2: 3,804,648,900 bp Quality-trimmed: 1,026,416 bp (0.0%) Read 1: 475,642 bp Read 2: 550,774 bp Total written (filtered): 7,442,564,649 bp (97.8%) Read 1: 3,722,456,537 bp Read 2: 3,720,108,112 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 3406159 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: 27.4% C: 20.2% G: 31.4% T: 19.9% none/other: 1.1% Overview of removed sequences length count expect max.err error counts 3 532379 396317.6 0 532379 4 161577 99079.4 0 161577 5 81480 24769.8 0 81480 6 67259 6192.5 0 67259 7 74297 1548.1 0 74297 8 66613 387.0 0 66613 9 68282 96.8 0 67970 312 10 68483 24.2 1 60388 8095 11 65908 6.0 1 58244 7664 12 65735 1.5 1 58403 7332 13 75767 0.4 1 67553 8214 14 73573 0.1 1 65309 8264 15 76811 0.0 1 68490 8321 16 71649 0.0 1 63903 7746 17 69309 0.0 1 62017 7292 18 64119 0.0 1 57310 6785 24 19 58254 0.0 1 51353 6766 135 20 62114 0.0 2 52383 6494 3237 21 60618 0.0 2 51245 6400 2973 22 59504 0.0 2 50416 6124 2964 23 61626 0.0 2 52044 6534 3048 24 59578 0.0 2 50255 6300 3023 25 61007 0.0 2 51579 6373 3055 26 61140 0.0 2 51981 6323 2836 27 59026 0.0 2 50070 6186 2762 8 28 60038 0.0 2 50825 6383 2820 10 29 51210 0.0 2 43121 5552 2505 32 30 47883 0.0 3 39239 4922 2211 1511 31 48215 0.0 3 39796 4832 2080 1507 32 46962 0.0 3 38795 4672 2076 1419 33 49358 0.0 3 40715 4951 2168 1524 34 48407 0.0 3 39870 5034 2094 1409 35 45248 0.0 3 37184 4586 2039 1439 36 43265 0.0 3 35598 4411 1913 1343 37 42715 0.0 3 35382 4323 1800 1210 38 39516 0.0 3 32677 3886 1774 1179 39 39495 0.0 3 32781 3960 1658 1096 40 35617 0.0 3 29505 3656 1433 1023 41 33022 0.0 3 27423 3245 1427 927 42 31167 0.0 3 25823 3148 1296 900 43 30098 0.0 3 24846 3108 1296 848 44 29437 0.0 3 24473 2845 1297 822 45 28132 0.0 3 23293 2850 1174 815 46 27803 0.0 3 23156 2745 1170 732 47 25243 0.0 3 20950 2550 1060 683 48 24634 0.0 3 20512 2464 992 666 49 21864 0.0 3 18133 2132 955 644 50 22542 0.0 3 18767 2233 921 621 51 19330 0.0 3 16279 1760 759 532 52 18033 0.0 3 15095 1708 764 466 53 18218 0.0 3 15349 1716 694 459 54 16980 0.0 3 14343 1548 639 450 55 16292 0.0 3 13748 1478 651 415 56 14204 0.0 3 11940 1374 522 368 57 15996 0.0 3 13588 1454 593 361 58 13217 0.0 3 11128 1276 487 326 59 12562 0.0 3 10686 1077 476 323 60 10683 0.0 3 9013 1002 389 279 61 8900 0.0 3 7477 831 356 236 62 7936 0.0 3 6650 776 335 175 63 8002 0.0 3 6780 721 323 178 64 7804 0.0 3 6643 700 284 177 65 6663 0.0 3 5668 573 247 175 66 6515 0.0 3 5494 611 240 170 67 6263 0.0 3 5315 576 208 164 68 5322 0.0 3 4546 454 200 122 69 4269 0.0 3 3596 388 177 108 70 3905 0.0 3 3255 396 151 103 71 3441 0.0 3 2892 339 120 90 72 2942 0.0 3 2431 293 126 92 73 2729 0.0 3 2288 264 106 71 74 2435 0.0 3 2034 229 108 64 75 2278 0.0 3 1911 207 100 60 76 2059 0.0 3 1744 185 74 56 77 1972 0.0 3 1680 186 66 40 78 1750 0.0 3 1455 162 73 60 79 1587 0.0 3 1325 138 75 49 80 1481 0.0 3 1237 139 60 45 81 1328 0.0 3 1086 131 67 44 82 1190 0.0 3 995 118 46 31 83 1054 0.0 3 856 116 55 27 84 910 0.0 3 731 92 48 39 85 816 0.0 3 651 93 47 25 86 778 0.0 3 626 97 33 22 87 689 0.0 3 558 75 27 29 88 727 0.0 3 574 69 53 31 89 675 0.0 3 513 92 40 30 90 623 0.0 3 496 65 35 27 91 628 0.0 3 509 56 36 27 92 564 0.0 3 442 69 24 29 93 509 0.0 3 394 59 30 26 94 428 0.0 3 320 51 23 34 95 403 0.0 3 299 52 29 23 96 352 0.0 3 268 39 25 20 97 315 0.0 3 221 53 20 21 98 364 0.0 3 273 46 24 21 99 359 0.0 3 262 49 27 21 100 341 0.0 3 243 45 36 17 101 303 0.0 3 230 32 22 19 102 332 0.0 3 239 41 28 24 103 390 0.0 3 301 51 19 19 104 3360 0.0 3 2892 327 84 57 105 268 0.0 3 197 33 19 19 106 239 0.0 3 156 48 18 17 107 212 0.0 3 141 36 21 14 108 196 0.0 3 116 35 24 21 109 176 0.0 3 118 22 17 19 110 235 0.0 3 161 37 17 20 111 189 0.0 3 122 32 18 17 112 191 0.0 3 119 31 21 20 113 144 0.0 3 91 28 13 12 114 150 0.0 3 91 25 22 12 115 147 0.0 3 99 19 18 11 116 159 0.0 3 104 25 16 14 117 121 0.0 3 80 21 11 9 118 178 0.0 3 108 34 17 19 119 142 0.0 3 86 30 19 7 120 160 0.0 3 108 19 15 18 121 118 0.0 3 77 22 10 9 122 130 0.0 3 76 23 19 12 123 103 0.0 3 63 18 11 11 124 176 0.0 3 131 26 8 11 125 86 0.0 3 55 16 8 7 126 117 0.0 3 85 11 11 10 127 121 0.0 3 95 16 6 4 128 275 0.0 3 236 19 11 9 129 585 0.0 3 537 36 9 3 130 404 0.0 3 360 31 9 4 131 1020 0.0 3 945 61 9 5 132 242 0.0 3 226 14 2 133 186 0.0 3 172 11 3 134 182 0.0 3 159 16 3 4 135 103 0.0 3 98 3 1 1 136 70 0.0 3 62 4 3 1 137 84 0.0 3 78 5 1 138 99 0.0 3 92 5 1 1 139 43 0.0 3 37 5 0 1 140 47 0.0 3 41 4 2 141 41 0.0 3 37 3 1 142 39 0.0 3 33 3 2 1 143 19 0.0 3 15 4 144 8 0.0 3 8 145 9 0.0 3 7 0 0 2 146 33 0.0 3 29 2 0 2 147 20 0.0 3 16 1 0 3 148 44 0.0 3 19 5 5 15 149 4085 0.0 3 6 3082 907 90 150 35578 0.0 3 1267 32183 1985 143 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 3458319 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: 27.5% C: 20.7% G: 31.0% T: 20.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 519536 396317.6 0 519536 4 168967 99079.4 0 168967 5 84867 24769.8 0 84867 6 71135 6192.5 0 71135 7 78556 1548.1 0 78556 8 71173 387.0 0 71173 9 71864 96.8 0 71602 262 10 71975 24.2 1 63670 8305 11 69188 6.0 1 61196 7992 12 68932 1.5 1 61642 7290 13 79626 0.4 1 71459 8167 14 77343 0.1 1 69194 8149 15 80732 0.0 1 72207 8525 16 74426 0.0 1 66523 7903 17 72722 0.0 1 65218 7504 18 66443 0.0 1 58274 8161 8 19 61584 0.0 1 53349 8116 119 20 64941 0.0 2 52222 9169 3550 21 62330 0.0 2 49417 9059 3854 22 60814 0.0 2 48013 9097 3704 23 63030 0.0 2 49932 9163 3935 24 61003 0.0 2 48692 8653 3658 25 62489 0.0 2 50243 8700 3546 26 62937 0.0 2 48713 10289 3935 27 60178 0.0 2 46245 9902 4028 3 28 61314 0.0 2 47386 9979 3944 5 29 52246 0.0 2 40214 8605 3389 38 30 49038 0.0 3 36555 7606 3021 1856 31 49484 0.0 3 37093 7548 3030 1813 32 48141 0.0 3 36032 7518 2885 1706 33 50664 0.0 3 38134 7814 2955 1761 34 49478 0.0 3 37228 7628 2908 1714 35 46590 0.0 3 35337 6894 2689 1670 36 44239 0.0 3 33270 6745 2656 1568 37 43892 0.0 3 33208 6473 2651 1560 38 40539 0.0 3 30855 5873 2374 1437 39 40461 0.0 3 31092 5724 2260 1385 40 36441 0.0 3 27602 5446 2135 1258 41 33878 0.0 3 25743 5050 1994 1091 42 31786 0.0 3 24114 4602 1967 1103 43 30833 0.0 3 23502 4618 1692 1021 44 30115 0.0 3 22974 4350 1788 1003 45 28797 0.0 3 22060 4128 1629 980 46 28410 0.0 3 21715 4059 1673 963 47 25716 0.0 3 19736 3659 1447 874 48 25078 0.0 3 19299 3462 1447 870 49 22240 0.0 3 16922 3332 1243 743 50 22996 0.0 3 17720 3261 1278 737 51 19807 0.0 3 15365 2799 995 648 52 18590 0.0 3 14491 2539 952 608 53 18684 0.0 3 14710 2455 992 527 54 17380 0.0 3 13636 2306 894 544 55 16714 0.0 3 13041 2325 853 495 56 14640 0.0 3 11420 1973 790 457 57 16185 0.0 3 13019 1967 714 485 58 13521 0.0 3 10666 1763 669 423 59 12764 0.0 3 10235 1571 623 335 60 10949 0.0 3 8609 1449 560 331 61 9120 0.0 3 7112 1216 468 324 62 8140 0.0 3 6303 1134 427 276 63 8145 0.0 3 6422 1075 387 261 64 7991 0.0 3 6307 1070 374 240 65 6865 0.0 3 5404 905 362 194 66 6681 0.0 3 5277 874 326 204 67 6434 0.0 3 5055 899 312 168 68 5516 0.0 3 4357 686 289 184 69 4379 0.0 3 3492 533 213 141 70 4002 0.0 3 3157 471 235 139 71 3607 0.0 3 2793 494 199 121 72 3038 0.0 3 2329 423 178 108 73 2846 0.0 3 2190 399 170 87 74 2524 0.0 3 2004 309 114 97 75 2400 0.0 3 1860 323 125 92 76 2170 0.0 3 1683 289 122 76 77 2099 0.0 3 1581 295 127 96 78 1829 0.0 3 1420 229 97 83 79 1687 0.0 3 1271 237 114 65 80 1596 0.0 3 1156 248 131 61 81 1409 0.0 3 1046 221 80 62 82 1275 0.0 3 967 183 66 59 83 1145 0.0 3 838 170 78 59 84 973 0.0 3 718 135 70 50 85 916 0.0 3 673 117 66 60 86 858 0.0 3 635 122 61 40 87 760 0.0 3 548 115 53 44 88 826 0.0 3 592 125 62 47 89 750 0.0 3 532 103 71 44 90 708 0.0 3 511 99 57 41 91 704 0.0 3 494 102 63 45 92 657 0.0 3 458 104 59 36 93 583 0.0 3 404 88 52 39 94 499 0.0 3 331 81 55 32 95 449 0.0 3 307 66 45 31 96 429 0.0 3 296 73 29 31 97 410 0.0 3 243 66 56 45 98 429 0.0 3 283 70 53 23 99 440 0.0 3 278 76 47 39 100 430 0.0 3 249 87 55 39 101 383 0.0 3 248 67 33 35 102 385 0.0 3 244 62 42 37 103 450 0.0 3 298 78 42 32 104 3477 0.0 3 2971 342 101 63 105 343 0.0 3 203 60 42 38 106 307 0.0 3 177 65 44 21 107 262 0.0 3 145 52 33 32 108 254 0.0 3 126 63 30 35 109 236 0.0 3 140 45 26 25 110 294 0.0 3 165 53 43 33 111 236 0.0 3 118 61 29 28 112 236 0.0 3 118 52 44 22 113 192 0.0 3 96 43 28 25 114 198 0.0 3 98 43 27 30 115 200 0.0 3 117 37 25 21 116 190 0.0 3 103 44 24 19 117 154 0.0 3 85 32 17 20 118 208 0.0 3 110 38 32 28 119 173 0.0 3 100 40 21 12 120 192 0.0 3 97 43 29 23 121 143 0.0 3 86 29 15 13 122 156 0.0 3 68 38 25 25 123 121 0.0 3 68 20 23 10 124 199 0.0 3 133 32 18 16 125 109 0.0 3 59 20 16 14 126 126 0.0 3 85 17 12 12 127 137 0.0 3 87 27 8 15 128 276 0.0 3 203 50 13 10 129 589 0.0 3 430 100 37 22 130 395 0.0 3 295 66 21 13 131 983 0.0 3 656 226 69 32 132 234 0.0 3 177 35 14 8 133 175 0.0 3 137 24 9 5 134 171 0.0 3 140 25 5 1 135 101 0.0 3 82 14 3 2 136 66 0.0 3 54 6 3 3 137 82 0.0 3 73 8 1 138 96 0.0 3 91 4 1 139 42 0.0 3 37 4 1 140 43 0.0 3 39 4 141 38 0.0 3 35 3 142 35 0.0 3 30 3 1 1 143 16 0.0 3 11 4 0 1 144 8 0.0 3 7 0 0 1 145 7 0.0 3 6 0 1 146 30 0.0 3 28 1 1 147 17 0.0 3 14 2 1 148 23 0.0 3 17 4 1 1 149 18 0.0 3 5 10 2 1 150 1393 0.0 3 1214 111 42 26