This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH03-33.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH03-33.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH03-33_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH03-33_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 115.853 s (6.067 µs/read; 9.89 M reads/minute). === Summary === Total read pairs processed: 19,096,421 Read 1 with adapter: 4,094,576 (21.4%) Read 2 with adapter: 4,134,344 (21.6%) == Read fate breakdown == Pairs that were too short: 121,215 (0.6%) Pairs written (passing filters): 18,975,206 (99.4%) Total basepairs processed: 5,728,926,300 bp Read 1: 2,864,463,150 bp Read 2: 2,864,463,150 bp Quality-trimmed: 720,916 bp (0.0%) Read 1: 357,745 bp Read 2: 363,171 bp Total written (filtered): 5,479,565,278 bp (95.6%) Read 1: 2,741,737,616 bp Read 2: 2,737,827,662 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 4094576 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: 27.0% C: 20.4% G: 30.3% T: 19.7% none/other: 2.6% Overview of removed sequences length count expect max.err error counts 3 389698 298381.6 0 389698 4 137447 74595.4 0 137447 5 83355 18648.8 0 83355 6 74537 4662.2 0 74537 7 80541 1165.6 0 80541 8 72164 291.4 0 72164 9 74498 72.8 0 74187 311 10 73901 18.2 1 65406 8495 11 75352 4.6 1 66808 8544 12 74812 1.1 1 66814 7998 13 89587 0.3 1 80334 9253 14 86473 0.1 1 77141 9332 15 92319 0.0 1 82744 9575 16 86092 0.0 1 77257 8835 17 82868 0.0 1 74313 8555 18 75159 0.0 1 67405 7723 31 19 68397 0.0 1 60771 7462 164 20 74832 0.0 2 63624 7573 3635 21 70251 0.0 2 60049 6969 3233 22 69708 0.0 2 59492 6875 3341 23 74371 0.0 2 63737 7298 3336 24 72115 0.0 2 61504 7092 3519 25 76306 0.0 2 65443 7350 3513 26 77161 0.0 2 66218 7536 3407 27 74769 0.0 2 64112 7313 3337 7 28 71380 0.0 2 61062 7159 3146 13 29 62342 0.0 2 52835 6572 2908 27 30 61068 0.0 3 50435 6054 2777 1802 31 61209 0.0 3 50776 6012 2669 1752 32 60849 0.0 3 50518 5986 2538 1807 33 63640 0.0 3 52764 6201 2776 1899 34 62227 0.0 3 51796 6064 2620 1747 35 59315 0.0 3 49180 5809 2518 1808 36 57623 0.0 3 48062 5489 2391 1681 37 59335 0.0 3 49517 5661 2399 1758 38 54976 0.0 3 45763 5336 2269 1608 39 52701 0.0 3 44211 4944 2140 1406 40 48949 0.0 3 40864 4681 2033 1371 41 47931 0.0 3 40048 4608 1952 1323 42 44214 0.0 3 36894 4196 1813 1311 43 42918 0.0 3 35849 4091 1769 1209 44 44708 0.0 3 37586 4095 1785 1242 45 41750 0.0 3 35068 3945 1681 1056 46 41951 0.0 3 35286 3890 1685 1090 47 40041 0.0 3 33564 3733 1571 1173 48 39602 0.0 3 33523 3596 1501 982 49 35141 0.0 3 29636 3205 1393 907 50 38658 0.0 3 32846 3505 1416 891 51 31905 0.0 3 27127 2865 1142 771 52 31579 0.0 3 26723 2924 1196 736 53 31545 0.0 3 26843 2825 1125 752 54 29184 0.0 3 24892 2594 1026 672 55 30531 0.0 3 26091 2695 1080 665 56 25861 0.0 3 22110 2258 919 574 57 30428 0.0 3 26213 2551 1033 631 58 23749 0.0 3 20407 1989 818 535 59 23868 0.0 3 20510 2024 809 525 60 19556 0.0 3 16678 1748 693 437 61 16310 0.0 3 13934 1414 582 380 62 15253 0.0 3 13115 1259 546 333 63 15000 0.0 3 12886 1280 516 318 64 14823 0.0 3 12876 1176 488 283 65 12513 0.0 3 10667 1110 461 275 66 12402 0.0 3 10673 1015 439 275 67 12478 0.0 3 10764 1081 385 248 68 10848 0.0 3 9330 921 373 224 69 8269 0.0 3 7105 723 280 161 70 7359 0.0 3 6319 617 264 159 71 6530 0.0 3 5626 541 228 135 72 5723 0.0 3 4962 479 160 122 73 5308 0.0 3 4592 431 163 122 74 4752 0.0 3 4076 397 180 99 75 4620 0.0 3 4008 369 136 107 76 3841 0.0 3 3316 332 105 88 77 3623 0.0 3 3166 284 88 85 78 3395 0.0 3 2936 273 118 68 79 3165 0.0 3 2738 257 109 61 80 2853 0.0 3 2483 217 86 67 81 2564 0.0 3 2213 193 84 74 82 2162 0.0 3 1887 175 67 33 83 2097 0.0 3 1808 163 81 45 84 1645 0.0 3 1389 138 62 56 85 1406 0.0 3 1204 109 46 47 86 1362 0.0 3 1167 103 49 43 87 1377 0.0 3 1158 113 62 44 88 1224 0.0 3 1057 104 36 27 89 1263 0.0 3 1075 107 49 32 90 1119 0.0 3 955 93 37 34 91 1177 0.0 3 1027 73 44 33 92 966 0.0 3 818 84 33 31 93 835 0.0 3 704 77 27 27 94 737 0.0 3 611 74 28 24 95 606 0.0 3 502 49 32 23 96 589 0.0 3 502 50 23 14 97 602 0.0 3 490 64 28 20 98 593 0.0 3 490 55 29 19 99 527 0.0 3 444 47 22 14 100 492 0.0 3 410 47 19 16 101 462 0.0 3 383 37 22 20 102 418 0.0 3 341 39 20 18 103 378 0.0 3 317 34 15 12 104 1451 0.0 3 1264 113 39 35 105 285 0.0 3 234 27 11 13 106 272 0.0 3 211 33 17 11 107 217 0.0 3 165 26 7 19 108 227 0.0 3 161 28 20 18 109 236 0.0 3 174 27 17 18 110 216 0.0 3 152 32 18 14 111 184 0.0 3 139 19 16 10 112 181 0.0 3 130 23 12 16 113 180 0.0 3 131 25 14 10 114 159 0.0 3 99 31 17 12 115 148 0.0 3 97 25 16 10 116 137 0.0 3 93 25 7 12 117 99 0.0 3 67 16 12 4 118 157 0.0 3 116 20 9 12 119 129 0.0 3 91 15 9 14 120 96 0.0 3 69 12 8 7 121 95 0.0 3 63 14 7 11 122 130 0.0 3 99 17 9 5 123 90 0.0 3 67 8 8 7 124 624 0.0 3 569 31 16 8 125 80 0.0 3 49 14 6 11 126 79 0.0 3 61 11 5 2 127 73 0.0 3 51 8 6 8 128 116 0.0 3 99 10 2 5 129 136 0.0 3 122 8 5 1 130 407 0.0 3 354 36 11 6 131 1393 0.0 3 1294 77 12 10 132 170 0.0 3 143 21 3 3 133 141 0.0 3 122 14 4 1 134 203 0.0 3 190 12 1 135 70 0.0 3 66 4 136 103 0.0 3 98 5 137 69 0.0 3 63 4 1 1 138 121 0.0 3 116 5 139 79 0.0 3 75 3 0 1 140 88 0.0 3 82 4 1 1 141 42 0.0 3 39 2 0 1 142 138 0.0 3 112 23 2 1 143 30 0.0 3 19 10 0 1 144 14 0.0 3 9 0 2 3 145 14 0.0 3 14 146 18 0.0 3 14 4 147 19 0.0 3 13 3 1 2 148 80 0.0 3 22 16 12 30 149 11017 0.0 3 21 8251 2514 231 150 103450 0.0 3 2119 95647 5362 322 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 4134344 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: 21.3% G: 30.1% T: 21.1% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 383131 298381.6 0 383131 4 142632 74595.4 0 142632 5 86914 18648.8 0 86914 6 79413 4662.2 0 79413 7 85558 1165.6 0 85558 8 77598 291.4 0 77598 9 79957 72.8 0 79706 251 10 78340 18.2 1 70066 8274 11 79540 4.6 1 71174 8366 12 78635 1.1 1 71006 7629 13 95346 0.3 1 86225 9121 14 91593 0.1 1 82542 9051 15 98211 0.0 1 88687 9524 16 90656 0.0 1 81648 9008 17 87272 0.0 1 78809 8463 18 79074 0.0 1 70660 8401 13 19 73339 0.0 1 64930 8246 163 20 79150 0.0 2 65829 9559 3762 21 73355 0.0 2 60191 9277 3887 22 72470 0.0 2 58858 9594 4018 23 77173 0.0 2 63187 9849 4137 24 74634 0.0 2 61283 9472 3879 25 79596 0.0 2 65390 10042 4164 26 80500 0.0 2 64983 11109 4408 27 77786 0.0 2 62416 11019 4346 5 28 74209 0.0 2 59570 10471 4160 8 29 64838 0.0 2 51876 9205 3721 36 30 63608 0.0 3 49446 8621 3478 2063 31 63827 0.0 3 49530 8587 3562 2148 32 63291 0.0 3 49394 8566 3341 1990 33 66112 0.0 3 51694 8872 3465 2081 34 64462 0.0 3 50375 8637 3293 2157 35 61637 0.0 3 48510 8006 3208 1913 36 60081 0.0 3 47179 8047 2975 1880 37 61733 0.0 3 48752 7878 3162 1941 38 56877 0.0 3 45018 7196 2932 1731 39 54543 0.0 3 43321 6861 2687 1674 40 50652 0.0 3 39645 6795 2600 1612 41 49563 0.0 3 39335 6331 2413 1484 42 45645 0.0 3 36082 5782 2404 1377 43 44584 0.0 3 35395 5724 2142 1323 44 46150 0.0 3 36603 5806 2369 1372 45 43249 0.0 3 34426 5438 2094 1291 46 43306 0.0 3 34666 5283 2068 1289 47 41165 0.0 3 32745 5131 2116 1173 48 40701 0.0 3 32421 5141 1954 1185 49 36071 0.0 3 28588 4642 1736 1105 50 39640 0.0 3 31905 4817 1856 1062 51 32859 0.0 3 26542 3985 1433 899 52 32399 0.0 3 26185 3875 1458 881 53 32276 0.0 3 26299 3647 1457 873 54 29994 0.0 3 24572 3389 1234 799 55 31384 0.0 3 25574 3642 1335 833 56 26594 0.0 3 21808 3004 1119 663 57 31057 0.0 3 25596 3445 1295 721 58 24347 0.0 3 20063 2719 1003 562 59 24219 0.0 3 19997 2592 1001 629 60 20104 0.0 3 16512 2247 852 493 61 16688 0.0 3 13638 1858 733 459 62 15721 0.0 3 12848 1799 672 402 63 15382 0.0 3 12671 1702 603 406 64 15076 0.0 3 12563 1653 527 333 65 12846 0.0 3 10567 1406 528 345 66 12729 0.0 3 10440 1432 546 311 67 12847 0.0 3 10493 1477 560 317 68 11095 0.0 3 9082 1262 479 272 69 8489 0.0 3 7028 896 354 211 70 7492 0.0 3 6147 834 314 197 71 6696 0.0 3 5472 728 311 185 72 5904 0.0 3 4897 610 246 151 73 5414 0.0 3 4443 617 228 126 74 4907 0.0 3 4026 547 210 124 75 4687 0.0 3 3847 519 198 123 76 3955 0.0 3 3253 413 187 102 77 3751 0.0 3 3112 394 158 87 78 3512 0.0 3 2855 418 140 99 79 3270 0.0 3 2623 396 160 91 80 2973 0.0 3 2405 328 141 99 81 2610 0.0 3 2099 306 132 73 82 2278 0.0 3 1839 255 113 71 83 2192 0.0 3 1791 217 107 77 84 1736 0.0 3 1387 197 98 54 85 1476 0.0 3 1170 181 80 45 86 1443 0.0 3 1174 143 75 51 87 1434 0.0 3 1135 168 78 53 88 1281 0.0 3 1025 163 48 45 89 1344 0.0 3 1064 163 70 47 90 1213 0.0 3 949 157 59 48 91 1261 0.0 3 1035 137 61 28 92 1034 0.0 3 827 114 61 32 93 894 0.0 3 685 112 58 39 94 799 0.0 3 627 80 49 43 95 677 0.0 3 514 90 39 34 96 663 0.0 3 480 97 53 33 97 657 0.0 3 496 99 26 36 98 636 0.0 3 490 69 43 34 99 583 0.0 3 443 78 38 24 100 560 0.0 3 411 75 39 35 101 509 0.0 3 367 71 44 27 102 452 0.0 3 341 61 28 22 103 420 0.0 3 321 45 33 21 104 1495 0.0 3 1283 131 46 35 105 341 0.0 3 245 46 27 23 106 316 0.0 3 218 38 38 22 107 268 0.0 3 177 44 29 18 108 277 0.0 3 174 47 28 28 109 272 0.0 3 185 45 28 14 110 248 0.0 3 162 38 27 21 111 216 0.0 3 145 40 19 12 112 215 0.0 3 146 26 25 18 113 219 0.0 3 130 42 29 18 114 189 0.0 3 107 41 23 18 115 170 0.0 3 111 33 17 9 116 157 0.0 3 102 24 20 11 117 114 0.0 3 72 21 8 13 118 176 0.0 3 103 42 19 12 119 154 0.0 3 91 31 15 17 120 120 0.0 3 70 27 10 13 121 116 0.0 3 69 18 16 13 122 143 0.0 3 90 25 17 11 123 111 0.0 3 78 14 10 9 124 629 0.0 3 531 74 11 13 125 76 0.0 3 49 13 7 7 126 90 0.0 3 60 15 11 4 127 74 0.0 3 49 13 8 4 128 123 0.0 3 91 15 8 9 129 144 0.0 3 104 26 9 5 130 399 0.0 3 346 37 11 5 131 1193 0.0 3 836 236 85 36 132 150 0.0 3 127 12 10 1 133 129 0.0 3 100 19 7 3 134 191 0.0 3 167 18 4 2 135 68 0.0 3 57 9 1 1 136 99 0.0 3 86 12 0 1 137 68 0.0 3 60 8 138 117 0.0 3 106 8 2 1 139 76 0.0 3 64 9 3 140 85 0.0 3 76 7 1 1 141 40 0.0 3 31 9 142 117 0.0 3 106 6 2 3 143 21 0.0 3 18 3 144 10 0.0 3 6 3 1 145 15 0.0 3 13 1 0 1 146 16 0.0 3 15 1 147 13 0.0 3 12 1 148 25 0.0 3 18 6 0 1 149 50 0.0 3 19 13 5 13 150 2373 0.0 3 1968 247 96 62