This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 0 -o /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-09.trimmed.R1.fastq.gz -p /share/nwfsc/ggoetz/202212-l.staminea/trimmed/CH05-09.trimmed.R2.fastq.gz -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,10 -m 40 --trim-n /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-09_R1_001.fastq.gz /share/nwfsc/knichols/Dungeness/RNAseq_gill/CH05-09_R2_001.fastq.gz Processing paired-end reads on 20 cores ... Finished in 191.415 s (6.403 µs/read; 9.37 M reads/minute). === Summary === Total read pairs processed: 29,893,608 Read 1 with adapter: 5,307,320 (17.8%) Read 2 with adapter: 5,411,584 (18.1%) == Read fate breakdown == Pairs that were too short: 78,916 (0.3%) Pairs written (passing filters): 29,814,692 (99.7%) Total basepairs processed: 8,968,082,400 bp Read 1: 4,484,041,200 bp Read 2: 4,484,041,200 bp Quality-trimmed: 1,225,834 bp (0.0%) Read 1: 570,444 bp Read 2: 655,390 bp Total written (filtered): 8,679,661,738 bp (96.8%) Read 1: 4,342,272,658 bp Read 2: 4,337,389,080 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Type: regular 3'; Length: 33; Trimmed: 5307320 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: 26.5% C: 18.9% G: 32.4% T: 21.0% none/other: 1.2% Overview of removed sequences length count expect max.err error counts 3 651906 467087.6 0 651906 4 205366 116771.9 0 205366 5 110183 29193.0 0 110183 6 97110 7298.2 0 97110 7 110398 1824.6 0 110398 8 95586 456.1 0 95586 9 99291 114.0 0 98858 433 10 97867 28.5 1 86464 11403 11 98334 7.1 1 86924 11410 12 95404 1.8 1 84835 10569 13 115030 0.4 1 102760 12270 14 109444 0.1 1 96968 12476 15 113156 0.0 1 100756 12400 16 109933 0.0 1 98401 11532 17 104116 0.0 1 93125 10991 18 98498 0.0 1 87903 10567 28 19 90334 0.0 1 79803 10318 213 20 97733 0.0 2 82175 10587 4971 21 94716 0.0 2 79898 10121 4697 22 93672 0.0 2 79004 9937 4731 23 97432 0.0 2 82645 10159 4628 24 94957 0.0 2 80174 10011 4772 25 97472 0.0 2 82462 10187 4823 26 99884 0.0 2 84522 10557 4805 27 95749 0.0 2 81361 9981 4395 12 28 97024 0.0 2 82289 10190 4520 25 29 82474 0.0 2 69602 8790 4030 52 30 78677 0.0 3 64428 8246 3572 2431 31 81053 0.0 3 66795 8259 3567 2432 32 78414 0.0 3 64470 7953 3608 2383 33 82796 0.0 3 68337 8278 3628 2553 34 81285 0.0 3 67031 8361 3477 2416 35 76862 0.0 3 63335 7878 3436 2213 36 76566 0.0 3 63096 7880 3283 2307 37 75948 0.0 3 62766 7624 3293 2265 38 69941 0.0 3 57941 7044 2999 1957 39 69562 0.0 3 57710 7047 2829 1976 40 63032 0.0 3 52436 6192 2630 1774 41 60752 0.0 3 50413 6168 2536 1635 42 56579 0.0 3 46849 5705 2408 1617 43 54333 0.0 3 44883 5583 2323 1544 44 54374 0.0 3 45155 5436 2282 1501 45 52691 0.0 3 43911 5123 2167 1490 46 51239 0.0 3 42628 5147 1983 1481 47 48445 0.0 3 39973 5087 2067 1318 48 46487 0.0 3 38818 4525 1906 1238 49 42818 0.0 3 35702 4225 1733 1158 50 42987 0.0 3 35991 4150 1677 1169 51 38051 0.0 3 31835 3738 1501 977 52 36254 0.0 3 30447 3524 1405 878 53 36023 0.0 3 30184 3517 1430 892 54 35207 0.0 3 29744 3294 1324 845 55 32344 0.0 3 27309 3016 1260 759 56 29527 0.0 3 24826 2810 1149 742 57 32127 0.0 3 27368 2879 1164 716 58 26485 0.0 3 22581 2373 938 593 59 26073 0.0 3 22081 2415 968 609 60 22191 0.0 3 18705 2120 846 520 61 18157 0.0 3 15313 1694 673 477 62 16963 0.0 3 14333 1628 600 402 63 16514 0.0 3 14007 1495 612 400 64 16330 0.0 3 13979 1444 520 387 65 13898 0.0 3 11846 1216 530 306 66 13437 0.0 3 11495 1165 478 299 67 13485 0.0 3 11466 1240 467 312 68 11591 0.0 3 9794 1058 471 268 69 8965 0.0 3 7620 803 323 219 70 7954 0.0 3 6795 694 274 191 71 7576 0.0 3 6437 685 274 180 72 6007 0.0 3 5076 565 207 159 73 5926 0.0 3 5079 491 217 139 74 4957 0.0 3 4233 436 171 117 75 4915 0.0 3 4162 461 181 111 76 4000 0.0 3 3374 371 156 99 77 4156 0.0 3 3557 371 143 85 78 3747 0.0 3 3161 342 139 105 79 3537 0.0 3 3034 313 112 78 80 3212 0.0 3 2695 306 132 79 81 2826 0.0 3 2425 229 111 61 82 2469 0.0 3 2070 233 101 65 83 2243 0.0 3 1942 172 75 54 84 1603 0.0 3 1336 149 62 56 85 1567 0.0 3 1307 141 65 54 86 1531 0.0 3 1308 125 64 34 87 1363 0.0 3 1131 126 54 52 88 1446 0.0 3 1212 111 78 45 89 1511 0.0 3 1261 144 60 46 90 1341 0.0 3 1112 135 53 41 91 1351 0.0 3 1106 130 66 49 92 1097 0.0 3 889 117 50 41 93 857 0.0 3 684 95 40 38 94 730 0.0 3 569 84 44 33 95 665 0.0 3 517 66 42 40 96 621 0.0 3 478 70 30 43 97 549 0.0 3 439 59 26 25 98 611 0.0 3 459 83 41 28 99 594 0.0 3 463 72 29 30 100 640 0.0 3 489 78 37 36 101 531 0.0 3 428 57 30 16 102 428 0.0 3 335 43 26 24 103 497 0.0 3 394 48 29 26 104 3212 0.0 3 2829 253 72 58 105 365 0.0 3 258 50 31 26 106 299 0.0 3 204 40 31 24 107 265 0.0 3 180 38 29 18 108 268 0.0 3 181 43 24 20 109 260 0.0 3 180 42 20 18 110 266 0.0 3 164 34 37 31 111 208 0.0 3 143 31 17 17 112 267 0.0 3 182 41 24 20 113 220 0.0 3 151 28 21 20 114 229 0.0 3 151 29 24 25 115 193 0.0 3 117 33 25 18 116 194 0.0 3 118 31 22 23 117 176 0.0 3 120 26 19 11 118 189 0.0 3 110 38 26 15 119 154 0.0 3 99 29 14 12 120 164 0.0 3 95 31 23 15 121 153 0.0 3 98 25 17 13 122 185 0.0 3 108 35 27 15 123 135 0.0 3 89 30 10 6 124 328 0.0 3 253 43 15 17 125 120 0.0 3 78 24 11 7 126 130 0.0 3 96 18 6 10 127 98 0.0 3 60 22 10 6 128 167 0.0 3 143 14 5 5 129 413 0.0 3 376 23 8 6 130 229 0.0 3 203 19 5 2 131 2186 0.0 3 2011 147 22 6 132 222 0.0 3 183 25 6 8 133 120 0.0 3 106 10 2 2 134 245 0.0 3 217 18 7 3 135 82 0.0 3 73 8 1 136 90 0.0 3 80 6 3 1 137 88 0.0 3 77 8 2 1 138 140 0.0 3 129 7 3 1 139 47 0.0 3 40 6 1 140 30 0.0 3 27 1 2 141 44 0.0 3 34 3 5 2 142 40 0.0 3 27 8 3 2 143 25 0.0 3 19 2 1 3 144 6 0.0 3 5 0 1 145 15 0.0 3 12 2 0 1 146 20 0.0 3 16 2 2 147 21 0.0 3 18 1 0 2 148 55 0.0 3 27 8 4 16 149 7157 0.0 3 10 5377 1613 157 150 63210 0.0 3 1300 58212 3459 239 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; Type: regular 3'; Length: 33; Trimmed: 5411584 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: 26.4% C: 19.5% G: 32.1% T: 22.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 631940 467087.6 0 631940 4 214783 116771.9 0 214783 5 114727 29193.0 0 114727 6 102567 7298.2 0 102567 7 115861 1824.6 0 115861 8 101973 456.1 0 101973 9 105281 114.0 0 104860 421 10 103233 28.5 1 91831 11402 11 103204 7.1 1 91763 11441 12 99709 1.8 1 89254 10455 13 121328 0.4 1 109218 12110 14 115018 0.1 1 103088 11930 15 119044 0.0 1 106880 12164 16 114658 0.0 1 102745 11913 17 109222 0.0 1 98143 11079 18 102993 0.0 1 92337 10642 14 19 96269 0.0 1 86111 9957 201 20 103581 0.0 2 88889 10403 4289 21 99155 0.0 2 84764 9892 4499 22 97345 0.0 2 82684 10124 4537 23 100758 0.0 2 85191 10748 4819 24 98367 0.0 2 83241 10391 4735 25 101695 0.0 2 86443 10554 4698 26 104561 0.0 2 86244 13086 5231 27 99689 0.0 2 81302 13287 5095 5 28 100992 0.0 2 82142 13909 4934 7 29 85535 0.0 2 69669 11402 4387 77 30 81392 0.0 3 64583 10078 4078 2653 31 84148 0.0 3 66641 10625 4219 2663 32 81226 0.0 3 64461 10305 3852 2608 33 85850 0.0 3 67977 10767 4316 2790 34 83867 0.0 3 66628 10403 4135 2701 35 79695 0.0 3 63536 9768 3904 2487 36 79124 0.0 3 62898 9740 3942 2544 37 78745 0.0 3 63206 9460 3751 2328 38 72383 0.0 3 58110 8747 3342 2184 39 71984 0.0 3 58031 8532 3304 2117 40 65015 0.0 3 52278 7700 3108 1929 41 62750 0.0 3 50793 7223 2850 1884 42 58115 0.0 3 46987 6658 2716 1754 43 56275 0.0 3 45644 6391 2630 1610 44 56002 0.0 3 45401 6332 2595 1674 45 54362 0.0 3 44042 6150 2542 1628 46 52789 0.0 3 43090 5920 2350 1429 47 49950 0.0 3 40679 5584 2262 1425 48 47771 0.0 3 38990 5334 2084 1363 49 43937 0.0 3 35789 4895 1940 1313 50 44327 0.0 3 36261 4918 1930 1218 51 39331 0.0 3 32385 4193 1676 1077 52 37328 0.0 3 30768 3939 1592 1029 53 36940 0.0 3 30445 3922 1540 1033 54 36177 0.0 3 29752 3924 1532 969 55 33277 0.0 3 27573 3547 1327 830 56 30454 0.0 3 25173 3299 1219 763 57 33061 0.0 3 27585 3322 1259 895 58 27259 0.0 3 22726 2812 1067 654 59 26535 0.0 3 22064 2695 1089 687 60 22756 0.0 3 18837 2407 926 586 61 18709 0.0 3 15604 1911 728 466 62 17411 0.0 3 14509 1743 712 447 63 16970 0.0 3 14174 1713 667 416 64 16734 0.0 3 14074 1631 620 409 65 14402 0.0 3 12012 1462 547 381 66 13841 0.0 3 11601 1360 534 346 67 13865 0.0 3 11664 1351 512 338 68 11877 0.0 3 9892 1191 490 304 69 9246 0.0 3 7677 904 403 262 70 8217 0.0 3 6778 868 338 233 71 7803 0.0 3 6452 777 338 236 72 6290 0.0 3 5144 644 297 205 73 6083 0.0 3 5068 599 248 168 74 5127 0.0 3 4279 508 208 132 75 5077 0.0 3 4262 507 187 121 76 4202 0.0 3 3453 448 177 124 77 4339 0.0 3 3643 397 165 134 78 3946 0.0 3 3252 415 157 122 79 3672 0.0 3 3050 356 142 124 80 3378 0.0 3 2772 342 148 116 81 2983 0.0 3 2453 293 146 91 82 2616 0.0 3 2128 252 144 92 83 2345 0.0 3 1934 229 101 81 84 1739 0.0 3 1388 172 107 72 85 1671 0.0 3 1338 165 98 70 86 1623 0.0 3 1323 158 88 54 87 1492 0.0 3 1178 164 92 58 88 1569 0.0 3 1254 172 90 53 89 1598 0.0 3 1271 177 95 55 90 1437 0.0 3 1143 154 78 62 91 1465 0.0 3 1159 163 86 57 92 1211 0.0 3 973 124 66 48 93 964 0.0 3 737 120 65 42 94 827 0.0 3 599 124 60 44 95 737 0.0 3 539 110 46 42 96 725 0.0 3 518 92 64 51 97 639 0.0 3 465 74 57 43 98 717 0.0 3 522 103 45 47 99 685 0.0 3 490 99 53 43 100 744 0.0 3 548 96 52 48 101 636 0.0 3 469 80 39 48 102 534 0.0 3 375 69 46 44 103 561 0.0 3 424 81 37 19 104 3330 0.0 3 2947 261 73 49 105 430 0.0 3 305 67 27 31 106 380 0.0 3 246 60 33 41 107 350 0.0 3 214 65 43 28 108 340 0.0 3 206 66 34 34 109 318 0.0 3 207 47 34 30 110 328 0.0 3 202 50 44 32 111 254 0.0 3 160 49 25 20 112 343 0.0 3 192 84 35 32 113 259 0.0 3 167 31 38 23 114 294 0.0 3 181 53 32 28 115 239 0.0 3 143 41 25 30 116 239 0.0 3 141 41 32 25 117 205 0.0 3 135 29 19 22 118 220 0.0 3 128 38 30 24 119 188 0.0 3 107 39 24 18 120 205 0.0 3 108 32 40 25 121 174 0.0 3 113 26 19 16 122 217 0.0 3 119 45 29 24 123 166 0.0 3 98 35 15 18 124 366 0.0 3 273 40 35 18 125 130 0.0 3 88 12 16 14 126 154 0.0 3 102 27 10 15 127 105 0.0 3 73 14 9 9 128 176 0.0 3 136 24 9 7 129 418 0.0 3 341 55 12 10 130 215 0.0 3 172 23 14 6 131 1866 0.0 3 1394 309 116 47 132 189 0.0 3 149 25 12 3 133 120 0.0 3 102 9 7 2 134 236 0.0 3 206 18 6 6 135 77 0.0 3 69 5 1 2 136 83 0.0 3 73 6 2 2 137 87 0.0 3 75 11 1 138 138 0.0 3 123 12 2 1 139 44 0.0 3 36 5 1 2 140 27 0.0 3 23 3 1 141 37 0.0 3 32 5 142 33 0.0 3 27 6 143 21 0.0 3 21 144 6 0.0 3 5 0 0 1 145 14 0.0 3 13 0 0 1 146 16 0.0 3 13 3 147 19 0.0 3 16 0 0 3 148 28 0.0 3 25 3 149 30 0.0 3 12 3 8 7 150 1450 0.0 3 1291 70 47 42