SUMMARISING RUN PARAMETERS ========================== Input filename: ctenidia_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.7 Cutadapt version: 3.4 Python version: could not detect Number of cores used for trimming: 4 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 2004). Second best hit was smallRNA (count: 15) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 2-colour high quality G-trimming enabled, with quality cutoff: --nextseq-trim=20 Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Output file will be GZIP compressed This is cutadapt 3.4 with Python 3.9.6 Command line parameters: -j 4 -e 0.1 --nextseq-trim=20 -O 1 -a AGATCGGAAGAGC ctenidia_2.fastq.gz Processing reads on 4 cores in single-end mode ... Finished in 613.44 s (10 µs/read; 5.90 M reads/minute). === Summary === Total reads processed: 60,302,305 Reads with adapters: 18,719,692 (31.0%) Reads written (passing filters): 60,302,305 (100.0%) Total basepairs processed: 8,729,141,812 bp Quality-trimmed: 321,742,877 bp (3.7%) Total written (filtered): 8,106,551,507 bp (92.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18719692 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 42.0% C: 23.9% G: 13.1% T: 20.8% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 14522406 15075576.2 0 14522406 3 886464 942223.5 0 886464 4 259984 235555.9 0 259984 5 64394 58889.0 0 64394 8 4589 920.1 0 4589 9 5316 230.0 0 5316 10 412 57.5 1 0 412 11 8491 14.4 1 4156 4335 12 1710 3.6 1 0 1710 13 18443 0.9 1 9443 9000 14 2204 0.9 1 222 1982 15 4551 0.9 1 2029 2522 16 12734 0.9 1 6447 6287 17 3311 0.9 1 961 2350 18 3943 0.9 1 2713 1230 19 3620 0.9 1 1677 1943 20 5595 0.9 1 3384 2211 21 9410 0.9 1 7185 2225 22 2993 0.9 1 1783 1210 23 274 0.9 1 206 68 24 1464 0.9 1 941 523 25 6547 0.9 1 4545 2002 26 8264 0.9 1 5662 2602 27 9791 0.9 1 7127 2664 28 3135 0.9 1 2256 879 29 4362 0.9 1 3201 1161 30 4141 0.9 1 3077 1064 31 5202 0.9 1 4646 556 32 10225 0.9 1 7667 2558 33 3254 0.9 1 2413 841 34 7549 0.9 1 5522 2027 35 279 0.9 1 192 87 36 938 0.9 1 600 338 37 2345 0.9 1 1950 395 38 2208 0.9 1 1510 698 39 6302 0.9 1 4753 1549 40 3057 0.9 1 1823 1234 41 3570 0.9 1 2618 952 42 2789 0.9 1 2116 673 43 734 0.9 1 422 312 44 2105 0.9 1 1512 593 45 701 0.9 1 527 174 46 2159 0.9 1 1524 635 47 961 0.9 1 570 391 48 2180 0.9 1 1676 504 49 2645 0.9 1 1866 779 50 1402 0.9 1 791 611 51 2071 0.9 1 1524 547 52 349 0.9 1 205 144 53 1009 0.9 1 686 323 54 1366 0.9 1 945 421 55 851 0.9 1 453 398 56 1511 0.9 1 1029 482 57 1389 0.9 1 832 557 58 1366 0.9 1 776 590 59 1480 0.9 1 952 528 60 1073 0.9 1 629 444 61 1011 0.9 1 579 432 62 1137 0.9 1 586 551 63 1122 0.9 1 556 566 64 1282 0.9 1 497 785 65 1700 0.9 1 423 1277 66 4223 0.9 1 402 3821 67 44380 0.9 1 620 43760 68 160401 0.9 1 779 159622 69 201393 0.9 1 663 200730 70 200426 0.9 1 542 199884 71 151038 0.9 1 401 150637 72 135996 0.9 1 258 135738 73 119801 0.9 1 213 119588 74 77383 0.9 1 169 77214 75 77084 0.9 1 164 76920 76 70068 0.9 1 149 69919 77 50382 0.9 1 99 50283 78 56090 0.9 1 108 55982 79 55541 0.9 1 109 55432 80 54427 0.9 1 99 54328 81 48267 0.9 1 78 48189 82 45338 0.9 1 79 45259 83 37582 0.9 1 55 37527 84 29030 0.9 1 62 28968 85 26155 0.9 1 50 26105 86 22237 0.9 1 56 22181 87 18325 0.9 1 56 18269 88 15646 0.9 1 49 15597 89 14194 0.9 1 43 14151 90 10225 0.9 1 48 10177 91 9372 0.9 1 42 9330 92 8436 0.9 1 33 8403 93 7613 0.9 1 41 7572 94 6682 0.9 1 31 6651 95 6269 0.9 1 30 6239 96 5328 0.9 1 34 5294 97 4665 0.9 1 48 4617 98 4587 0.9 1 36 4551 99 4243 0.9 1 41 4202 100 4210 0.9 1 44 4166 101 4239 0.9 1 38 4201 102 4390 0.9 1 41 4349 103 4591 0.9 1 60 4531 104 4732 0.9 1 72 4660 105 5252 0.9 1 60 5192 106 6094 0.9 1 50 6044 107 6548 0.9 1 42 6506 108 7241 0.9 1 57 7184 109 7654 0.9 1 66 7588 110 7704 0.9 1 57 7647 111 7742 0.9 1 78 7664 112 7909 0.9 1 78 7831 113 7589 0.9 1 53 7536 114 7321 0.9 1 68 7253 115 6584 0.9 1 57 6527 116 6028 0.9 1 38 5990 117 5501 0.9 1 38 5463 118 5082 0.9 1 31 5051 119 4711 0.9 1 25 4686 120 4533 0.9 1 37 4496 121 4097 0.9 1 29 4068 122 3596 0.9 1 23 3573 123 3419 0.9 1 35 3384 124 2903 0.9 1 40 2863 125 2679 0.9 1 21 2658 126 2488 0.9 1 23 2465 127 2330 0.9 1 12 2318 128 2069 0.9 1 18 2051 129 1952 0.9 1 16 1936 130 1750 0.9 1 19 1731 131 1808 0.9 1 16 1792 132 1784 0.9 1 15 1769 133 1788 0.9 1 11 1777 134 1579 0.9 1 6 1573 135 1704 0.9 1 4 1700 136 1808 0.9 1 10 1798 137 1889 0.9 1 10 1879 138 2173 0.9 1 15 2158 139 2364 0.9 1 7 2357 140 2666 0.9 1 8 2658 141 3276 0.9 1 3 3273 142 4109 0.9 1 3 4106 143 5169 0.9 1 1 5168 144 6924 0.9 1 2 6922 145 9488 0.9 1 3 9485 146 13619 0.9 1 2 13617 147 23802 0.9 1 3 23799 148 45414 0.9 1 9 45405 149 90340 0.9 1 1 90339 150 502217 0.9 1 0 502217 151 122136 0.9 1 0 122136 RUN STATISTICS FOR INPUT FILE: ctenidia_2.fastq.gz ============================================= 60302305 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 60302305 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3022509 (5.01%)