SUMMARISING RUN PARAMETERS ========================== Input filename: gonad_1.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: 2115). Second best hit was Nextera (count: 9) 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 gonad_1.fastq.gz Processing reads on 4 cores in single-end mode ... Finished in 680.62 s (10 µs/read; 6.14 M reads/minute). === Summary === Total reads processed: 69,648,408 Reads with adapters: 22,836,005 (32.8%) Reads written (passing filters): 69,648,408 (100.0%) Total basepairs processed: 10,092,146,653 bp Quality-trimmed: 388,797,285 bp (3.9%) Total written (filtered): 9,339,103,670 bp (92.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22836005 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 42.7% C: 25.7% G: 13.3% T: 17.7% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 16533252 17412102.0 0 16533252 3 939460 1088256.4 0 939460 4 302989 272064.1 0 302989 5 186236 68016.0 0 186236 8 55220 1062.8 0 55220 9 81125 265.7 0 81125 10 1349 66.4 1 0 1349 11 91337 16.6 1 81655 9682 12 3419 4.2 1 0 3419 13 45534 1.0 1 39608 5926 14 49894 1.0 1 38346 11548 15 48121 1.0 1 41316 6805 16 52645 1.0 1 40617 12028 17 100345 1.0 1 85889 14456 18 7016 1.0 1 2529 4487 19 34442 1.0 1 29013 5429 20 48079 1.0 1 38731 9348 21 76609 1.0 1 68557 8052 22 8740 1.0 1 4464 4276 23 39120 1.0 1 35057 4063 24 40922 1.0 1 34385 6537 25 40444 1.0 1 34287 6157 26 37907 1.0 1 31865 6042 27 45921 1.0 1 37096 8825 28 38613 1.0 1 32125 6488 29 72380 1.0 1 63644 8736 30 5088 1.0 1 2985 2103 31 29633 1.0 1 24412 5221 32 32784 1.0 1 28813 3971 33 36051 1.0 1 29342 6709 34 50598 1.0 1 45359 5239 35 9291 1.0 1 6052 3239 36 30990 1.0 1 25810 5180 37 29634 1.0 1 24618 5016 38 27439 1.0 1 22904 4535 39 28200 1.0 1 23430 4770 40 21920 1.0 1 18395 3525 41 24754 1.0 1 20808 3946 42 20932 1.0 1 17021 3911 43 31365 1.0 1 27831 3534 44 10290 1.0 1 6947 3343 45 29498 1.0 1 26608 2890 46 5969 1.0 1 3350 2619 47 13631 1.0 1 11932 1699 48 18662 1.0 1 13824 4838 49 23094 1.0 1 20860 2234 50 4574 1.0 1 2424 2150 51 20369 1.0 1 11619 8750 52 21812 1.0 1 19380 2432 53 6255 1.0 1 1799 4456 54 14996 1.0 1 6415 8581 55 21845 1.0 1 9636 12209 56 23846 1.0 1 11057 12789 57 15475 1.0 1 5640 9835 58 16550 1.0 1 8933 7617 59 10942 1.0 1 9475 1467 60 28140 1.0 1 1187 26953 61 37584 1.0 1 8980 28604 62 39470 1.0 1 9364 30106 63 9650 1.0 1 7914 1736 64 58432 1.0 1 1184 57248 65 224642 1.0 1 8913 215729 66 123916 1.0 1 18122 105794 67 118866 1.0 1 9393 109473 68 16626 1.0 1 12896 3730 69 2366 1.0 1 756 1610 70 1964 1.0 1 506 1458 71 2672 1.0 1 483 2189 72 5257 1.0 1 405 4852 73 33702 1.0 1 545 33157 74 153185 1.0 1 651 152534 75 211887 1.0 1 669 211218 76 158276 1.0 1 722 157554 77 180153 1.0 1 470 179683 78 155928 1.0 1 355 155573 79 132822 1.0 1 223 132599 80 111466 1.0 1 175 111291 81 88230 1.0 1 118 88112 82 72088 1.0 1 94 71994 83 68695 1.0 1 119 68576 84 59893 1.0 1 79 59814 85 49638 1.0 1 82 49556 86 42097 1.0 1 52 42045 87 36967 1.0 1 37 36930 88 29837 1.0 1 44 29793 89 24985 1.0 1 47 24938 90 21961 1.0 1 47 21914 91 18700 1.0 1 44 18656 92 15461 1.0 1 43 15418 93 13387 1.0 1 42 13345 94 11377 1.0 1 46 11331 95 9943 1.0 1 38 9905 96 9552 1.0 1 23 9529 97 8219 1.0 1 37 8182 98 7024 1.0 1 34 6990 99 6007 1.0 1 30 5977 100 6007 1.0 1 28 5979 101 5928 1.0 1 17 5911 102 6430 1.0 1 21 6409 103 6751 1.0 1 23 6728 104 7068 1.0 1 18 7050 105 7443 1.0 1 20 7423 106 8146 1.0 1 37 8109 107 8211 1.0 1 24 8187 108 8382 1.0 1 12 8370 109 8625 1.0 1 17 8608 110 8551 1.0 1 22 8529 111 8124 1.0 1 14 8110 112 8080 1.0 1 12 8068 113 7156 1.0 1 17 7139 114 6844 1.0 1 16 6828 115 6568 1.0 1 9 6559 116 5800 1.0 1 14 5786 117 5606 1.0 1 16 5590 118 4889 1.0 1 19 4870 119 4618 1.0 1 19 4599 120 4202 1.0 1 11 4191 121 4059 1.0 1 14 4045 122 3811 1.0 1 23 3788 123 3491 1.0 1 10 3481 124 3509 1.0 1 11 3498 125 3575 1.0 1 7 3568 126 3539 1.0 1 11 3528 127 3624 1.0 1 7 3617 128 3584 1.0 1 7 3577 129 3227 1.0 1 13 3214 130 3105 1.0 1 6 3099 131 2908 1.0 1 4 2904 132 2607 1.0 1 13 2594 133 2349 1.0 1 16 2333 134 2386 1.0 1 11 2375 135 2355 1.0 1 11 2344 136 2324 1.0 1 6 2318 137 2376 1.0 1 11 2365 138 2534 1.0 1 5 2529 139 2536 1.0 1 4 2532 140 2676 1.0 1 4 2672 141 3208 1.0 1 4 3204 142 3772 1.0 1 2 3770 143 4415 1.0 1 2 4413 144 5596 1.0 1 2 5594 145 7818 1.0 1 2 7816 146 10793 1.0 1 2 10791 147 19023 1.0 1 2 19021 148 41430 1.0 1 1 41429 149 70478 1.0 1 0 70478 150 316783 1.0 1 3 316780 151 130014 1.0 1 0 130014 RUN STATISTICS FOR INPUT FILE: gonad_1.fastq.gz ============================================= 69648408 sequences processed in total