SUMMARISING RUN PARAMETERS ========================== Input filename: gonad_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: 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_2.fastq.gz Processing reads on 4 cores in single-end mode ... Finished in 685.66 s (10 µs/read; 6.09 M reads/minute). === Summary === Total reads processed: 69,648,408 Reads with adapters: 23,578,643 (33.9%) Reads written (passing filters): 69,648,408 (100.0%) Total basepairs processed: 10,095,423,700 bp Quality-trimmed: 542,690,366 bp (5.4%) Total written (filtered): 9,234,428,766 bp (91.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23578643 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.8% C: 23.9% G: 13.7% T: 18.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17696821 17412102.0 0 17696821 3 1115222 1088256.4 0 1115222 4 348936 272064.1 0 348936 5 206760 68016.0 0 206760 8 66519 1062.8 0 66519 9 77565 265.7 0 77565 10 1274 66.4 1 0 1274 11 90146 16.6 1 80593 9553 12 2352 4.2 1 0 2352 13 110810 1.0 1 92717 18093 14 2303 1.0 1 309 1994 15 38990 1.0 1 33428 5562 16 144806 1.0 1 126600 18206 17 4667 1.0 1 1799 2868 18 87153 1.0 1 79928 7225 19 5125 1.0 1 2645 2480 20 63815 1.0 1 57505 6310 21 197515 1.0 1 185900 11615 22 4570 1.0 1 3011 1559 23 459 1.0 1 358 101 24 2375 1.0 1 1536 839 25 67506 1.0 1 62484 5022 26 90450 1.0 1 83280 7170 27 122402 1.0 1 114795 7607 28 4715 1.0 1 3483 1232 29 63999 1.0 1 60102 3897 30 5701 1.0 1 4180 1521 31 94330 1.0 1 90670 3660 32 13248 1.0 1 10197 3051 33 44563 1.0 1 41549 3014 34 27031 1.0 1 23728 3303 35 1023 1.0 1 757 266 36 6590 1.0 1 5543 1047 37 28448 1.0 1 26635 1813 38 5681 1.0 1 4397 1284 39 21839 1.0 1 19165 2674 40 12309 1.0 1 10381 1928 41 3821 1.0 1 2686 1135 42 3635 1.0 1 2833 802 43 5734 1.0 1 4952 782 44 1941 1.0 1 1368 573 45 781 1.0 1 522 259 46 5689 1.0 1 4485 1204 47 2021 1.0 1 1441 580 48 2434 1.0 1 1797 637 49 3962 1.0 1 3025 937 50 3637 1.0 1 2844 793 51 2156 1.0 1 1495 661 52 713 1.0 1 498 215 53 1511 1.0 1 1122 389 54 2808 1.0 1 2232 576 55 1515 1.0 1 995 520 56 2447 1.0 1 1705 742 57 3186 1.0 1 1880 1306 58 3227 1.0 1 2219 1008 59 2318 1.0 1 1452 866 60 2363 1.0 1 1506 857 61 2601 1.0 1 1756 845 62 3202 1.0 1 1623 1579 63 2802 1.0 1 1536 1266 64 2370 1.0 1 1188 1182 65 2360 1.0 1 631 1729 66 5450 1.0 1 566 4884 67 50131 1.0 1 814 49317 68 188576 1.0 1 978 187598 69 234118 1.0 1 988 233130 70 213853 1.0 1 873 212980 71 170181 1.0 1 698 169483 72 122861 1.0 1 398 122463 73 104257 1.0 1 352 103905 74 69239 1.0 1 253 68986 75 70264 1.0 1 206 70058 76 67089 1.0 1 183 66906 77 42280 1.0 1 162 42118 78 43371 1.0 1 114 43257 79 45946 1.0 1 122 45824 80 41191 1.0 1 106 41085 81 36192 1.0 1 94 36098 82 32961 1.0 1 96 32865 83 29070 1.0 1 95 28975 84 22951 1.0 1 68 22883 85 19115 1.0 1 50 19065 86 16516 1.0 1 49 16467 87 12844 1.0 1 49 12795 88 11654 1.0 1 67 11587 89 9714 1.0 1 58 9656 90 8097 1.0 1 64 8033 91 6910 1.0 1 35 6875 92 6521 1.0 1 35 6486 93 5967 1.0 1 26 5941 94 5074 1.0 1 37 5037 95 4452 1.0 1 47 4405 96 4198 1.0 1 39 4159 97 3869 1.0 1 84 3785 98 3555 1.0 1 51 3504 99 3441 1.0 1 60 3381 100 3251 1.0 1 62 3189 101 3169 1.0 1 66 3103 102 3138 1.0 1 31 3107 103 3313 1.0 1 31 3282 104 3468 1.0 1 25 3443 105 3552 1.0 1 19 3533 106 4197 1.0 1 42 4155 107 4782 1.0 1 45 4737 108 5099 1.0 1 49 5050 109 5689 1.0 1 40 5649 110 5928 1.0 1 42 5886 111 6001 1.0 1 37 5964 112 5766 1.0 1 48 5718 113 5905 1.0 1 52 5853 114 5799 1.0 1 38 5761 115 5154 1.0 1 24 5130 116 5162 1.0 1 17 5145 117 4661 1.0 1 24 4637 118 4376 1.0 1 17 4359 119 3944 1.0 1 11 3933 120 3443 1.0 1 13 3430 121 3402 1.0 1 17 3385 122 3140 1.0 1 14 3126 123 2674 1.0 1 18 2656 124 2364 1.0 1 18 2346 125 2323 1.0 1 20 2303 126 2182 1.0 1 18 2164 127 1937 1.0 1 15 1922 128 1761 1.0 1 13 1748 129 1708 1.0 1 20 1688 130 1709 1.0 1 8 1701 131 1584 1.0 1 9 1575 132 1562 1.0 1 10 1552 133 1574 1.0 1 12 1562 134 1448 1.0 1 7 1441 135 1546 1.0 1 11 1535 136 1707 1.0 1 7 1700 137 1717 1.0 1 12 1705 138 2054 1.0 1 6 2048 139 2192 1.0 1 6 2186 140 2739 1.0 1 4 2735 141 3109 1.0 1 2 3107 142 3893 1.0 1 1 3892 143 4897 1.0 1 2 4895 144 6465 1.0 1 0 6465 145 9120 1.0 1 1 9119 146 13095 1.0 1 1 13094 147 21867 1.0 1 3 21864 148 41971 1.0 1 0 41971 149 83490 1.0 1 1 83489 150 490387 1.0 1 3 490384 151 104069 1.0 1 1 104068 RUN STATISTICS FOR INPUT FILE: gonad_2.fastq.gz ============================================= 69648408 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 69648408 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4055431 (5.82%)