SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/CTRL_8C_26psu_1_S17_L001_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 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 All Read 1 sequences will be trimmed by 5 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 5 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Users/strigg/Desktop/Salmo_Calig/TRIM/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Users/strigg/Desktop/Salmo_Calig/CTRL_8C_26psu_1_S17_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 561.78 s (41 us/read; 1.47 M reads/minute). === Summary === Total reads processed: 13,781,290 Reads with adapters: 10,393,178 (75.4%) Reads written (passing filters): 13,781,290 (100.0%) Total basepairs processed: 2,067,193,500 bp Quality-trimmed: 10,332,398 bp (0.5%) Total written (filtered): 1,650,693,153 bp (79.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10393178 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.0% C: 12.4% G: 22.9% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2177342 3445322.5 0 2177342 2 279599 861330.6 0 279599 3 156926 215332.7 0 156926 4 90665 53833.2 0 90665 5 76306 13458.3 0 76306 6 64993 3364.6 0 64993 7 53352 841.1 0 53352 8 75967 210.3 0 75967 9 61280 52.6 0 61074 206 10 66110 13.1 1 62970 3140 11 69828 3.3 1 65500 4328 12 69328 0.8 1 64877 4451 13 77454 0.2 1 72977 4477 14 71203 0.2 1 66291 4912 15 59758 0.2 1 55879 3879 16 86601 0.2 1 81117 5484 17 65384 0.2 1 60933 4451 18 67208 0.2 1 63111 4097 19 81178 0.2 1 76029 5149 20 77499 0.2 1 72833 4666 21 68546 0.2 1 64113 4433 22 76276 0.2 1 71754 4522 23 78702 0.2 1 73839 4863 24 78191 0.2 1 73447 4744 25 88316 0.2 1 83190 5126 26 73679 0.2 1 68983 4696 27 82923 0.2 1 77281 5642 28 76296 0.2 1 72446 3850 29 82111 0.2 1 77123 4988 30 79614 0.2 1 75308 4306 31 89456 0.2 1 84223 5233 32 78118 0.2 1 73947 4171 33 86787 0.2 1 81520 5267 34 111454 0.2 1 105036 6418 35 64200 0.2 1 60716 3484 36 89863 0.2 1 84483 5380 37 97027 0.2 1 91271 5756 38 90403 0.2 1 85738 4665 39 89856 0.2 1 85089 4767 40 98244 0.2 1 92516 5728 41 92652 0.2 1 87737 4915 42 94536 0.2 1 89519 5017 43 85154 0.2 1 80486 4668 44 96817 0.2 1 91511 5306 45 102115 0.2 1 96823 5292 46 77381 0.2 1 73350 4031 47 94700 0.2 1 89756 4944 48 92948 0.2 1 88160 4788 49 96945 0.2 1 91985 4960 50 91133 0.2 1 86206 4927 51 111309 0.2 1 105778 5531 52 80724 0.2 1 76802 3922 53 97109 0.2 1 92582 4527 54 75460 0.2 1 71575 3885 55 96939 0.2 1 92436 4503 56 100452 0.2 1 95531 4921 57 93931 0.2 1 89647 4284 58 91630 0.2 1 87584 4046 59 91476 0.2 1 87193 4283 60 94295 0.2 1 89743 4552 61 96075 0.2 1 91458 4617 62 103947 0.2 1 98742 5205 63 139881 0.2 1 133644 6237 64 115738 0.2 1 111196 4542 65 76600 0.2 1 73143 3457 66 81388 0.2 1 77826 3562 67 79784 0.2 1 76063 3721 68 81137 0.2 1 77492 3645 69 80187 0.2 1 76468 3719 70 85090 0.2 1 81074 4016 71 89717 0.2 1 85778 3939 72 84263 0.2 1 80409 3854 73 87216 0.2 1 83465 3751 74 81093 0.2 1 77528 3565 75 77500 0.2 1 74052 3448 76 75266 0.2 1 71946 3320 77 75853 0.2 1 72329 3524 78 72260 0.2 1 68950 3310 79 68908 0.2 1 65817 3091 80 69469 0.2 1 66410 3059 81 68119 0.2 1 65042 3077 82 65495 0.2 1 62627 2868 83 64033 0.2 1 61248 2785 84 61976 0.2 1 59216 2760 85 61317 0.2 1 58515 2802 86 60982 0.2 1 58300 2682 87 61128 0.2 1 58498 2630 88 60002 0.2 1 57306 2696 89 53699 0.2 1 51332 2367 90 51966 0.2 1 49630 2336 91 49026 0.2 1 46908 2118 92 46213 0.2 1 44244 1969 93 44796 0.2 1 42840 1956 94 44237 0.2 1 42309 1928 95 41556 0.2 1 39752 1804 96 39335 0.2 1 37550 1785 97 36382 0.2 1 34875 1507 98 33450 0.2 1 32005 1445 99 32975 0.2 1 31610 1365 100 29764 0.2 1 28510 1254 101 27741 0.2 1 26626 1115 102 25948 0.2 1 24908 1040 103 23781 0.2 1 22799 982 104 22951 0.2 1 22001 950 105 20726 0.2 1 19855 871 106 19269 0.2 1 18460 809 107 17116 0.2 1 16344 772 108 16142 0.2 1 15422 720 109 14186 0.2 1 13581 605 110 13235 0.2 1 12682 553 111 12589 0.2 1 12054 535 112 10912 0.2 1 10466 446 113 9393 0.2 1 8942 451 114 8457 0.2 1 8091 366 115 7197 0.2 1 6874 323 116 6211 0.2 1 5908 303 117 5216 0.2 1 4981 235 118 4612 0.2 1 4406 206 119 3969 0.2 1 3800 169 120 3391 0.2 1 3233 158 121 3136 0.2 1 3000 136 122 2549 0.2 1 2419 130 123 2350 0.2 1 2231 119 124 1891 0.2 1 1802 89 125 1725 0.2 1 1617 108 126 1554 0.2 1 1484 70 127 1178 0.2 1 1121 57 128 930 0.2 1 883 47 129 904 0.2 1 851 53 130 653 0.2 1 624 29 131 560 0.2 1 529 31 132 495 0.2 1 468 27 133 660 0.2 1 626 34 134 1423 0.2 1 1385 38 135 575 0.2 1 556 19 136 211 0.2 1 198 13 137 131 0.2 1 127 4 138 83 0.2 1 76 7 139 59 0.2 1 52 7 140 46 0.2 1 40 6 141 37 0.2 1 35 2 142 28 0.2 1 27 1 143 41 0.2 1 38 3 144 59 0.2 1 58 1 145 179 0.2 1 178 1 146 263 0.2 1 249 14 147 1229 0.2 1 1166 63 148 791 0.2 1 756 35 149 435 0.2 1 415 20 150 2389 0.2 1 2255 134 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/CTRL_8C_26psu_1_S17_L001_R2_001.fastq.gz ============================================= 13781290 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 13781290 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 36197 (0.26%)