SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/16C_32psu_4_S4_L002_R1_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/16C_32psu_4_S4_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 634.36 s (41 us/read; 1.47 M reads/minute). === Summary === Total reads processed: 15,591,852 Reads with adapters: 11,241,936 (72.1%) Reads written (passing filters): 15,591,852 (100.0%) Total basepairs processed: 2,338,777,800 bp Quality-trimmed: 7,762,195 bp (0.3%) Total written (filtered): 1,950,418,217 bp (83.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11241936 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.8% C: 13.2% G: 19.5% T: 35.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2728314 3897963.0 0 2728314 2 352949 974490.8 0 352949 3 189042 243622.7 0 189042 4 110295 60905.7 0 110295 5 86754 15226.4 0 86754 6 84318 3806.6 0 84318 7 67898 951.7 0 67898 8 84774 237.9 0 84774 9 86162 59.5 0 85323 839 10 77737 14.9 1 73221 4516 11 88459 3.7 1 81353 7106 12 84258 0.9 1 78502 5756 13 83829 0.2 1 77646 6183 14 87427 0.2 1 80554 6873 15 88669 0.2 1 82188 6481 16 87155 0.2 1 79865 7290 17 108105 0.2 1 98581 9524 18 88189 0.2 1 82109 6080 19 75841 0.2 1 70534 5307 20 90690 0.2 1 84354 6336 21 100155 0.2 1 92424 7731 22 84109 0.2 1 78568 5541 23 100437 0.2 1 93211 7226 24 89008 0.2 1 81375 7633 25 97433 0.2 1 90437 6996 26 86900 0.2 1 81328 5572 27 98051 0.2 1 90237 7814 28 106220 0.2 1 97819 8401 29 94302 0.2 1 86322 7980 30 107823 0.2 1 101345 6478 31 77079 0.2 1 71662 5417 32 102558 0.2 1 95070 7488 33 91366 0.2 1 84409 6957 34 99532 0.2 1 91471 8061 35 107666 0.2 1 99772 7894 36 89079 0.2 1 83528 5551 37 100059 0.2 1 92531 7528 38 104683 0.2 1 96200 8483 39 105342 0.2 1 97340 8002 40 103603 0.2 1 95197 8406 41 116472 0.2 1 105109 11363 42 91799 0.2 1 84082 7717 43 151482 0.2 1 141550 9932 44 48893 0.2 1 44323 4570 45 107330 0.2 1 98158 9172 46 169588 0.2 1 157239 12349 47 115292 0.2 1 107496 7796 48 81237 0.2 1 73490 7747 49 158364 0.2 1 148089 10275 50 62839 0.2 1 58050 4789 51 90568 0.2 1 83874 6694 52 192734 0.2 1 181187 11547 53 137640 0.2 1 130713 6927 54 59884 0.2 1 55438 4446 55 102380 0.2 1 96895 5485 56 71739 0.2 1 66587 5152 57 121813 0.2 1 115448 6365 58 43981 0.2 1 41008 2973 59 41261 0.2 1 37490 3771 60 111430 0.2 1 105252 6178 61 87063 0.2 1 82619 4444 62 47900 0.2 1 44309 3591 63 85477 0.2 1 80258 5219 64 72824 0.2 1 68588 4236 65 60641 0.2 1 56399 4242 66 87315 0.2 1 81607 5708 67 100034 0.2 1 92897 7137 68 160033 0.2 1 150907 9126 69 87754 0.2 1 82192 5562 70 34259 0.2 1 30999 3260 71 22148 0.2 1 20058 2090 72 59270 0.2 1 55764 3506 73 72359 0.2 1 68127 4232 74 73545 0.2 1 68961 4584 75 72172 0.2 1 67396 4776 76 70342 0.2 1 65617 4725 77 69830 0.2 1 65084 4746 78 66115 0.2 1 61597 4518 79 64360 0.2 1 60010 4350 80 63230 0.2 1 58997 4233 81 61274 0.2 1 57172 4102 82 59014 0.2 1 55084 3930 83 57125 0.2 1 53358 3767 84 54574 0.2 1 50808 3766 85 52527 0.2 1 48940 3587 86 50257 0.2 1 46911 3346 87 48208 0.2 1 45026 3182 88 45866 0.2 1 42781 3085 89 44045 0.2 1 41050 2995 90 43438 0.2 1 40512 2926 91 40328 0.2 1 37640 2688 92 38164 0.2 1 35615 2549 93 35352 0.2 1 32983 2369 94 33785 0.2 1 31458 2327 95 31871 0.2 1 29668 2203 96 29463 0.2 1 27470 1993 97 27711 0.2 1 25891 1820 98 25451 0.2 1 23610 1841 99 24415 0.2 1 22590 1825 100 21725 0.2 1 20167 1558 101 20433 0.2 1 19008 1425 102 18660 0.2 1 17274 1386 103 16794 0.2 1 15616 1178 104 15844 0.2 1 14677 1167 105 14021 0.2 1 13036 985 106 12448 0.2 1 11562 886 107 11573 0.2 1 10706 867 108 10412 0.2 1 9602 810 109 8989 0.2 1 8297 692 110 8150 0.2 1 7523 627 111 7254 0.2 1 6680 574 112 6183 0.2 1 5709 474 113 5353 0.2 1 4937 416 114 4766 0.2 1 4364 402 115 4132 0.2 1 3707 425 116 3477 0.2 1 3165 312 117 3036 0.2 1 2738 298 118 2618 0.2 1 2398 220 119 2115 0.2 1 1918 197 120 1769 0.2 1 1599 170 121 1495 0.2 1 1327 168 122 1258 0.2 1 1133 125 123 1079 0.2 1 967 112 124 920 0.2 1 808 112 125 777 0.2 1 674 103 126 681 0.2 1 592 89 127 553 0.2 1 494 59 128 387 0.2 1 336 51 129 401 0.2 1 353 48 130 291 0.2 1 256 35 131 270 0.2 1 235 35 132 242 0.2 1 222 20 133 268 0.2 1 225 43 134 327 0.2 1 297 30 135 148 0.2 1 131 17 136 79 0.2 1 65 14 137 63 0.2 1 55 8 138 35 0.2 1 28 7 139 28 0.2 1 22 6 140 22 0.2 1 20 2 141 16 0.2 1 14 2 142 13 0.2 1 11 2 143 16 0.2 1 11 5 144 10 0.2 1 5 5 145 13 0.2 1 8 5 146 16 0.2 1 12 4 147 29 0.2 1 25 4 148 26 0.2 1 23 3 149 19 0.2 1 18 1 150 167 0.2 1 150 17 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/16C_32psu_4_S4_L002_R1_001.fastq.gz ============================================= 15591852 sequences processed in total