SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/8C_26psu_4_S12_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/8C_26psu_4_S12_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 480.47 s (38 us/read; 1.56 M reads/minute). === Summary === Total reads processed: 12,486,748 Reads with adapters: 8,893,888 (71.2%) Reads written (passing filters): 12,486,748 (100.0%) Total basepairs processed: 1,873,012,200 bp Quality-trimmed: 5,043,033 bp (0.3%) Total written (filtered): 1,556,339,778 bp (83.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8893888 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.5% C: 15.6% G: 17.3% T: 35.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2335523 3121687.0 0 2335523 2 288272 780421.8 0 288272 3 160403 195105.4 0 160403 4 85608 48776.4 0 85608 5 58915 12194.1 0 58915 6 57362 3048.5 0 57362 7 44207 762.1 0 44207 8 57380 190.5 0 57380 9 58488 47.6 0 57517 971 10 52992 11.9 1 48842 4150 11 61046 3.0 1 54898 6148 12 57274 0.7 1 52182 5092 13 56700 0.2 1 51661 5039 14 59620 0.2 1 53923 5697 15 59755 0.2 1 54283 5472 16 59818 0.2 1 53514 6304 17 74695 0.2 1 66802 7893 18 60082 0.2 1 55008 5074 19 51866 0.2 1 47284 4582 20 63201 0.2 1 57371 5830 21 69970 0.2 1 63395 6575 22 57953 0.2 1 53164 4789 23 68365 0.2 1 61918 6447 24 63806 0.2 1 56950 6856 25 67673 0.2 1 61556 6117 26 61661 0.2 1 56449 5212 27 70143 0.2 1 63185 6958 28 67771 0.2 1 61544 6227 29 71226 0.2 1 63790 7436 30 75482 0.2 1 69371 6111 31 58014 0.2 1 52857 5157 32 74386 0.2 1 67729 6657 33 63663 0.2 1 57495 6168 34 74108 0.2 1 66532 7576 35 70037 0.2 1 63230 6807 36 76753 0.2 1 69831 6922 37 67916 0.2 1 61720 6196 38 71617 0.2 1 65621 5996 39 75012 0.2 1 68484 6528 40 71594 0.2 1 64730 6864 41 78317 0.2 1 70095 8222 42 72352 0.2 1 64854 7498 43 105118 0.2 1 97302 7816 44 39192 0.2 1 34640 4552 45 76811 0.2 1 69875 6936 46 73857 0.2 1 67212 6645 47 78745 0.2 1 71969 6776 48 69568 0.2 1 62853 6715 49 81769 0.2 1 74077 7692 50 65947 0.2 1 60677 5270 51 71662 0.2 1 65506 6156 52 80128 0.2 1 72415 7713 53 85941 0.2 1 79178 6763 54 61047 0.2 1 55540 5507 55 75533 0.2 1 69160 6373 56 87285 0.2 1 80207 7078 57 70909 0.2 1 64686 6223 58 68890 0.2 1 64023 4867 59 56798 0.2 1 51598 5200 60 76540 0.2 1 70247 6293 61 72774 0.2 1 66897 5877 62 72381 0.2 1 66643 5738 63 67661 0.2 1 61998 5663 64 65324 0.2 1 60081 5243 65 70599 0.2 1 64735 5864 66 77128 0.2 1 70592 6536 67 84260 0.2 1 76015 8245 68 144203 0.2 1 134904 9299 69 43407 0.2 1 39642 3765 70 15848 0.2 1 13317 2531 71 33644 0.2 1 30540 3104 72 56928 0.2 1 52537 4391 73 61080 0.2 1 56221 4859 74 61529 0.2 1 56438 5091 75 60533 0.2 1 55505 5028 76 58948 0.2 1 53903 5045 77 59043 0.2 1 53976 5067 78 55894 0.2 1 51078 4816 79 55224 0.2 1 50589 4635 80 53749 0.2 1 49095 4654 81 52818 0.2 1 48513 4305 82 51098 0.2 1 46773 4325 83 49182 0.2 1 45013 4169 84 47970 0.2 1 43859 4111 85 46307 0.2 1 42293 4014 86 45032 0.2 1 41160 3872 87 42066 0.2 1 38573 3493 88 42344 0.2 1 38592 3752 89 39930 0.2 1 36464 3466 90 40509 0.2 1 36927 3582 91 36941 0.2 1 33684 3257 92 35322 0.2 1 32274 3048 93 32946 0.2 1 30001 2945 94 32705 0.2 1 29772 2933 95 29601 0.2 1 27010 2591 96 28129 0.2 1 25553 2576 97 26467 0.2 1 24046 2421 98 25094 0.2 1 22854 2240 99 24292 0.2 1 21966 2326 100 22228 0.2 1 20140 2088 101 20127 0.2 1 18275 1852 102 18734 0.2 1 17008 1726 103 17312 0.2 1 15695 1617 104 16349 0.2 1 14760 1589 105 14697 0.2 1 13311 1386 106 13248 0.2 1 11852 1396 107 12309 0.2 1 11095 1214 108 11118 0.2 1 10010 1108 109 9883 0.2 1 8876 1007 110 9429 0.2 1 8493 936 111 8334 0.2 1 7393 941 112 7520 0.2 1 6729 791 113 6506 0.2 1 5771 735 114 5675 0.2 1 5040 635 115 4923 0.2 1 4354 569 116 4197 0.2 1 3676 521 117 3761 0.2 1 3289 472 118 3198 0.2 1 2835 363 119 2789 0.2 1 2461 328 120 2403 0.2 1 2050 353 121 1996 0.2 1 1771 225 122 1692 0.2 1 1462 230 123 1495 0.2 1 1306 189 124 1325 0.2 1 1129 196 125 1099 0.2 1 932 167 126 1059 0.2 1 919 140 127 931 0.2 1 822 109 128 654 0.2 1 548 106 129 550 0.2 1 477 73 130 491 0.2 1 418 73 131 529 0.2 1 438 91 132 576 0.2 1 513 63 133 972 0.2 1 858 114 134 2641 0.2 1 2458 183 135 835 0.2 1 788 47 136 183 0.2 1 162 21 137 124 0.2 1 105 19 138 78 0.2 1 70 8 139 41 0.2 1 32 9 140 43 0.2 1 37 6 141 24 0.2 1 20 4 142 18 0.2 1 15 3 143 16 0.2 1 12 4 144 54 0.2 1 49 5 145 231 0.2 1 211 20 146 231 0.2 1 210 21 147 1327 0.2 1 1201 126 148 804 0.2 1 738 66 149 437 0.2 1 393 44 150 3016 0.2 1 2525 491 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/8C_26psu_4_S12_L002_R1_001.fastq.gz ============================================= 12486748 sequences processed in total