SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_L001_R2_001.fastq.gz Trimming mode: single-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; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/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 /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 767.43 s (42 us/read; 1.42 M reads/minute). === Summary === Total reads processed: 18,172,174 Reads with adapters: 13,925,142 (76.6%) Reads written (passing filters): 18,172,174 (100.0%) Total basepairs processed: 2,725,826,100 bp Quality-trimmed: 12,772,261 bp (0.5%) Total written (filtered): 2,156,656,577 bp (79.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13925142 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 12.4% G: 23.9% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2593588 4543043.5 0 2593588 2 376254 1135760.9 0 376254 3 210205 283940.2 0 210205 4 119037 70985.1 0 119037 5 104651 17746.3 0 104651 6 89236 4436.6 0 89236 7 73097 1109.1 0 73097 8 103442 277.3 0 103442 9 83266 69.3 0 82975 291 10 90702 17.3 1 86533 4169 11 96126 4.3 1 90174 5952 12 96465 1.1 1 90519 5946 13 107004 0.3 1 100993 6011 14 100898 0.3 1 93952 6946 15 82733 0.3 1 77655 5078 16 119602 0.3 1 112441 7161 17 94839 0.3 1 88603 6236 18 92099 0.3 1 86695 5404 19 114214 0.3 1 107016 7198 20 107713 0.3 1 101500 6213 21 95562 0.3 1 89784 5778 22 107588 0.3 1 101222 6366 23 111031 0.3 1 104295 6736 24 110341 0.3 1 103677 6664 25 124129 0.3 1 117008 7121 26 103231 0.3 1 96892 6339 27 114476 0.3 1 106707 7769 28 107750 0.3 1 102430 5320 29 114219 0.3 1 107523 6696 30 113089 0.3 1 107416 5673 31 123120 0.3 1 116178 6942 32 110386 0.3 1 104842 5544 33 123147 0.3 1 116091 7056 34 156685 0.3 1 148041 8644 35 89283 0.3 1 84701 4582 36 120443 0.3 1 113382 7061 37 129458 0.3 1 122208 7250 38 122546 0.3 1 116642 5904 39 119280 0.3 1 113530 5750 40 132471 0.3 1 125158 7313 41 126758 0.3 1 120385 6373 42 130992 0.3 1 124472 6520 43 120675 0.3 1 114532 6143 44 136598 0.3 1 129517 7081 45 144732 0.3 1 137448 7284 46 106581 0.3 1 101258 5323 47 132125 0.3 1 125807 6318 48 130489 0.3 1 124465 6024 49 135590 0.3 1 129070 6520 50 128632 0.3 1 122091 6541 51 159357 0.3 1 151626 7731 52 116120 0.3 1 110786 5334 53 139419 0.3 1 133495 5924 54 106851 0.3 1 101979 4872 55 135687 0.3 1 129810 5877 56 138774 0.3 1 132432 6342 57 131848 0.3 1 126296 5552 58 127061 0.3 1 121713 5348 59 129536 0.3 1 124051 5485 60 133143 0.3 1 127312 5831 61 136216 0.3 1 129973 6243 62 147811 0.3 1 140964 6847 63 197994 0.3 1 190073 7921 64 157927 0.3 1 152075 5852 65 105906 0.3 1 101567 4339 66 114677 0.3 1 109835 4842 67 114010 0.3 1 108938 5072 68 114564 0.3 1 109670 4894 69 112505 0.3 1 107761 4744 70 118303 0.3 1 113227 5076 71 123531 0.3 1 118496 5035 72 117539 0.3 1 112405 5134 73 122781 0.3 1 117929 4852 74 113055 0.3 1 108472 4583 75 107896 0.3 1 103502 4394 76 106239 0.3 1 101975 4264 77 105105 0.3 1 100663 4442 78 99929 0.3 1 95794 4135 79 96680 0.3 1 92707 3973 80 95740 0.3 1 91762 3978 81 93945 0.3 1 90030 3915 82 89626 0.3 1 86049 3577 83 87905 0.3 1 84339 3566 84 84781 0.3 1 81246 3535 85 83386 0.3 1 79899 3487 86 83197 0.3 1 79728 3469 87 82660 0.3 1 79311 3349 88 81067 0.3 1 77676 3391 89 73343 0.3 1 70291 3052 90 69973 0.3 1 67072 2901 91 65096 0.3 1 62445 2651 92 61646 0.3 1 59119 2527 93 59393 0.3 1 56935 2458 94 57203 0.3 1 54848 2355 95 53756 0.3 1 51532 2224 96 50956 0.3 1 49026 1930 97 47276 0.3 1 45371 1905 98 44746 0.3 1 43017 1729 99 42641 0.3 1 41013 1628 100 39899 0.3 1 38401 1498 101 36809 0.3 1 35396 1413 102 34264 0.3 1 32958 1306 103 31058 0.3 1 29842 1216 104 30002 0.3 1 28912 1090 105 26784 0.3 1 25668 1116 106 24257 0.3 1 23303 954 107 21941 0.3 1 21141 800 108 20010 0.3 1 19251 759 109 18313 0.3 1 17584 729 110 16702 0.3 1 16007 695 111 15559 0.3 1 14968 591 112 13419 0.3 1 12890 529 113 11631 0.3 1 11113 518 114 10507 0.3 1 10110 397 115 8927 0.3 1 8561 366 116 7354 0.3 1 7008 346 117 6258 0.3 1 5993 265 118 5422 0.3 1 5194 228 119 4575 0.3 1 4365 210 120 3972 0.3 1 3799 173 121 3338 0.3 1 3179 159 122 2723 0.3 1 2578 145 123 2312 0.3 1 2208 104 124 2044 0.3 1 1948 96 125 1725 0.3 1 1623 102 126 1567 0.3 1 1498 69 127 1207 0.3 1 1135 72 128 957 0.3 1 886 71 129 782 0.3 1 739 43 130 614 0.3 1 575 39 131 601 0.3 1 565 36 132 573 0.3 1 543 30 133 862 0.3 1 829 33 134 1185 0.3 1 1148 37 135 434 0.3 1 412 22 136 191 0.3 1 179 12 137 150 0.3 1 137 13 138 67 0.3 1 59 8 139 66 0.3 1 55 11 140 41 0.3 1 35 6 141 28 0.3 1 25 3 142 18 0.3 1 17 1 143 17 0.3 1 17 144 10 0.3 1 7 3 145 31 0.3 1 30 1 146 24 0.3 1 21 3 147 69 0.3 1 63 6 148 53 0.3 1 49 4 149 41 0.3 1 39 2 150 371 0.3 1 357 14 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_L001_R2_001.fastq.gz ============================================= 18172174 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 23837 (0.1%)