SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_L001_R1_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/16C_32psu_2_S2_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 674.03 s (38 us/read; 1.58 M reads/minute). === Summary === Total reads processed: 17,734,461 Reads with adapters: 14,777,967 (83.3%) Reads written (passing filters): 17,734,461 (100.0%) Total basepairs processed: 2,660,169,150 bp Quality-trimmed: 5,148,925 bp (0.2%) Total written (filtered): 1,960,839,520 bp (73.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14777967 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 12.9% G: 21.9% T: 35.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1738050 4433615.2 0 1738050 2 278207 1108403.8 0 278207 3 163757 277101.0 0 163757 4 100314 69275.2 0 100314 5 85611 17318.8 0 85611 6 82934 4329.7 0 82934 7 71901 1082.4 0 71901 8 92752 270.6 0 92752 9 83307 67.7 0 82257 1050 10 83535 16.9 1 78970 4565 11 92909 4.2 1 85625 7284 12 89396 1.1 1 83407 5989 13 91391 0.3 1 85129 6262 14 92986 0.3 1 86205 6781 15 95417 0.3 1 88994 6423 16 96485 0.3 1 89177 7308 17 117735 0.3 1 108243 9492 18 99811 0.3 1 93600 6211 19 87560 0.3 1 81823 5737 20 104404 0.3 1 97366 7038 21 115608 0.3 1 107491 8117 22 99044 0.3 1 93521 5523 23 114295 0.3 1 106563 7732 24 108405 0.3 1 99404 9001 25 115898 0.3 1 108064 7834 26 106400 0.3 1 100103 6297 27 119862 0.3 1 110913 8949 28 117009 0.3 1 108719 8290 29 126066 0.3 1 115846 10220 30 135672 0.3 1 127802 7870 31 103769 0.3 1 96862 6907 32 134576 0.3 1 125712 8864 33 115506 0.3 1 107678 7828 34 131922 0.3 1 122476 9446 35 139540 0.3 1 128729 10811 36 129944 0.3 1 121921 8023 37 155181 0.3 1 145058 10123 38 125033 0.3 1 115777 9256 39 137711 0.3 1 129241 8470 40 145763 0.3 1 136531 9232 41 145406 0.3 1 134994 10412 42 140227 0.3 1 129509 10718 43 213869 0.3 1 202923 10946 44 71935 0.3 1 65627 6308 45 151697 0.3 1 142261 9436 46 139466 0.3 1 130673 8793 47 151314 0.3 1 141909 9405 48 149772 0.3 1 140199 9573 49 163566 0.3 1 152198 11368 50 142863 0.3 1 134146 8717 51 154145 0.3 1 144042 10103 52 159345 0.3 1 148339 11006 53 168861 0.3 1 158401 10460 54 140944 0.3 1 132160 8784 55 163358 0.3 1 152729 10629 56 198374 0.3 1 186858 11516 57 129041 0.3 1 119923 9118 58 168939 0.3 1 159723 9216 59 149936 0.3 1 140432 9504 60 161773 0.3 1 151304 10469 61 159837 0.3 1 150130 9707 62 178889 0.3 1 168432 10457 63 140394 0.3 1 131036 9358 64 159197 0.3 1 149784 9413 65 178150 0.3 1 167258 10892 66 185093 0.3 1 173786 11307 67 199374 0.3 1 184232 15142 68 376952 0.3 1 359289 17663 69 53765 0.3 1 48910 4855 70 23496 0.3 1 19245 4251 71 105909 0.3 1 99682 6227 72 143025 0.3 1 134667 8358 73 150010 0.3 1 141153 8857 74 148858 0.3 1 139863 8995 75 147559 0.3 1 138722 8837 76 146256 0.3 1 137657 8599 77 146473 0.3 1 137642 8831 78 139439 0.3 1 130923 8516 79 138812 0.3 1 130392 8420 80 134925 0.3 1 126986 7939 81 132740 0.3 1 124849 7891 82 129707 0.3 1 121848 7859 83 125045 0.3 1 117720 7325 84 120955 0.3 1 113756 7199 85 117638 0.3 1 110705 6933 86 114999 0.3 1 108021 6978 87 110985 0.3 1 104322 6663 88 108344 0.3 1 101912 6432 89 103347 0.3 1 97100 6247 90 102084 0.3 1 95939 6145 91 97477 0.3 1 91376 6101 92 92174 0.3 1 86611 5563 93 86985 0.3 1 81755 5230 94 84316 0.3 1 79155 5161 95 78474 0.3 1 73684 4790 96 73594 0.3 1 68994 4600 97 68665 0.3 1 64422 4243 98 65130 0.3 1 60988 4142 99 62724 0.3 1 58428 4296 100 57069 0.3 1 53328 3741 101 53096 0.3 1 49656 3440 102 48453 0.3 1 45307 3146 103 44883 0.3 1 41855 3028 104 41860 0.3 1 39145 2715 105 37319 0.3 1 34804 2515 106 33117 0.3 1 30846 2271 107 30224 0.3 1 28086 2138 108 28577 0.3 1 26568 2009 109 24900 0.3 1 23148 1752 110 22182 0.3 1 20539 1643 111 19835 0.3 1 18458 1377 112 17455 0.3 1 16149 1306 113 15019 0.3 1 13793 1226 114 13036 0.3 1 12026 1010 115 11314 0.3 1 10380 934 116 9567 0.3 1 8809 758 117 8005 0.3 1 7289 716 118 6890 0.3 1 6310 580 119 5712 0.3 1 5183 529 120 4607 0.3 1 4200 407 121 4029 0.3 1 3642 387 122 3364 0.3 1 3030 334 123 2640 0.3 1 2382 258 124 2162 0.3 1 1941 221 125 1794 0.3 1 1596 198 126 1531 0.3 1 1353 178 127 1215 0.3 1 1098 117 128 1005 0.3 1 879 126 129 809 0.3 1 695 114 130 661 0.3 1 597 64 131 509 0.3 1 455 54 132 443 0.3 1 389 54 133 409 0.3 1 355 54 134 483 0.3 1 430 53 135 256 0.3 1 227 29 136 159 0.3 1 133 26 137 104 0.3 1 91 13 138 67 0.3 1 53 14 139 54 0.3 1 47 7 140 47 0.3 1 39 8 141 21 0.3 1 15 6 142 21 0.3 1 19 2 143 8 0.3 1 4 4 144 21 0.3 1 20 1 145 51 0.3 1 46 5 146 37 0.3 1 29 8 147 70 0.3 1 63 7 148 65 0.3 1 52 13 149 39 0.3 1 35 4 150 480 0.3 1 358 122 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_L001_R1_001.fastq.gz ============================================= 17734461 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3391 (0.0%)