SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_1_S13_L002_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/16C_26psu_1_S13_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 984.11 s (45 us/read; 1.34 M reads/minute). === Summary === Total reads processed: 22,055,675 Reads with adapters: 17,164,009 (77.8%) Reads written (passing filters): 22,055,675 (100.0%) Total basepairs processed: 3,308,351,250 bp Quality-trimmed: 16,172,247 bp (0.5%) Total written (filtered): 2,590,121,341 bp (78.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17164009 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.4% G: 23.7% T: 35.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2956348 5513918.8 0 2956348 2 421838 1378479.7 0 421838 3 248359 344619.9 0 248359 4 140787 86155.0 0 140787 5 125775 21538.7 0 125775 6 111856 5384.7 0 111856 7 89214 1346.2 0 89214 8 128837 336.5 0 128837 9 101494 84.1 0 101161 333 10 109255 21.0 1 101714 7541 11 118195 5.3 1 108364 9831 12 117038 1.3 1 107170 9868 13 134296 0.3 1 123167 11129 14 123942 0.3 1 112784 11158 15 100887 0.3 1 92534 8353 16 146698 0.3 1 134607 12091 17 124219 0.3 1 113532 10687 18 108678 0.3 1 99668 9010 19 144281 0.3 1 132500 11781 20 133615 0.3 1 123129 10486 21 116612 0.3 1 107459 9153 22 133618 0.3 1 123290 10328 23 141009 0.3 1 130007 11002 24 139397 0.3 1 128279 11118 25 156124 0.3 1 144895 11229 26 130436 0.3 1 119727 10709 27 145243 0.3 1 132821 12422 28 129948 0.3 1 120966 8982 29 147371 0.3 1 136169 11202 30 140000 0.3 1 130086 9914 31 156053 0.3 1 144716 11337 32 135242 0.3 1 125682 9560 33 156256 0.3 1 144163 12093 34 200062 0.3 1 185381 14681 35 108741 0.3 1 100819 7922 36 156564 0.3 1 144598 11966 37 165143 0.3 1 153098 12045 38 153915 0.3 1 143649 10266 39 147077 0.3 1 137848 9229 40 167810 0.3 1 155933 11877 41 163682 0.3 1 152622 11060 42 166228 0.3 1 154981 11247 43 150608 0.3 1 140711 9897 44 176387 0.3 1 164024 12363 45 185146 0.3 1 172572 12574 46 132758 0.3 1 123550 9208 47 167253 0.3 1 156952 10301 48 165177 0.3 1 154705 10472 49 173975 0.3 1 162376 11599 50 166191 0.3 1 155002 11189 51 203241 0.3 1 190158 13083 52 146701 0.3 1 137201 9500 53 181035 0.3 1 170415 10620 54 130972 0.3 1 122872 8100 55 173160 0.3 1 163051 10109 56 176881 0.3 1 165551 11330 57 169136 0.3 1 159682 9454 58 163469 0.3 1 154161 9308 59 163465 0.3 1 153708 9757 60 171325 0.3 1 161169 10156 61 174265 0.3 1 164163 10102 62 189943 0.3 1 178404 11539 63 247557 0.3 1 234468 13089 64 202460 0.3 1 193222 9238 65 135184 0.3 1 127502 7682 66 146610 0.3 1 138357 8253 67 145979 0.3 1 137259 8720 68 147766 0.3 1 139368 8398 69 145296 0.3 1 136585 8711 70 155955 0.3 1 146888 9067 71 158414 0.3 1 149557 8857 72 151267 0.3 1 142345 8922 73 157245 0.3 1 148240 9005 74 144510 0.3 1 136069 8441 75 137730 0.3 1 129832 7898 76 133886 0.3 1 125901 7985 77 133306 0.3 1 125623 7683 78 127271 0.3 1 119937 7334 79 123387 0.3 1 116350 7037 80 122486 0.3 1 115616 6870 81 120050 0.3 1 113299 6751 82 115066 0.3 1 108580 6486 83 111130 0.3 1 104980 6150 84 106741 0.3 1 100726 6015 85 105619 0.3 1 99800 5819 86 104981 0.3 1 99314 5667 87 105156 0.3 1 99595 5561 88 102130 0.3 1 96657 5473 89 91200 0.3 1 86213 4987 90 88189 0.3 1 83375 4814 91 82519 0.3 1 77931 4588 92 77564 0.3 1 73377 4187 93 74406 0.3 1 70415 3991 94 71559 0.3 1 67703 3856 95 67768 0.3 1 64110 3658 96 64417 0.3 1 60976 3441 97 59309 0.3 1 56218 3091 98 54600 0.3 1 51799 2801 99 53526 0.3 1 50607 2919 100 48940 0.3 1 46308 2632 101 44993 0.3 1 42581 2412 102 41335 0.3 1 39097 2238 103 37548 0.3 1 35551 1997 104 35714 0.3 1 33829 1885 105 32156 0.3 1 30392 1764 106 29290 0.3 1 27775 1515 107 26004 0.3 1 24590 1414 108 24018 0.3 1 22665 1353 109 21637 0.3 1 20542 1095 110 19578 0.3 1 18483 1095 111 18464 0.3 1 17459 1005 112 15937 0.3 1 15101 836 113 14018 0.3 1 13272 746 114 12104 0.3 1 11450 654 115 10138 0.3 1 9597 541 116 8616 0.3 1 8197 419 117 7239 0.3 1 6863 376 118 6371 0.3 1 6012 359 119 5403 0.3 1 5093 310 120 4535 0.3 1 4258 277 121 3911 0.3 1 3687 224 122 3351 0.3 1 3130 221 123 2870 0.3 1 2695 175 124 2400 0.3 1 2272 128 125 2105 0.3 1 1957 148 126 1712 0.3 1 1597 115 127 1490 0.3 1 1401 89 128 1075 0.3 1 998 77 129 923 0.3 1 859 64 130 711 0.3 1 666 45 131 624 0.3 1 582 42 132 524 0.3 1 489 35 133 507 0.3 1 469 38 134 649 0.3 1 623 26 135 367 0.3 1 349 18 136 204 0.3 1 188 16 137 158 0.3 1 144 14 138 102 0.3 1 92 10 139 75 0.3 1 67 8 140 58 0.3 1 57 1 141 47 0.3 1 40 7 142 38 0.3 1 34 4 143 23 0.3 1 20 3 144 21 0.3 1 20 1 145 27 0.3 1 23 4 146 22 0.3 1 20 2 147 86 0.3 1 82 4 148 43 0.3 1 41 2 149 33 0.3 1 32 1 150 345 0.3 1 321 24 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_1_S13_L002_R2_001.fastq.gz ============================================= 22055675 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 27448 (0.1%)