SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_2_S10_L002_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/8C_26psu_2_S10_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 730.98 s (40 us/read; 1.51 M reads/minute). === Summary === Total reads processed: 18,388,474 Reads with adapters: 14,774,548 (80.3%) Reads written (passing filters): 18,388,474 (100.0%) Total basepairs processed: 2,758,271,100 bp Quality-trimmed: 5,422,014 bp (0.2%) Total written (filtered): 2,096,179,695 bp (76.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14774548 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.0% C: 14.7% G: 20.4% T: 34.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2179283 4597118.5 0 2179283 2 319389 1149279.6 0 319389 3 179573 287319.9 0 179573 4 108126 71830.0 0 108126 5 90944 17957.5 0 90944 6 89410 4489.4 0 89410 7 72797 1122.3 0 72797 8 91422 280.6 0 91422 9 93678 70.1 0 92415 1263 10 84673 17.5 1 79267 5406 11 97249 4.4 1 88769 8480 12 93054 1.1 1 86160 6894 13 93570 0.3 1 86447 7123 14 97334 0.3 1 89025 8309 15 99065 0.3 1 91404 7661 16 99365 0.3 1 90487 8878 17 122566 0.3 1 111250 11316 18 102597 0.3 1 95121 7476 19 88093 0.3 1 81291 6802 20 107045 0.3 1 98814 8231 21 119128 0.3 1 109388 9740 22 98363 0.3 1 91503 6860 23 118120 0.3 1 108869 9251 24 109512 0.3 1 99530 9982 25 117620 0.3 1 108476 9144 26 107233 0.3 1 99745 7488 27 121679 0.3 1 111586 10093 28 118815 0.3 1 109364 9451 29 129909 0.3 1 118061 11848 30 136643 0.3 1 127560 9083 31 99248 0.3 1 91716 7532 32 129461 0.3 1 119254 10207 33 120389 0.3 1 110237 10152 34 133674 0.3 1 122112 11562 35 135326 0.3 1 125969 9357 36 125558 0.3 1 113748 11810 37 131811 0.3 1 122131 9680 38 134596 0.3 1 124192 10404 39 144370 0.3 1 133180 11190 40 130508 0.3 1 120297 10211 41 146230 0.3 1 133678 12552 42 134185 0.3 1 121889 12296 43 205437 0.3 1 192857 12580 44 71406 0.3 1 64241 7165 45 146811 0.3 1 136113 10698 46 133431 0.3 1 123482 9949 47 146963 0.3 1 136319 10644 48 142772 0.3 1 132090 10682 49 156871 0.3 1 144261 12610 50 134522 0.3 1 125136 9386 51 145234 0.3 1 134471 10763 52 151741 0.3 1 139780 11961 53 160323 0.3 1 148993 11330 54 129391 0.3 1 119763 9628 55 153504 0.3 1 142065 11439 56 189438 0.3 1 176473 12965 57 121885 0.3 1 111816 10069 58 156277 0.3 1 146133 10144 59 138166 0.3 1 127798 10368 60 151809 0.3 1 140696 11113 61 148378 0.3 1 138229 10149 62 164350 0.3 1 153017 11333 63 132176 0.3 1 121776 10400 64 146283 0.3 1 136343 9940 65 162567 0.3 1 150970 11597 66 169475 0.3 1 157430 12045 67 180215 0.3 1 164843 15372 68 335801 0.3 1 317089 18712 69 66723 0.3 1 60845 5878 70 26090 0.3 1 21811 4279 71 91663 0.3 1 85518 6145 72 129140 0.3 1 120846 8294 73 135992 0.3 1 126800 9192 74 136581 0.3 1 127154 9427 75 134341 0.3 1 124926 9415 76 133080 0.3 1 123316 9764 77 133409 0.3 1 123959 9450 78 126607 0.3 1 117538 9069 79 125070 0.3 1 116034 9036 80 121818 0.3 1 113223 8595 81 121825 0.3 1 113140 8685 82 118244 0.3 1 109604 8640 83 114640 0.3 1 106502 8138 84 109963 0.3 1 101985 7978 85 107204 0.3 1 99478 7726 86 104741 0.3 1 97192 7549 87 100621 0.3 1 93543 7078 88 98776 0.3 1 91675 7101 89 94677 0.3 1 87957 6720 90 94332 0.3 1 87620 6712 91 89612 0.3 1 83296 6316 92 85598 0.3 1 79627 5971 93 79579 0.3 1 73824 5755 94 77934 0.3 1 72425 5509 95 72110 0.3 1 66875 5235 96 68840 0.3 1 63845 4995 97 64799 0.3 1 60100 4699 98 60773 0.3 1 56257 4516 99 58381 0.3 1 53874 4507 100 53848 0.3 1 49904 3944 101 49943 0.3 1 46245 3698 102 46241 0.3 1 42732 3509 103 43196 0.3 1 39990 3206 104 40167 0.3 1 37244 2923 105 35834 0.3 1 33163 2671 106 33023 0.3 1 30489 2534 107 30207 0.3 1 27948 2259 108 28472 0.3 1 26245 2227 109 25094 0.3 1 23102 1992 110 22988 0.3 1 21194 1794 111 20538 0.3 1 18949 1589 112 18521 0.3 1 17080 1441 113 15947 0.3 1 14645 1302 114 14330 0.3 1 13057 1273 115 12384 0.3 1 11329 1055 116 11096 0.3 1 10163 933 117 9114 0.3 1 8363 751 118 8187 0.3 1 7390 797 119 6803 0.3 1 6183 620 120 5832 0.3 1 5301 531 121 5072 0.3 1 4620 452 122 4206 0.3 1 3803 403 123 3440 0.3 1 3104 336 124 3042 0.3 1 2726 316 125 2501 0.3 1 2242 259 126 2111 0.3 1 1904 207 127 1791 0.3 1 1610 181 128 1444 0.3 1 1292 152 129 1148 0.3 1 1034 114 130 877 0.3 1 785 92 131 693 0.3 1 607 86 132 646 0.3 1 559 87 133 689 0.3 1 596 93 134 1090 0.3 1 1005 85 135 492 0.3 1 440 52 136 216 0.3 1 190 26 137 184 0.3 1 157 27 138 124 0.3 1 103 21 139 70 0.3 1 60 10 140 61 0.3 1 49 12 141 35 0.3 1 30 5 142 23 0.3 1 21 2 143 27 0.3 1 25 2 144 40 0.3 1 34 6 145 86 0.3 1 71 15 146 101 0.3 1 97 4 147 403 0.3 1 365 38 148 275 0.3 1 252 23 149 182 0.3 1 169 13 150 1714 0.3 1 1347 367 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_2_S10_L002_R1_001.fastq.gz ============================================= 18388474 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 7210 (0.0%)