SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_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_32psu_4_S8_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 621.57 s (43 us/read; 1.41 M reads/minute). === Summary === Total reads processed: 14,607,942 Reads with adapters: 11,056,021 (75.7%) Reads written (passing filters): 14,607,942 (100.0%) Total basepairs processed: 2,191,191,300 bp Quality-trimmed: 9,138,103 bp (0.4%) Total written (filtered): 1,772,690,067 bp (80.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11056021 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.7% C: 11.8% G: 21.0% T: 36.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2179670 3651985.5 0 2179670 2 288357 912996.4 0 288357 3 156435 228249.1 0 156435 4 98004 57062.3 0 98004 5 83153 14265.6 0 83153 6 80849 3566.4 0 80849 7 66215 891.6 0 66215 8 83652 222.9 0 83652 9 81421 55.7 0 80631 790 10 76420 13.9 1 72069 4351 11 85164 3.5 1 78240 6924 12 81348 0.9 1 75711 5637 13 83598 0.2 1 77773 5825 14 83352 0.2 1 76916 6436 15 87371 0.2 1 80774 6597 16 86829 0.2 1 79522 7307 17 105942 0.2 1 96774 9168 18 88487 0.2 1 82567 5920 19 76290 0.2 1 70996 5294 20 90707 0.2 1 84433 6274 21 101596 0.2 1 93808 7788 22 84911 0.2 1 79523 5388 23 99744 0.2 1 92683 7061 24 90626 0.2 1 82850 7776 25 98474 0.2 1 91331 7143 26 89046 0.2 1 83387 5659 27 100470 0.2 1 92717 7753 28 97480 0.2 1 90362 7118 29 103196 0.2 1 94309 8887 30 114370 0.2 1 107320 7050 31 79392 0.2 1 73939 5453 32 105208 0.2 1 97664 7544 33 95289 0.2 1 88120 7169 34 103964 0.2 1 96266 7698 35 100819 0.2 1 93035 7784 36 104164 0.2 1 96092 8072 37 105927 0.2 1 98240 7687 38 112135 0.2 1 103582 8553 39 96387 0.2 1 90041 6346 40 110619 0.2 1 102036 8583 41 118329 0.2 1 106686 11643 42 106988 0.2 1 97227 9761 43 165097 0.2 1 154382 10715 44 56454 0.2 1 50914 5540 45 117022 0.2 1 106731 10291 46 248165 0.2 1 231776 16389 47 141744 0.2 1 132412 9332 48 71383 0.2 1 63944 7439 49 214966 0.2 1 202098 12868 50 67123 0.2 1 61729 5394 51 84537 0.2 1 77868 6669 52 227448 0.2 1 214969 12479 53 153876 0.2 1 146571 7305 54 58063 0.2 1 53681 4382 55 96470 0.2 1 91390 5080 56 61719 0.2 1 56899 4820 57 135082 0.2 1 128247 6835 58 34302 0.2 1 31774 2528 59 37018 0.2 1 33361 3657 60 120449 0.2 1 114261 6188 61 79440 0.2 1 75334 4106 62 40303 0.2 1 37043 3260 63 92254 0.2 1 86676 5578 64 78944 0.2 1 74628 4316 65 54545 0.2 1 50567 3978 66 92915 0.2 1 86970 5945 67 106337 0.2 1 98786 7551 68 178710 0.2 1 168688 10022 69 108665 0.2 1 102241 6424 70 43742 0.2 1 39918 3824 71 19154 0.2 1 17119 2035 72 62321 0.2 1 58726 3595 73 80997 0.2 1 76319 4678 74 82292 0.2 1 77235 5057 75 80453 0.2 1 75230 5223 76 78946 0.2 1 73647 5299 77 78496 0.2 1 73454 5042 78 73891 0.2 1 68991 4900 79 72359 0.2 1 67790 4569 80 70385 0.2 1 65644 4741 81 70687 0.2 1 66072 4615 82 67765 0.2 1 63360 4405 83 64119 0.2 1 59858 4261 84 61128 0.2 1 56996 4132 85 58834 0.2 1 54971 3863 86 56645 0.2 1 52920 3725 87 53397 0.2 1 50007 3390 88 52020 0.2 1 48563 3457 89 48843 0.2 1 45677 3166 90 48488 0.2 1 45284 3204 91 45775 0.2 1 42701 3074 92 42633 0.2 1 39741 2892 93 39061 0.2 1 36500 2561 94 37084 0.2 1 34707 2377 95 34306 0.2 1 31956 2350 96 31990 0.2 1 29804 2186 97 29916 0.2 1 28016 1900 98 27386 0.2 1 25513 1873 99 26105 0.2 1 24176 1929 100 23728 0.2 1 22014 1714 101 21360 0.2 1 19893 1467 102 19677 0.2 1 18296 1381 103 17691 0.2 1 16474 1217 104 16298 0.2 1 15194 1104 105 14499 0.2 1 13498 1001 106 13016 0.2 1 12109 907 107 11299 0.2 1 10529 770 108 10657 0.2 1 9906 751 109 9041 0.2 1 8358 683 110 8101 0.2 1 7484 617 111 7203 0.2 1 6631 572 112 6115 0.2 1 5677 438 113 5247 0.2 1 4830 417 114 4477 0.2 1 4092 385 115 3837 0.2 1 3499 338 116 3178 0.2 1 2885 293 117 2717 0.2 1 2476 241 118 2308 0.2 1 2079 229 119 1913 0.2 1 1734 179 120 1562 0.2 1 1431 131 121 1324 0.2 1 1204 120 122 1075 0.2 1 965 110 123 859 0.2 1 768 91 124 724 0.2 1 640 84 125 591 0.2 1 519 72 126 475 0.2 1 409 66 127 455 0.2 1 404 51 128 340 0.2 1 294 46 129 243 0.2 1 193 50 130 216 0.2 1 182 34 131 170 0.2 1 146 24 132 150 0.2 1 133 17 133 129 0.2 1 114 15 134 222 0.2 1 199 23 135 80 0.2 1 75 5 136 46 0.2 1 42 4 137 44 0.2 1 37 7 138 28 0.2 1 28 139 21 0.2 1 18 3 140 10 0.2 1 6 4 141 12 0.2 1 8 4 142 16 0.2 1 13 3 143 7 0.2 1 3 4 144 10 0.2 1 10 145 6 0.2 1 4 2 146 6 0.2 1 4 2 147 26 0.2 1 24 2 148 13 0.2 1 11 2 149 11 0.2 1 11 150 141 0.2 1 126 15 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_L002_R1_001.fastq.gz ============================================= 14607942 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 1190 (0.0%)