SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_2_S14_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/16C_26psu_2_S14_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 753.42 s (44 us/read; 1.37 M reads/minute). === Summary === Total reads processed: 17,243,447 Reads with adapters: 13,270,528 (77.0%) Reads written (passing filters): 17,243,447 (100.0%) Total basepairs processed: 2,586,517,050 bp Quality-trimmed: 11,661,219 bp (0.5%) Total written (filtered): 2,049,890,632 bp (79.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13270528 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.8% G: 23.5% T: 35.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2410570 4310861.8 0 2410570 2 362455 1077715.4 0 362455 3 204625 269428.9 0 204625 4 116204 67357.2 0 116204 5 102265 16839.3 0 102265 6 87780 4209.8 0 87780 7 72496 1052.5 0 72496 8 102751 263.1 0 102751 9 81658 65.8 0 81386 272 10 89121 16.4 1 84631 4490 11 93864 4.1 1 87983 5881 12 94565 1.0 1 88491 6074 13 105522 0.3 1 99372 6150 14 98340 0.3 1 91512 6828 15 80980 0.3 1 75936 5044 16 116316 0.3 1 109001 7315 17 93497 0.3 1 87166 6331 18 89538 0.3 1 84129 5409 19 112544 0.3 1 105239 7305 20 105651 0.3 1 99238 6413 21 93625 0.3 1 87782 5843 22 104844 0.3 1 98723 6121 23 109552 0.3 1 102808 6744 24 108841 0.3 1 101825 7016 25 121233 0.3 1 114032 7201 26 101015 0.3 1 94639 6376 27 112490 0.3 1 104790 7700 28 105074 0.3 1 99527 5547 29 111755 0.3 1 104926 6829 30 110664 0.3 1 104658 6006 31 120328 0.3 1 113206 7122 32 108098 0.3 1 102252 5846 33 119317 0.3 1 112198 7119 34 151071 0.3 1 142232 8839 35 87186 0.3 1 82458 4728 36 120833 0.3 1 113650 7183 37 128643 0.3 1 121059 7584 38 120495 0.3 1 114429 6066 39 117189 0.3 1 111171 6018 40 129860 0.3 1 122333 7527 41 123836 0.3 1 117366 6470 42 127654 0.3 1 120939 6715 43 116428 0.3 1 110085 6343 44 133061 0.3 1 125767 7294 45 139911 0.3 1 132604 7307 46 103489 0.3 1 98069 5420 47 129515 0.3 1 122821 6694 48 126933 0.3 1 120634 6299 49 132432 0.3 1 125535 6897 50 125382 0.3 1 118618 6764 51 155910 0.3 1 147950 7960 52 112001 0.3 1 106554 5447 53 134464 0.3 1 128383 6081 54 103158 0.3 1 98052 5106 55 131983 0.3 1 126024 5959 56 136358 0.3 1 129807 6551 57 127296 0.3 1 121594 5702 58 122071 0.3 1 116674 5397 59 124219 0.3 1 118380 5839 60 128066 0.3 1 121909 6157 61 132129 0.3 1 125705 6424 62 142837 0.3 1 135944 6893 63 190582 0.3 1 182484 8098 64 150467 0.3 1 144624 5843 65 101740 0.3 1 97088 4652 66 109816 0.3 1 104968 4848 67 107749 0.3 1 102613 5136 68 108633 0.3 1 103740 4893 69 107596 0.3 1 102648 4948 70 114794 0.3 1 109576 5218 71 116610 0.3 1 111540 5070 72 110184 0.3 1 105059 5125 73 115749 0.3 1 110692 5057 74 106275 0.3 1 101612 4663 75 101750 0.3 1 97259 4491 76 99053 0.3 1 94705 4348 77 99069 0.3 1 94745 4324 78 94226 0.3 1 90009 4217 79 90763 0.3 1 86805 3958 80 89778 0.3 1 85958 3820 81 88669 0.3 1 84684 3985 82 84401 0.3 1 80642 3759 83 81824 0.3 1 78236 3588 84 78990 0.3 1 75425 3565 85 76455 0.3 1 73024 3431 86 76386 0.3 1 73029 3357 87 75988 0.3 1 72761 3227 88 73818 0.3 1 70558 3260 89 65970 0.3 1 63085 2885 90 63019 0.3 1 60213 2806 91 58914 0.3 1 56366 2548 92 54704 0.3 1 52314 2390 93 52692 0.3 1 50404 2288 94 51139 0.3 1 48941 2198 95 47428 0.3 1 45341 2087 96 45523 0.3 1 43617 1906 97 43074 0.3 1 41264 1810 98 39986 0.3 1 38323 1663 99 40439 0.3 1 38720 1719 100 35462 0.3 1 34051 1411 101 31343 0.3 1 29998 1345 102 28451 0.3 1 27239 1212 103 26443 0.3 1 25307 1136 104 24686 0.3 1 23698 988 105 22319 0.3 1 21394 925 106 20298 0.3 1 19438 860 107 18363 0.3 1 17549 814 108 16498 0.3 1 15775 723 109 15075 0.3 1 14486 589 110 13470 0.3 1 12883 587 111 12724 0.3 1 12179 545 112 10843 0.3 1 10385 458 113 9574 0.3 1 9156 418 114 8065 0.3 1 7698 367 115 6969 0.3 1 6632 337 116 5939 0.3 1 5624 315 117 5106 0.3 1 4872 234 118 4425 0.3 1 4206 219 119 3716 0.3 1 3520 196 120 3161 0.3 1 3007 154 121 2854 0.3 1 2727 127 122 2418 0.3 1 2305 113 123 2039 0.3 1 1907 132 124 1593 0.3 1 1516 77 125 1395 0.3 1 1318 77 126 1136 0.3 1 1075 61 127 1068 0.3 1 1004 64 128 801 0.3 1 764 37 129 660 0.3 1 625 35 130 510 0.3 1 471 39 131 432 0.3 1 407 25 132 400 0.3 1 378 22 133 460 0.3 1 436 24 134 592 0.3 1 573 19 135 262 0.3 1 249 13 136 158 0.3 1 150 8 137 105 0.3 1 102 3 138 83 0.3 1 78 5 139 62 0.3 1 57 5 140 55 0.3 1 49 6 141 58 0.3 1 56 2 142 36 0.3 1 36 143 49 0.3 1 47 2 144 33 0.3 1 30 3 145 52 0.3 1 45 7 146 154 0.3 1 152 2 147 543 0.3 1 532 11 148 399 0.3 1 383 16 149 287 0.3 1 273 14 150 2663 0.3 1 2573 90 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_2_S14_L001_R2_001.fastq.gz ============================================= 17243447 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 23344 (0.1%)