SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_2_S6_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/8C_32psu_2_S6_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 547.25 s (43 us/read; 1.41 M reads/minute). === Summary === Total reads processed: 12,868,767 Reads with adapters: 10,225,148 (79.5%) Reads written (passing filters): 12,868,767 (100.0%) Total basepairs processed: 1,930,315,050 bp Quality-trimmed: 8,911,212 bp (0.5%) Total written (filtered): 1,486,049,208 bp (77.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10225148 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 13.1% G: 23.9% T: 34.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1581903 3217191.8 0 1581903 2 233784 804297.9 0 233784 3 139412 201074.5 0 139412 4 79292 50268.6 0 79292 5 72507 12567.2 0 72507 6 64695 3141.8 0 64695 7 50784 785.4 0 50784 8 73943 196.4 0 73943 9 59253 49.1 0 59073 180 10 62906 12.3 1 58824 4082 11 69220 3.1 1 63844 5376 12 67633 0.8 1 62443 5190 13 78337 0.2 1 72455 5882 14 72684 0.2 1 66542 6142 15 59253 0.2 1 54996 4257 16 85878 0.2 1 79407 6471 17 71616 0.2 1 66058 5558 18 64381 0.2 1 59775 4606 19 83620 0.2 1 77611 6009 20 78383 0.2 1 72906 5477 21 69471 0.2 1 64687 4784 22 78479 0.2 1 73016 5463 23 83210 0.2 1 77230 5980 24 82011 0.2 1 76117 5894 25 93094 0.2 1 87025 6069 26 77459 0.2 1 71634 5825 27 86527 0.2 1 79790 6737 28 77466 0.2 1 72862 4604 29 87078 0.2 1 81023 6055 30 83340 0.2 1 78135 5205 31 92587 0.2 1 86504 6083 32 80491 0.2 1 75656 4835 33 92967 0.2 1 86621 6346 34 120697 0.2 1 112803 7894 35 64048 0.2 1 59979 4069 36 95138 0.2 1 88610 6528 37 100610 0.2 1 93904 6706 38 93157 0.2 1 87717 5440 39 88669 0.2 1 83789 4880 40 101334 0.2 1 95182 6152 41 98089 0.2 1 92269 5820 42 100106 0.2 1 94212 5894 43 90866 0.2 1 85570 5296 44 106583 0.2 1 100029 6554 45 108549 0.2 1 101877 6672 46 84237 0.2 1 79394 4843 47 103605 0.2 1 98067 5538 48 100222 0.2 1 94797 5425 49 105528 0.2 1 99377 6151 50 101252 0.2 1 95306 5946 51 124662 0.2 1 117482 7180 52 89980 0.2 1 85108 4872 53 112122 0.2 1 106274 5848 54 81922 0.2 1 77760 4162 55 105894 0.2 1 100558 5336 56 109567 0.2 1 103471 6096 57 105084 0.2 1 100060 5024 58 101375 0.2 1 96453 4922 59 101412 0.2 1 96219 5193 60 106019 0.2 1 100584 5435 61 107866 0.2 1 102516 5350 62 117046 0.2 1 111012 6034 63 155210 0.2 1 148115 7095 64 127345 0.2 1 122328 5017 65 83662 0.2 1 79683 3979 66 91095 0.2 1 86676 4419 67 90432 0.2 1 85682 4750 68 91566 0.2 1 87021 4545 69 91038 0.2 1 86455 4583 70 97071 0.2 1 92328 4743 71 100160 0.2 1 95222 4938 72 95370 0.2 1 90793 4577 73 99146 0.2 1 94377 4769 74 90186 0.2 1 85699 4487 75 87292 0.2 1 82908 4384 76 84846 0.2 1 80550 4296 77 84110 0.2 1 79782 4328 78 80083 0.2 1 76044 4039 79 77641 0.2 1 73764 3877 80 76649 0.2 1 72933 3716 81 75643 0.2 1 71998 3645 82 72511 0.2 1 69001 3510 83 70456 0.2 1 67059 3397 84 67826 0.2 1 64473 3353 85 66652 0.2 1 63633 3019 86 65922 0.2 1 62797 3125 87 65939 0.2 1 62926 3013 88 64115 0.2 1 61226 2889 89 57559 0.2 1 54978 2581 90 55692 0.2 1 53148 2544 91 51986 0.2 1 49669 2317 92 49131 0.2 1 46914 2217 93 46886 0.2 1 44668 2218 94 45747 0.2 1 43801 1946 95 42950 0.2 1 40887 2063 96 40716 0.2 1 38860 1856 97 37404 0.2 1 35730 1674 98 34443 0.2 1 32843 1600 99 33264 0.2 1 31734 1530 100 30705 0.2 1 29262 1443 101 28943 0.2 1 27671 1272 102 27964 0.2 1 26691 1273 103 25366 0.2 1 24255 1111 104 24064 0.2 1 22990 1074 105 21070 0.2 1 20080 990 106 19078 0.2 1 18244 834 107 17343 0.2 1 16582 761 108 15238 0.2 1 14525 713 109 14062 0.2 1 13403 659 110 12670 0.2 1 12101 569 111 11892 0.2 1 11362 530 112 10243 0.2 1 9780 463 113 8834 0.2 1 8449 385 114 7653 0.2 1 7300 353 115 6468 0.2 1 6167 301 116 5767 0.2 1 5513 254 117 4744 0.2 1 4519 225 118 4267 0.2 1 4031 236 119 3534 0.2 1 3331 203 120 2971 0.2 1 2813 158 121 2616 0.2 1 2484 132 122 2300 0.2 1 2180 120 123 1889 0.2 1 1769 120 124 1591 0.2 1 1513 78 125 1198 0.2 1 1143 55 126 1107 0.2 1 1053 54 127 843 0.2 1 791 52 128 694 0.2 1 650 44 129 581 0.2 1 539 42 130 407 0.2 1 381 26 131 412 0.2 1 395 17 132 294 0.2 1 275 19 133 274 0.2 1 263 11 134 295 0.2 1 282 13 135 162 0.2 1 152 10 136 127 0.2 1 120 7 137 72 0.2 1 67 5 138 53 0.2 1 46 7 139 48 0.2 1 43 5 140 33 0.2 1 30 3 141 23 0.2 1 20 3 142 13 0.2 1 11 2 143 12 0.2 1 11 1 144 5 0.2 1 3 2 145 11 0.2 1 11 146 13 0.2 1 12 1 147 30 0.2 1 28 2 148 16 0.2 1 14 2 149 14 0.2 1 13 1 150 92 0.2 1 87 5 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_2_S6_L002_R2_001.fastq.gz ============================================= 12868767 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 14322 (0.1%)