SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_1_S17_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/CTRL_8C_26psu_1_S17_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 600.51 s (44 us/read; 1.36 M reads/minute). === Summary === Total reads processed: 13,627,098 Reads with adapters: 10,276,263 (75.4%) Reads written (passing filters): 13,627,098 (100.0%) Total basepairs processed: 2,044,064,700 bp Quality-trimmed: 9,937,551 bp (0.5%) Total written (filtered): 1,630,739,955 bp (79.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10276263 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 12.4% G: 23.0% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2146357 3406774.5 0 2146357 2 269360 851693.6 0 269360 3 157893 212923.4 0 157893 4 87930 53230.9 0 87930 5 73543 13307.7 0 73543 6 64791 3326.9 0 64791 7 52189 831.7 0 52189 8 74756 207.9 0 74756 9 60599 52.0 0 60366 233 10 63543 13.0 1 59315 4228 11 68667 3.2 1 63268 5399 12 67618 0.8 1 62224 5394 13 77226 0.2 1 71131 6095 14 69709 0.2 1 63900 5809 15 58686 0.2 1 54055 4631 16 84262 0.2 1 77680 6582 17 67924 0.2 1 62515 5409 18 64114 0.2 1 59144 4970 19 80499 0.2 1 74211 6288 20 76034 0.2 1 70274 5760 21 67847 0.2 1 62554 5293 22 74609 0.2 1 68953 5656 23 78584 0.2 1 72661 5923 24 77507 0.2 1 71592 5915 25 87777 0.2 1 81767 6010 26 72611 0.2 1 66753 5858 27 83123 0.2 1 76411 6712 28 73079 0.2 1 68272 4807 29 82291 0.2 1 76291 6000 30 76541 0.2 1 71237 5304 31 89563 0.2 1 83077 6486 32 74346 0.2 1 69371 4975 33 86840 0.2 1 80487 6353 34 112360 0.2 1 104461 7899 35 60619 0.2 1 56337 4282 36 90028 0.2 1 83414 6614 37 96370 0.2 1 89511 6859 38 89130 0.2 1 83444 5686 39 86200 0.2 1 80889 5311 40 97029 0.2 1 90271 6758 41 93202 0.2 1 87114 6088 42 93307 0.2 1 87268 6039 43 83469 0.2 1 77943 5526 44 97590 0.2 1 91014 6576 45 100276 0.2 1 93792 6484 46 75444 0.2 1 70447 4997 47 93307 0.2 1 87603 5704 48 90968 0.2 1 85370 5598 49 95545 0.2 1 89305 6240 50 91141 0.2 1 85291 5850 51 108887 0.2 1 102107 6780 52 80355 0.2 1 75335 5020 53 99048 0.2 1 93311 5737 54 72741 0.2 1 68334 4407 55 95947 0.2 1 90438 5509 56 99513 0.2 1 93368 6145 57 93556 0.2 1 88452 5104 58 90539 0.2 1 85415 5124 59 90467 0.2 1 85091 5376 60 93608 0.2 1 88124 5484 61 95101 0.2 1 89698 5403 62 102226 0.2 1 96046 6180 63 136011 0.2 1 129004 7007 64 112722 0.2 1 107622 5100 65 75623 0.2 1 71479 4144 66 81004 0.2 1 76564 4440 67 79874 0.2 1 75268 4606 68 81531 0.2 1 76952 4579 69 80094 0.2 1 75476 4618 70 85599 0.2 1 80759 4840 71 89528 0.2 1 84657 4871 72 84362 0.2 1 79637 4725 73 87554 0.2 1 82710 4844 74 81739 0.2 1 77139 4600 75 76846 0.2 1 72538 4308 76 75616 0.2 1 71298 4318 77 75671 0.2 1 71375 4296 78 71297 0.2 1 67330 3967 79 68959 0.2 1 65062 3897 80 69385 0.2 1 65444 3941 81 68113 0.2 1 64379 3734 82 65128 0.2 1 61578 3550 83 63398 0.2 1 59890 3508 84 61642 0.2 1 58327 3315 85 61077 0.2 1 57799 3278 86 60708 0.2 1 57467 3241 87 60697 0.2 1 57594 3103 88 59562 0.2 1 56463 3099 89 54239 0.2 1 51398 2841 90 51773 0.2 1 48980 2793 91 49319 0.2 1 46756 2563 92 46223 0.2 1 43736 2487 93 44798 0.2 1 42455 2343 94 43852 0.2 1 41584 2268 95 41908 0.2 1 39647 2261 96 39622 0.2 1 37536 2086 97 36420 0.2 1 34621 1799 98 33185 0.2 1 31489 1696 99 32771 0.2 1 31125 1646 100 29865 0.2 1 28321 1544 101 27753 0.2 1 26308 1445 102 25712 0.2 1 24349 1363 103 23843 0.2 1 22528 1315 104 23330 0.2 1 22084 1246 105 20720 0.2 1 19658 1062 106 19342 0.2 1 18364 978 107 17248 0.2 1 16375 873 108 15847 0.2 1 15052 795 109 14536 0.2 1 13807 729 110 12976 0.2 1 12292 684 111 12529 0.2 1 11885 644 112 10963 0.2 1 10373 590 113 9349 0.2 1 8908 441 114 8548 0.2 1 8120 428 115 7299 0.2 1 6916 383 116 6237 0.2 1 5941 296 117 5243 0.2 1 4920 323 118 4696 0.2 1 4465 231 119 3975 0.2 1 3763 212 120 3508 0.2 1 3309 199 121 3040 0.2 1 2875 165 122 2575 0.2 1 2428 147 123 2186 0.2 1 2073 113 124 1945 0.2 1 1832 113 125 1652 0.2 1 1551 101 126 1464 0.2 1 1388 76 127 1181 0.2 1 1120 61 128 990 0.2 1 926 64 129 867 0.2 1 802 65 130 639 0.2 1 610 29 131 564 0.2 1 532 32 132 517 0.2 1 490 27 133 691 0.2 1 653 38 134 1520 0.2 1 1458 62 135 553 0.2 1 527 26 136 201 0.2 1 194 7 137 155 0.2 1 146 9 138 95 0.2 1 92 3 139 52 0.2 1 49 3 140 44 0.2 1 40 4 141 42 0.2 1 38 4 142 33 0.2 1 31 2 143 49 0.2 1 44 5 144 63 0.2 1 60 3 145 162 0.2 1 155 7 146 237 0.2 1 226 11 147 1276 0.2 1 1212 64 148 739 0.2 1 700 39 149 423 0.2 1 396 27 150 2548 0.2 1 2400 148 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_1_S17_L002_R2_001.fastq.gz ============================================= 13627098 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 24804 (0.2%)