SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_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/16C_32psu_2_S2_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 713.19 s (40 us/read; 1.49 M reads/minute). === Summary === Total reads processed: 17,682,252 Reads with adapters: 14,653,341 (82.9%) Reads written (passing filters): 17,682,252 (100.0%) Total basepairs processed: 2,652,337,800 bp Quality-trimmed: 13,059,983 bp (0.5%) Total written (filtered): 1,958,600,443 bp (73.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14653341 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 12.0% G: 24.7% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1817135 4420563.0 0 1817135 2 279096 1105140.8 0 279096 3 175846 276285.2 0 175846 4 97770 69071.3 0 97770 5 91322 17267.8 0 91322 6 82979 4317.0 0 82979 7 65452 1079.2 0 65452 8 95994 269.8 0 95994 9 76273 67.5 0 76051 222 10 81686 16.9 1 76699 4987 11 88683 4.2 1 82075 6608 12 88254 1.1 1 81734 6520 13 102186 0.3 1 94885 7301 14 94341 0.3 1 86650 7691 15 77377 0.3 1 72050 5327 16 111829 0.3 1 103609 8220 17 95099 0.3 1 87974 7125 18 85068 0.3 1 79390 5678 19 110655 0.3 1 102928 7727 20 104031 0.3 1 97040 6991 21 92000 0.3 1 85864 6136 22 104100 0.3 1 97146 6954 23 109645 0.3 1 102128 7517 24 108307 0.3 1 100742 7565 25 123264 0.3 1 115703 7561 26 104401 0.3 1 96855 7546 27 119574 0.3 1 110821 8753 28 105530 0.3 1 99453 6077 29 120646 0.3 1 112687 7959 30 114291 0.3 1 107348 6943 31 129583 0.3 1 121518 8065 32 112118 0.3 1 105486 6632 33 129638 0.3 1 121053 8585 34 165788 0.3 1 155262 10526 35 90769 0.3 1 85358 5411 36 134484 0.3 1 125338 9146 37 141040 0.3 1 132135 8905 38 130890 0.3 1 123508 7382 39 125992 0.3 1 119419 6573 40 143114 0.3 1 134816 8298 41 141161 0.3 1 133004 8157 42 150560 0.3 1 142032 8528 43 126059 0.3 1 119274 6785 44 153119 0.3 1 144163 8956 45 156350 0.3 1 146944 9406 46 124535 0.3 1 117729 6806 47 151106 0.3 1 143277 7829 48 145709 0.3 1 138077 7632 49 153645 0.3 1 144717 8928 50 152443 0.3 1 143810 8633 51 186444 0.3 1 176105 10339 52 135339 0.3 1 128275 7064 53 167309 0.3 1 158978 8331 54 122506 0.3 1 116488 6018 55 159881 0.3 1 152187 7694 56 166549 0.3 1 157620 8929 57 159405 0.3 1 152142 7263 58 154742 0.3 1 147569 7173 59 154815 0.3 1 147039 7776 60 162353 0.3 1 154259 8094 61 164751 0.3 1 156984 7767 62 181848 0.3 1 172769 9079 63 243575 0.3 1 232900 10675 64 204233 0.3 1 196775 7458 65 131464 0.3 1 125558 5906 66 143870 0.3 1 137254 6616 67 143305 0.3 1 136348 6957 68 146020 0.3 1 139340 6680 69 145720 0.3 1 138556 7164 70 152388 0.3 1 145229 7159 71 160483 0.3 1 152923 7560 72 153910 0.3 1 146668 7242 73 161080 0.3 1 153734 7346 74 148742 0.3 1 141577 7165 75 142283 0.3 1 135459 6824 76 139212 0.3 1 132662 6550 77 138672 0.3 1 132174 6498 78 134120 0.3 1 127702 6418 79 128493 0.3 1 122569 5924 80 128817 0.3 1 123042 5775 81 126667 0.3 1 120859 5808 82 120873 0.3 1 115386 5487 83 118191 0.3 1 112948 5243 84 114338 0.3 1 109255 5083 85 112679 0.3 1 107691 4988 86 112861 0.3 1 107936 4925 87 113253 0.3 1 108504 4749 88 112053 0.3 1 107404 4649 89 99896 0.3 1 95509 4387 90 94224 0.3 1 90152 4072 91 88708 0.3 1 84909 3799 92 84091 0.3 1 80464 3627 93 80972 0.3 1 77474 3498 94 78965 0.3 1 75719 3246 95 74676 0.3 1 71434 3242 96 70973 0.3 1 67917 3056 97 64791 0.3 1 62029 2762 98 59852 0.3 1 57281 2571 99 56272 0.3 1 53840 2432 100 50916 0.3 1 48630 2286 101 48192 0.3 1 46113 2079 102 45225 0.3 1 43338 1887 103 42981 0.3 1 41068 1913 104 41627 0.3 1 39818 1809 105 36524 0.3 1 34997 1527 106 32960 0.3 1 31559 1401 107 28968 0.3 1 27743 1225 108 25878 0.3 1 24765 1113 109 23275 0.3 1 22256 1019 110 21045 0.3 1 20178 867 111 19919 0.3 1 19038 881 112 16987 0.3 1 16274 713 113 14633 0.3 1 14022 611 114 12693 0.3 1 12155 538 115 10546 0.3 1 10065 481 116 8985 0.3 1 8625 360 117 7253 0.3 1 6908 345 118 6254 0.3 1 5971 283 119 5291 0.3 1 5043 248 120 4411 0.3 1 4200 211 121 3756 0.3 1 3560 196 122 3023 0.3 1 2867 156 123 2649 0.3 1 2500 149 124 2061 0.3 1 1951 110 125 1723 0.3 1 1623 100 126 1447 0.3 1 1342 105 127 1137 0.3 1 1082 55 128 888 0.3 1 830 58 129 801 0.3 1 760 41 130 520 0.3 1 487 33 131 493 0.3 1 458 35 132 407 0.3 1 377 30 133 444 0.3 1 414 30 134 445 0.3 1 433 12 135 251 0.3 1 241 10 136 140 0.3 1 129 11 137 98 0.3 1 90 8 138 74 0.3 1 66 8 139 51 0.3 1 50 1 140 46 0.3 1 45 1 141 23 0.3 1 22 1 142 21 0.3 1 19 2 143 18 0.3 1 16 2 144 19 0.3 1 19 145 44 0.3 1 42 2 146 27 0.3 1 26 1 147 73 0.3 1 69 4 148 42 0.3 1 38 4 149 58 0.3 1 55 3 150 398 0.3 1 372 26 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_L002_R2_001.fastq.gz ============================================= 17682252 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 19996 (0.1%)