SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_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/8C_26psu_3_S11_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 667.73 s (39 us/read; 1.55 M reads/minute). === Summary === Total reads processed: 17,221,011 Reads with adapters: 14,791,093 (85.9%) Reads written (passing filters): 17,221,011 (100.0%) Total basepairs processed: 2,583,151,650 bp Quality-trimmed: 13,446,962 bp (0.5%) Total written (filtered): 1,830,093,875 bp (70.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14791093 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.4% C: 12.3% G: 25.7% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1396647 4305252.8 0 1396647 2 233877 1076313.2 0 233877 3 144492 269078.3 0 144492 4 87098 67269.6 0 87098 5 86055 16817.4 0 86055 6 74999 4204.3 0 74999 7 60602 1051.1 0 60602 8 88349 262.8 0 88349 9 70295 65.7 0 70075 220 10 78524 16.4 1 74626 3898 11 82895 4.1 1 77738 5157 12 84476 1.0 1 79233 5243 13 94326 0.3 1 88847 5479 14 89984 0.3 1 83845 6139 15 72879 0.3 1 68520 4359 16 107100 0.3 1 100533 6567 17 87871 0.3 1 82033 5838 18 83139 0.3 1 78397 4742 19 107298 0.3 1 100402 6896 20 100171 0.3 1 94390 5781 21 88114 0.3 1 82713 5401 22 101076 0.3 1 95306 5770 23 105877 0.3 1 99537 6340 24 106645 0.3 1 100049 6596 25 121932 0.3 1 115168 6764 26 100476 0.3 1 94344 6132 27 110166 0.3 1 102758 7408 28 107176 0.3 1 101924 5252 29 114111 0.3 1 107493 6618 30 115359 0.3 1 109345 6014 31 124714 0.3 1 117673 7041 32 113114 0.3 1 107249 5865 33 126653 0.3 1 119283 7370 34 161416 0.3 1 152249 9167 35 95165 0.3 1 90366 4799 36 130060 0.3 1 122395 7665 37 137916 0.3 1 130202 7714 38 132706 0.3 1 126385 6321 39 129385 0.3 1 123068 6317 40 145600 0.3 1 137496 8104 41 141184 0.3 1 134070 7114 42 147655 0.3 1 140213 7442 43 133334 0.3 1 126611 6723 44 155705 0.3 1 147696 8009 45 171369 0.3 1 162810 8559 46 117297 0.3 1 111483 5814 47 154795 0.3 1 147535 7260 48 153124 0.3 1 145909 7215 49 161825 0.3 1 153802 8023 50 152605 0.3 1 145077 7528 51 196303 0.3 1 186610 9693 52 140348 0.3 1 134075 6273 53 169943 0.3 1 162909 7034 54 129681 0.3 1 123901 5780 55 171452 0.3 1 164350 7102 56 175614 0.3 1 167693 7921 57 166121 0.3 1 159314 6807 58 161387 0.3 1 155069 6318 59 166619 0.3 1 159538 7081 60 171867 0.3 1 164363 7504 61 178391 0.3 1 170609 7782 62 196679 0.3 1 188081 8598 63 261274 0.3 1 251029 10245 64 223191 0.3 1 215765 7426 65 140786 0.3 1 135022 5764 66 154538 0.3 1 148311 6227 67 154027 0.3 1 147524 6503 68 155618 0.3 1 149295 6323 69 156069 0.3 1 149599 6470 70 165853 0.3 1 158998 6855 71 174385 0.3 1 167574 6811 72 166867 0.3 1 160011 6856 73 177560 0.3 1 170679 6881 74 163422 0.3 1 157175 6247 75 155704 0.3 1 149734 5970 76 153010 0.3 1 147031 5979 77 153177 0.3 1 146921 6256 78 148366 0.3 1 142418 5948 79 143302 0.3 1 137662 5640 80 143393 0.3 1 137924 5469 81 142595 0.3 1 137094 5501 82 136572 0.3 1 131469 5103 83 132737 0.3 1 127619 5118 84 127991 0.3 1 122783 5208 85 126965 0.3 1 121917 5048 86 125977 0.3 1 120895 5082 87 128246 0.3 1 123231 5015 88 125283 0.3 1 120412 4871 89 112372 0.3 1 108049 4323 90 108791 0.3 1 104559 4232 91 102461 0.3 1 98288 4173 92 96447 0.3 1 92722 3725 93 93869 0.3 1 90286 3583 94 91252 0.3 1 87743 3509 95 86357 0.3 1 83052 3305 96 82971 0.3 1 79818 3153 97 76434 0.3 1 73514 2920 98 72048 0.3 1 69275 2773 99 70150 0.3 1 67632 2518 100 63666 0.3 1 61347 2319 101 59861 0.3 1 57732 2129 102 55598 0.3 1 53622 1976 103 51026 0.3 1 49092 1934 104 48386 0.3 1 46675 1711 105 42639 0.3 1 41080 1559 106 39613 0.3 1 38200 1413 107 35228 0.3 1 33949 1279 108 31897 0.3 1 30649 1248 109 28672 0.3 1 27578 1094 110 25914 0.3 1 24951 963 111 24295 0.3 1 23481 814 112 21304 0.3 1 20453 851 113 18350 0.3 1 17653 697 114 16256 0.3 1 15627 629 115 13357 0.3 1 12793 564 116 11612 0.3 1 11150 462 117 9484 0.3 1 9116 368 118 8205 0.3 1 7826 379 119 6936 0.3 1 6629 307 120 5765 0.3 1 5525 240 121 5231 0.3 1 5015 216 122 4247 0.3 1 4080 167 123 3547 0.3 1 3416 131 124 2936 0.3 1 2808 128 125 2425 0.3 1 2314 111 126 2011 0.3 1 1915 96 127 1702 0.3 1 1617 85 128 1242 0.3 1 1178 64 129 1065 0.3 1 1006 59 130 766 0.3 1 721 45 131 781 0.3 1 739 42 132 668 0.3 1 634 34 133 887 0.3 1 866 21 134 1489 0.3 1 1430 59 135 583 0.3 1 560 23 136 206 0.3 1 191 15 137 151 0.3 1 146 5 138 116 0.3 1 111 5 139 72 0.3 1 65 7 140 56 0.3 1 54 2 141 35 0.3 1 27 8 142 30 0.3 1 26 4 143 21 0.3 1 18 3 144 19 0.3 1 17 2 145 37 0.3 1 35 2 146 25 0.3 1 22 3 147 50 0.3 1 46 4 148 39 0.3 1 37 2 149 45 0.3 1 42 3 150 451 0.3 1 418 33 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_L001_R2_001.fastq.gz ============================================= 17221011 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 26089 (0.2%)