SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_3_S7_L001_R1_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_3_S7_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 537.88 s (38 us/read; 1.58 M reads/minute). === Summary === Total reads processed: 14,166,205 Reads with adapters: 11,846,180 (83.6%) Reads written (passing filters): 14,166,205 (100.0%) Total basepairs processed: 2,124,930,750 bp Quality-trimmed: 4,298,957 bp (0.2%) Total written (filtered): 1,559,729,002 bp (73.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11846180 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.1% C: 15.1% G: 21.0% T: 34.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1373757 3541551.2 0 1373757 2 216270 885387.8 0 216270 3 129588 221347.0 0 129588 4 80077 55336.7 0 80077 5 69163 13834.2 0 69163 6 67518 3458.5 0 67518 7 56035 864.6 0 56035 8 70267 216.2 0 70267 9 70629 54.0 0 69702 927 10 66297 13.5 1 62862 3435 11 73903 3.4 1 68283 5620 12 71104 0.8 1 66580 4524 13 72370 0.2 1 67647 4723 14 73869 0.2 1 68608 5261 15 77649 0.2 1 72603 5046 16 76835 0.2 1 71293 5542 17 93103 0.2 1 85654 7449 18 80962 0.2 1 76131 4831 19 69251 0.2 1 64739 4512 20 83140 0.2 1 77746 5394 21 91983 0.2 1 85635 6348 22 78972 0.2 1 74340 4632 23 91741 0.2 1 85612 6129 24 86730 0.2 1 79637 7093 25 93905 0.2 1 87575 6330 26 84785 0.2 1 79850 4935 27 95659 0.2 1 88641 7018 28 93289 0.2 1 86777 6512 29 102324 0.2 1 94020 8304 30 106573 0.2 1 100735 5838 31 82302 0.2 1 76920 5382 32 102146 0.2 1 95503 6643 33 96707 0.2 1 90380 6327 34 106974 0.2 1 99423 7551 35 107836 0.2 1 100264 7572 36 113175 0.2 1 105186 7989 37 100704 0.2 1 95019 5685 38 121468 0.2 1 112012 9456 39 103157 0.2 1 96822 6335 40 115108 0.2 1 108010 7098 41 129750 0.2 1 120171 9579 42 102179 0.2 1 94823 7356 43 171532 0.2 1 162826 8706 44 55606 0.2 1 50892 4714 45 120800 0.2 1 113289 7511 46 113431 0.2 1 106413 7018 47 120541 0.2 1 113256 7285 48 119747 0.2 1 111882 7865 49 130730 0.2 1 121756 8974 50 111508 0.2 1 104914 6594 51 122095 0.2 1 114233 7862 52 127642 0.2 1 118613 9029 53 137409 0.2 1 129309 8100 54 108827 0.2 1 102141 6686 55 130904 0.2 1 122687 8217 56 157783 0.2 1 148768 9015 57 104771 0.2 1 97389 7382 58 132433 0.2 1 125333 7100 59 115612 0.2 1 108308 7304 60 130650 0.2 1 122277 8373 61 128910 0.2 1 121303 7607 62 139690 0.2 1 131489 8201 63 114068 0.2 1 106664 7404 64 125901 0.2 1 118809 7092 65 141358 0.2 1 132756 8602 66 146823 0.2 1 137956 8867 67 159981 0.2 1 148074 11907 68 301471 0.2 1 287602 13869 69 51550 0.2 1 47181 4369 70 21339 0.2 1 17862 3477 71 81265 0.2 1 76296 4969 72 113463 0.2 1 106973 6490 73 120176 0.2 1 113199 6977 74 119128 0.2 1 112036 7092 75 118829 0.2 1 111689 7140 76 117859 0.2 1 110976 6883 77 119047 0.2 1 112165 6882 78 111406 0.2 1 104659 6747 79 110628 0.2 1 103829 6799 80 108577 0.2 1 102197 6380 81 107611 0.2 1 101254 6357 82 104685 0.2 1 98322 6363 83 101689 0.2 1 95553 6136 84 99042 0.2 1 93220 5822 85 96588 0.2 1 90890 5698 86 93102 0.2 1 87585 5517 87 89497 0.2 1 84148 5349 88 88681 0.2 1 83310 5371 89 83884 0.2 1 78862 5022 90 83820 0.2 1 78644 5176 91 79519 0.2 1 74630 4889 92 75751 0.2 1 71312 4439 93 71060 0.2 1 66734 4326 94 68805 0.2 1 64395 4410 95 63794 0.2 1 59908 3886 96 60732 0.2 1 57025 3707 97 57614 0.2 1 54075 3539 98 53272 0.2 1 49912 3360 99 52704 0.2 1 49079 3625 100 47213 0.2 1 44245 2968 101 43905 0.2 1 41069 2836 102 40757 0.2 1 38090 2667 103 36990 0.2 1 34581 2409 104 34678 0.2 1 32449 2229 105 30517 0.2 1 28453 2064 106 28231 0.2 1 26371 1860 107 25422 0.2 1 23676 1746 108 24129 0.2 1 22480 1649 109 20909 0.2 1 19298 1611 110 19145 0.2 1 17778 1367 111 17228 0.2 1 15946 1282 112 14959 0.2 1 13818 1141 113 12878 0.2 1 11894 984 114 11383 0.2 1 10467 916 115 9899 0.2 1 9096 803 116 8618 0.2 1 7872 746 117 7168 0.2 1 6561 607 118 6256 0.2 1 5711 545 119 5200 0.2 1 4764 436 120 4401 0.2 1 4012 389 121 3754 0.2 1 3388 366 122 3023 0.2 1 2711 312 123 2648 0.2 1 2374 274 124 2210 0.2 1 1991 219 125 1851 0.2 1 1661 190 126 1538 0.2 1 1379 159 127 1281 0.2 1 1146 135 128 1028 0.2 1 906 122 129 844 0.2 1 750 94 130 578 0.2 1 506 72 131 477 0.2 1 408 69 132 403 0.2 1 349 54 133 425 0.2 1 364 61 134 500 0.2 1 457 43 135 253 0.2 1 229 24 136 154 0.2 1 133 21 137 116 0.2 1 99 17 138 91 0.2 1 74 17 139 63 0.2 1 48 15 140 40 0.2 1 34 6 141 25 0.2 1 20 5 142 20 0.2 1 12 8 143 19 0.2 1 15 4 144 21 0.2 1 17 4 145 20 0.2 1 16 4 146 14 0.2 1 12 2 147 31 0.2 1 27 4 148 15 0.2 1 13 2 149 18 0.2 1 14 4 150 240 0.2 1 195 45 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_3_S7_L001_R1_001.fastq.gz ============================================= 14166205 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 2985 (0.0%)