SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_4_S4_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_4_S4_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 724.45 s (46 us/read; 1.29 M reads/minute). === Summary === Total reads processed: 15,591,852 Reads with adapters: 11,164,940 (71.6%) Reads written (passing filters): 15,591,852 (100.0%) Total basepairs processed: 2,338,777,800 bp Quality-trimmed: 8,987,489 bp (0.4%) Total written (filtered): 1,952,377,119 bp (83.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11164940 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 12.2% G: 21.8% T: 35.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2716063 3897963.0 0 2716063 2 365801 974490.8 0 365801 3 204110 243622.7 0 204110 4 111706 60905.7 0 111706 5 93686 15226.4 0 93686 6 82310 3806.6 0 82310 7 64821 951.7 0 64821 8 93347 237.9 0 93347 9 74551 59.5 0 74263 288 10 78346 14.9 1 72991 5355 11 85380 3.7 1 78328 7052 12 84150 0.9 1 77541 6609 13 96178 0.2 1 88615 7563 14 88433 0.2 1 80671 7762 15 72019 0.2 1 66503 5516 16 102952 0.2 1 94755 8197 17 86769 0.2 1 79687 7082 18 76619 0.2 1 70853 5766 19 98606 0.2 1 91042 7564 20 91841 0.2 1 84883 6958 21 80822 0.2 1 74556 6266 22 90084 0.2 1 83382 6702 23 95275 0.2 1 87967 7308 24 93761 0.2 1 86637 7124 25 105154 0.2 1 98108 7046 26 87685 0.2 1 80687 6998 27 96238 0.2 1 88248 7990 28 86982 0.2 1 81506 5476 29 96532 0.2 1 89458 7074 30 91145 0.2 1 85081 6064 31 100852 0.2 1 93803 7049 32 86615 0.2 1 80885 5730 33 99917 0.2 1 92622 7295 34 128321 0.2 1 119309 9012 35 68466 0.2 1 63767 4699 36 99171 0.2 1 91848 7323 37 104228 0.2 1 97074 7154 38 95840 0.2 1 89901 5939 39 91223 0.2 1 85899 5324 40 103901 0.2 1 97025 6876 41 100699 0.2 1 94360 6339 42 101648 0.2 1 95335 6313 43 91398 0.2 1 85693 5705 44 105931 0.2 1 98930 7001 45 111589 0.2 1 104455 7134 46 79183 0.2 1 74169 5014 47 99997 0.2 1 94251 5746 48 97219 0.2 1 91470 5749 49 102240 0.2 1 95693 6547 50 96699 0.2 1 90628 6071 51 118228 0.2 1 110940 7288 52 84607 0.2 1 79439 5168 53 104742 0.2 1 98960 5782 54 75371 0.2 1 71116 4255 55 98114 0.2 1 92755 5359 56 100972 0.2 1 94974 5998 57 94787 0.2 1 89866 4921 58 91176 0.2 1 86320 4856 59 91225 0.2 1 86196 5029 60 94303 0.2 1 88940 5363 61 95802 0.2 1 90516 5286 62 104062 0.2 1 98063 5999 63 134017 0.2 1 127276 6741 64 107807 0.2 1 103277 4530 65 71585 0.2 1 67908 3677 66 78177 0.2 1 74035 4142 67 77189 0.2 1 72913 4276 68 77503 0.2 1 73378 4125 69 76227 0.2 1 72009 4218 70 77805 0.2 1 73707 4098 71 80348 0.2 1 76129 4219 72 76686 0.2 1 72546 4140 73 78718 0.2 1 74553 4165 74 72998 0.2 1 69110 3888 75 69291 0.2 1 65521 3770 76 66128 0.2 1 62546 3582 77 65756 0.2 1 62222 3534 78 62918 0.2 1 59420 3498 79 59982 0.2 1 56797 3185 80 59872 0.2 1 56761 3111 81 57826 0.2 1 54814 3012 82 55215 0.2 1 52336 2879 83 53442 0.2 1 50600 2842 84 50951 0.2 1 48209 2742 85 49724 0.2 1 47191 2533 86 49032 0.2 1 46473 2559 87 49028 0.2 1 46704 2324 88 46498 0.2 1 44150 2348 89 42159 0.2 1 40004 2155 90 40296 0.2 1 38283 2013 91 37292 0.2 1 35403 1889 92 34841 0.2 1 33039 1802 93 33152 0.2 1 31479 1673 94 31763 0.2 1 30149 1614 95 30241 0.2 1 28665 1576 96 27836 0.2 1 26423 1413 97 25827 0.2 1 24589 1238 98 24001 0.2 1 22767 1234 99 23498 0.2 1 22301 1197 100 21732 0.2 1 20644 1088 101 19788 0.2 1 18836 952 102 17924 0.2 1 16990 934 103 15850 0.2 1 15000 850 104 14943 0.2 1 14170 773 105 13279 0.2 1 12646 633 106 11897 0.2 1 11297 600 107 10895 0.2 1 10336 559 108 9562 0.2 1 9057 505 109 8353 0.2 1 7873 480 110 7641 0.2 1 7229 412 111 7111 0.2 1 6763 348 112 6029 0.2 1 5694 335 113 5217 0.2 1 4974 243 114 4567 0.2 1 4342 225 115 3814 0.2 1 3593 221 116 3236 0.2 1 3069 167 117 2708 0.2 1 2550 158 118 2402 0.2 1 2269 133 119 1976 0.2 1 1850 126 120 1573 0.2 1 1480 93 121 1360 0.2 1 1290 70 122 1161 0.2 1 1085 76 123 1044 0.2 1 961 83 124 817 0.2 1 759 58 125 740 0.2 1 678 62 126 632 0.2 1 586 46 127 507 0.2 1 481 26 128 371 0.2 1 328 43 129 368 0.2 1 334 34 130 272 0.2 1 248 24 131 250 0.2 1 232 18 132 226 0.2 1 220 6 133 268 0.2 1 248 20 134 319 0.2 1 304 15 135 142 0.2 1 138 4 136 65 0.2 1 62 3 137 61 0.2 1 60 1 138 31 0.2 1 25 6 139 26 0.2 1 21 5 140 13 0.2 1 11 2 141 16 0.2 1 13 3 142 11 0.2 1 8 3 143 13 0.2 1 11 2 144 7 0.2 1 5 2 145 9 0.2 1 6 3 146 13 0.2 1 12 1 147 30 0.2 1 26 4 148 17 0.2 1 16 1 149 16 0.2 1 14 2 150 117 0.2 1 107 10 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_4_S4_L002_R2_001.fastq.gz ============================================= 15591852 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 13005 (0.1%)