SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_1_S13_L002_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/16C_26psu_1_S13_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 940.13 s (43 us/read; 1.41 M reads/minute). === Summary === Total reads processed: 22,055,675 Reads with adapters: 17,288,884 (78.4%) Reads written (passing filters): 22,055,675 (100.0%) Total basepairs processed: 3,308,351,250 bp Quality-trimmed: 20,473,501 bp (0.6%) Total written (filtered): 2,585,092,173 bp (78.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17288884 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.0% G: 20.5% T: 35.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2888739 5513918.8 0 2888739 2 417982 1378479.7 0 417982 3 229648 344619.9 0 229648 4 140558 86155.0 0 140558 5 117330 21538.7 0 117330 6 114463 5384.7 0 114463 7 92119 1346.2 0 92119 8 118305 336.5 0 118305 9 116870 84.1 0 115423 1447 10 109085 21.0 1 102190 6895 11 122273 5.3 1 111534 10739 12 117728 1.3 1 108915 8813 13 119559 0.3 1 110607 8952 14 120718 0.3 1 110803 9915 15 126246 0.3 1 116067 10179 16 124980 0.3 1 114018 10962 17 152992 0.3 1 138965 14027 18 127404 0.3 1 118125 9279 19 110945 0.3 1 102558 8387 20 133534 0.3 1 123405 10129 21 147067 0.3 1 135223 11844 22 124353 0.3 1 115585 8768 23 146038 0.3 1 134941 11097 24 136315 0.3 1 124052 12263 25 144095 0.3 1 132766 11329 26 132325 0.3 1 123014 9311 27 148607 0.3 1 136108 12499 28 145176 0.3 1 133796 11380 29 153982 0.3 1 140231 13751 30 162931 0.3 1 151904 11027 31 127590 0.3 1 117988 9602 32 158563 0.3 1 146202 12361 33 143459 0.3 1 131864 11595 34 158293 0.3 1 145587 12706 35 161600 0.3 1 146632 14968 36 173713 0.3 1 161385 12328 37 138576 0.3 1 128088 10488 38 164914 0.3 1 152362 12552 39 166196 0.3 1 152847 13349 40 174913 0.3 1 159838 15075 41 195923 0.3 1 172793 23130 42 162924 0.3 1 146209 16715 43 267611 0.3 1 248773 18838 44 88981 0.3 1 79036 9945 45 199179 0.3 1 175262 23917 46 690085 0.3 1 650909 39176 47 257754 0.3 1 240653 17101 48 117426 0.3 1 103023 14403 49 402804 0.3 1 380078 22726 50 126965 0.3 1 116321 10644 51 110357 0.3 1 99078 11279 52 376565 0.3 1 356163 20402 53 193192 0.3 1 182832 10360 54 64424 0.3 1 58616 5808 55 110681 0.3 1 104197 6484 56 61759 0.3 1 55308 6451 57 169454 0.3 1 160172 9282 58 37968 0.3 1 34229 3739 59 46940 0.3 1 41198 5742 60 169988 0.3 1 161028 8960 61 86428 0.3 1 81402 5026 62 43888 0.3 1 39006 4882 63 131951 0.3 1 123251 8700 64 119378 0.3 1 112438 6940 65 67995 0.3 1 61783 6212 66 148705 0.3 1 138293 10412 67 175463 0.3 1 161782 13681 68 280115 0.3 1 262817 17298 69 200997 0.3 1 188546 12451 70 91468 0.3 1 84121 7347 71 26418 0.3 1 22702 3716 72 93747 0.3 1 87405 6342 73 136042 0.3 1 127373 8669 74 142888 0.3 1 133128 9760 75 142439 0.3 1 132394 10045 76 141347 0.3 1 131130 10217 77 141016 0.3 1 131311 9705 78 132511 0.3 1 122849 9662 79 132027 0.3 1 122622 9405 80 128769 0.3 1 119387 9382 81 126902 0.3 1 118148 8754 82 123681 0.3 1 114826 8855 83 118947 0.3 1 110667 8280 84 114559 0.3 1 106314 8245 85 111485 0.3 1 103536 7949 86 107436 0.3 1 99695 7741 87 103344 0.3 1 96004 7340 88 100991 0.3 1 93808 7183 89 95415 0.3 1 88771 6644 90 94998 0.3 1 88363 6635 91 89676 0.3 1 83270 6406 92 85299 0.3 1 79247 6052 93 79596 0.3 1 73937 5659 94 76506 0.3 1 71043 5463 95 71120 0.3 1 65893 5227 96 67197 0.3 1 62368 4829 97 63520 0.3 1 59045 4475 98 58336 0.3 1 54045 4291 99 56900 0.3 1 52530 4370 100 51732 0.3 1 47977 3755 101 47750 0.3 1 44264 3486 102 44471 0.3 1 41149 3322 103 40594 0.3 1 37603 2991 104 37603 0.3 1 34872 2731 105 33894 0.3 1 31456 2438 106 30780 0.3 1 28387 2393 107 27659 0.3 1 25538 2121 108 26065 0.3 1 24009 2056 109 23274 0.3 1 21434 1840 110 20689 0.3 1 19111 1578 111 18796 0.3 1 17291 1505 112 16460 0.3 1 15232 1228 113 14306 0.3 1 13173 1133 114 12558 0.3 1 11518 1040 115 10829 0.3 1 9919 910 116 9235 0.3 1 8487 748 117 7908 0.3 1 7205 703 118 6968 0.3 1 6363 605 119 5769 0.3 1 5245 524 120 4920 0.3 1 4475 445 121 4219 0.3 1 3831 388 122 3544 0.3 1 3202 342 123 3058 0.3 1 2744 314 124 2517 0.3 1 2275 242 125 2174 0.3 1 1950 224 126 1777 0.3 1 1603 174 127 1561 0.3 1 1396 165 128 1149 0.3 1 1015 134 129 996 0.3 1 899 97 130 753 0.3 1 670 83 131 665 0.3 1 585 80 132 569 0.3 1 501 68 133 543 0.3 1 476 67 134 671 0.3 1 623 48 135 378 0.3 1 347 31 136 222 0.3 1 190 32 137 159 0.3 1 149 10 138 107 0.3 1 97 10 139 82 0.3 1 68 14 140 62 0.3 1 55 7 141 48 0.3 1 42 6 142 40 0.3 1 35 5 143 27 0.3 1 21 6 144 22 0.3 1 19 3 145 23 0.3 1 21 2 146 31 0.3 1 24 7 147 94 0.3 1 87 7 148 48 0.3 1 41 7 149 39 0.3 1 31 8 150 382 0.3 1 330 52 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_1_S13_L002_R1_001.fastq.gz ============================================= 22055675 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 4286 (0.0%)