SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/20181211_metagenomics_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA Library_Geoduck_MG_2_S4_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2784.93 s (34 us/read; 1.78 M reads/minute). === Summary === Total reads processed: 82,486,730 Reads with adapters: 38,274,870 (46.4%) Reads written (passing filters): 82,486,730 (100.0%) Total basepairs processed: 12,455,496,230 bp Quality-trimmed: 264,631,747 bp (2.1%) Total written (filtered): 11,010,453,787 bp (88.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38274870 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 17.1% C: 33.2% G: 23.1% T: 26.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11725056 20621682.5 0 11725056 2 3280128 5155420.6 0 3280128 3 963449 1288855.2 0 963449 4 401452 322213.8 0 401452 5 261325 80553.4 0 261325 6 158333 20138.4 0 158333 7 157607 5034.6 0 157607 8 171108 1258.6 0 171108 9 205103 314.7 0 203751 1352 10 137969 78.7 1 132074 5895 11 180155 19.7 1 173508 6647 12 213900 4.9 1 205595 8305 13 238400 4.9 1 229890 8510 14 195370 4.9 1 188715 6655 15 252163 4.9 1 242863 9300 16 216508 4.9 1 207634 8874 17 205638 4.9 1 199278 6360 18 191036 4.9 1 184900 6136 19 120447 4.9 1 116812 3635 20 166610 4.9 1 159936 6674 21 207880 4.9 1 198398 9482 22 249693 4.9 1 241559 8134 23 173429 4.9 1 167860 5569 24 206132 4.9 1 200823 5309 25 229667 4.9 1 223599 6068 26 247752 4.9 1 240522 7230 27 291878 4.9 1 284067 7811 28 130828 4.9 1 126695 4133 29 199559 4.9 1 193296 6263 30 173097 4.9 1 168864 4233 31 114253 4.9 1 110610 3643 32 207034 4.9 1 202218 4816 33 154640 4.9 1 150635 4005 34 237200 4.9 1 231064 6136 35 235068 4.9 1 229848 5220 36 212699 4.9 1 207829 4870 37 234889 4.9 1 228445 6444 38 224954 4.9 1 219263 5691 39 203397 4.9 1 197551 5846 40 193552 4.9 1 187411 6141 41 127103 4.9 1 123662 3441 42 200888 4.9 1 196045 4843 43 239476 4.9 1 233735 5741 44 171744 4.9 1 168191 3553 45 466702 4.9 1 458945 7757 46 51379 4.9 1 49260 2119 47 197247 4.9 1 194032 3215 48 193514 4.9 1 190060 3454 49 209464 4.9 1 205739 3725 50 136862 4.9 1 133560 3302 51 144293 4.9 1 140927 3366 52 137842 4.9 1 135078 2764 53 195711 4.9 1 191138 4573 54 261223 4.9 1 255142 6081 55 347395 4.9 1 340803 6592 56 207843 4.9 1 204044 3799 57 154897 4.9 1 152025 2872 58 215278 4.9 1 211116 4162 59 212556 4.9 1 208846 3710 60 154607 4.9 1 151744 2863 61 140087 4.9 1 137295 2792 62 125300 4.9 1 122588 2712 63 182736 4.9 1 178552 4184 64 220852 4.9 1 216486 4366 65 220283 4.9 1 215796 4487 66 285864 4.9 1 280390 5474 67 250173 4.9 1 245361 4812 68 265510 4.9 1 260221 5289 69 286648 4.9 1 280734 5914 70 316323 4.9 1 309924 6399 71 473200 4.9 1 464391 8809 72 5163834 4.9 1 5134507 29327 73 1022434 4.9 1 1013705 8729 74 223373 4.9 1 220799 2574 75 86601 4.9 1 85162 1439 76 55595 4.9 1 54368 1227 77 56037 4.9 1 54890 1147 78 47598 4.9 1 46535 1063 79 43401 4.9 1 42425 976 80 36923 4.9 1 35980 943 81 32142 4.9 1 31364 778 82 29493 4.9 1 28714 779 83 32336 4.9 1 31590 746 84 35856 4.9 1 34989 867 85 41646 4.9 1 40715 931 86 43060 4.9 1 42063 997 87 42339 4.9 1 41325 1014 88 41248 4.9 1 40274 974 89 37918 4.9 1 37105 813 90 31605 4.9 1 30831 774 91 25082 4.9 1 24369 713 92 21938 4.9 1 21315 623 93 21656 4.9 1 21029 627 94 25159 4.9 1 24383 776 95 30605 4.9 1 29842 763 96 37429 4.9 1 36542 887 97 37394 4.9 1 36619 775 98 35706 4.9 1 34853 853 99 32370 4.9 1 31587 783 100 28818 4.9 1 28117 701 101 24745 4.9 1 24135 610 102 35942 4.9 1 35410 532 103 19684 4.9 1 19182 502 104 19216 4.9 1 18660 556 105 25362 4.9 1 24645 717 106 31783 4.9 1 30989 794 107 35654 4.9 1 34844 810 108 33272 4.9 1 32430 842 109 28906 4.9 1 28203 703 110 24876 4.9 1 24215 661 111 20282 4.9 1 19778 504 112 16027 4.9 1 15519 508 113 13581 4.9 1 13118 463 114 14971 4.9 1 14504 467 115 19661 4.9 1 19171 490 116 22732 4.9 1 22212 520 117 22251 4.9 1 21743 508 118 20389 4.9 1 19897 492 119 16406 4.9 1 16007 399 120 13120 4.9 1 12695 425 121 12140 4.9 1 11700 440 122 11639 4.9 1 11226 413 123 10704 4.9 1 10326 378 124 8916 4.9 1 8602 314 125 2129 4.9 1 1926 203 126 867 4.9 1 655 212 127 628 4.9 1 424 204 128 552 4.9 1 287 265 129 366 4.9 1 148 218 130 413 4.9 1 181 232 131 359 4.9 1 102 257 132 352 4.9 1 135 217 133 269 4.9 1 43 226 134 299 4.9 1 40 259 135 273 4.9 1 27 246 136 270 4.9 1 27 243 137 220 4.9 1 13 207 138 291 4.9 1 9 282 139 261 4.9 1 4 257 140 217 4.9 1 9 208 141 226 4.9 1 9 217 142 408 4.9 1 29 379 143 858 4.9 1 14 844 144 169 4.9 1 2 167 145 243 4.9 1 4 239 146 75 4.9 1 0 75 147 168 4.9 1 1 167 148 429 4.9 1 6 423 149 155 4.9 1 0 155 150 106 4.9 1 2 104 151 54 4.9 1 0 54 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R1_001.fastq.gz ============================================= 82486730 sequences processed in total