SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_L002_R2_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_1_S3_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 3003.16 s (36 us/read; 1.67 M reads/minute). === Summary === Total reads processed: 83,562,471 Reads with adapters: 38,976,691 (46.6%) Reads written (passing filters): 83,562,471 (100.0%) Total basepairs processed: 12,617,933,121 bp Quality-trimmed: 635,723,981 bp (5.0%) Total written (filtered): 10,961,342,640 bp (86.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38976691 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 15.7% C: 35.1% G: 25.4% T: 23.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15985248 20890617.8 0 15985248 2 2627012 5222654.4 0 2627012 3 796767 1305663.6 0 796767 4 429050 326415.9 0 429050 5 317613 81604.0 0 317613 6 70847 20401.0 0 70847 7 172411 5100.2 0 172411 8 99936 1275.1 0 99936 9 243504 318.8 0 242492 1012 10 101789 79.7 1 86963 14826 11 199930 19.9 1 181681 18249 12 198461 5.0 1 180164 18297 13 306225 5.0 1 274776 31449 14 112339 5.0 1 100848 11491 15 304539 5.0 1 274391 30148 16 233147 5.0 1 208921 24226 17 101079 5.0 1 91745 9334 18 207715 5.0 1 186118 21597 19 193564 5.0 1 178163 15401 20 133698 5.0 1 121605 12093 21 127245 5.0 1 117135 10110 22 309141 5.0 1 283633 25508 23 101416 5.0 1 92303 9113 24 418239 5.0 1 387251 30988 25 208860 5.0 1 195437 13423 26 126211 5.0 1 116958 9253 27 160842 5.0 1 150939 9903 28 277558 5.0 1 262073 15485 29 142250 5.0 1 134318 7932 30 123649 5.0 1 116200 7449 31 183906 5.0 1 173414 10492 32 144806 5.0 1 137622 7184 33 128347 5.0 1 121334 7013 34 267701 5.0 1 255015 12686 35 220267 5.0 1 211967 8300 36 81538 5.0 1 76706 4832 37 203550 5.0 1 194248 9302 38 392847 5.0 1 376337 16510 39 178050 5.0 1 170010 8040 40 52141 5.0 1 49395 2746 41 110296 5.0 1 105771 4525 42 247384 5.0 1 240726 6658 43 125698 5.0 1 120762 4936 44 199058 5.0 1 193031 6027 45 235209 5.0 1 228574 6635 46 234181 5.0 1 227004 7177 47 171147 5.0 1 166343 4804 48 216342 5.0 1 210513 5829 49 122293 5.0 1 118792 3501 50 226118 5.0 1 220739 5379 51 44843 5.0 1 42790 2053 52 141470 5.0 1 137510 3960 53 175291 5.0 1 170146 5145 54 391152 5.0 1 382553 8599 55 94303 5.0 1 90753 3550 56 254503 5.0 1 246874 7629 57 363063 5.0 1 355127 7936 58 140400 5.0 1 137037 3363 59 110647 5.0 1 108053 2594 60 164297 5.0 1 160658 3639 61 121528 5.0 1 118184 3344 62 174843 5.0 1 170922 3921 63 265359 5.0 1 260233 5126 64 83357 5.0 1 81484 1873 65 129288 5.0 1 126903 2385 66 96911 5.0 1 94836 2075 67 281446 5.0 1 277124 4322 68 85202 5.0 1 83077 2125 69 140438 5.0 1 137910 2528 70 168623 5.0 1 165554 3069 71 99212 5.0 1 96947 2265 72 135577 5.0 1 132461 3116 73 163868 5.0 1 160423 3445 74 227202 5.0 1 222650 4552 75 390706 5.0 1 383560 7146 76 4064022 5.0 1 4037400 26622 77 786999 5.0 1 778958 8041 78 144903 5.0 1 142401 2502 79 45259 5.0 1 44001 1258 80 27900 5.0 1 26891 1009 81 22947 5.0 1 22158 789 82 17925 5.0 1 17189 736 83 18841 5.0 1 18067 774 84 24692 5.0 1 23696 996 85 29249 5.0 1 28377 872 86 36553 5.0 1 35389 1164 87 39381 5.0 1 38151 1230 88 37646 5.0 1 36681 965 89 32725 5.0 1 31842 883 90 26576 5.0 1 25736 840 91 21940 5.0 1 21129 811 92 18185 5.0 1 17508 677 93 17646 5.0 1 16897 749 94 20408 5.0 1 19729 679 95 25161 5.0 1 24357 804 96 29739 5.0 1 28847 892 97 31887 5.0 1 30920 967 98 28667 5.0 1 27763 904 99 25701 5.0 1 24816 885 100 22281 5.0 1 21396 885 101 17369 5.0 1 16757 612 102 14319 5.0 1 13630 689 103 13084 5.0 1 12383 701 104 14965 5.0 1 14139 826 105 20362 5.0 1 19289 1073 106 25963 5.0 1 24671 1292 107 27536 5.0 1 26653 883 108 25858 5.0 1 25025 833 109 22122 5.0 1 21347 775 110 18239 5.0 1 17598 641 111 14855 5.0 1 14317 538 112 11995 5.0 1 11490 505 113 9967 5.0 1 9516 451 114 10872 5.0 1 10404 468 115 14247 5.0 1 13763 484 116 16257 5.0 1 15728 529 117 15490 5.0 1 14967 523 118 13882 5.0 1 13361 521 119 11034 5.0 1 10595 439 120 8447 5.0 1 8037 410 121 8015 5.0 1 7609 406 122 7693 5.0 1 7318 375 123 7087 5.0 1 6742 345 124 5915 5.0 1 5619 296 125 1421 5.0 1 1170 251 126 621 5.0 1 368 253 127 534 5.0 1 289 245 128 419 5.0 1 204 215 129 364 5.0 1 123 241 130 438 5.0 1 154 284 131 350 5.0 1 101 249 132 349 5.0 1 99 250 133 276 5.0 1 50 226 134 262 5.0 1 45 217 135 246 5.0 1 34 212 136 270 5.0 1 50 220 137 266 5.0 1 32 234 138 281 5.0 1 19 262 139 289 5.0 1 26 263 140 234 5.0 1 13 221 141 273 5.0 1 18 255 142 424 5.0 1 40 384 143 598 5.0 1 25 573 144 191 5.0 1 7 184 145 192 5.0 1 7 185 146 103 5.0 1 4 99 147 204 5.0 1 7 197 148 303 5.0 1 13 290 149 161 5.0 1 1 160 150 87 5.0 1 1 86 151 36 5.0 1 0 36 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R2_001.fastq.gz ============================================= 83562471 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 83562471 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 311720 (0.37%)