SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_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_5_S6_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2548.95 s (35 us/read; 1.70 M reads/minute). === Summary === Total reads processed: 72,142,506 Reads with adapters: 32,074,902 (44.5%) Reads written (passing filters): 72,142,506 (100.0%) Total basepairs processed: 10,893,518,406 bp Quality-trimmed: 470,539,858 bp (4.3%) Total written (filtered): 9,503,775,392 bp (87.2%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 32074902 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 17.1% C: 33.3% G: 22.4% T: 27.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11307470 18035626.5 0 11307470 2 2484973 4508906.6 0 2484973 3 637659 1127226.7 0 637659 4 409601 281806.7 0 409601 5 264543 70451.7 0 264543 6 71888 17612.9 0 71888 7 145923 4403.2 0 145923 8 97639 1100.8 0 97639 9 226293 275.2 0 225304 989 10 89599 68.8 1 77343 12256 11 182727 17.2 1 167164 15563 12 179100 4.3 1 164096 15004 13 261706 4.3 1 237527 24179 14 105947 4.3 1 95776 10171 15 265605 4.3 1 241818 23787 16 210655 4.3 1 190587 20068 17 101016 4.3 1 92642 8374 18 171663 4.3 1 155176 16487 19 187990 4.3 1 173831 14159 20 110613 4.3 1 101198 9415 21 118508 4.3 1 109730 8778 22 274149 4.3 1 253126 21023 23 90441 4.3 1 82687 7754 24 360500 4.3 1 336352 24148 25 199998 4.3 1 187858 12140 26 111309 4.3 1 103725 7584 27 149081 4.3 1 140654 8427 28 248423 4.3 1 235687 12736 29 122477 4.3 1 116311 6166 30 107749 4.3 1 101542 6207 31 162871 4.3 1 154226 8645 32 120631 4.3 1 115234 5397 33 118489 4.3 1 112271 6218 34 245793 4.3 1 234939 10854 35 190517 4.3 1 183691 6826 36 79929 4.3 1 75288 4641 37 185327 4.3 1 177678 7649 38 350817 4.3 1 337845 12972 39 160243 4.3 1 153509 6734 40 49523 4.3 1 47055 2468 41 99720 4.3 1 95846 3874 42 209961 4.3 1 204671 5290 43 122898 4.3 1 118531 4367 44 166079 4.3 1 161517 4562 45 218520 4.3 1 212794 5726 46 216230 4.3 1 210165 6065 47 150848 4.3 1 146896 3952 48 195313 4.3 1 190410 4903 49 119864 4.3 1 116907 2957 50 198149 4.3 1 193710 4439 51 44470 4.3 1 42705 1765 52 125312 4.3 1 122091 3221 53 160350 4.3 1 156164 4186 54 350097 4.3 1 343329 6768 55 90527 4.3 1 87468 3059 56 228576 4.3 1 222949 5627 57 314847 4.3 1 308798 6049 58 130101 4.3 1 127078 3023 59 103061 4.3 1 100655 2406 60 145738 4.3 1 142665 3073 61 110959 4.3 1 108380 2579 62 157053 4.3 1 153657 3396 63 232486 4.3 1 228299 4187 64 77784 4.3 1 76130 1654 65 113617 4.3 1 111623 1994 66 91230 4.3 1 89405 1825 67 255083 4.3 1 251507 3576 68 76869 4.3 1 75081 1788 69 130744 4.3 1 128354 2390 70 155408 4.3 1 152773 2635 71 87764 4.3 1 85962 1802 72 122270 4.3 1 119725 2545 73 148448 4.3 1 145724 2724 74 209849 4.3 1 206144 3705 75 367609 4.3 1 361553 6056 76 3686459 4.3 1 3664819 21640 77 697823 4.3 1 691400 6423 78 126948 4.3 1 125058 1890 79 40096 4.3 1 39112 984 80 24645 4.3 1 23902 743 81 20367 4.3 1 19755 612 82 16078 4.3 1 15494 584 83 16099 4.3 1 15502 597 84 22100 4.3 1 21363 737 85 27271 4.3 1 26557 714 86 32766 4.3 1 31943 823 87 35764 4.3 1 34863 901 88 34412 4.3 1 33651 761 89 29649 4.3 1 28854 795 90 24331 4.3 1 23662 669 91 19647 4.3 1 19057 590 92 16184 4.3 1 15655 529 93 15805 4.3 1 15266 539 94 18042 4.3 1 17484 558 95 23214 4.3 1 22574 640 96 27102 4.3 1 26399 703 97 29599 4.3 1 28831 768 98 26939 4.3 1 26231 708 99 23593 4.3 1 22861 732 100 20037 4.3 1 19411 626 101 15643 4.3 1 15085 558 102 12701 4.3 1 12170 531 103 11370 4.3 1 10864 506 104 13052 4.3 1 12479 573 105 18499 4.3 1 17748 751 106 23737 4.3 1 22878 859 107 25678 4.3 1 25001 677 108 24121 4.3 1 23475 646 109 21133 4.3 1 20494 639 110 16788 4.3 1 16309 479 111 13356 4.3 1 12937 419 112 10717 4.3 1 10310 407 113 8871 4.3 1 8444 427 114 9976 4.3 1 9609 367 115 13191 4.3 1 12784 407 116 15663 4.3 1 15218 445 117 14717 4.3 1 14265 452 118 13298 4.3 1 12886 412 119 10198 4.3 1 9859 339 120 7835 4.3 1 7503 332 121 6923 4.3 1 6583 340 122 6487 4.3 1 6134 353 123 6011 4.3 1 5666 345 124 5052 4.3 1 4766 286 125 1232 4.3 1 993 239 126 453 4.3 1 276 177 127 417 4.3 1 198 219 128 338 4.3 1 117 221 129 278 4.3 1 74 204 130 327 4.3 1 76 251 131 235 4.3 1 44 191 132 245 4.3 1 46 199 133 201 4.3 1 26 175 134 217 4.3 1 19 198 135 219 4.3 1 9 210 136 233 4.3 1 11 222 137 183 4.3 1 13 170 138 242 4.3 1 8 234 139 251 4.3 1 7 244 140 235 4.3 1 11 224 141 245 4.3 1 5 240 142 401 4.3 1 25 376 143 537 4.3 1 15 522 144 182 4.3 1 6 176 145 176 4.3 1 2 174 146 99 4.3 1 1 98 147 204 4.3 1 2 202 148 315 4.3 1 3 312 149 117 4.3 1 1 116 150 65 4.3 1 4 61 151 49 4.3 1 3 46 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R2_001.fastq.gz ============================================= 72142506 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 72142506 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 228753 (0.32%)