SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-153_S4_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/EPI-153_S4_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 595.70 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 31,826,247 Reads with adapters: 21,047,023 (66.1%) Reads written (passing filters): 31,826,247 (100.0%) Total basepairs processed: 3,123,507,456 bp Total written (filtered): 2,374,167,438 bp (76.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21047023 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.7% C: 22.7% G: 22.3% T: 32.7% none/other: 1.6% Overview of removed sequences length count expect max.err error counts 1 4625438 7956561.8 0 4625438 2 1220566 1989140.4 0 1220566 3 493817 497285.1 0 493817 4 346503 124321.3 0 346503 5 194730 31080.3 0 194730 6 190334 7770.1 0 190334 7 175288 1942.5 0 175288 8 194249 485.6 0 194249 9 188770 121.4 0 187141 1629 10 185203 30.4 1 177928 7275 11 182418 7.6 1 174332 8086 12 175257 1.9 1 167798 7459 13 168305 0.5 1 161383 6922 14 185877 0.5 1 176407 9470 15 175416 0.5 1 167095 8321 16 187348 0.5 1 177533 9815 17 175691 0.5 1 166765 8926 18 165818 0.5 1 158065 7753 19 179243 0.5 1 168887 10356 20 166381 0.5 1 158820 7561 21 178125 0.5 1 168200 9925 22 169549 0.5 1 161592 7957 23 164350 0.5 1 156222 8128 24 166411 0.5 1 157453 8958 25 157902 0.5 1 150292 7610 26 169905 0.5 1 160447 9458 27 157525 0.5 1 150269 7256 28 149350 0.5 1 142674 6676 29 160034 0.5 1 152335 7699 30 150998 0.5 1 144820 6178 31 159200 0.5 1 151231 7969 32 146368 0.5 1 140073 6295 33 150597 0.5 1 143880 6717 34 142387 0.5 1 136216 6171 35 143129 0.5 1 136725 6404 36 142571 0.5 1 135738 6833 37 150217 0.5 1 142781 7436 38 135584 0.5 1 129336 6248 39 127103 0.5 1 121545 5558 40 129962 0.5 1 123847 6115 41 186631 0.5 1 178880 7751 42 103895 0.5 1 99312 4583 43 75381 0.5 1 71635 3746 44 111173 0.5 1 106236 4937 45 107699 0.5 1 102921 4778 46 102780 0.5 1 98365 4415 47 110712 0.5 1 105689 5023 48 102770 0.5 1 98164 4606 49 109258 0.5 1 104131 5127 50 98670 0.5 1 94442 4228 51 96138 0.5 1 92057 4081 52 92719 0.5 1 88722 3997 53 87427 0.5 1 84015 3412 54 86335 0.5 1 82803 3532 55 86669 0.5 1 83296 3373 56 82237 0.5 1 79002 3235 57 77657 0.5 1 74599 3058 58 76728 0.5 1 73931 2797 59 69963 0.5 1 67293 2670 60 63246 0.5 1 60841 2405 61 65713 0.5 1 63251 2462 62 66262 0.5 1 63882 2380 63 60636 0.5 1 58371 2265 64 59097 0.5 1 57071 2026 65 55777 0.5 1 53772 2005 66 54211 0.5 1 52166 2045 67 53850 0.5 1 51817 2033 68 51283 0.5 1 49189 2094 69 56589 0.5 1 54314 2275 70 59002 0.5 1 56394 2608 71 71697 0.5 1 68376 3321 72 101134 0.5 1 95104 6030 73 264449 0.5 1 238909 25540 74 1368072 0.5 1 1322221 45851 75 1090622 0.5 1 1056344 34278 76 539434 0.5 1 520458 18976 77 302992 0.5 1 292488 10504 78 170691 0.5 1 164686 6005 79 92705 0.5 1 89167 3538 80 59113 0.5 1 56910 2203 81 38234 0.5 1 36688 1546 82 26531 0.5 1 25412 1119 83 21530 0.5 1 20593 937 84 18625 0.5 1 17733 892 85 17507 0.5 1 16705 802 86 16821 0.5 1 16025 796 87 15641 0.5 1 14918 723 88 14464 0.5 1 13778 686 89 14908 0.5 1 14162 746 90 18712 0.5 1 17847 865 91 26035 0.5 1 24787 1248 92 43360 0.5 1 41318 2042 93 110016 0.5 1 105281 4735 94 322772 0.5 1 309585 13187 95 529080 0.5 1 507864 21216 96 237065 0.5 1 226449 10616 97 143662 0.5 1 136962 6700 98 55818 0.5 1 53007 2811 99 51190 0.5 1 48654 2536 100 48314 0.5 1 45507 2807 101 77402 0.5 1 71601 5801 RUN STATISTICS FOR INPUT FILE: EPI-153_S4_L002_R1_001.fastq.gz ============================================= 31826247 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 6634320 (20.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 20571442 (64.6%)