SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-187_S20_L003_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-187_S20_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 498.35 s (19 us/read; 3.16 M reads/minute). === Summary === Total reads processed: 26,246,829 Reads with adapters: 16,449,015 (62.7%) Reads written (passing filters): 26,246,829 (100.0%) Total basepairs processed: 2,593,337,302 bp Total written (filtered): 2,078,917,984 bp (80.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16449015 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.5% C: 19.9% G: 22.8% T: 34.6% none/other: 1.2% Overview of removed sequences length count expect max.err error counts 1 4244715 6561707.2 0 4244715 2 1060175 1640426.8 0 1060175 3 413693 410106.7 0 413693 4 282195 102526.7 0 282195 5 144390 25631.7 0 144390 6 141912 6407.9 0 141912 7 134414 1602.0 0 134414 8 156994 400.5 0 156994 9 148896 100.1 0 147505 1391 10 144337 25.0 1 138719 5618 11 137865 6.3 1 131819 6046 12 132764 1.6 1 127093 5671 13 129873 0.4 1 124237 5636 14 143251 0.4 1 133597 9654 15 138035 0.4 1 128365 9670 16 147473 0.4 1 136702 10771 17 136487 0.4 1 126639 9848 18 126615 0.4 1 118153 8462 19 139919 0.4 1 128493 11426 20 132191 0.4 1 123113 9078 21 144948 0.4 1 133689 11259 22 137722 0.4 1 128110 9612 23 129888 0.4 1 120318 9570 24 132686 0.4 1 122563 10123 25 126757 0.4 1 117708 9049 26 137413 0.4 1 126321 11092 27 125944 0.4 1 118619 7325 28 119288 0.4 1 113400 5888 29 132108 0.4 1 124879 7229 30 123707 0.4 1 117468 6239 31 130174 0.4 1 122780 7394 32 122811 0.4 1 116745 6066 33 130283 0.4 1 123422 6861 34 121550 0.4 1 115464 6086 35 111925 0.4 1 106408 5517 36 118696 0.4 1 112776 5920 37 121686 0.4 1 115958 5728 38 112942 0.4 1 107294 5648 39 112577 0.4 1 107196 5381 40 110053 0.4 1 104734 5319 41 159914 0.4 1 153346 6568 42 97693 0.4 1 93634 4059 43 59254 0.4 1 56188 3066 44 94896 0.4 1 90631 4265 45 92690 0.4 1 88619 4071 46 89796 0.4 1 85968 3828 47 95248 0.4 1 90688 4560 48 88606 0.4 1 84627 3979 49 90331 0.4 1 86100 4231 50 80684 0.4 1 77254 3430 51 79681 0.4 1 76237 3444 52 75912 0.4 1 72672 3240 53 70777 0.4 1 68094 2683 54 70078 0.4 1 67176 2902 55 72964 0.4 1 70188 2776 56 68333 0.4 1 65619 2714 57 63265 0.4 1 60628 2637 58 63217 0.4 1 60773 2444 59 59673 0.4 1 57386 2287 60 53633 0.4 1 51590 2043 61 55413 0.4 1 53331 2082 62 56841 0.4 1 54829 2012 63 51980 0.4 1 50121 1859 64 50023 0.4 1 48327 1696 65 46167 0.4 1 44604 1563 66 43174 0.4 1 41572 1602 67 43106 0.4 1 41597 1509 68 41677 0.4 1 40022 1655 69 48505 0.4 1 46644 1861 70 51819 0.4 1 49745 2074 71 58432 0.4 1 55831 2601 72 81850 0.4 1 77696 4154 73 167025 0.4 1 153027 13998 74 727912 0.4 1 702275 25637 75 694359 0.4 1 672926 21433 76 359256 0.4 1 347059 12197 77 208533 0.4 1 201550 6983 78 119844 0.4 1 115863 3981 79 63747 0.4 1 61442 2305 80 40304 0.4 1 38924 1380 81 24617 0.4 1 23657 960 82 16714 0.4 1 16009 705 83 13303 0.4 1 12735 568 84 10934 0.4 1 10439 495 85 10091 0.4 1 9652 439 86 9324 0.4 1 8893 431 87 8620 0.4 1 8204 416 88 7782 0.4 1 7377 405 89 7972 0.4 1 7534 438 90 9487 0.4 1 9043 444 91 13460 0.4 1 12815 645 92 22675 0.4 1 21660 1015 93 58262 0.4 1 55709 2553 94 181576 0.4 1 174031 7545 95 318758 0.4 1 305951 12807 96 141409 0.4 1 135217 6192 97 84367 0.4 1 80376 3991 98 31873 0.4 1 30251 1622 99 29542 0.4 1 28124 1418 100 26918 0.4 1 25502 1416 101 45367 0.4 1 42282 3085 RUN STATISTICS FOR INPUT FILE: EPI-187_S20_L003_R1_001.fastq.gz ============================================= 26246829 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4675160 (17.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 16171584 (61.6%)