SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-162_S9_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-162_S9_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 447.15 s (19 us/read; 3.13 M reads/minute). === Summary === Total reads processed: 23,358,871 Reads with adapters: 15,082,440 (64.6%) Reads written (passing filters): 23,358,871 (100.0%) Total basepairs processed: 2,345,251,531 bp Total written (filtered): 1,964,326,382 bp (83.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15082440 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.3% C: 11.6% G: 27.5% T: 37.3% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 3472743 5839717.8 0 3472743 2 877721 1459929.4 0 877721 3 358182 364982.4 0 358182 4 265552 91245.6 0 265552 5 160493 22811.4 0 160493 6 159328 5702.8 0 159328 7 148914 1425.7 0 148914 8 160777 356.4 0 160777 9 161442 89.1 0 160178 1264 10 156524 22.3 1 150460 6064 11 160998 5.6 1 153933 7065 12 155999 1.4 1 149545 6454 13 152254 0.3 1 146023 6231 14 167336 0.3 1 158912 8424 15 159129 0.3 1 151907 7222 16 172902 0.3 1 163959 8943 17 167060 0.3 1 158756 8304 18 157020 0.3 1 150009 7011 19 174867 0.3 1 165110 9757 20 161476 0.3 1 154054 7422 21 184225 0.3 1 173763 10462 22 169979 0.3 1 161864 8115 23 163065 0.3 1 155197 7868 24 173997 0.3 1 164808 9189 25 163854 0.3 1 156265 7589 26 183676 0.3 1 173605 10071 27 168702 0.3 1 161074 7628 28 161314 0.3 1 154188 7126 29 180526 0.3 1 172061 8465 30 169775 0.3 1 162836 6939 31 182450 0.3 1 173629 8821 32 175034 0.3 1 167729 7305 33 182145 0.3 1 174102 8043 34 172123 0.3 1 165062 7061 35 170896 0.3 1 163607 7289 36 168902 0.3 1 161901 7001 37 183418 0.3 1 175171 8247 38 176674 0.3 1 168235 8439 39 170579 0.3 1 163529 7050 40 174217 0.3 1 165825 8392 41 236625 0.3 1 226849 9776 42 162106 0.3 1 155810 6296 43 80156 0.3 1 75959 4197 44 150457 0.3 1 144087 6370 45 144333 0.3 1 138129 6204 46 139909 0.3 1 134179 5730 47 149450 0.3 1 142871 6579 48 136289 0.3 1 130330 5959 49 144906 0.3 1 138309 6597 50 131066 0.3 1 125598 5468 51 127807 0.3 1 122706 5101 52 120833 0.3 1 116032 4801 53 115383 0.3 1 111264 4119 54 113740 0.3 1 109263 4477 55 113786 0.3 1 109559 4227 56 105762 0.3 1 101857 3905 57 99203 0.3 1 95383 3820 58 96443 0.3 1 92988 3455 59 94088 0.3 1 90746 3342 60 85105 0.3 1 82121 2984 61 86903 0.3 1 83817 3086 62 85520 0.3 1 82715 2805 63 77089 0.3 1 74492 2597 64 73179 0.3 1 70890 2289 65 67232 0.3 1 64946 2286 66 62945 0.3 1 60766 2179 67 61279 0.3 1 59226 2053 68 56405 0.3 1 54518 1887 69 56763 0.3 1 54758 2005 70 52329 0.3 1 50579 1750 71 54319 0.3 1 52453 1866 72 53635 0.3 1 51458 2177 73 72384 0.3 1 68271 4113 74 184067 0.3 1 178541 5526 75 121760 0.3 1 117897 3863 76 73542 0.3 1 71188 2354 77 45489 0.3 1 43948 1541 78 28789 0.3 1 27865 924 79 17211 0.3 1 16626 585 80 11793 0.3 1 11396 397 81 7623 0.3 1 7337 286 82 5514 0.3 1 5316 198 83 4548 0.3 1 4384 164 84 3887 0.3 1 3740 147 85 3050 0.3 1 2950 100 86 2321 0.3 1 2215 106 87 2020 0.3 1 1945 75 88 1420 0.3 1 1356 64 89 1324 0.3 1 1236 88 90 1700 0.3 1 1619 81 91 2122 0.3 1 2029 93 92 3350 0.3 1 3206 144 93 7577 0.3 1 7234 343 94 21629 0.3 1 20710 919 95 36305 0.3 1 34922 1383 96 17518 0.3 1 16743 775 97 12554 0.3 1 11956 598 98 5528 0.3 1 5264 264 99 5812 0.3 1 5501 311 100 7152 0.3 1 6759 393 101 13138 0.3 1 12035 1103 RUN STATISTICS FOR INPUT FILE: EPI-162_S9_L002_R1_001.fastq.gz ============================================= 23358871 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2425928 (10.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 15005695 (64.2%)