SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-209_S29_L004_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 File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_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/20180514_geoduck_trimgalore_rrbs/EPI-209_S29_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 580.02 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 31,419,769 Reads with adapters: 19,519,447 (62.1%) Reads written (passing filters): 31,419,769 (100.0%) Total basepairs processed: 3,141,568,143 bp Total written (filtered): 2,631,717,250 bp (83.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19519447 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 22.1% C: 12.5% G: 27.7% T: 37.0% none/other: 0.8% Overview of removed sequences length count expect max.err error counts 1 5104196 7854942.2 0 5104196 2 1282874 1963735.6 0 1282874 3 514153 490933.9 0 514153 4 349457 122733.5 0 349457 5 195510 30683.4 0 195510 6 190326 7670.8 0 190326 7 183372 1917.7 0 183372 8 202905 479.4 0 202905 9 199640 119.9 0 197870 1770 10 194368 30.0 1 187590 6778 11 189733 7.5 1 182475 7258 12 182180 1.9 1 175300 6880 13 184222 0.5 1 177153 7069 14 198823 0.5 1 190364 8459 15 196851 0.5 1 188778 8073 16 202180 0.5 1 193418 8762 17 198555 0.5 1 189996 8559 18 182062 0.5 1 175373 6689 19 196052 0.5 1 186860 9192 20 187921 0.5 1 180726 7195 21 206080 0.5 1 196647 9433 22 193887 0.5 1 186272 7615 23 181692 0.5 1 174212 7480 24 187410 0.5 1 178783 8627 25 184943 0.5 1 177127 7816 26 187840 0.5 1 179218 8622 27 184194 0.5 1 176303 7891 28 179633 0.5 1 172277 7356 29 191726 0.5 1 183145 8581 30 181975 0.5 1 174674 7301 31 187719 0.5 1 178878 8841 32 182624 0.5 1 175038 7586 33 185522 0.5 1 177628 7894 34 177640 0.5 1 169998 7642 35 181591 0.5 1 173240 8351 36 170667 0.5 1 163695 6972 37 181543 0.5 1 173774 7769 38 171122 0.5 1 163872 7250 39 165615 0.5 1 158843 6772 40 179315 0.5 1 170652 8663 41 235130 0.5 1 225337 9793 42 157713 0.5 1 151789 5924 43 85281 0.5 1 81053 4228 44 145801 0.5 1 139772 6029 45 147140 0.5 1 140916 6224 46 139829 0.5 1 134243 5586 47 148474 0.5 1 141906 6568 48 139363 0.5 1 133346 6017 49 145909 0.5 1 139440 6469 50 130224 0.5 1 125073 5151 51 131571 0.5 1 126221 5350 52 128157 0.5 1 122752 5405 53 120069 0.5 1 115539 4530 54 116872 0.5 1 112196 4676 55 124682 0.5 1 119775 4907 56 116193 0.5 1 111791 4402 57 108076 0.5 1 103823 4253 58 109899 0.5 1 105738 4161 59 105070 0.5 1 100977 4093 60 95180 0.5 1 91566 3614 61 99151 0.5 1 95315 3836 62 99915 0.5 1 96349 3566 63 90990 0.5 1 87651 3339 64 86701 0.5 1 83827 2874 65 82223 0.5 1 79324 2899 66 75672 0.5 1 72920 2752 67 73713 0.5 1 71104 2609 68 68779 0.5 1 66283 2496 69 71095 0.5 1 68631 2464 70 65006 0.5 1 62701 2305 71 65658 0.5 1 63230 2428 72 70391 0.5 1 67161 3230 73 113761 0.5 1 105157 8604 74 410703 0.5 1 397705 12998 75 326509 0.5 1 315762 10747 76 218507 0.5 1 211021 7486 77 145002 0.5 1 139982 5020 78 93139 0.5 1 89993 3146 79 53657 0.5 1 51738 1919 80 35115 0.5 1 33804 1311 81 20856 0.5 1 20105 751 82 13667 0.5 1 13144 523 83 10300 0.5 1 9823 477 84 8464 0.5 1 8099 365 85 6719 0.5 1 6426 293 86 5679 0.5 1 5431 248 87 4950 0.5 1 4690 260 88 4318 0.5 1 4113 205 89 4302 0.5 1 4083 219 90 5657 0.5 1 5405 252 91 7704 0.5 1 7377 327 92 12356 0.5 1 11782 574 93 28465 0.5 1 27252 1213 94 84696 0.5 1 81371 3325 95 140821 0.5 1 135476 5345 96 59706 0.5 1 57173 2533 97 38364 0.5 1 36616 1748 98 16332 0.5 1 15538 794 99 15904 0.5 1 15079 825 100 18771 0.5 1 17701 1070 101 36978 0.5 1 33665 3313 RUN STATISTICS FOR INPUT FILE: EPI-209_S29_L004_R1_001.fastq.gz ============================================= 31419769 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3579716 (11.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 19039132 (60.6%) RRBS reads trimmed by 2 bp at the start when read started with CAA (249171) or CGA (197761) in total: 446932 (1.4%)