SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-206_S27_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-206_S27_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 638.44 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 36,712,077 Reads with adapters: 29,247,131 (79.7%) Reads written (passing filters): 36,712,077 (100.0%) Total basepairs processed: 3,485,949,730 bp Total written (filtered): 1,846,929,548 bp (53.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29247131 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.3% C: 36.7% G: 17.0% T: 25.9% none/other: 2.0% Overview of removed sequences length count expect max.err error counts 1 3228855 9178019.2 0 3228855 2 814430 2294504.8 0 814430 3 323288 573626.2 0 323288 4 220035 143406.6 0 220035 5 124648 35851.6 0 124648 6 121803 8962.9 0 121803 7 116957 2240.7 0 116957 8 130219 560.2 0 130219 9 130167 140.0 0 129052 1115 10 125078 35.0 1 120883 4195 11 125724 8.8 1 120887 4837 12 120484 2.2 1 115911 4573 13 122421 0.5 1 117731 4690 14 130138 0.5 1 124528 5610 15 130148 0.5 1 124953 5195 16 136032 0.5 1 130023 6009 17 132431 0.5 1 126691 5740 18 123569 0.5 1 118966 4603 19 131617 0.5 1 125498 6119 20 129634 0.5 1 124584 5050 21 142335 0.5 1 135582 6753 22 134128 0.5 1 128746 5382 23 126897 0.5 1 121655 5242 24 130045 0.5 1 124045 6000 25 127496 0.5 1 122227 5269 26 134662 0.5 1 128482 6180 27 130063 0.5 1 124530 5533 28 128046 0.5 1 122757 5289 29 139706 0.5 1 133546 6160 30 130865 0.5 1 125790 5075 31 138710 0.5 1 132463 6247 32 134740 0.5 1 129257 5483 33 144832 0.5 1 138249 6583 34 138218 0.5 1 131875 6343 35 133525 0.5 1 127491 6034 36 136714 0.5 1 130957 5757 37 139782 0.5 1 134007 5775 38 131438 0.5 1 125998 5440 39 130390 0.5 1 125180 5210 40 142223 0.5 1 135330 6893 41 189428 0.5 1 181863 7565 42 117382 0.5 1 112605 4777 43 94979 0.5 1 90901 4078 44 124642 0.5 1 119370 5272 45 128246 0.5 1 122953 5293 46 124709 0.5 1 119544 5165 47 132828 0.5 1 126978 5850 48 128158 0.5 1 122535 5623 49 134060 0.5 1 128165 5895 50 124069 0.5 1 119057 5012 51 126845 0.5 1 121676 5169 52 126625 0.5 1 121326 5299 53 121173 0.5 1 116572 4601 54 121838 0.5 1 116915 4923 55 130660 0.5 1 125499 5161 56 125599 0.5 1 120844 4755 57 120552 0.5 1 115965 4587 58 123941 0.5 1 119245 4696 59 121828 0.5 1 117052 4776 60 112908 0.5 1 108589 4319 61 122789 0.5 1 118060 4729 62 125836 0.5 1 121097 4739 63 117881 0.5 1 113473 4408 64 116746 0.5 1 112719 4027 65 112511 0.5 1 108481 4030 66 108222 0.5 1 104369 3853 67 108994 0.5 1 104944 4050 68 107321 0.5 1 103251 4070 69 120596 0.5 1 116105 4491 70 129211 0.5 1 124393 4818 71 143554 0.5 1 137739 5815 72 186702 0.5 1 177231 9471 73 427521 0.5 1 387842 39679 74 2525331 0.5 1 2442119 83212 75 2615473 0.5 1 2532407 83066 76 1999179 0.5 1 1932714 66465 77 1471290 0.5 1 1424015 47275 78 908981 0.5 1 880086 28895 79 502729 0.5 1 486185 16544 80 298845 0.5 1 288920 9925 81 168462 0.5 1 162592 5870 82 103554 0.5 1 99754 3800 83 76679 0.5 1 73665 3014 84 64723 0.5 1 62123 2600 85 58219 0.5 1 55923 2296 86 53725 0.5 1 51554 2171 87 48028 0.5 1 46069 1959 88 43918 0.5 1 42134 1784 89 44831 0.5 1 42946 1885 90 57596 0.5 1 55145 2451 91 84494 0.5 1 80992 3502 92 135295 0.5 1 129986 5309 93 321595 0.5 1 309254 12341 94 971543 0.5 1 935718 35825 95 1564005 0.5 1 1507217 56788 96 620451 0.5 1 595489 24962 97 305173 0.5 1 292193 12980 98 111347 0.5 1 106178 5169 99 90919 0.5 1 86935 3984 100 83337 0.5 1 79356 3981 101 146562 0.5 1 137385 9177 RUN STATISTICS FOR INPUT FILE: EPI-206_S27_L004_R1_001.fastq.gz ============================================= 36712077 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 13606605 (37.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 27829282 (75.8%) RRBS reads trimmed by 2 bp at the start when read started with CAA (368302) or CGA (302859) in total: 671161 (1.8%)