SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-136_S36_L005_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-136_S36_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 530.62 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 27,877,100 Reads with adapters: 16,122,592 (57.8%) Reads written (passing filters): 27,877,100 (100.0%) Total basepairs processed: 2,804,301,508 bp Total written (filtered): 2,502,412,318 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16122592 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.8% C: 7.6% G: 25.4% T: 41.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5196614 6969275.0 0 5196614 2 1244905 1742318.8 0 1244905 3 501582 435579.7 0 501582 4 338073 108894.9 0 338073 5 169656 27223.7 0 169656 6 179724 6805.9 0 179724 7 172693 1701.5 0 172693 8 231764 425.4 0 231764 9 165809 106.3 0 164445 1364 10 160172 26.6 1 153356 6816 11 162993 6.6 1 155130 7863 12 157704 1.7 1 150559 7145 13 148611 0.4 1 142127 6484 14 171446 0.4 1 162006 9440 15 160449 0.4 1 152773 7676 16 175407 0.4 1 165670 9737 17 165080 0.4 1 157018 8062 18 153200 0.4 1 146214 6986 19 168296 0.4 1 158798 9498 20 152313 0.4 1 145742 6571 21 173998 0.4 1 164337 9661 22 164852 0.4 1 157490 7362 23 157208 0.4 1 149541 7667 24 167696 0.4 1 158719 8977 25 152708 0.4 1 145880 6828 26 174012 0.4 1 164488 9524 27 154046 0.4 1 147312 6734 28 145487 0.4 1 139109 6378 29 162347 0.4 1 154433 7914 30 152830 0.4 1 146395 6435 31 166871 0.4 1 158168 8703 32 148862 0.4 1 142519 6343 33 157197 0.4 1 149801 7396 34 147790 0.4 1 141345 6445 35 155986 0.4 1 148222 7764 36 156743 0.4 1 148890 7853 37 156023 0.4 1 149042 6981 38 147693 0.4 1 141559 6134 39 141920 0.4 1 135509 6411 40 144191 0.4 1 137190 7001 41 200095 0.4 1 192440 7655 42 126136 0.4 1 121116 5020 43 82424 0.4 1 78498 3926 44 131182 0.4 1 125324 5858 45 126408 0.4 1 121109 5299 46 123228 0.4 1 118236 4992 47 133105 0.4 1 126953 6152 48 123425 0.4 1 117800 5625 49 123931 0.4 1 118087 5844 50 111801 0.4 1 107001 4800 51 106300 0.4 1 101957 4343 52 100591 0.4 1 96500 4091 53 99701 0.4 1 95844 3857 54 97598 0.4 1 93567 4031 55 101037 0.4 1 97284 3753 56 93645 0.4 1 89839 3806 57 91658 0.4 1 88400 3258 58 84440 0.4 1 81627 2813 59 81684 0.4 1 78742 2942 60 73534 0.4 1 71056 2478 61 74083 0.4 1 71663 2420 62 75564 0.4 1 73057 2507 63 72157 0.4 1 69600 2557 64 71180 0.4 1 68951 2229 65 63455 0.4 1 61410 2045 66 60342 0.4 1 58363 1979 67 53750 0.4 1 52041 1709 68 45861 0.4 1 44319 1542 69 45044 0.4 1 43643 1401 70 40256 0.4 1 38890 1366 71 35878 0.4 1 34745 1133 72 33633 0.4 1 32494 1139 73 35316 0.4 1 33942 1374 74 48697 0.4 1 47601 1096 75 19819 0.4 1 19269 550 76 10023 0.4 1 9708 315 77 6396 0.4 1 6198 198 78 4341 0.4 1 4205 136 79 2782 0.4 1 2683 99 80 1934 0.4 1 1885 49 81 1232 0.4 1 1196 36 82 781 0.4 1 752 29 83 479 0.4 1 464 15 84 326 0.4 1 314 12 85 205 0.4 1 198 7 86 111 0.4 1 104 7 87 86 0.4 1 82 4 88 70 0.4 1 65 5 89 50 0.4 1 43 7 90 62 0.4 1 62 91 76 0.4 1 68 8 92 118 0.4 1 105 13 93 149 0.4 1 136 13 94 253 0.4 1 235 18 95 393 0.4 1 352 41 96 330 0.4 1 304 26 97 173 0.4 1 159 14 98 60 0.4 1 56 4 99 43 0.4 1 31 12 100 50 0.4 1 39 11 101 160 0.4 1 109 51 RUN STATISTICS FOR INPUT FILE: EPI-136_S36_L005_R1_001.fastq.gz ============================================= 27877100 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2879950 (10.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 15942796 (57.2%) RRBS reads trimmed by 2 bp at the start when read started with CAA (179709) or CGA (147099) in total: 326808 (1.2%)