SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-194_S23_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-194_S23_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 537.94 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 28,208,567 Reads with adapters: 15,045,577 (53.3%) Reads written (passing filters): 28,208,567 (100.0%) Total basepairs processed: 2,830,822,900 bp Total written (filtered): 2,567,816,031 bp (90.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15045577 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.5% C: 9.6% G: 24.5% T: 40.9% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 5701855 7052141.8 0 5701855 2 1366830 1763035.4 0 1366830 3 505105 440758.9 0 505105 4 335399 110189.7 0 335399 5 155820 27547.4 0 155820 6 151231 6886.9 0 151231 7 139651 1721.7 0 139651 8 148867 430.4 0 148867 9 150107 107.6 0 148537 1570 10 144690 26.9 1 138759 5931 11 146830 6.7 1 140326 6504 12 140014 1.7 1 133914 6100 13 134739 0.4 1 128815 5924 14 148474 0.4 1 138356 10118 15 138714 0.4 1 128789 9925 16 149283 0.4 1 138221 11062 17 142221 0.4 1 131736 10485 18 130527 0.4 1 121671 8856 19 141515 0.4 1 129915 11600 20 128653 0.4 1 119693 8960 21 143907 0.4 1 132526 11381 22 131450 0.4 1 122220 9230 23 127279 0.4 1 117926 9353 24 130328 0.4 1 120698 9630 25 122124 0.4 1 113200 8924 26 133641 0.4 1 122948 10693 27 121426 0.4 1 114512 6914 28 114200 0.4 1 108441 5759 29 124102 0.4 1 117423 6679 30 116555 0.4 1 110772 5783 31 123000 0.4 1 115935 7065 32 113084 0.4 1 107365 5719 33 118150 0.4 1 112087 6063 34 109161 0.4 1 103863 5298 35 110503 0.4 1 104378 6125 36 108377 0.4 1 102830 5547 37 111622 0.4 1 106080 5542 38 104783 0.4 1 99878 4905 39 99005 0.4 1 94570 4435 40 98479 0.4 1 93307 5172 41 131127 0.4 1 125506 5621 42 86898 0.4 1 83214 3684 43 56668 0.4 1 53867 2801 44 82797 0.4 1 78869 3928 45 79234 0.4 1 75628 3606 46 74623 0.4 1 71520 3103 47 78701 0.4 1 74951 3750 48 71547 0.4 1 68185 3362 49 73739 0.4 1 70270 3469 50 66094 0.4 1 63284 2810 51 64176 0.4 1 61353 2823 52 60943 0.4 1 58345 2598 53 56901 0.4 1 54650 2251 54 56378 0.4 1 53992 2386 55 56566 0.4 1 54222 2344 56 51864 0.4 1 49812 2052 57 49033 0.4 1 47010 2023 58 47116 0.4 1 45335 1781 59 46402 0.4 1 44522 1880 60 41353 0.4 1 39801 1552 61 41571 0.4 1 39996 1575 62 41036 0.4 1 39513 1523 63 37275 0.4 1 35899 1376 64 34809 0.4 1 33566 1243 65 32306 0.4 1 31149 1157 66 29648 0.4 1 28556 1092 67 29551 0.4 1 28475 1076 68 27653 0.4 1 26608 1045 69 28947 0.4 1 27874 1073 70 26933 0.4 1 25831 1102 71 27899 0.4 1 26658 1241 72 32985 0.4 1 31259 1726 73 58102 0.4 1 53935 4167 74 172153 0.4 1 165868 6285 75 135085 0.4 1 130389 4696 76 76877 0.4 1 74011 2866 77 46227 0.4 1 44571 1656 78 27768 0.4 1 26770 998 79 15738 0.4 1 15133 605 80 10556 0.4 1 10129 427 81 6661 0.4 1 6379 282 82 4485 0.4 1 4266 219 83 3621 0.4 1 3451 170 84 2967 0.4 1 2826 141 85 2541 0.4 1 2409 132 86 2241 0.4 1 2136 105 87 1852 0.4 1 1756 96 88 1717 0.4 1 1629 88 89 1673 0.4 1 1575 98 90 1965 0.4 1 1867 98 91 2647 0.4 1 2498 149 92 4302 0.4 1 4074 228 93 10429 0.4 1 9933 496 94 30690 0.4 1 29401 1289 95 54070 0.4 1 51821 2249 96 24809 0.4 1 23669 1140 97 17676 0.4 1 16852 824 98 7974 0.4 1 7544 430 99 8333 0.4 1 7872 461 100 9937 0.4 1 9302 635 101 18007 0.4 1 16318 1689 RUN STATISTICS FOR INPUT FILE: EPI-194_S23_L003_R1_001.fastq.gz ============================================= 28208567 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2960108 (10.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 14939966 (53.0%)