SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-103_S27_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-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 390.67 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 20,420,261 Reads with adapters: 10,283,712 (50.4%) Reads written (passing filters): 20,420,261 (100.0%) Total basepairs processed: 2,054,126,666 bp Total written (filtered): 1,925,748,290 bp (93.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10283712 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.7% C: 5.9% G: 24.5% T: 42.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4475714 5105065.2 0 4475714 2 1023849 1276266.3 0 1023849 3 388885 319066.6 0 388885 4 258450 79766.6 0 258450 5 111458 19941.7 0 111458 6 115643 4985.4 0 115643 7 106247 1246.4 0 106247 8 141870 311.6 0 141870 9 107898 77.9 0 106798 1100 10 98957 19.5 1 93927 5030 11 102966 4.9 1 96927 6039 12 95747 1.2 1 90547 5200 13 87695 0.3 1 82877 4818 14 101667 0.3 1 94968 6699 15 93139 0.3 1 87800 5339 16 103499 0.3 1 96374 7125 17 95053 0.3 1 89414 5639 18 87319 0.3 1 82373 4946 19 93614 0.3 1 87354 6260 20 83374 0.3 1 78697 4677 21 94369 0.3 1 88145 6224 22 87215 0.3 1 82399 4816 23 81878 0.3 1 76955 4923 24 84292 0.3 1 78848 5444 25 75958 0.3 1 71702 4256 26 85493 0.3 1 79989 5504 27 75013 0.3 1 70780 4233 28 69434 0.3 1 65743 3691 29 76872 0.3 1 72314 4558 30 70549 0.3 1 66780 3769 31 76672 0.3 1 72027 4645 32 65989 0.3 1 62622 3367 33 77921 0.3 1 73000 4921 34 64015 0.3 1 60557 3458 35 65390 0.3 1 61390 4000 36 69532 0.3 1 65320 4212 37 62340 0.3 1 58957 3383 38 61893 0.3 1 58232 3661 39 59034 0.3 1 55683 3351 40 60466 0.3 1 56940 3526 41 85039 0.3 1 81239 3800 42 48849 0.3 1 46798 2051 43 21450 0.3 1 19928 1522 44 48314 0.3 1 45718 2596 45 45581 0.3 1 43091 2490 46 43704 0.3 1 41474 2230 47 46686 0.3 1 44129 2557 48 44652 0.3 1 42070 2582 49 44260 0.3 1 41731 2529 50 38780 0.3 1 36820 1960 51 36753 0.3 1 34893 1860 52 34328 0.3 1 32602 1726 53 32419 0.3 1 30876 1543 54 32948 0.3 1 31303 1645 55 32703 0.3 1 31200 1503 56 31231 0.3 1 29705 1526 57 30278 0.3 1 28832 1446 58 27855 0.3 1 26666 1189 59 27604 0.3 1 26347 1257 60 24122 0.3 1 23057 1065 61 23675 0.3 1 22682 993 62 24513 0.3 1 23477 1036 63 23046 0.3 1 22005 1041 64 22440 0.3 1 21524 916 65 20291 0.3 1 19482 809 66 18819 0.3 1 18005 814 67 17210 0.3 1 16470 740 68 14805 0.3 1 14163 642 69 14715 0.3 1 14065 650 70 13133 0.3 1 12521 612 71 12548 0.3 1 12020 528 72 11994 0.3 1 11476 518 73 11872 0.3 1 11190 682 74 18800 0.3 1 18184 616 75 7934 0.3 1 7639 295 76 3757 0.3 1 3618 139 77 2203 0.3 1 2106 97 78 1531 0.3 1 1470 61 79 1078 0.3 1 1043 35 80 755 0.3 1 716 39 81 508 0.3 1 483 25 82 324 0.3 1 311 13 83 230 0.3 1 220 10 84 142 0.3 1 132 10 85 110 0.3 1 103 7 86 59 0.3 1 50 9 87 46 0.3 1 39 7 88 61 0.3 1 52 9 89 53 0.3 1 48 5 90 66 0.3 1 55 11 91 82 0.3 1 73 9 92 124 0.3 1 107 17 93 190 0.3 1 169 21 94 305 0.3 1 277 28 95 464 0.3 1 429 35 96 389 0.3 1 358 31 97 180 0.3 1 159 21 98 73 0.3 1 58 15 99 41 0.3 1 36 5 100 58 0.3 1 42 16 101 163 0.3 1 99 64 RUN STATISTICS FOR INPUT FILE: EPI-103_S27_L005_R1_001.fastq.gz ============================================= 20420261 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2158450 (10.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 10160052 (49.8%) RRBS reads trimmed by 2 bp at the start when read started with CAA (131912) or CGA (121074) in total: 252986 (1.2%)