SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-187_S20_L003_R2_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-187_S20_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 491.38 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 26,246,829 Reads with adapters: 18,079,996 (68.9%) Reads written (passing filters): 26,246,829 (100.0%) Total basepairs processed: 2,562,531,825 bp Total written (filtered): 2,078,239,304 bp (81.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18079996 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.3% C: 21.4% G: 14.7% T: 30.5% none/other: 1.1% Overview of removed sequences length count expect max.err error counts 1 7197400 6561707.2 0 7197400 2 208041 1640426.8 0 208041 3 179414 410106.7 0 179414 4 146048 102526.7 0 146048 5 144214 25631.7 0 144214 6 145283 6407.9 0 145283 7 143582 1602.0 0 143582 8 163621 400.5 0 163621 9 146933 100.1 0 146256 677 10 151352 25.0 1 146932 4420 11 134637 6.3 1 129506 5131 12 138103 1.6 1 132888 5215 13 135057 0.4 1 130076 4981 14 147047 0.4 1 141385 5662 15 139777 0.4 1 134667 5110 16 140779 0.4 1 135746 5033 17 142731 0.4 1 137574 5157 18 126595 0.4 1 122122 4473 19 135811 0.4 1 130985 4826 20 136504 0.4 1 131429 5075 21 137456 0.4 1 132014 5442 22 143704 0.4 1 138117 5587 23 134653 0.4 1 129634 5019 24 142073 0.4 1 136438 5635 25 127208 0.4 1 122513 4695 26 128819 0.4 1 123271 5548 27 131855 0.4 1 125462 6393 28 135502 0.4 1 130263 5239 29 131794 0.4 1 126055 5739 30 142291 0.4 1 137045 5246 31 122142 0.4 1 117081 5061 32 128071 0.4 1 123616 4455 33 135833 0.4 1 130415 5418 34 136191 0.4 1 130330 5861 35 126312 0.4 1 122171 4141 36 122726 0.4 1 117832 4894 37 123477 0.4 1 118865 4612 38 110807 0.4 1 106631 4176 39 114676 0.4 1 110170 4506 40 113286 0.4 1 108811 4475 41 112410 0.4 1 108517 3893 42 111362 0.4 1 107841 3521 43 97740 0.4 1 94019 3721 44 100517 0.4 1 96940 3577 45 134194 0.4 1 130057 4137 46 96989 0.4 1 93586 3403 47 71321 0.4 1 68666 2655 48 100363 0.4 1 97308 3055 49 70531 0.4 1 68086 2445 50 73040 0.4 1 70462 2578 51 101498 0.4 1 98722 2776 52 63528 0.4 1 61264 2264 53 63983 0.4 1 61851 2132 54 56577 0.4 1 54589 1988 55 68949 0.4 1 66917 2032 56 66324 0.4 1 64164 2160 57 60719 0.4 1 58726 1993 58 59731 0.4 1 57776 1955 59 56014 0.4 1 54085 1929 60 54245 0.4 1 52358 1887 61 54615 0.4 1 52670 1945 62 58953 0.4 1 56684 2269 63 63724 0.4 1 61073 2651 64 69537 0.4 1 66564 2973 65 83985 0.4 1 80179 3806 66 114477 0.4 1 108588 5889 67 242825 0.4 1 221431 21394 68 1183029 0.4 1 1152131 30898 69 419202 0.4 1 404483 14719 70 226689 0.4 1 218702 7987 71 112634 0.4 1 108143 4491 72 71882 0.4 1 68760 3122 73 45455 0.4 1 43140 2315 74 33995 0.4 1 32240 1755 75 27024 0.4 1 25405 1619 76 22819 0.4 1 21457 1362 77 19789 0.4 1 18481 1308 78 17353 0.4 1 16228 1125 79 15176 0.4 1 14174 1002 80 13223 0.4 1 12332 891 81 12034 0.4 1 11163 871 82 10716 0.4 1 9894 822 83 9504 0.4 1 8757 747 84 8644 0.4 1 7929 715 85 7827 0.4 1 7195 632 86 7588 0.4 1 6933 655 87 7608 0.4 1 6901 707 88 7988 0.4 1 7242 746 89 9046 0.4 1 8176 870 90 11397 0.4 1 10382 1015 91 15547 0.4 1 14164 1383 92 23220 0.4 1 21201 2019 93 53648 0.4 1 49322 4326 94 165866 0.4 1 154238 11628 95 293669 0.4 1 273891 19778 96 129153 0.4 1 120733 8420 97 78881 0.4 1 73531 5350 98 28211 0.4 1 26227 1984 99 26325 0.4 1 24397 1928 100 23058 0.4 1 21347 1711 101 41840 0.4 1 38569 3271 RUN STATISTICS FOR INPUT FILE: EPI-187_S20_L003_R2_001.fastq.gz ============================================= 26246829 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 5001798 (19.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (687828) or CGA (247537) in total: 935365 (3.6%) Total number of sequences analysed for the sequence pair length validation: 26246829 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3510835 (13.38%)