SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-160_S7_L002_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-160_S7_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 626.10 s (18 us/read; 3.28 M reads/minute). === Summary === Total reads processed: 34,201,339 Reads with adapters: 22,442,614 (65.6%) Reads written (passing filters): 34,201,339 (100.0%) Total basepairs processed: 3,411,765,051 bp Total written (filtered): 2,769,402,003 bp (81.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22442614 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 22.0% C: 14.1% G: 27.0% T: 36.2% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 5019206 8550334.8 0 5019206 2 1289783 2137583.7 0 1289783 3 525372 534395.9 0 525372 4 380883 133599.0 0 380883 5 220606 33399.7 0 220606 6 219998 8349.9 0 219998 7 204382 2087.5 0 204382 8 228062 521.9 0 228062 9 224699 130.5 0 222798 1901 10 219010 32.6 1 209917 9093 11 220348 8.2 1 210137 10211 12 212955 2.0 1 203595 9360 13 206578 0.5 1 197497 9081 14 229297 0.5 1 217258 12039 15 216738 0.5 1 206132 10606 16 239034 0.5 1 225574 13460 17 224515 0.5 1 212493 12022 18 216107 0.5 1 205667 10440 19 232913 0.5 1 219303 13610 20 218825 0.5 1 208151 10674 21 239205 0.5 1 225519 13686 22 223544 0.5 1 212499 11045 23 220892 0.5 1 209446 11446 24 231082 0.5 1 218068 13014 25 220243 0.5 1 209147 11096 26 243771 0.5 1 229463 14308 27 221326 0.5 1 210527 10799 28 210566 0.5 1 200741 9825 29 235974 0.5 1 224155 11819 30 218044 0.5 1 208594 9450 31 246826 0.5 1 233326 13500 32 221255 0.5 1 211293 9962 33 234166 0.5 1 222748 11418 34 231544 0.5 1 220261 11283 35 223754 0.5 1 213728 10026 36 222030 0.5 1 212188 9842 37 227557 0.5 1 217598 9959 38 223271 0.5 1 213089 10182 39 221366 0.5 1 210688 10678 40 229726 0.5 1 217855 11871 41 301624 0.5 1 288051 13573 42 187019 0.5 1 178435 8584 43 142917 0.5 1 135932 6985 44 198743 0.5 1 189487 9256 45 193594 0.5 1 184841 8753 46 186487 0.5 1 178310 8177 47 205294 0.5 1 195350 9944 48 187137 0.5 1 178307 8830 49 200535 0.5 1 190847 9688 50 177272 0.5 1 169298 7974 51 175412 0.5 1 167766 7646 52 169322 0.5 1 161900 7422 53 158138 0.5 1 151766 6372 54 159285 0.5 1 152592 6693 55 164157 0.5 1 157795 6362 56 152731 0.5 1 146569 6162 57 142822 0.5 1 136962 5860 58 142548 0.5 1 137106 5442 59 137182 0.5 1 131890 5292 60 122415 0.5 1 117811 4604 61 126453 0.5 1 121846 4607 62 125590 0.5 1 120997 4593 63 112934 0.5 1 108784 4150 64 110439 0.5 1 106601 3838 65 101766 0.5 1 98039 3727 66 94539 0.5 1 90977 3562 67 92615 0.5 1 89233 3382 68 85891 0.5 1 82566 3325 69 92983 0.5 1 89389 3594 70 92049 0.5 1 88258 3791 71 105556 0.5 1 101150 4406 72 129793 0.5 1 124001 5792 73 196938 0.5 1 184016 12922 74 583060 0.5 1 563331 19729 75 404775 0.5 1 390773 14002 76 231178 0.5 1 222864 8314 77 140161 0.5 1 135125 5036 78 84186 0.5 1 81311 2875 79 46850 0.5 1 45102 1748 80 29248 0.5 1 28140 1108 81 18659 0.5 1 17939 720 82 13298 0.5 1 12765 533 83 10240 0.5 1 9813 427 84 8761 0.5 1 8359 402 85 7647 0.5 1 7297 350 86 6378 0.5 1 6074 304 87 5745 0.5 1 5444 301 88 4859 0.5 1 4588 271 89 4812 0.5 1 4563 249 90 6434 0.5 1 6111 323 91 8871 0.5 1 8444 427 92 14202 0.5 1 13536 666 93 34335 0.5 1 32733 1602 94 104995 0.5 1 100638 4357 95 177431 0.5 1 170053 7378 96 78635 0.5 1 75070 3565 97 51048 0.5 1 48632 2416 98 20791 0.5 1 19611 1180 99 20397 0.5 1 19352 1045 100 20624 0.5 1 19341 1283 101 37361 0.5 1 34213 3148 RUN STATISTICS FOR INPUT FILE: EPI-160_S7_L002_R1_001.fastq.gz ============================================= 34201339 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4687406 (13.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 21913270 (64.1%) RRBS reads trimmed by 2 bp at the start when read started with CAA (283100) or CGA (182524) in total: 465624 (1.4%)