SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-151_S2_L002_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-151_S2_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 550.10 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 29,567,647 Reads with adapters: 20,251,861 (68.5%) Reads written (passing filters): 29,567,647 (100.0%) Total basepairs processed: 2,866,651,146 bp Total written (filtered): 2,294,002,231 bp (80.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20251861 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.6% C: 19.5% G: 16.0% T: 31.7% none/other: 1.2% Overview of removed sequences length count expect max.err error counts 1 8165392 7391911.8 0 8165392 2 235104 1847977.9 0 235104 3 194458 461994.5 0 194458 4 164533 115498.6 0 164533 5 165580 28874.7 0 165580 6 162894 7218.7 0 162894 7 156516 1804.7 0 156516 8 161660 451.2 0 161660 9 157728 112.8 0 157071 657 10 160765 28.2 1 155960 4805 11 152110 7.0 1 146309 5801 12 155532 1.8 1 149763 5769 13 148937 0.4 1 143462 5475 14 161274 0.4 1 155066 6208 15 149744 0.4 1 144178 5566 16 149975 0.4 1 144410 5565 17 155298 0.4 1 149510 5788 18 136836 0.4 1 131847 4989 19 145583 0.4 1 140410 5173 20 141477 0.4 1 135970 5507 21 144639 0.4 1 138644 5995 22 146689 0.4 1 140775 5914 23 138178 0.4 1 132739 5439 24 145636 0.4 1 139707 5929 25 127827 0.4 1 122891 4936 26 128850 0.4 1 123095 5755 27 131049 0.4 1 124377 6672 28 135222 0.4 1 129844 5378 29 129620 0.4 1 123449 6171 30 141404 0.4 1 135745 5659 31 121274 0.4 1 116012 5262 32 125686 0.4 1 121049 4637 33 131396 0.4 1 125657 5739 34 131793 0.4 1 125645 6148 35 123111 0.4 1 118935 4176 36 112356 0.4 1 107640 4716 37 112254 0.4 1 107774 4480 38 99569 0.4 1 95638 3931 39 104413 0.4 1 100160 4253 40 102571 0.4 1 98412 4159 41 100299 0.4 1 96860 3439 42 100287 0.4 1 97076 3211 43 85646 0.4 1 82264 3382 44 89002 0.4 1 85764 3238 45 129650 0.4 1 125856 3794 46 84200 0.4 1 81325 2875 47 57353 0.4 1 55097 2256 48 85602 0.4 1 82993 2609 49 55807 0.4 1 53868 1939 50 59070 0.4 1 56857 2213 51 84802 0.4 1 82477 2325 52 49919 0.4 1 48136 1783 53 49742 0.4 1 47934 1808 54 44319 0.4 1 42733 1586 55 53186 0.4 1 51448 1738 56 50774 0.4 1 48898 1876 57 47249 0.4 1 45538 1711 58 46803 0.4 1 45045 1758 59 44144 0.4 1 42411 1733 60 42975 0.4 1 41266 1709 61 44635 0.4 1 42702 1933 62 49646 0.4 1 47443 2203 63 55590 0.4 1 52994 2596 64 66103 0.4 1 62890 3213 65 89115 0.4 1 84663 4452 66 136551 0.4 1 129288 7263 67 316522 0.4 1 289022 27500 68 1526661 0.4 1 1487224 39437 69 562709 0.4 1 543585 19124 70 307948 0.4 1 297586 10362 71 154507 0.4 1 148485 6022 72 96877 0.4 1 92909 3968 73 61127 0.4 1 58264 2863 74 46025 0.4 1 43623 2402 75 35831 0.4 1 33972 1859 76 29677 0.4 1 27985 1692 77 25803 0.4 1 24274 1529 78 22576 0.4 1 21133 1443 79 20254 0.4 1 18918 1336 80 18234 0.4 1 16959 1275 81 16482 0.4 1 15297 1185 82 14710 0.4 1 13633 1077 83 13223 0.4 1 12223 1000 84 12462 0.4 1 11462 1000 85 11680 0.4 1 10703 977 86 11343 0.4 1 10336 1007 87 11920 0.4 1 10881 1039 88 12462 0.4 1 11317 1145 89 14437 0.4 1 13090 1347 90 17865 0.4 1 16251 1614 91 24387 0.4 1 22217 2170 92 37283 0.4 1 33900 3383 93 85016 0.4 1 78146 6870 94 258000 0.4 1 239765 18235 95 454864 0.4 1 425420 29444 96 198723 0.4 1 185801 12922 97 114300 0.4 1 106602 7698 98 38732 0.4 1 36089 2643 99 35897 0.4 1 33421 2476 100 30365 0.4 1 28226 2139 101 55557 0.4 1 51415 4142 RUN STATISTICS FOR INPUT FILE: EPI-151_S2_L002_R2_001.fastq.gz ============================================= 29567647 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 6230800 (21.1%) 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 (840262) or CGA (272734) in total: 1112996 (3.8%) Total number of sequences analysed for the sequence pair length validation: 29567647 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5060296 (17.11%)