SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-176_S15_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 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-176_S15_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 682.60 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 36,578,520 Reads with adapters: 20,012,705 (54.7%) Reads written (passing filters): 36,578,520 (100.0%) Total basepairs processed: 3,682,480,253 bp Total written (filtered): 3,344,434,499 bp (90.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20012705 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.3% C: 8.3% G: 26.3% T: 40.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 6848493 9144630.0 0 6848493 2 1646843 2286157.5 0 1646843 3 644966 571539.4 0 644966 4 460007 142884.8 0 460007 5 248785 35721.2 0 248785 6 241295 8930.3 0 241295 7 224134 2232.6 0 224134 8 237199 558.1 0 237199 9 237076 139.5 0 235297 1779 10 222556 34.9 1 213595 8961 11 232535 8.7 1 222078 10457 12 222455 2.2 1 212703 9752 13 216618 0.5 1 207307 9311 14 234963 0.5 1 219122 15841 15 220375 0.5 1 204482 15893 16 234123 0.5 1 216824 17299 17 222550 0.5 1 206363 16187 18 204626 0.5 1 190802 13824 19 222546 0.5 1 204295 18251 20 205436 0.5 1 191555 13881 21 231296 0.5 1 212984 18312 22 209829 0.5 1 194909 14920 23 194692 0.5 1 180324 14368 24 205956 0.5 1 190332 15624 25 190073 0.5 1 176397 13676 26 209285 0.5 1 192526 16759 27 194286 0.5 1 183109 11177 28 182448 0.5 1 173286 9162 29 201399 0.5 1 190522 10877 30 185277 0.5 1 176234 9043 31 197606 0.5 1 186504 11102 32 189179 0.5 1 179886 9293 33 202441 0.5 1 191462 10979 34 181542 0.5 1 172110 9432 35 168863 0.5 1 160175 8688 36 172629 0.5 1 164698 7931 37 171774 0.5 1 163803 7971 38 158570 0.5 1 150759 7811 39 152328 0.5 1 145799 6529 40 167052 0.5 1 158382 8670 41 217948 0.5 1 208829 9119 42 130331 0.5 1 124531 5800 43 88977 0.5 1 84757 4220 44 130452 0.5 1 124601 5851 45 125656 0.5 1 120061 5595 46 119369 0.5 1 114334 5035 47 125167 0.5 1 119479 5688 48 114327 0.5 1 109104 5223 49 120640 0.5 1 115007 5633 50 107503 0.5 1 102950 4553 51 104415 0.5 1 100035 4380 52 97810 0.5 1 93572 4238 53 92164 0.5 1 88584 3580 54 90481 0.5 1 86613 3868 55 90758 0.5 1 87196 3562 56 84767 0.5 1 81419 3348 57 80286 0.5 1 77063 3223 58 75474 0.5 1 72580 2894 59 74041 0.5 1 71224 2817 60 66669 0.5 1 64231 2438 61 67341 0.5 1 64802 2539 62 67749 0.5 1 65271 2478 63 60232 0.5 1 58112 2120 64 56800 0.5 1 54850 1950 65 51689 0.5 1 49911 1778 66 48403 0.5 1 46633 1770 67 46380 0.5 1 44794 1586 68 41847 0.5 1 40300 1547 69 42558 0.5 1 41043 1515 70 40147 0.5 1 38644 1503 71 37008 0.5 1 35539 1469 72 35684 0.5 1 34111 1573 73 41601 0.5 1 39197 2404 74 79133 0.5 1 76244 2889 75 52519 0.5 1 50595 1924 76 28093 0.5 1 26993 1100 77 17013 0.5 1 16330 683 78 10853 0.5 1 10391 462 79 6610 0.5 1 6327 283 80 4649 0.5 1 4451 198 81 3188 0.5 1 3056 132 82 2242 0.5 1 2121 121 83 1733 0.5 1 1660 73 84 1313 0.5 1 1244 69 85 970 0.5 1 902 68 86 748 0.5 1 703 45 87 585 0.5 1 555 30 88 405 0.5 1 376 29 89 391 0.5 1 364 27 90 506 0.5 1 468 38 91 612 0.5 1 568 44 92 871 0.5 1 820 51 93 1676 0.5 1 1566 110 94 4526 0.5 1 4293 233 95 8000 0.5 1 7621 379 96 4159 0.5 1 3904 255 97 2970 0.5 1 2768 202 98 1081 0.5 1 994 87 99 1079 0.5 1 982 97 100 1919 0.5 1 1741 178 101 6081 0.5 1 5291 790 RUN STATISTICS FOR INPUT FILE: EPI-176_S15_L003_R1_001.fastq.gz ============================================= 36578520 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3084379 (8.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 19726321 (53.9%) RRBS reads trimmed by 2 bp at the start when read started with CAA (280760) or CGA (189215) in total: 469975 (1.3%)