SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-161_S8_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-161_S8_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 462.15 s (19 us/read; 3.23 M reads/minute). === Summary === Total reads processed: 24,900,290 Reads with adapters: 15,699,376 (63.0%) Reads written (passing filters): 24,900,290 (100.0%) Total basepairs processed: 2,503,455,282 bp Total written (filtered): 2,146,909,273 bp (85.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15699376 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.7% C: 10.6% G: 27.2% T: 38.2% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 3889186 6225072.5 0 3889186 2 982506 1556268.1 0 982506 3 408254 389067.0 0 408254 4 304747 97266.8 0 304747 5 184045 24316.7 0 184045 6 182672 6079.2 0 182672 7 169787 1519.8 0 169787 8 184362 379.9 0 184362 9 186084 95.0 0 184460 1624 10 175966 23.7 1 169365 6601 11 182201 5.9 1 174487 7714 12 176369 1.5 1 169062 7307 13 172555 0.4 1 165391 7164 14 190187 0.4 1 180788 9399 15 180330 0.4 1 172199 8131 16 191556 0.4 1 181714 9842 17 185987 0.4 1 177077 8910 18 175911 0.4 1 168020 7891 19 192495 0.4 1 182048 10447 20 180688 0.4 1 172553 8135 21 200854 0.4 1 189882 10972 22 186589 0.4 1 177923 8666 23 180090 0.4 1 171514 8576 24 188240 0.4 1 178282 9958 25 178148 0.4 1 169861 8287 26 196349 0.4 1 185809 10540 27 179582 0.4 1 171607 7975 28 172454 0.4 1 165023 7431 29 188141 0.4 1 179315 8826 30 178450 0.4 1 171283 7167 31 189465 0.4 1 180090 9375 32 179240 0.4 1 171665 7575 33 189373 0.4 1 180971 8402 34 180804 0.4 1 173034 7770 35 169480 0.4 1 162463 7017 36 178790 0.4 1 170836 7954 37 180146 0.4 1 172739 7407 38 169981 0.4 1 162650 7331 39 169741 0.4 1 162293 7448 40 166317 0.4 1 158276 8041 41 237933 0.4 1 228293 9640 42 145447 0.4 1 139578 5869 43 91684 0.4 1 87417 4267 44 146754 0.4 1 140444 6310 45 141120 0.4 1 135120 6000 46 136163 0.4 1 130622 5541 47 143054 0.4 1 136750 6304 48 130903 0.4 1 125188 5715 49 136341 0.4 1 130282 6059 50 123011 0.4 1 117828 5183 51 119488 0.4 1 114581 4907 52 113493 0.4 1 108759 4734 53 107776 0.4 1 103811 3965 54 104804 0.4 1 100785 4019 55 105043 0.4 1 101113 3930 56 97887 0.4 1 94223 3664 57 89832 0.4 1 86497 3335 58 87538 0.4 1 84443 3095 59 84829 0.4 1 81787 3042 60 75897 0.4 1 73123 2774 61 76679 0.4 1 73941 2738 62 74799 0.4 1 72325 2474 63 67749 0.4 1 65443 2306 64 64425 0.4 1 62372 2053 65 58683 0.4 1 56745 1938 66 54810 0.4 1 52854 1956 67 52396 0.4 1 50640 1756 68 48122 0.4 1 46462 1660 69 48271 0.4 1 46611 1660 70 45929 0.4 1 44415 1514 71 42075 0.4 1 40636 1439 72 44032 0.4 1 42278 1754 73 53826 0.4 1 50499 3327 74 127917 0.4 1 123682 4235 75 95916 0.4 1 93160 2756 76 46008 0.4 1 44407 1601 77 26443 0.4 1 25547 896 78 16349 0.4 1 15752 597 79 9783 0.4 1 9446 337 80 6915 0.4 1 6654 261 81 4560 0.4 1 4389 171 82 3334 0.4 1 3203 131 83 2706 0.4 1 2613 93 84 2221 0.4 1 2125 96 85 1700 0.4 1 1618 82 86 1372 0.4 1 1315 57 87 1107 0.4 1 1069 38 88 834 0.4 1 784 50 89 820 0.4 1 773 47 90 982 0.4 1 928 54 91 1237 0.4 1 1150 87 92 2050 0.4 1 1941 109 93 4390 0.4 1 4187 203 94 12425 0.4 1 11875 550 95 20989 0.4 1 20168 821 96 10877 0.4 1 10369 508 97 7893 0.4 1 7527 366 98 3100 0.4 1 2943 157 99 3212 0.4 1 3021 191 100 4611 0.4 1 4305 306 101 10710 0.4 1 9669 1041 RUN STATISTICS FOR INPUT FILE: EPI-161_S8_L002_R1_001.fastq.gz ============================================= 24900290 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2310949 (9.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 15443920 (62.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (194756) or CGA (123491) in total: 318247 (1.3%)