SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-226_S34_L004_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-226_S34_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 213.84 s (18 us/read; 3.26 M reads/minute). === Summary === Total reads processed: 11,630,377 Reads with adapters: 6,623,434 (56.9%) Reads written (passing filters): 11,630,377 (100.0%) Total basepairs processed: 1,165,424,439 bp Total written (filtered): 1,026,779,257 bp (88.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6623434 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.2% C: 11.9% G: 25.6% T: 38.7% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 2228223 2907594.2 0 2228223 2 528338 726898.6 0 528338 3 209311 181724.6 0 209311 4 135647 45431.2 0 135647 5 72670 11357.8 0 72670 6 69549 2839.4 0 69549 7 64308 709.9 0 64308 8 74269 177.5 0 74269 9 70830 44.4 0 70109 721 10 68819 11.1 1 66375 2444 11 65207 2.8 1 62583 2624 12 61672 0.7 1 59216 2456 13 61634 0.2 1 59102 2532 14 65805 0.2 1 62892 2913 15 66707 0.2 1 63810 2897 16 67078 0.2 1 64091 2987 17 63433 0.2 1 60574 2859 18 58501 0.2 1 56219 2282 19 62289 0.2 1 59205 3084 20 60713 0.2 1 58090 2623 21 64828 0.2 1 61612 3216 22 61281 0.2 1 58765 2516 23 55911 0.2 1 53485 2426 24 57373 0.2 1 54617 2756 25 56233 0.2 1 53777 2456 26 57511 0.2 1 54789 2722 27 55687 0.2 1 53249 2438 28 53255 0.2 1 50916 2339 29 56502 0.2 1 53749 2753 30 52204 0.2 1 49972 2232 31 54263 0.2 1 51572 2691 32 51280 0.2 1 48960 2320 33 52309 0.2 1 49899 2410 34 50471 0.2 1 48040 2431 35 48305 0.2 1 46179 2126 36 47365 0.2 1 45295 2070 37 50360 0.2 1 48131 2229 38 46217 0.2 1 44224 1993 39 46955 0.2 1 44790 2165 40 46970 0.2 1 44593 2377 41 66071 0.2 1 63358 2713 42 40087 0.2 1 38507 1580 43 21793 0.2 1 20607 1186 44 38365 0.2 1 36760 1605 45 38765 0.2 1 37014 1751 46 36631 0.2 1 35073 1558 47 37938 0.2 1 36123 1815 48 35965 0.2 1 34321 1644 49 36015 0.2 1 34420 1595 50 32274 0.2 1 30916 1358 51 32368 0.2 1 30974 1394 52 31742 0.2 1 30370 1372 53 29692 0.2 1 28504 1188 54 29285 0.2 1 28033 1252 55 30486 0.2 1 29252 1234 56 28328 0.2 1 27224 1104 57 26174 0.2 1 25107 1067 58 26840 0.2 1 25791 1049 59 24874 0.2 1 23861 1013 60 22495 0.2 1 21627 868 61 22796 0.2 1 21842 954 62 22603 0.2 1 21716 887 63 21315 0.2 1 20505 810 64 20278 0.2 1 19541 737 65 19205 0.2 1 18475 730 66 17795 0.2 1 17121 674 67 16876 0.2 1 16254 622 68 15527 0.2 1 14953 574 69 15922 0.2 1 15333 589 70 14898 0.2 1 14350 548 71 14814 0.2 1 14196 618 72 16447 0.2 1 15567 880 73 25417 0.2 1 23340 2077 74 86842 0.2 1 83391 3451 75 93055 0.2 1 89883 3172 76 64013 0.2 1 61697 2316 77 44496 0.2 1 42925 1571 78 28109 0.2 1 27123 986 79 15874 0.2 1 15267 607 80 10003 0.2 1 9624 379 81 5862 0.2 1 5619 243 82 3872 0.2 1 3694 178 83 2855 0.2 1 2723 132 84 2340 0.2 1 2242 98 85 1877 0.2 1 1791 86 86 1664 0.2 1 1576 88 87 1397 0.2 1 1331 66 88 1236 0.2 1 1189 47 89 1174 0.2 1 1116 58 90 1443 0.2 1 1378 65 91 2043 0.2 1 1949 94 92 3208 0.2 1 3060 148 93 7472 0.2 1 7155 317 94 22822 0.2 1 21875 947 95 38871 0.2 1 37276 1595 96 16979 0.2 1 16200 779 97 11521 0.2 1 10953 568 98 4779 0.2 1 4517 262 99 4734 0.2 1 4477 257 100 5104 0.2 1 4808 296 101 9425 0.2 1 8621 804 RUN STATISTICS FOR INPUT FILE: EPI-226_S34_L004_R1_001.fastq.gz ============================================= 11630377 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1152822 (9.9%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 6473641 (55.7%) RRBS reads trimmed by 2 bp at the start when read started with CAA (98443) or CGA (71020) in total: 169463 (1.5%)