SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-220_S32_L004_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 All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_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/20180516_geoduck_trimgalore_rrbs/EPI-220_S32_L004_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 340.32 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 17,825,268 Reads with adapters: 12,471,618 (70.0%) Reads written (passing filters): 17,825,268 (100.0%) Total basepairs processed: 1,747,315,749 bp Total written (filtered): 1,406,236,646 bp (80.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12471618 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.6% C: 21.3% G: 14.7% T: 30.5% none/other: 1.0% Overview of removed sequences length count expect max.err error counts 1 4621914 4456317.0 0 4621914 2 166859 1114079.2 0 166859 3 126817 278519.8 0 126817 4 101954 69630.0 0 101954 5 98852 17407.5 0 98852 6 102602 4351.9 0 102602 7 101917 1088.0 0 101917 8 113398 272.0 0 113398 9 101405 68.0 0 100930 475 10 107071 17.0 1 104274 2797 11 93666 4.2 1 90872 2794 12 98440 1.1 1 95258 3182 13 95236 0.3 1 92401 2835 14 104322 0.3 1 100838 3484 15 99978 0.3 1 96856 3122 16 100311 0.3 1 97344 2967 17 104120 0.3 1 100841 3279 18 95020 0.3 1 92203 2817 19 100566 0.3 1 97416 3150 20 98715 0.3 1 95715 3000 21 98392 0.3 1 95280 3112 22 103928 0.3 1 100585 3343 23 98308 0.3 1 95099 3209 24 105191 0.3 1 101624 3567 25 94681 0.3 1 91784 2897 26 96304 0.3 1 92877 3427 27 95287 0.3 1 91576 3711 28 101502 0.3 1 98245 3257 29 96833 0.3 1 93391 3442 30 105724 0.3 1 102439 3285 31 91080 0.3 1 87941 3139 32 97946 0.3 1 95106 2840 33 100904 0.3 1 97431 3473 34 99312 0.3 1 95607 3705 35 99341 0.3 1 96475 2866 36 94648 0.3 1 91439 3209 37 95146 0.3 1 92073 3073 38 86863 0.3 1 84001 2862 39 88850 0.3 1 85837 3013 40 87359 0.3 1 84304 3055 41 90386 0.3 1 87409 2977 42 89289 0.3 1 86603 2686 43 78958 0.3 1 76301 2657 44 83193 0.3 1 80331 2862 45 101831 0.3 1 98739 3092 46 78777 0.3 1 76365 2412 47 61033 0.3 1 58970 2063 48 83366 0.3 1 80880 2486 49 63416 0.3 1 61416 2000 50 63344 0.3 1 61221 2123 51 86577 0.3 1 84242 2335 52 57186 0.3 1 55478 1708 53 57738 0.3 1 56077 1661 54 50529 0.3 1 48998 1531 55 61235 0.3 1 59485 1750 56 57061 0.3 1 55434 1627 57 53649 0.3 1 51993 1656 58 52604 0.3 1 50964 1640 59 48946 0.3 1 47422 1524 60 46906 0.3 1 45404 1502 61 46488 0.3 1 45002 1486 62 46769 0.3 1 45211 1558 63 47286 0.3 1 45619 1667 64 47458 0.3 1 45667 1791 65 51140 0.3 1 48996 2144 66 59239 0.3 1 56378 2861 67 112519 0.3 1 100178 12341 68 735846 0.3 1 715188 20658 69 331317 0.3 1 319846 11471 70 182639 0.3 1 176064 6575 71 89799 0.3 1 85994 3805 72 53587 0.3 1 51200 2387 73 32474 0.3 1 30820 1654 74 23284 0.3 1 22058 1226 75 17810 0.3 1 16759 1051 76 14412 0.3 1 13531 881 77 12438 0.3 1 11598 840 78 10676 0.3 1 9968 708 79 9448 0.3 1 8776 672 80 8301 0.3 1 7721 580 81 7185 0.3 1 6639 546 82 6422 0.3 1 5940 482 83 5763 0.3 1 5305 458 84 5044 0.3 1 4624 420 85 4780 0.3 1 4357 423 86 4586 0.3 1 4140 446 87 4544 0.3 1 4122 422 88 4988 0.3 1 4510 478 89 5756 0.3 1 5204 552 90 7077 0.3 1 6403 674 91 9745 0.3 1 8821 924 92 14845 0.3 1 13508 1337 93 33296 0.3 1 30468 2828 94 103822 0.3 1 96245 7577 95 181013 0.3 1 168722 12291 96 77793 0.3 1 72506 5287 97 47585 0.3 1 44365 3220 98 17320 0.3 1 16119 1201 99 16595 0.3 1 15430 1165 100 15501 0.3 1 14327 1174 101 28242 0.3 1 25855 2387 RUN STATISTICS FOR INPUT FILE: EPI-220_S32_L004_R2_001.fastq.gz ============================================= 17825268 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3035562 (17.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 17825268 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2154676 (12.09%)