SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-205_S26_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 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-205_S26_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 462.25 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 26,556,310 Reads with adapters: 21,157,951 (79.7%) Reads written (passing filters): 26,556,310 (100.0%) Total basepairs processed: 2,541,028,762 bp Total written (filtered): 1,406,384,870 bp (55.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21157951 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 17.7% C: 33.4% G: 21.0% T: 25.7% none/other: 2.3% Overview of removed sequences length count expect max.err error counts 1 2329226 6639077.5 0 2329226 2 582334 1659769.4 0 582334 3 245704 414942.3 0 245704 4 170613 103735.6 0 170613 5 105071 25933.9 0 105071 6 99765 6483.5 0 99765 7 93143 1620.9 0 93143 8 106146 405.2 0 106146 9 107479 101.3 0 106583 896 10 102320 25.3 1 98638 3682 11 103609 6.3 1 99268 4341 12 97090 1.6 1 93371 3719 13 98412 0.4 1 94340 4072 14 108648 0.4 1 103594 5054 15 107673 0.4 1 102981 4692 16 112874 0.4 1 107377 5497 17 110262 0.4 1 105053 5209 18 102499 0.4 1 98478 4021 19 109005 0.4 1 103559 5446 20 107747 0.4 1 103285 4462 21 117498 0.4 1 111762 5736 22 112197 0.4 1 107596 4601 23 107244 0.4 1 102595 4649 24 109761 0.4 1 104509 5252 25 109228 0.4 1 104507 4721 26 114125 0.4 1 108499 5626 27 113279 0.4 1 108357 4922 28 109396 0.4 1 104638 4758 29 118978 0.4 1 113508 5470 30 113699 0.4 1 108985 4714 31 120309 0.4 1 114593 5716 32 116116 0.4 1 111320 4796 33 128749 0.4 1 122354 6395 34 115724 0.4 1 110552 5172 35 118592 0.4 1 112894 5698 36 120388 0.4 1 114668 5720 37 122529 0.4 1 117248 5281 38 117783 0.4 1 112350 5433 39 124717 0.4 1 118768 5949 40 126513 0.4 1 120298 6215 41 180856 0.4 1 173440 7416 42 114095 0.4 1 109834 4261 43 56446 0.4 1 53592 2854 44 109904 0.4 1 105147 4757 45 115290 0.4 1 110312 4978 46 109450 0.4 1 104957 4493 47 118493 0.4 1 113191 5302 48 116006 0.4 1 110603 5403 49 125480 0.4 1 119768 5712 50 110010 0.4 1 105397 4613 51 114871 0.4 1 109949 4922 52 116309 0.4 1 111443 4866 53 106713 0.4 1 102586 4127 54 109689 0.4 1 105061 4628 55 119096 0.4 1 114290 4806 56 113261 0.4 1 108743 4518 57 108160 0.4 1 103902 4258 58 112971 0.4 1 108604 4367 59 110075 0.4 1 105726 4349 60 100793 0.4 1 96897 3896 61 110308 0.4 1 105971 4337 62 113382 0.4 1 109217 4165 63 107136 0.4 1 103179 3957 64 103583 0.4 1 99929 3654 65 101262 0.4 1 97642 3620 66 97619 0.4 1 94026 3593 67 97977 0.4 1 94515 3462 68 92277 0.4 1 88858 3419 69 99905 0.4 1 96222 3683 70 98910 0.4 1 95171 3739 71 111670 0.4 1 107157 4513 72 148118 0.4 1 141053 7065 73 292531 0.4 1 264987 27544 74 1723655 0.4 1 1666842 56813 75 1702184 0.4 1 1648580 53604 76 1232488 0.4 1 1192458 40030 77 872626 0.4 1 844141 28485 78 566266 0.4 1 548269 17997 79 328585 0.4 1 317660 10925 80 208407 0.4 1 201569 6838 81 122439 0.4 1 118197 4242 82 79399 0.4 1 76469 2930 83 58160 0.4 1 55872 2288 84 49549 0.4 1 47694 1855 85 41731 0.4 1 40084 1647 86 37141 0.4 1 35685 1456 87 32074 0.4 1 30787 1287 88 28425 0.4 1 27145 1280 89 28857 0.4 1 27694 1163 90 36569 0.4 1 35069 1500 91 53109 0.4 1 50988 2121 92 84110 0.4 1 80831 3279 93 198243 0.4 1 190499 7744 94 601021 0.4 1 578712 22309 95 955372 0.4 1 920442 34930 96 387732 0.4 1 372209 15523 97 213780 0.4 1 204545 9235 98 79272 0.4 1 75753 3519 99 69348 0.4 1 66270 3078 100 67686 0.4 1 64465 3221 101 120632 0.4 1 113172 7460 RUN STATISTICS FOR INPUT FILE: EPI-205_S26_L004_R1_001.fastq.gz ============================================= 26556310 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 9080776 (34.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 20476080 (77.1%)