SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-113_S30_L005_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-113_S30_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 513.43 s (19 us/read; 3.09 M reads/minute). === Summary === Total reads processed: 26,402,719 Reads with adapters: 16,194,524 (61.3%) Reads written (passing filters): 26,402,719 (100.0%) Total basepairs processed: 2,644,650,289 bp Total written (filtered): 2,439,521,152 bp (92.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16194524 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.3% C: 25.0% G: 7.3% T: 28.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9284506 6600679.8 0 9284506 2 203723 1650169.9 0 203723 3 196913 412542.5 0 196913 4 152936 103135.6 0 152936 5 154306 25783.9 0 154306 6 157559 6446.0 0 157559 7 152903 1611.5 0 152903 8 201089 402.9 0 201089 9 141877 100.7 0 141269 608 10 144403 25.2 1 139215 5188 11 136055 6.3 1 129529 6526 12 138006 1.6 1 131634 6372 13 130562 0.4 1 124539 6023 14 147233 0.4 1 140590 6643 15 133290 0.4 1 127075 6215 16 132239 0.4 1 126176 6063 17 141140 0.4 1 134961 6179 18 116661 0.4 1 111193 5468 19 127587 0.4 1 121919 5668 20 123418 0.4 1 117560 5858 21 129601 0.4 1 122845 6756 22 131627 0.4 1 125290 6337 23 121053 0.4 1 115303 5750 24 131866 0.4 1 125698 6168 25 109296 0.4 1 104120 5176 26 115734 0.4 1 109430 6304 27 119397 0.4 1 112077 7320 28 122549 0.4 1 116974 5575 29 116204 0.4 1 109498 6706 30 129810 0.4 1 124421 5389 31 103387 0.4 1 98118 5269 32 111348 0.4 1 106820 4528 33 113279 0.4 1 107624 5655 34 117651 0.4 1 111307 6344 35 112260 0.4 1 108079 4181 36 100584 0.4 1 95506 5078 37 96108 0.4 1 91654 4454 38 89462 0.4 1 85119 4343 39 90793 0.4 1 86230 4563 40 90680 0.4 1 86126 4554 41 88457 0.4 1 84645 3812 42 95588 0.4 1 92056 3532 43 72358 0.4 1 68807 3551 44 82211 0.4 1 78580 3631 45 127700 0.4 1 123788 3912 46 71689 0.4 1 68670 3019 47 47206 0.4 1 44510 2696 48 82688 0.4 1 79908 2780 49 45076 0.4 1 43074 2002 50 51977 0.4 1 49445 2532 51 84905 0.4 1 82334 2571 52 39360 0.4 1 37339 2021 53 44703 0.4 1 42442 2261 54 38800 0.4 1 36864 1936 55 52774 0.4 1 50527 2247 56 51002 0.4 1 48550 2452 57 46946 0.4 1 44890 2056 58 45258 0.4 1 43267 1991 59 42147 0.4 1 40119 2028 60 42832 0.4 1 40777 2055 61 43849 0.4 1 41626 2223 62 48659 0.4 1 46409 2250 63 53530 0.4 1 51126 2404 64 54792 0.4 1 52278 2514 65 54622 0.4 1 52241 2381 66 54444 0.4 1 52083 2361 67 56517 0.4 1 53786 2731 68 102816 0.4 1 100375 2441 69 32244 0.4 1 30905 1339 70 15282 0.4 1 14432 850 71 10129 0.4 1 9441 688 72 8152 0.4 1 7565 587 73 6705 0.4 1 6252 453 74 5701 0.4 1 5284 417 75 4969 0.4 1 4605 364 76 4107 0.4 1 3821 286 77 3541 0.4 1 3278 263 78 2856 0.4 1 2630 226 79 2270 0.4 1 2104 166 80 1566 0.4 1 1460 106 81 1166 0.4 1 1089 77 82 827 0.4 1 760 67 83 481 0.4 1 436 45 84 322 0.4 1 302 20 85 180 0.4 1 169 11 86 102 0.4 1 96 6 87 71 0.4 1 67 4 88 43 0.4 1 37 6 89 42 0.4 1 38 4 90 54 0.4 1 48 6 91 66 0.4 1 58 8 92 89 0.4 1 78 11 93 131 0.4 1 114 17 94 239 0.4 1 210 29 95 394 0.4 1 345 49 96 335 0.4 1 301 34 97 180 0.4 1 163 17 98 57 0.4 1 52 5 99 33 0.4 1 30 3 100 57 0.4 1 54 3 101 132 0.4 1 119 13 RUN STATISTICS FOR INPUT FILE: EPI-113_S30_L005_R2_001.fastq.gz ============================================= 26402719 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3059179 (11.6%) 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: 26402719 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 100528 (0.38%)