SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-182_S17_L003_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-182_S17_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 613.25 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 32,071,199 Reads with adapters: 17,601,776 (54.9%) Reads written (passing filters): 32,071,199 (100.0%) Total basepairs processed: 3,221,874,465 bp Total written (filtered): 2,909,186,838 bp (90.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17601776 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.2% C: 9.3% G: 24.9% T: 40.4% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 6124334 8017799.8 0 6124334 2 1458709 2004449.9 0 1458709 3 580137 501112.5 0 580137 4 407512 125278.1 0 407512 5 211933 31319.5 0 211933 6 213707 7829.9 0 213707 7 197236 1957.5 0 197236 8 238888 489.4 0 238888 9 201191 122.3 0 199500 1691 10 188835 30.6 1 181071 7764 11 189998 7.6 1 181218 8780 12 181416 1.9 1 173285 8131 13 173758 0.5 1 165913 7845 14 191895 0.5 1 178377 13518 15 180080 0.5 1 167088 12992 16 191280 0.5 1 176943 14337 17 183121 0.5 1 169456 13665 18 167999 0.5 1 156503 11496 19 183307 0.5 1 167680 15627 20 166686 0.5 1 154919 11767 21 186499 0.5 1 171254 15245 22 173950 0.5 1 161531 12419 23 161215 0.5 1 149075 12140 24 168824 0.5 1 155480 13344 25 158190 0.5 1 146370 11820 26 168858 0.5 1 154983 13875 27 157026 0.5 1 147882 9144 28 146903 0.5 1 139175 7728 29 159599 0.5 1 150412 9187 30 148998 0.5 1 141473 7525 31 159428 0.5 1 149803 9625 32 146015 0.5 1 138554 7461 33 150031 0.5 1 142162 7869 34 141191 0.5 1 133789 7402 35 146763 0.5 1 138264 8499 36 133975 0.5 1 127520 6455 37 141493 0.5 1 134164 7329 38 131930 0.5 1 125301 6629 39 122547 0.5 1 117052 5495 40 136625 0.5 1 129507 7118 41 179023 0.5 1 170983 8040 42 115575 0.5 1 110822 4753 43 54418 0.5 1 51317 3101 44 107466 0.5 1 102553 4913 45 103314 0.5 1 98555 4759 46 99834 0.5 1 95438 4396 47 105310 0.5 1 100276 5034 48 95966 0.5 1 91467 4499 49 99310 0.5 1 94733 4577 50 88017 0.5 1 84232 3785 51 86574 0.5 1 82712 3862 52 82604 0.5 1 79050 3554 53 78220 0.5 1 75197 3023 54 75947 0.5 1 72630 3317 55 78285 0.5 1 75091 3194 56 72293 0.5 1 69336 2957 57 66858 0.5 1 64086 2772 58 66260 0.5 1 63637 2623 59 62808 0.5 1 60284 2524 60 57398 0.5 1 55205 2193 61 58100 0.5 1 55951 2149 62 59612 0.5 1 57474 2138 63 53289 0.5 1 51302 1987 64 51538 0.5 1 49748 1790 65 47599 0.5 1 45960 1639 66 44289 0.5 1 42689 1600 67 42047 0.5 1 40594 1453 68 38200 0.5 1 36814 1386 69 39728 0.5 1 38342 1386 70 36347 0.5 1 34921 1426 71 35844 0.5 1 34402 1442 72 37989 0.5 1 36152 1837 73 60271 0.5 1 56373 3898 74 169559 0.5 1 164217 5342 75 104986 0.5 1 101449 3537 76 55692 0.5 1 53671 2021 77 31389 0.5 1 30263 1126 78 18842 0.5 1 18076 766 79 10921 0.5 1 10499 422 80 7467 0.5 1 7164 303 81 4663 0.5 1 4448 215 82 3249 0.5 1 3097 152 83 2482 0.5 1 2367 115 84 1887 0.5 1 1803 84 85 1588 0.5 1 1516 72 86 1404 0.5 1 1333 71 87 1225 0.5 1 1158 67 88 1080 0.5 1 1013 67 89 1063 0.5 1 1008 55 90 1414 0.5 1 1330 84 91 1998 0.5 1 1880 118 92 3298 0.5 1 3153 145 93 8391 0.5 1 7993 398 94 24958 0.5 1 23871 1087 95 42052 0.5 1 40243 1809 96 17823 0.5 1 16958 865 97 10756 0.5 1 10166 590 98 4431 0.5 1 4186 245 99 4326 0.5 1 4107 219 100 4458 0.5 1 4182 276 101 7959 0.5 1 7261 698 RUN STATISTICS FOR INPUT FILE: EPI-182_S17_L003_R1_001.fastq.gz ============================================= 32071199 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3339897 (10.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 17552713 (54.7%)