SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-229_S36_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-229_S36_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 382.26 s (18 us/read; 3.28 M reads/minute). === Summary === Total reads processed: 20,924,617 Reads with adapters: 13,199,077 (63.1%) Reads written (passing filters): 20,924,617 (100.0%) Total basepairs processed: 2,094,290,523 bp Total written (filtered): 1,746,269,414 bp (83.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13199077 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 22.3% C: 12.8% G: 27.0% T: 37.2% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 3344770 5231154.2 0 3344770 2 836961 1307788.6 0 836961 3 331696 326947.1 0 331696 4 226780 81736.8 0 226780 5 129298 20434.2 0 129298 6 126121 5108.5 0 126121 7 117341 1277.1 0 117341 8 131935 319.3 0 131935 9 134277 79.8 0 132895 1382 10 127465 20.0 1 122689 4776 11 128063 5.0 1 122882 5181 12 120478 1.2 1 115720 4758 13 122064 0.3 1 117017 5047 14 131182 0.3 1 125156 6026 15 129968 0.3 1 124277 5691 16 136769 0.3 1 130338 6431 17 133125 0.3 1 126995 6130 18 125508 0.3 1 120365 5143 19 128972 0.3 1 122877 6095 20 129498 0.3 1 124184 5314 21 136412 0.3 1 129882 6530 22 130849 0.3 1 125453 5396 23 127277 0.3 1 121722 5555 24 127843 0.3 1 121545 6298 25 126134 0.3 1 120523 5611 26 133030 0.3 1 126420 6610 27 126421 0.3 1 120711 5710 28 123700 0.3 1 118296 5404 29 134214 0.3 1 127942 6272 30 125023 0.3 1 119911 5112 31 134541 0.3 1 127779 6762 32 128000 0.3 1 122507 5493 33 131320 0.3 1 125382 5938 34 132898 0.3 1 126532 6366 35 125216 0.3 1 119790 5426 36 119404 0.3 1 114378 5026 37 129439 0.3 1 123947 5492 38 125333 0.3 1 119871 5462 39 122345 0.3 1 116840 5505 40 128927 0.3 1 122346 6581 41 173412 0.3 1 166232 7180 42 105830 0.3 1 101492 4338 43 81210 0.3 1 77330 3880 44 109177 0.3 1 104508 4669 45 111479 0.3 1 106498 4981 46 105771 0.3 1 101243 4528 47 111425 0.3 1 106386 5039 48 106764 0.3 1 101835 4929 49 109569 0.3 1 104541 5028 50 98673 0.3 1 94600 4073 51 99078 0.3 1 94747 4331 52 98087 0.3 1 93733 4354 53 91092 0.3 1 87528 3564 54 89184 0.3 1 85390 3794 55 95086 0.3 1 91180 3906 56 87537 0.3 1 84069 3468 57 81516 0.3 1 78255 3261 58 83397 0.3 1 80140 3257 59 79537 0.3 1 76269 3268 60 70507 0.3 1 67696 2811 61 74471 0.3 1 71530 2941 62 73952 0.3 1 71132 2820 63 67800 0.3 1 65264 2536 64 65424 0.3 1 63103 2321 65 61732 0.3 1 59465 2267 66 56848 0.3 1 54691 2157 67 54674 0.3 1 52628 2046 68 51074 0.3 1 49103 1971 69 52040 0.3 1 50176 1864 70 49029 0.3 1 47174 1855 71 49769 0.3 1 47809 1960 72 54450 0.3 1 52072 2378 73 72918 0.3 1 67610 5308 74 218320 0.3 1 209983 8337 75 223198 0.3 1 215966 7232 76 132920 0.3 1 128288 4632 77 86787 0.3 1 83762 3025 78 52565 0.3 1 50670 1895 79 29587 0.3 1 28476 1111 80 18814 0.3 1 18099 715 81 11612 0.3 1 11178 434 82 7759 0.3 1 7436 323 83 5758 0.3 1 5477 281 84 4712 0.3 1 4494 218 85 3732 0.3 1 3563 169 86 3139 0.3 1 3002 137 87 2698 0.3 1 2575 123 88 2435 0.3 1 2285 150 89 2273 0.3 1 2160 113 90 2847 0.3 1 2705 142 91 3949 0.3 1 3749 200 92 6327 0.3 1 6015 312 93 14844 0.3 1 14189 655 94 44473 0.3 1 42656 1817 95 78220 0.3 1 75102 3118 96 33418 0.3 1 31968 1450 97 23445 0.3 1 22275 1170 98 9920 0.3 1 9370 550 99 10137 0.3 1 9624 513 100 11073 0.3 1 10426 647 101 21006 0.3 1 19182 1824 RUN STATISTICS FOR INPUT FILE: EPI-229_S36_L004_R1_001.fastq.gz ============================================= 20924617 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2262392 (10.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 12906327 (61.7%) RRBS reads trimmed by 2 bp at the start when read started with CAA (157665) or CGA (119194) in total: 276859 (1.3%)