SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-143_S37_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-143_S37_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 420.27 s (20 us/read; 3.04 M reads/minute). === Summary === Total reads processed: 21,282,370 Reads with adapters: 13,027,408 (61.2%) Reads written (passing filters): 21,282,370 (100.0%) Total basepairs processed: 2,124,411,278 bp Total written (filtered): 1,962,976,192 bp (92.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13027408 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.9% C: 24.5% G: 7.0% T: 28.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7570183 5320592.5 0 7570183 2 169088 1330148.1 0 169088 3 155339 332537.0 0 155339 4 116704 83134.3 0 116704 5 119849 20783.6 0 119849 6 119840 5195.9 0 119840 7 112621 1299.0 0 112621 8 134585 324.7 0 134585 9 109153 81.2 0 108674 479 10 110332 20.3 1 105546 4786 11 105439 5.1 1 99378 6061 12 106573 1.3 1 100821 5752 13 101561 0.3 1 95954 5607 14 114307 0.3 1 107992 6315 15 100728 0.3 1 95051 5677 16 104005 0.3 1 98208 5797 17 112778 0.3 1 106855 5923 18 92790 0.3 1 87610 5180 19 101104 0.3 1 95759 5345 20 95792 0.3 1 90285 5507 21 102674 0.3 1 96230 6444 22 104353 0.3 1 98196 6157 23 99596 0.3 1 94004 5592 24 111383 0.3 1 104901 6482 25 89523 0.3 1 84463 5060 26 94054 0.3 1 87855 6199 27 98439 0.3 1 91256 7183 28 102326 0.3 1 96812 5514 29 95156 0.3 1 88384 6772 30 109808 0.3 1 104292 5516 31 86563 0.3 1 81193 5370 32 95967 0.3 1 91467 4500 33 97689 0.3 1 92035 5654 34 99871 0.3 1 93400 6471 35 96197 0.3 1 91983 4214 36 83486 0.3 1 78334 5152 37 80668 0.3 1 76061 4607 38 74494 0.3 1 70286 4208 39 75544 0.3 1 70933 4611 40 76512 0.3 1 71951 4561 41 75425 0.3 1 71691 3734 42 82038 0.3 1 78530 3508 43 60020 0.3 1 56516 3504 44 69220 0.3 1 65717 3503 45 108829 0.3 1 104875 3954 46 57524 0.3 1 54537 2987 47 38125 0.3 1 35504 2621 48 67781 0.3 1 65046 2735 49 36354 0.3 1 34356 1998 50 41493 0.3 1 39096 2397 51 68737 0.3 1 66286 2451 52 30652 0.3 1 28801 1851 53 34592 0.3 1 32422 2170 54 29373 0.3 1 27616 1757 55 40300 0.3 1 38255 2045 56 38663 0.3 1 36339 2324 57 34333 0.3 1 32503 1830 58 33274 0.3 1 31520 1754 59 31764 0.3 1 29862 1902 60 32023 0.3 1 30018 2005 61 32374 0.3 1 30500 1874 62 33876 0.3 1 31841 2035 63 35211 0.3 1 33134 2077 64 34577 0.3 1 32504 2073 65 35845 0.3 1 33820 2025 66 36419 0.3 1 34395 2024 67 40180 0.3 1 37727 2453 68 68045 0.3 1 65759 2286 69 20752 0.3 1 19500 1252 70 10678 0.3 1 9809 869 71 7230 0.3 1 6531 699 72 5929 0.3 1 5328 601 73 4906 0.3 1 4400 506 74 4110 0.3 1 3718 392 75 3571 0.3 1 3187 384 76 3029 0.3 1 2764 265 77 2428 0.3 1 2192 236 78 2108 0.3 1 1886 222 79 1610 0.3 1 1457 153 80 1131 0.3 1 1012 119 81 888 0.3 1 799 89 82 621 0.3 1 549 72 83 438 0.3 1 395 43 84 255 0.3 1 228 27 85 134 0.3 1 122 12 86 111 0.3 1 94 17 87 57 0.3 1 52 5 88 49 0.3 1 43 6 89 49 0.3 1 33 16 90 56 0.3 1 45 11 91 107 0.3 1 83 24 92 167 0.3 1 131 36 93 222 0.3 1 185 37 94 471 0.3 1 381 90 95 646 0.3 1 560 86 96 613 0.3 1 545 68 97 317 0.3 1 282 35 98 111 0.3 1 96 15 99 54 0.3 1 44 10 100 87 0.3 1 66 21 101 352 0.3 1 274 78 RUN STATISTICS FOR INPUT FILE: EPI-143_S37_L005_R2_001.fastq.gz ============================================= 21282370 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2883335 (13.5%) 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: 21282370 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 121498 (0.57%)