SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-145_S38_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-145_S38_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 500.39 s (20 us/read; 3.06 M reads/minute). === Summary === Total reads processed: 25,512,585 Reads with adapters: 15,613,126 (61.2%) Reads written (passing filters): 25,512,585 (100.0%) Total basepairs processed: 2,553,685,509 bp Total written (filtered): 2,356,058,789 bp (92.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15613126 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.3% C: 25.0% G: 7.1% T: 28.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 9077013 6378146.2 0 9077013 2 191849 1594536.6 0 191849 3 188524 398634.1 0 188524 4 143336 99658.5 0 143336 5 142647 24914.6 0 142647 6 146034 6228.7 0 146034 7 139792 1557.2 0 139792 8 178001 389.3 0 178001 9 135673 97.3 0 135104 569 10 136613 24.3 1 131617 4996 11 128613 6.1 1 122097 6516 12 128881 1.5 1 122858 6023 13 122163 0.4 1 116317 5846 14 136318 0.4 1 129872 6446 15 124861 0.4 1 118909 5952 16 124856 0.4 1 118914 5942 17 131964 0.4 1 125918 6046 18 110142 0.4 1 104971 5171 19 119375 0.4 1 114042 5333 20 115744 0.4 1 109986 5758 21 121855 0.4 1 115367 6488 22 123970 0.4 1 117835 6135 23 114419 0.4 1 108954 5465 24 122162 0.4 1 116393 5769 25 103220 0.4 1 98078 5142 26 109614 0.4 1 103443 6171 27 114021 0.4 1 106971 7050 28 114371 0.4 1 109126 5245 29 111847 0.4 1 105127 6720 30 121246 0.4 1 116039 5207 31 98509 0.4 1 93194 5315 32 103407 0.4 1 99169 4238 33 107769 0.4 1 102375 5394 34 113829 0.4 1 107389 6440 35 101643 0.4 1 97779 3864 36 96504 0.4 1 91368 5136 37 91281 0.4 1 86804 4477 38 83854 0.4 1 79689 4165 39 85543 0.4 1 81147 4396 40 85429 0.4 1 80999 4430 41 83091 0.4 1 79482 3609 42 87925 0.4 1 84702 3223 43 69788 0.4 1 66229 3559 44 77087 0.4 1 73629 3458 45 115625 0.4 1 111938 3687 46 68373 0.4 1 65332 3041 47 46242 0.4 1 43635 2607 48 77224 0.4 1 74590 2634 49 43134 0.4 1 41113 2021 50 49609 0.4 1 47114 2495 51 77797 0.4 1 75369 2428 52 37403 0.4 1 35614 1789 53 42599 0.4 1 40472 2127 54 36131 0.4 1 34264 1867 55 48945 0.4 1 46830 2115 56 47254 0.4 1 44959 2295 57 42774 0.4 1 40818 1956 58 41425 0.4 1 39658 1767 59 38922 0.4 1 36999 1923 60 39145 0.4 1 37236 1909 61 40063 0.4 1 38092 1971 62 43002 0.4 1 40884 2118 63 46639 0.4 1 44376 2263 64 47439 0.4 1 45216 2223 65 48155 0.4 1 45925 2230 66 49461 0.4 1 47212 2249 67 56049 0.4 1 53086 2963 68 119070 0.4 1 115969 3101 69 39067 0.4 1 37462 1605 70 19519 0.4 1 18466 1053 71 11722 0.4 1 11006 716 72 9271 0.4 1 8616 655 73 7363 0.4 1 6876 487 74 6135 0.4 1 5668 467 75 5168 0.4 1 4792 376 76 4305 0.4 1 4012 293 77 3649 0.4 1 3390 259 78 2978 0.4 1 2768 210 79 2470 0.4 1 2295 175 80 1809 0.4 1 1691 118 81 1380 0.4 1 1281 99 82 1043 0.4 1 968 75 83 721 0.4 1 663 58 84 549 0.4 1 491 58 85 401 0.4 1 362 39 86 315 0.4 1 281 34 87 296 0.4 1 253 43 88 304 0.4 1 264 40 89 339 0.4 1 291 48 90 379 0.4 1 320 59 91 540 0.4 1 499 41 92 974 0.4 1 889 85 93 2147 0.4 1 1910 237 94 5784 0.4 1 5196 588 95 9468 0.4 1 8607 861 96 3934 0.4 1 3588 346 97 1691 0.4 1 1544 147 98 549 0.4 1 503 46 99 438 0.4 1 403 35 100 398 0.4 1 355 43 101 757 0.4 1 670 87 RUN STATISTICS FOR INPUT FILE: EPI-145_S38_L005_R2_001.fastq.gz ============================================= 25512585 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3020088 (11.8%) 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: 25512585 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 198072 (0.78%)