SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-120_S32_L005_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-120_S32_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 462.20 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 24,230,515 Reads with adapters: 12,658,640 (52.2%) Reads written (passing filters): 24,230,515 (100.0%) Total basepairs processed: 2,437,190,550 bp Total written (filtered): 2,256,141,500 bp (92.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12658640 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.3% C: 6.5% G: 23.3% T: 42.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5215044 6057628.8 0 5215044 2 1185935 1514407.2 0 1185935 3 460477 378601.8 0 460477 4 296960 94650.4 0 296960 5 133281 23662.6 0 133281 6 138907 5915.7 0 138907 7 128511 1478.9 0 128511 8 177430 369.7 0 177430 9 124932 92.4 0 123911 1021 10 116833 23.1 1 111658 5175 11 121640 5.8 1 115370 6270 12 114792 1.4 1 109069 5723 13 106189 0.4 1 101127 5062 14 122087 0.4 1 115054 7033 15 111513 0.4 1 105783 5730 16 125555 0.4 1 117828 7727 17 114696 0.4 1 108704 5992 18 107816 0.4 1 102380 5436 19 113462 0.4 1 106741 6721 20 103254 0.4 1 98238 5016 21 113071 0.4 1 106544 6527 22 105599 0.4 1 100469 5130 23 103483 0.4 1 97997 5486 24 107198 0.4 1 100795 6403 25 96683 0.4 1 91913 4770 26 110944 0.4 1 104410 6534 27 95948 0.4 1 91120 4828 28 90299 0.4 1 85864 4435 29 99521 0.4 1 94254 5267 30 90050 0.4 1 85805 4245 31 103444 0.4 1 97313 6131 32 87356 0.4 1 83081 4275 33 93863 0.4 1 88815 5048 34 89063 0.4 1 84550 4513 35 85201 0.4 1 81038 4163 36 84371 0.4 1 80312 4059 37 84859 0.4 1 80808 4051 38 82966 0.4 1 78897 4069 39 78946 0.4 1 74844 4102 40 83184 0.4 1 78895 4289 41 111555 0.4 1 106865 4690 42 63250 0.4 1 60484 2766 43 46411 0.4 1 44104 2307 44 69225 0.4 1 65943 3282 45 66749 0.4 1 63572 3177 46 64450 0.4 1 61513 2937 47 70139 0.4 1 66753 3386 48 65721 0.4 1 62383 3338 49 64466 0.4 1 61226 3240 50 57318 0.4 1 54609 2709 51 55150 0.4 1 52692 2458 52 52411 0.4 1 50029 2382 53 50902 0.4 1 48752 2150 54 50526 0.4 1 48234 2292 55 52702 0.4 1 50474 2228 56 48694 0.4 1 46581 2113 57 46977 0.4 1 45095 1882 58 44308 0.4 1 42724 1584 59 42824 0.4 1 41163 1661 60 39196 0.4 1 37749 1447 61 39715 0.4 1 38354 1361 62 40924 0.4 1 39422 1502 63 38937 0.4 1 37492 1445 64 38718 0.4 1 37370 1348 65 35814 0.4 1 34571 1243 66 33718 0.4 1 32521 1197 67 31361 0.4 1 30228 1133 68 28395 0.4 1 27324 1071 69 28452 0.4 1 27377 1075 70 26168 0.4 1 25172 996 71 25293 0.4 1 24396 897 72 24159 0.4 1 23197 962 73 23897 0.4 1 22820 1077 74 35524 0.4 1 34649 875 75 14487 0.4 1 14040 447 76 7396 0.4 1 7122 274 77 4762 0.4 1 4581 181 78 3111 0.4 1 2995 116 79 2139 0.4 1 2051 88 80 1458 0.4 1 1386 72 81 1002 0.4 1 959 43 82 650 0.4 1 636 14 83 468 0.4 1 444 24 84 319 0.4 1 304 15 85 180 0.4 1 172 8 86 112 0.4 1 108 4 87 90 0.4 1 84 6 88 66 0.4 1 58 8 89 53 0.4 1 51 2 90 78 0.4 1 72 6 91 99 0.4 1 94 5 92 164 0.4 1 148 16 93 239 0.4 1 221 18 94 430 0.4 1 395 35 95 626 0.4 1 580 46 96 531 0.4 1 482 49 97 306 0.4 1 285 21 98 99 0.4 1 85 14 99 48 0.4 1 44 4 100 82 0.4 1 64 18 101 233 0.4 1 164 69 RUN STATISTICS FOR INPUT FILE: EPI-120_S32_L005_R1_001.fastq.gz ============================================= 24230515 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2582413 (10.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 12657281 (52.2%)