SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-44_S41_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-44_S41_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 656.53 s (17 us/read; 3.56 M reads/minute). === Summary === Total reads processed: 38,920,722 Reads with adapters: 33,753,969 (86.7%) Reads written (passing filters): 38,920,722 (100.0%) Total basepairs processed: 3,561,410,805 bp Total written (filtered): 1,308,776,257 bp (36.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 33753969 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 15.6% C: 49.5% G: 11.2% T: 19.2% none/other: 4.4% Overview of removed sequences length count expect max.err error counts 1 2342573 9730180.5 0 2342573 2 554938 2432545.1 0 554938 3 221265 608136.3 0 221265 4 145862 152034.1 0 145862 5 79262 38008.5 0 79262 6 74365 9502.1 0 74365 7 68535 2375.5 0 68535 8 73161 593.9 0 73161 9 75634 148.5 0 74906 728 10 73838 37.1 1 70554 3284 11 76989 9.3 1 73011 3978 12 71519 2.3 1 68135 3384 13 72547 0.6 1 68937 3610 14 78117 0.6 1 73480 4637 15 77734 0.6 1 73487 4247 16 82661 0.6 1 77734 4927 17 81476 0.6 1 76679 4797 18 73276 0.6 1 69726 3550 19 81430 0.6 1 76202 5228 20 75957 0.6 1 71914 4043 21 88967 0.6 1 82938 6029 22 80446 0.6 1 76041 4405 23 76909 0.6 1 72469 4440 24 82026 0.6 1 76846 5180 25 79151 0.6 1 74633 4518 26 86459 0.6 1 80705 5754 27 81877 0.6 1 77304 4573 28 79192 0.6 1 75012 4180 29 86917 0.6 1 81848 5069 30 79601 0.6 1 75563 4038 31 86906 0.6 1 81731 5175 32 84384 0.6 1 79799 4585 33 85562 0.6 1 80892 4670 34 82994 0.6 1 78724 4270 35 80689 0.6 1 76590 4099 36 84355 0.6 1 79712 4643 37 93276 0.6 1 88115 5161 38 89826 0.6 1 84466 5360 39 86579 0.6 1 82054 4525 40 90843 0.6 1 85488 5355 41 126158 0.6 1 119845 6313 42 78660 0.6 1 74942 3718 43 45571 0.6 1 42883 2688 44 79131 0.6 1 75220 3911 45 81433 0.6 1 76954 4479 46 76799 0.6 1 72769 4030 47 86512 0.6 1 81461 5051 48 81813 0.6 1 77114 4699 49 87931 0.6 1 82571 5360 50 77386 0.6 1 73221 4165 51 80366 0.6 1 75725 4641 52 83103 0.6 1 78038 5065 53 75421 0.6 1 71345 4076 54 74440 0.6 1 70157 4283 55 83961 0.6 1 79105 4856 56 77031 0.6 1 72585 4446 57 72414 0.6 1 67939 4475 58 80952 0.6 1 76591 4361 59 77285 0.6 1 72993 4292 60 69052 0.6 1 65262 3790 61 84855 0.6 1 80251 4604 62 86341 0.6 1 81912 4429 63 78019 0.6 1 73748 4271 64 76757 0.6 1 73092 3665 65 71577 0.6 1 68252 3325 66 76047 0.6 1 72227 3820 67 88133 0.6 1 83699 4434 68 104595 0.6 1 99082 5513 69 142040 0.6 1 134938 7102 70 176038 0.6 1 166617 9421 71 273510 0.6 1 259119 14391 72 428585 0.6 1 401025 27560 73 1192617 0.6 1 1088803 103814 74 5405423 0.6 1 5221238 184185 75 3785488 0.6 1 3647387 138101 76 2430968 0.6 1 2340247 90721 77 1515538 0.6 1 1458921 56617 78 918766 0.6 1 884927 33839 79 500382 0.6 1 480379 20003 80 321065 0.6 1 308148 12917 81 196010 0.6 1 187564 8446 82 131075 0.6 1 124825 6250 83 102704 0.6 1 97686 5018 84 85341 0.6 1 80883 4458 85 79754 0.6 1 75579 4175 86 76363 0.6 1 72485 3878 87 68380 0.6 1 64669 3711 88 61474 0.6 1 58069 3405 89 61699 0.6 1 58308 3391 90 77739 0.6 1 73602 4137 91 107932 0.6 1 102340 5592 92 182417 0.6 1 173166 9251 93 475162 0.6 1 452932 22230 94 1427275 0.6 1 1364226 63049 95 2423675 0.6 1 2318373 105302 96 1068813 0.6 1 1018256 50557 97 608393 0.6 1 576295 32098 98 226087 0.6 1 213399 12688 99 217668 0.6 1 205620 12048 100 211381 0.6 1 198861 12520 101 344366 0.6 1 320919 23447 RUN STATISTICS FOR INPUT FILE: EPI-44_S41_L005_R1_001.fastq.gz ============================================= 38920722 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 20972027 (53.9%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 31654254 (81.3%)