SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-153_S4_L002_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-153_S4_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 602.20 s (19 us/read; 3.17 M reads/minute). === Summary === Total reads processed: 31,826,247 Reads with adapters: 22,817,768 (71.7%) Reads written (passing filters): 31,826,247 (100.0%) Total basepairs processed: 3,075,738,320 bp Total written (filtered): 2,375,711,352 bp (77.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22817768 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.3% C: 20.2% G: 16.5% T: 30.6% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 7922069 7956561.8 0 7922069 2 258609 1989140.4 0 258609 3 233096 497285.1 0 233096 4 194475 124321.3 0 194475 5 197777 31080.3 0 197777 6 196569 7770.1 0 196569 7 185297 1942.5 0 185297 8 201488 485.6 0 201488 9 188362 121.4 0 187597 765 10 192192 30.4 1 186722 5470 11 178615 7.6 1 171876 6739 12 181122 1.9 1 174566 6556 13 175852 0.5 1 169580 6272 14 189773 0.5 1 182860 6913 15 178529 0.5 1 172114 6415 16 178766 0.5 1 172346 6420 17 183382 0.5 1 176830 6552 18 163448 0.5 1 157626 5822 19 173181 0.5 1 167184 5997 20 171728 0.5 1 165391 6337 21 173957 0.5 1 166948 7009 22 179682 0.5 1 172635 7047 23 167727 0.5 1 161502 6225 24 175763 0.5 1 168934 6829 25 158888 0.5 1 152989 5899 26 160693 0.5 1 153752 6941 27 166236 0.5 1 158193 8043 28 168883 0.5 1 162413 6470 29 164648 0.5 1 157198 7450 30 176558 0.5 1 169917 6641 31 154566 0.5 1 148067 6499 32 158152 0.5 1 152630 5522 33 167719 0.5 1 160814 6905 34 171793 0.5 1 164263 7530 35 159102 0.5 1 153943 5159 36 149775 0.5 1 143848 5927 37 146987 0.5 1 141455 5532 38 132398 0.5 1 127357 5041 39 139811 0.5 1 134274 5537 40 137903 0.5 1 132692 5211 41 133844 0.5 1 129319 4525 42 132202 0.5 1 128170 4032 43 116343 0.5 1 112100 4243 44 122271 0.5 1 117983 4288 45 174349 0.5 1 169554 4795 46 116270 0.5 1 112497 3773 47 82602 0.5 1 79604 2998 48 121598 0.5 1 118108 3490 49 83774 0.5 1 81006 2768 50 87712 0.5 1 84652 3060 51 125946 0.5 1 122710 3236 52 76272 0.5 1 73627 2645 53 77332 0.5 1 74632 2700 54 68651 0.5 1 66273 2378 55 81764 0.5 1 79232 2532 56 78951 0.5 1 76244 2707 57 73850 0.5 1 71367 2483 58 73367 0.5 1 70967 2400 59 66099 0.5 1 63769 2330 60 64062 0.5 1 61741 2321 61 66824 0.5 1 64271 2553 62 73099 0.5 1 70108 2991 63 80726 0.5 1 77400 3326 64 91941 0.5 1 87912 4029 65 118843 0.5 1 113374 5469 66 175079 0.5 1 166343 8736 67 384862 0.5 1 351320 33542 68 1830643 0.5 1 1785180 45463 69 668933 0.5 1 646399 22534 70 361868 0.5 1 349588 12280 71 179208 0.5 1 172255 6953 72 112795 0.5 1 108156 4639 73 71202 0.5 1 67986 3216 74 53263 0.5 1 50690 2573 75 41584 0.5 1 39306 2278 76 33962 0.5 1 32021 1941 77 29850 0.5 1 28121 1729 78 26274 0.5 1 24726 1548 79 23163 0.5 1 21730 1433 80 20719 0.5 1 19366 1353 81 19152 0.5 1 17901 1251 82 17232 0.5 1 16027 1205 83 15522 0.5 1 14356 1166 84 14219 0.5 1 13155 1064 85 13174 0.5 1 12131 1043 86 12725 0.5 1 11683 1042 87 13159 0.5 1 12068 1091 88 13558 0.5 1 12362 1196 89 15786 0.5 1 14346 1440 90 19651 0.5 1 17952 1699 91 27601 0.5 1 25243 2358 92 41529 0.5 1 38116 3413 93 94805 0.5 1 87543 7262 94 290673 0.5 1 271388 19285 95 489711 0.5 1 459137 30574 96 217427 0.5 1 203871 13556 97 134960 0.5 1 126132 8828 98 50028 0.5 1 46696 3332 99 44940 0.5 1 41915 3025 100 40915 0.5 1 38066 2849 101 73333 0.5 1 67412 5921 RUN STATISTICS FOR INPUT FILE: EPI-153_S4_L002_R2_001.fastq.gz ============================================= 31826247 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7132912 (22.4%) 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: 31826247 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5816850 (18.28%)