SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-154_S5_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 File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_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/20180514_geoduck_trimgalore_rrbs/EPI-154_S5_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 492.66 s (19 us/read; 3.10 M reads/minute). === Summary === Total reads processed: 25,441,933 Reads with adapters: 16,256,132 (63.9%) Reads written (passing filters): 25,441,933 (100.0%) Total basepairs processed: 2,550,382,665 bp Total written (filtered): 2,318,095,620 bp (90.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16256132 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.6% C: 22.8% G: 7.7% T: 30.6% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 8207271 6360483.2 0 8207271 2 254722 1590120.8 0 254722 3 208896 397530.2 0 208896 4 178048 99382.6 0 178048 5 178049 24845.6 0 178049 6 179761 6211.4 0 179761 7 172613 1552.9 0 172613 8 179753 388.2 0 179753 9 170676 97.1 0 169954 722 10 173174 24.3 1 168413 4761 11 162623 6.1 1 157120 5503 12 166641 1.5 1 160992 5649 13 160850 0.4 1 155450 5400 14 173994 0.4 1 167940 6054 15 162177 0.4 1 156606 5571 16 161280 0.4 1 155847 5433 17 169197 0.4 1 163442 5755 18 149838 0.4 1 144787 5051 19 159544 0.4 1 154160 5384 20 155247 0.4 1 149804 5443 21 157290 0.4 1 151509 5781 22 158605 0.4 1 152873 5732 23 153119 0.4 1 147669 5450 24 163394 0.4 1 157633 5761 25 143699 0.4 1 138656 5043 26 144924 0.4 1 139071 5853 27 145792 0.4 1 139436 6356 28 150106 0.4 1 144880 5226 29 142310 0.4 1 136715 5595 30 154569 0.4 1 149534 5035 31 131574 0.4 1 126721 4853 32 137366 0.4 1 133109 4257 33 141626 0.4 1 136585 5041 34 142494 0.4 1 136953 5541 35 135337 0.4 1 131364 3973 36 125036 0.4 1 120628 4408 37 125521 0.4 1 121299 4222 38 110296 0.4 1 106682 3614 39 113794 0.4 1 110043 3751 40 110865 0.4 1 107262 3603 41 109863 0.4 1 106515 3348 42 107260 0.4 1 104408 2852 43 93456 0.4 1 90333 3123 44 94747 0.4 1 91737 3010 45 116428 0.4 1 113489 2939 46 87149 0.4 1 84633 2516 47 62242 0.4 1 60137 2105 48 86625 0.4 1 84428 2197 49 60756 0.4 1 58925 1831 50 62723 0.4 1 60827 1896 51 85886 0.4 1 83860 2026 52 50848 0.4 1 49248 1600 53 52338 0.4 1 50700 1638 54 45722 0.4 1 44257 1465 55 53891 0.4 1 52403 1488 56 50360 0.4 1 48804 1556 57 45719 0.4 1 44326 1393 58 43394 0.4 1 42094 1300 59 41271 0.4 1 39964 1307 60 38922 0.4 1 37711 1211 61 38021 0.4 1 36820 1201 62 37586 0.4 1 36327 1259 63 36031 0.4 1 34819 1212 64 33851 0.4 1 32709 1142 65 34527 0.4 1 33378 1149 66 35355 0.4 1 34018 1337 67 44812 0.4 1 42175 2637 68 128687 0.4 1 125915 2772 69 44857 0.4 1 43444 1413 70 20803 0.4 1 20005 798 71 11665 0.4 1 11105 560 72 8862 0.4 1 8451 411 73 6988 0.4 1 6622 366 74 5756 0.4 1 5468 288 75 4815 0.4 1 4551 264 76 4136 0.4 1 3936 200 77 3863 0.4 1 3651 212 78 3191 0.4 1 3032 159 79 2805 0.4 1 2637 168 80 2295 0.4 1 2162 133 81 1925 0.4 1 1829 96 82 1484 0.4 1 1400 84 83 1209 0.4 1 1138 71 84 1000 0.4 1 950 50 85 712 0.4 1 666 46 86 558 0.4 1 509 49 87 532 0.4 1 486 46 88 399 0.4 1 358 41 89 399 0.4 1 350 49 90 506 0.4 1 450 56 91 662 0.4 1 589 73 92 919 0.4 1 802 117 93 1797 0.4 1 1625 172 94 5182 0.4 1 4749 433 95 8946 0.4 1 8157 789 96 4491 0.4 1 4116 375 97 3529 0.4 1 3242 287 98 1446 0.4 1 1334 112 99 1318 0.4 1 1196 122 100 2069 0.4 1 1880 189 101 6472 0.4 1 5807 665 RUN STATISTICS FOR INPUT FILE: EPI-154_S5_L002_R2_001.fastq.gz ============================================= 25441933 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2468964 (9.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (849342) or CGA (260335) in total: 1109677 (4.4%) Total number of sequences analysed for the sequence pair length validation: 25441933 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 213577 (0.84%)