SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-111_S29_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-111_S29_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 528.58 s (20 us/read; 3.08 M reads/minute). === Summary === Total reads processed: 27,105,772 Reads with adapters: 17,090,015 (63.0%) Reads written (passing filters): 27,105,772 (100.0%) Total basepairs processed: 2,715,698,735 bp Total written (filtered): 2,479,517,591 bp (91.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17090015 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.0% C: 25.4% G: 7.9% T: 28.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9158844 6776443.0 0 9158844 2 222490 1694110.8 0 222490 3 216047 423527.7 0 216047 4 166659 105881.9 0 166659 5 172344 26470.5 0 172344 6 178822 6617.6 0 178822 7 166817 1654.4 0 166817 8 220773 413.6 0 220773 9 157247 103.4 0 156596 651 10 153696 25.9 1 147802 5894 11 152010 6.5 1 144082 7928 12 150846 1.6 1 143702 7144 13 145472 0.4 1 138406 7066 14 160748 0.4 1 153149 7599 15 146455 0.4 1 139136 7319 16 150185 0.4 1 142824 7361 17 160038 0.4 1 152581 7457 18 135658 0.4 1 129068 6590 19 145018 0.4 1 138565 6453 20 138966 0.4 1 131989 6977 21 147645 0.4 1 139417 8228 22 148856 0.4 1 141145 7711 23 140201 0.4 1 133287 6914 24 151063 0.4 1 143714 7349 25 128897 0.4 1 122411 6486 26 136236 0.4 1 128473 7763 27 142741 0.4 1 133346 9395 28 143480 0.4 1 136651 6829 29 139674 0.4 1 131300 8374 30 153019 0.4 1 146253 6766 31 125676 0.4 1 118982 6694 32 131953 0.4 1 126534 5419 33 138663 0.4 1 131359 7304 34 144968 0.4 1 136706 8262 35 130366 0.4 1 125164 5202 36 122790 0.4 1 116242 6548 37 116355 0.4 1 110456 5899 38 107681 0.4 1 102245 5436 39 110932 0.4 1 104998 5934 40 112384 0.4 1 106493 5891 41 108811 0.4 1 104118 4693 42 115043 0.4 1 110840 4203 43 89620 0.4 1 84943 4677 44 100678 0.4 1 96019 4659 45 150520 0.4 1 145569 4951 46 87397 0.4 1 83419 3978 47 58630 0.4 1 55185 3445 48 98762 0.4 1 95241 3521 49 55036 0.4 1 52388 2648 50 62761 0.4 1 59503 3258 51 101114 0.4 1 97935 3179 52 48558 0.4 1 46084 2474 53 54011 0.4 1 51100 2911 54 46507 0.4 1 44125 2382 55 62877 0.4 1 60204 2673 56 59358 0.4 1 56385 2973 57 53329 0.4 1 50874 2455 58 52458 0.4 1 50075 2383 59 48783 0.4 1 46309 2474 60 50071 0.4 1 47542 2529 61 50636 0.4 1 48169 2467 62 53169 0.4 1 50489 2680 63 54191 0.4 1 51516 2675 64 54339 0.4 1 51589 2750 65 55435 0.4 1 52777 2658 66 56343 0.4 1 53861 2482 67 61908 0.4 1 58856 3052 68 115266 0.4 1 112234 3032 69 35317 0.4 1 33723 1594 70 17245 0.4 1 16234 1011 71 11167 0.4 1 10374 793 72 9008 0.4 1 8316 692 73 7330 0.4 1 6732 598 74 6124 0.4 1 5629 495 75 5095 0.4 1 4690 405 76 4239 0.4 1 3947 292 77 3485 0.4 1 3206 279 78 2779 0.4 1 2565 214 79 2288 0.4 1 2121 167 80 1591 0.4 1 1486 105 81 1171 0.4 1 1062 109 82 823 0.4 1 758 65 83 509 0.4 1 461 48 84 327 0.4 1 298 29 85 191 0.4 1 173 18 86 117 0.4 1 105 12 87 73 0.4 1 69 4 88 44 0.4 1 39 5 89 45 0.4 1 41 4 90 56 0.4 1 48 8 91 95 0.4 1 84 11 92 138 0.4 1 120 18 93 197 0.4 1 178 19 94 361 0.4 1 313 48 95 585 0.4 1 512 73 96 485 0.4 1 427 58 97 263 0.4 1 240 23 98 72 0.4 1 65 7 99 57 0.4 1 52 5 100 71 0.4 1 56 15 101 341 0.4 1 267 74 RUN STATISTICS FOR INPUT FILE: EPI-111_S29_L005_R2_001.fastq.gz ============================================= 27105772 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3343823 (12.3%) 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: 27105772 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 90776 (0.33%)