SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-182_S17_L003_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-182_S17_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 613.44 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 32,071,199 Reads with adapters: 20,419,880 (63.7%) Reads written (passing filters): 32,071,199 (100.0%) Total basepairs processed: 3,209,416,264 bp Total written (filtered): 2,904,080,822 bp (90.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20419880 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.7% C: 23.5% G: 8.0% T: 29.6% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 10623142 8017799.8 0 10623142 2 292438 2004449.9 0 292438 3 258192 501112.5 0 258192 4 212983 125278.1 0 212983 5 212566 31319.5 0 212566 6 220116 7829.9 0 220116 7 210328 1957.5 0 210328 8 251658 489.4 0 251658 9 201768 122.3 0 200954 814 10 196456 30.6 1 191408 5048 11 185028 7.6 1 178769 6259 12 188526 1.9 1 182082 6444 13 181662 0.5 1 175741 5921 14 195325 0.5 1 188729 6596 15 183867 0.5 1 178042 5825 16 183908 0.5 1 177918 5990 17 191340 0.5 1 185062 6278 18 168444 0.5 1 162948 5496 19 176528 0.5 1 170822 5706 20 172879 0.5 1 167204 5675 21 175162 0.5 1 168989 6173 22 179093 0.5 1 172927 6166 23 170187 0.5 1 164481 5706 24 177316 0.5 1 171156 6160 25 159815 0.5 1 154281 5534 26 159759 0.5 1 153600 6159 27 161505 0.5 1 154452 7053 28 164634 0.5 1 158940 5694 29 156470 0.5 1 150360 6110 30 170791 0.5 1 165248 5543 31 144714 0.5 1 139634 5080 32 151411 0.5 1 146787 4624 33 157492 0.5 1 151790 5702 34 157103 0.5 1 151141 5962 35 146823 0.5 1 142573 4250 36 140641 0.5 1 135819 4822 37 138029 0.5 1 133476 4553 38 124782 0.5 1 120775 4007 39 128058 0.5 1 123805 4253 40 126252 0.5 1 121976 4276 41 124451 0.5 1 120410 4041 42 122367 0.5 1 118954 3413 43 108760 0.5 1 105175 3585 44 110087 0.5 1 106635 3452 45 135211 0.5 1 131515 3696 46 104781 0.5 1 101579 3202 47 77220 0.5 1 74594 2626 48 105214 0.5 1 102338 2876 49 76651 0.5 1 74336 2315 50 78921 0.5 1 76499 2422 51 107456 0.5 1 104757 2699 52 66527 0.5 1 64369 2158 53 69352 0.5 1 67364 1988 54 60817 0.5 1 58923 1894 55 72730 0.5 1 70743 1987 56 68646 0.5 1 66556 2090 57 63477 0.5 1 61663 1814 58 60594 0.5 1 58785 1809 59 57426 0.5 1 55579 1847 60 55546 0.5 1 53827 1719 61 54429 0.5 1 52664 1765 62 55442 0.5 1 53715 1727 63 55162 0.5 1 53405 1757 64 54622 0.5 1 52789 1833 65 56338 0.5 1 54455 1883 66 59877 0.5 1 57625 2252 67 81596 0.5 1 76599 4997 68 283845 0.5 1 277528 6317 69 98876 0.5 1 95754 3122 70 49650 0.5 1 47894 1756 71 26046 0.5 1 24993 1053 72 18388 0.5 1 17550 838 73 13473 0.5 1 12778 695 74 10532 0.5 1 10007 525 75 8960 0.5 1 8451 509 76 7680 0.5 1 7252 428 77 6568 0.5 1 6219 349 78 5626 0.5 1 5281 345 79 4815 0.5 1 4541 274 80 3954 0.5 1 3729 225 81 3292 0.5 1 3096 196 82 2634 0.5 1 2461 173 83 2132 0.5 1 1959 173 84 1691 0.5 1 1563 128 85 1447 0.5 1 1343 104 86 1236 0.5 1 1119 117 87 1194 0.5 1 1083 111 88 1189 0.5 1 1073 116 89 1377 0.5 1 1244 133 90 1709 0.5 1 1520 189 91 2521 0.5 1 2287 234 92 3494 0.5 1 3190 304 93 8032 0.5 1 7316 716 94 23132 0.5 1 21506 1626 95 39466 0.5 1 36784 2682 96 16809 0.5 1 15647 1162 97 9988 0.5 1 9289 699 98 3946 0.5 1 3659 287 99 3842 0.5 1 3565 277 100 3901 0.5 1 3608 293 101 7544 0.5 1 6860 684 RUN STATISTICS FOR INPUT FILE: EPI-182_S17_L003_R2_001.fastq.gz ============================================= 32071199 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3166821 (9.9%) 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 (1013152) or CGA (324660) in total: 1337812 (4.2%) Total number of sequences analysed for the sequence pair length validation: 32071199 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 569907 (1.78%)