SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-175_S14_L003_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-175_S14_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 479.10 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 25,152,012 Reads with adapters: 13,933,897 (55.4%) Reads written (passing filters): 25,152,012 (100.0%) Total basepairs processed: 2,526,221,747 bp Total written (filtered): 2,273,578,625 bp (90.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13933897 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.3% C: 9.2% G: 26.6% T: 39.6% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 4839745 6288003.0 0 4839745 2 1159616 1572000.8 0 1159616 3 457070 393000.2 0 457070 4 315225 98250.0 0 315225 5 161669 24562.5 0 161669 6 153209 6140.6 0 153209 7 139020 1535.2 0 139020 8 155720 383.8 0 155720 9 155752 95.9 0 154418 1334 10 144758 24.0 1 138390 6368 11 152068 6.0 1 144410 7658 12 141687 1.5 1 134879 6808 13 134537 0.4 1 128233 6304 14 151906 0.4 1 140481 11425 15 140254 0.4 1 129658 10596 16 153527 0.4 1 141017 12510 17 145060 0.4 1 133644 11416 18 133309 0.4 1 123823 9486 19 144446 0.4 1 131609 12837 20 131905 0.4 1 122252 9653 21 147076 0.4 1 134833 12243 22 136548 0.4 1 126453 10095 23 130124 0.4 1 120051 10073 24 134702 0.4 1 124049 10653 25 125168 0.4 1 115663 9505 26 136731 0.4 1 125147 11584 27 125965 0.4 1 118321 7644 28 116048 0.4 1 109937 6111 29 129529 0.4 1 121923 7606 30 119391 0.4 1 113089 6302 31 128450 0.4 1 120687 7763 32 116299 0.4 1 110275 6024 33 133567 0.4 1 125501 8066 34 112155 0.4 1 106254 5901 35 113072 0.4 1 106676 6396 36 116137 0.4 1 109448 6689 37 108496 0.4 1 103109 5387 38 106615 0.4 1 100713 5902 39 106353 0.4 1 101003 5350 40 106741 0.4 1 101308 5433 41 150121 0.4 1 143558 6563 42 93376 0.4 1 89559 3817 43 37838 0.4 1 35523 2315 44 85800 0.4 1 81848 3952 45 82286 0.4 1 78450 3836 46 77329 0.4 1 73819 3510 47 82981 0.4 1 78902 4079 48 77004 0.4 1 73171 3833 49 81031 0.4 1 76942 4089 50 70064 0.4 1 66922 3142 51 69042 0.4 1 65978 3064 52 65089 0.4 1 62314 2775 53 60110 0.4 1 57729 2381 54 60513 0.4 1 57896 2617 55 61351 0.4 1 58872 2479 56 56599 0.4 1 54261 2338 57 53049 0.4 1 50860 2189 58 51846 0.4 1 49797 2049 59 49859 0.4 1 47903 1956 60 44532 0.4 1 42765 1767 61 45539 0.4 1 43739 1800 62 45703 0.4 1 43940 1763 63 40907 0.4 1 39381 1526 64 39031 0.4 1 37600 1431 65 36262 0.4 1 34933 1329 66 33678 0.4 1 32396 1282 67 33205 0.4 1 31985 1220 68 29689 0.4 1 28603 1086 69 30870 0.4 1 29729 1141 70 28613 0.4 1 27541 1072 71 29155 0.4 1 27924 1231 72 32633 0.4 1 31107 1526 73 44088 0.4 1 41011 3077 74 135691 0.4 1 130999 4692 75 99615 0.4 1 96225 3390 76 53871 0.4 1 51948 1923 77 31749 0.4 1 30595 1154 78 19387 0.4 1 18692 695 79 11327 0.4 1 10897 430 80 7720 0.4 1 7388 332 81 5054 0.4 1 4843 211 82 3407 0.4 1 3235 172 83 2739 0.4 1 2613 126 84 2329 0.4 1 2227 102 85 1919 0.4 1 1826 93 86 1568 0.4 1 1480 88 87 1281 0.4 1 1217 64 88 1057 0.4 1 1003 54 89 1011 0.4 1 967 44 90 1326 0.4 1 1267 59 91 1746 0.4 1 1649 97 92 2823 0.4 1 2691 132 93 6839 0.4 1 6514 325 94 20927 0.4 1 20052 875 95 34297 0.4 1 32839 1458 96 14561 0.4 1 13848 713 97 9969 0.4 1 9501 468 98 4319 0.4 1 4086 233 99 4276 0.4 1 4048 228 100 4973 0.4 1 4673 300 101 9273 0.4 1 8487 786 RUN STATISTICS FOR INPUT FILE: EPI-175_S14_L003_R1_001.fastq.gz ============================================= 25152012 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2708883 (10.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 13879758 (55.2%)