SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-160_S7_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-160_S7_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 642.90 s (19 us/read; 3.19 M reads/minute). === Summary === Total reads processed: 34,201,339 Reads with adapters: 24,529,566 (71.7%) Reads written (passing filters): 34,201,339 (100.0%) Total basepairs processed: 3,383,075,458 bp Total written (filtered): 2,766,557,070 bp (81.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24529566 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.6% C: 22.5% G: 12.3% T: 29.9% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 8617664 8550334.8 0 8617664 2 295221 2137583.7 0 295221 3 259150 534395.9 0 259150 4 220226 133599.0 0 220226 5 223536 33399.7 0 223536 6 227905 8349.9 0 227905 7 219468 2087.5 0 219468 8 237286 521.9 0 237286 9 222804 130.5 0 221813 991 10 228933 32.6 1 222424 6509 11 214510 8.2 1 206636 7874 12 221414 2.0 1 213313 8101 13 216176 0.5 1 208574 7602 14 234753 0.5 1 226050 8703 15 222276 0.5 1 214263 8013 16 224060 0.5 1 216063 7997 17 234826 0.5 1 226488 8338 18 211638 0.5 1 204112 7526 19 227923 0.5 1 219759 8164 20 225650 0.5 1 217311 8339 21 232121 0.5 1 222981 9140 22 236862 0.5 1 227558 9304 23 226788 0.5 1 218120 8668 24 245980 0.5 1 236505 9475 25 221116 0.5 1 212824 8292 26 225213 0.5 1 215363 9850 27 231699 0.5 1 220696 11003 28 242200 0.5 1 232775 9425 29 234850 0.5 1 224725 10125 30 257222 0.5 1 247960 9262 31 224813 0.5 1 215784 9029 32 235820 0.5 1 227698 8122 33 248260 0.5 1 238351 9909 34 257740 0.5 1 246886 10854 35 246443 0.5 1 238693 7750 36 233198 0.5 1 224076 9122 37 235386 0.5 1 226931 8455 38 214218 0.5 1 206307 7911 39 226054 0.5 1 217764 8290 40 224350 0.5 1 216374 7976 41 223941 0.5 1 216800 7141 42 221404 0.5 1 214997 6407 43 198522 0.5 1 191659 6863 44 208297 0.5 1 201480 6817 45 268178 0.5 1 261095 7083 46 202468 0.5 1 196177 6291 47 147340 0.5 1 142016 5324 48 210671 0.5 1 205079 5592 49 148934 0.5 1 144333 4601 50 156130 0.5 1 150975 5155 51 219807 0.5 1 214411 5396 52 135080 0.5 1 130600 4480 53 139874 0.5 1 135277 4597 54 124772 0.5 1 120668 4104 55 150091 0.5 1 145643 4448 56 144984 0.5 1 140133 4851 57 133697 0.5 1 129565 4132 58 130646 0.5 1 126620 4026 59 124439 0.5 1 120255 4184 60 118229 0.5 1 114239 3990 61 118605 0.5 1 114637 3968 62 120500 0.5 1 116238 4262 63 122715 0.5 1 118394 4321 64 124710 0.5 1 120123 4587 65 135247 0.5 1 130209 5038 66 155463 0.5 1 149020 6443 67 247599 0.5 1 230154 17445 68 930607 0.5 1 908900 21707 69 330952 0.5 1 320292 10660 70 170296 0.5 1 164288 6008 71 88955 0.5 1 85265 3690 72 60204 0.5 1 57544 2660 73 42687 0.5 1 40619 2068 74 33938 0.5 1 32238 1700 75 28246 0.5 1 26705 1541 76 23785 0.5 1 22495 1290 77 21297 0.5 1 20092 1205 78 18888 0.5 1 17771 1117 79 16219 0.5 1 15253 966 80 14126 0.5 1 13310 816 81 12160 0.5 1 11440 720 82 10584 0.5 1 9891 693 83 8910 0.5 1 8315 595 84 7890 0.5 1 7369 521 85 6725 0.5 1 6225 500 86 5758 0.5 1 5295 463 87 5592 0.5 1 5129 463 88 5471 0.5 1 5050 421 89 6216 0.5 1 5684 532 90 7546 0.5 1 6870 676 91 10454 0.5 1 9589 865 92 15677 0.5 1 14339 1338 93 34355 0.5 1 31803 2552 94 102615 0.5 1 95615 7000 95 172175 0.5 1 161021 11154 96 76218 0.5 1 71263 4955 97 49748 0.5 1 46443 3305 98 19516 0.5 1 18218 1298 99 18915 0.5 1 17622 1293 100 18868 0.5 1 17573 1295 101 35878 0.5 1 32785 3093 RUN STATISTICS FOR INPUT FILE: EPI-160_S7_L002_R2_001.fastq.gz ============================================= 34201339 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 5524652 (16.2%) 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: 34201339 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2278767 (6.66%)