SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-194_S23_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 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-194_S23_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 552.20 s (20 us/read; 3.07 M reads/minute). === Summary === Total reads processed: 28,208,567 Reads with adapters: 17,396,852 (61.7%) Reads written (passing filters): 28,208,567 (100.0%) Total basepairs processed: 2,817,230,234 bp Total written (filtered): 2,563,216,887 bp (91.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17396852 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.3% C: 21.7% G: 8.5% T: 31.0% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 9720777 7052141.8 0 9720777 2 230372 1763035.4 0 230372 3 186338 440758.9 0 186338 4 156610 110189.7 0 156610 5 156122 27547.4 0 156122 6 154732 6886.9 0 154732 7 147921 1721.7 0 147921 8 152696 430.4 0 152696 9 149555 107.6 0 148909 646 10 149750 26.9 1 145495 4255 11 143430 6.7 1 138180 5250 12 145266 1.7 1 139899 5367 13 139706 0.4 1 134922 4784 14 151284 0.4 1 145879 5405 15 140797 0.4 1 135826 4971 16 142762 0.4 1 137801 4961 17 147648 0.4 1 142594 5054 18 130083 0.4 1 125490 4593 19 136651 0.4 1 131966 4685 20 133078 0.4 1 128381 4697 21 136112 0.4 1 130969 5143 22 136539 0.4 1 131477 5062 23 131712 0.4 1 127055 4657 24 137096 0.4 1 132103 4993 25 122452 0.4 1 117958 4494 26 123646 0.4 1 118517 5129 27 125639 0.4 1 119884 5755 28 127862 0.4 1 123323 4539 29 122968 0.4 1 117920 5048 30 132330 0.4 1 127925 4405 31 113381 0.4 1 109126 4255 32 116319 0.4 1 112579 3740 33 123190 0.4 1 118615 4575 34 122709 0.4 1 117789 4920 35 112238 0.4 1 108843 3395 36 110212 0.4 1 106072 4140 37 110932 0.4 1 107126 3806 38 97874 0.4 1 94521 3353 39 100200 0.4 1 96642 3558 40 99070 0.4 1 95491 3579 41 97227 0.4 1 93960 3267 42 93450 0.4 1 90645 2805 43 84066 0.4 1 80989 3077 44 83879 0.4 1 81101 2778 45 101429 0.4 1 98459 2970 46 78628 0.4 1 76044 2584 47 58071 0.4 1 55963 2108 48 77567 0.4 1 75282 2285 49 57035 0.4 1 55169 1866 50 58759 0.4 1 56828 1931 51 78795 0.4 1 76767 2028 52 49427 0.4 1 47742 1685 53 50869 0.4 1 49276 1593 54 44466 0.4 1 42932 1534 55 52365 0.4 1 50811 1554 56 49486 0.4 1 47873 1613 57 46100 0.4 1 44632 1468 58 43715 0.4 1 42293 1422 59 42086 0.4 1 40711 1375 60 40342 0.4 1 38962 1380 61 39133 0.4 1 37778 1355 62 39298 0.4 1 37901 1397 63 39394 0.4 1 37976 1418 64 38781 0.4 1 37331 1450 65 41561 0.4 1 40009 1552 66 46217 0.4 1 44271 1946 67 75403 0.4 1 69624 5779 68 301766 0.4 1 294344 7422 69 109024 0.4 1 105302 3722 70 56266 0.4 1 54177 2089 71 28933 0.4 1 27762 1171 72 19879 0.4 1 18943 936 73 13872 0.4 1 13180 692 74 10800 0.4 1 10169 631 75 8717 0.4 1 8245 472 76 7572 0.4 1 7168 404 77 6727 0.4 1 6342 385 78 5663 0.4 1 5330 333 79 5000 0.4 1 4696 304 80 4316 0.4 1 4045 271 81 3579 0.4 1 3334 245 82 3018 0.4 1 2801 217 83 2687 0.4 1 2476 211 84 2149 0.4 1 2004 145 85 1831 0.4 1 1685 146 86 1659 0.4 1 1526 133 87 1614 0.4 1 1457 157 88 1568 0.4 1 1423 145 89 1738 0.4 1 1586 152 90 2170 0.4 1 1952 218 91 2797 0.4 1 2514 283 92 4143 0.4 1 3766 377 93 9021 0.4 1 8260 761 94 27524 0.4 1 25440 2084 95 49612 0.4 1 46053 3559 96 22461 0.4 1 20882 1579 97 16359 0.4 1 15158 1201 98 6943 0.4 1 6395 548 99 7292 0.4 1 6746 546 100 8095 0.4 1 7497 598 101 16449 0.4 1 15042 1407 RUN STATISTICS FOR INPUT FILE: EPI-194_S23_L003_R2_001.fastq.gz ============================================= 28208567 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2999798 (10.6%) 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: 28208567 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 749414 (2.66%)