SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-188_S21_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-188_S21_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 452.14 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 24,209,277 Reads with adapters: 18,324,585 (75.7%) Reads written (passing filters): 24,209,277 (100.0%) Total basepairs processed: 2,370,780,374 bp Total written (filtered): 1,794,053,922 bp (75.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18324585 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.4% C: 22.5% G: 14.5% T: 28.4% none/other: 2.1% Overview of removed sequences length count expect max.err error counts 1 5299923 6052319.2 0 5299923 2 183481 1513079.8 0 183481 3 159429 378270.0 0 159429 4 136294 94567.5 0 136294 5 137372 23641.9 0 137372 6 139759 5910.5 0 139759 7 136524 1477.6 0 136524 8 149224 369.4 0 149224 9 140210 92.4 0 139638 572 10 141811 23.1 1 137800 4011 11 135594 5.8 1 130542 5052 12 139797 1.4 1 134853 4944 13 136693 0.4 1 132007 4686 14 149252 0.4 1 143799 5453 15 142464 0.4 1 137500 4964 16 143576 0.4 1 138665 4911 17 152456 0.4 1 147208 5248 18 137739 0.4 1 133032 4707 19 146182 0.4 1 141137 5045 20 147926 0.4 1 142555 5371 21 152752 0.4 1 146987 5765 22 158508 0.4 1 152577 5931 23 152920 0.4 1 147315 5605 24 163294 0.4 1 157195 6099 25 148970 0.4 1 143420 5550 26 154688 0.4 1 148144 6544 27 161143 0.4 1 153601 7542 28 166915 0.4 1 160709 6206 29 165758 0.4 1 158479 7279 30 181751 0.4 1 175443 6308 31 159562 0.4 1 153266 6296 32 168611 0.4 1 163041 5570 33 180848 0.4 1 173880 6968 34 187485 0.4 1 179696 7789 35 175711 0.4 1 170228 5483 36 175452 0.4 1 168783 6669 37 174726 0.4 1 168539 6187 38 161690 0.4 1 155892 5798 39 171263 0.4 1 165083 6180 40 171773 0.4 1 165433 6340 41 172093 0.4 1 166216 5877 42 171767 0.4 1 166531 5236 43 156983 0.4 1 151400 5583 44 163518 0.4 1 158003 5515 45 209498 0.4 1 203593 5905 46 163861 0.4 1 158430 5431 47 121760 0.4 1 117466 4294 48 171838 0.4 1 166863 4975 49 126787 0.4 1 122778 4009 50 133883 0.4 1 129505 4378 51 186576 0.4 1 181794 4782 52 118170 0.4 1 114214 3956 53 125277 0.4 1 121316 3961 54 111172 0.4 1 107806 3366 55 136318 0.4 1 132455 3863 56 132238 0.4 1 128153 4085 57 123866 0.4 1 120146 3720 58 121075 0.4 1 117380 3695 59 117079 0.4 1 113310 3769 60 115016 0.4 1 111362 3654 61 116669 0.4 1 112830 3839 62 122542 0.4 1 118266 4276 63 127855 0.4 1 123445 4410 64 132063 0.4 1 127222 4841 65 144626 0.4 1 139138 5488 66 165922 0.4 1 158676 7246 67 274571 0.4 1 250279 24292 68 1144857 0.4 1 1116410 28447 69 420217 0.4 1 406032 14185 70 218092 0.4 1 210343 7749 71 112680 0.4 1 107916 4764 72 75989 0.4 1 72513 3476 73 53033 0.4 1 50361 2672 74 41706 0.4 1 39465 2241 75 34273 0.4 1 32361 1912 76 29284 0.4 1 27586 1698 77 26174 0.4 1 24682 1492 78 22842 0.4 1 21513 1329 79 19707 0.4 1 18556 1151 80 16892 0.4 1 15851 1041 81 14629 0.4 1 13677 952 82 12601 0.4 1 11797 804 83 10478 0.4 1 9775 703 84 8838 0.4 1 8214 624 85 7559 0.4 1 6988 571 86 6544 0.4 1 5998 546 87 6430 0.4 1 5901 529 88 6191 0.4 1 5601 590 89 6832 0.4 1 6211 621 90 8330 0.4 1 7569 761 91 11024 0.4 1 10137 887 92 16439 0.4 1 15046 1393 93 34594 0.4 1 31907 2687 94 102839 0.4 1 95728 7111 95 180381 0.4 1 168603 11778 96 84567 0.4 1 79106 5461 97 62519 0.4 1 58257 4262 98 26820 0.4 1 24952 1868 99 28749 0.4 1 26641 2108 100 36423 0.4 1 33723 2700 101 83503 0.4 1 75214 8289 RUN STATISTICS FOR INPUT FILE: EPI-188_S21_L003_R2_001.fastq.gz ============================================= 24209277 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4864306 (20.1%) 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: 24209277 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2721139 (11.24%)