SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-167_S10_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-167_S10_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 487.90 s (20 us/read; 3.06 M reads/minute). === Summary === Total reads processed: 24,859,230 Reads with adapters: 15,369,391 (61.8%) Reads written (passing filters): 24,859,230 (100.0%) Total basepairs processed: 2,488,122,616 bp Total written (filtered): 2,292,740,401 bp (92.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15369391 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.1% C: 20.3% G: 7.3% T: 32.1% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 8551744 6214807.5 0 8551744 2 246148 1553701.9 0 246148 3 190565 388425.5 0 190565 4 163955 97106.4 0 163955 5 160213 24276.6 0 160213 6 158749 6069.1 0 158749 7 150000 1517.3 0 150000 8 152348 379.3 0 152348 9 152655 94.8 0 152020 635 10 150821 23.7 1 146396 4425 11 146653 5.9 1 141358 5295 12 148628 1.5 1 143175 5453 13 142195 0.4 1 137114 5081 14 151761 0.4 1 146219 5542 15 140774 0.4 1 135529 5245 16 140681 0.4 1 135637 5044 17 148111 0.4 1 142873 5238 18 131846 0.4 1 127220 4626 19 138041 0.4 1 133124 4917 20 134670 0.4 1 129536 5134 21 136338 0.4 1 130803 5535 22 137968 0.4 1 132680 5288 23 132322 0.4 1 127360 4962 24 137798 0.4 1 132572 5226 25 122164 0.4 1 117575 4589 26 122835 0.4 1 117672 5163 27 123407 0.4 1 117521 5886 28 125924 0.4 1 121369 4555 29 121485 0.4 1 116288 5197 30 128128 0.4 1 123665 4463 31 110876 0.4 1 106520 4356 32 113497 0.4 1 109642 3855 33 118175 0.4 1 113570 4605 34 120005 0.4 1 114905 5100 35 109616 0.4 1 106079 3537 36 102731 0.4 1 98816 3915 37 102246 0.4 1 98428 3818 38 88554 0.4 1 85388 3166 39 91579 0.4 1 88232 3347 40 88267 0.4 1 85088 3179 41 85974 0.4 1 83185 2789 42 82637 0.4 1 80194 2443 43 73211 0.4 1 70603 2608 44 72696 0.4 1 70279 2417 45 85138 0.4 1 82870 2268 46 65598 0.4 1 63595 2003 47 46515 0.4 1 44853 1662 48 63045 0.4 1 61242 1803 49 44347 0.4 1 42924 1423 50 46087 0.4 1 44500 1587 51 59933 0.4 1 58384 1549 52 37135 0.4 1 35811 1324 53 36863 0.4 1 35622 1241 54 32337 0.4 1 31205 1132 55 36994 0.4 1 35915 1079 56 34416 0.4 1 33218 1198 57 30866 0.4 1 29829 1037 58 28525 0.4 1 27569 956 59 26804 0.4 1 25894 910 60 25275 0.4 1 24330 945 61 24709 0.4 1 23797 912 62 24147 0.4 1 23270 877 63 22706 0.4 1 21820 886 64 21721 0.4 1 20890 831 65 22286 0.4 1 21358 928 66 24176 0.4 1 23085 1091 67 36009 0.4 1 33206 2803 68 129078 0.4 1 125717 3361 69 47386 0.4 1 45734 1652 70 24924 0.4 1 24012 912 71 13025 0.4 1 12410 615 72 8682 0.4 1 8278 404 73 6054 0.4 1 5733 321 74 4715 0.4 1 4403 312 75 3618 0.4 1 3425 193 76 2997 0.4 1 2803 194 77 2622 0.4 1 2433 189 78 2318 0.4 1 2156 162 79 1995 0.4 1 1863 132 80 1609 0.4 1 1513 96 81 1408 0.4 1 1302 106 82 1197 0.4 1 1109 88 83 1086 0.4 1 994 92 84 925 0.4 1 841 84 85 857 0.4 1 780 77 86 793 0.4 1 706 87 87 813 0.4 1 718 95 88 823 0.4 1 735 88 89 934 0.4 1 846 88 90 1158 0.4 1 1031 127 91 1444 0.4 1 1276 168 92 2210 0.4 1 1964 246 93 4655 0.4 1 4194 461 94 13593 0.4 1 12607 986 95 23945 0.4 1 22218 1727 96 11675 0.4 1 10828 847 97 8623 0.4 1 7964 659 98 3643 0.4 1 3391 252 99 3896 0.4 1 3601 295 100 4139 0.4 1 3843 296 101 7928 0.4 1 7181 747 RUN STATISTICS FOR INPUT FILE: EPI-167_S10_L002_R2_001.fastq.gz ============================================= 24859230 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2502338 (10.1%) 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: 24859230 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 377980 (1.52%)