SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-185_S19_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 File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_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/20180514_geoduck_trimgalore_rrbs/EPI-185_S19_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 214.60 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 11,279,672 Reads with adapters: 7,295,393 (64.7%) Reads written (passing filters): 11,279,672 (100.0%) Total basepairs processed: 1,125,100,133 bp Total written (filtered): 997,411,999 bp (88.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7295393 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.0% C: 22.9% G: 10.0% T: 30.7% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 3322845 2819918.0 0 3322845 2 144034 704979.5 0 144034 3 92220 176244.9 0 92220 4 77005 44061.2 0 77005 5 74295 11015.3 0 74295 6 76204 2753.8 0 76204 7 71835 688.5 0 71835 8 77207 172.1 0 77207 9 72915 43.0 0 72587 328 10 73603 10.8 1 71417 2186 11 68922 2.7 1 66311 2611 12 71024 0.7 1 68305 2719 13 68274 0.2 1 65775 2499 14 75243 0.2 1 72315 2928 15 70498 0.2 1 67808 2690 16 70863 0.2 1 68166 2697 17 74916 0.2 1 72082 2834 18 65237 0.2 1 62734 2503 19 70318 0.2 1 67728 2590 20 69171 0.2 1 66583 2588 21 69592 0.2 1 66808 2784 22 72429 0.2 1 69622 2807 23 68507 0.2 1 65951 2556 24 72929 0.2 1 69986 2943 25 62719 0.2 1 60300 2419 26 64131 0.2 1 61344 2787 27 66035 0.2 1 62878 3157 28 68935 0.2 1 66287 2648 29 65315 0.2 1 62482 2833 30 71418 0.2 1 68837 2581 31 60142 0.2 1 57847 2295 32 64656 0.2 1 62451 2205 33 67457 0.2 1 64803 2654 34 65817 0.2 1 62990 2827 35 64123 0.2 1 62012 2111 36 60309 0.2 1 58007 2302 37 60466 0.2 1 58336 2130 38 54250 0.2 1 52286 1964 39 55784 0.2 1 53700 2084 40 54373 0.2 1 52394 1979 41 54247 0.2 1 52433 1814 42 52797 0.2 1 51213 1584 43 46339 0.2 1 44721 1618 44 46847 0.2 1 45219 1628 45 58377 0.2 1 56657 1720 46 44368 0.2 1 42890 1478 47 32959 0.2 1 31699 1260 48 45075 0.2 1 43762 1313 49 33040 0.2 1 32011 1029 50 33797 0.2 1 32630 1167 51 46202 0.2 1 44983 1219 52 28220 0.2 1 27238 982 53 29055 0.2 1 28114 941 54 25714 0.2 1 24831 883 55 30807 0.2 1 29928 879 56 29318 0.2 1 28429 889 57 26697 0.2 1 25843 854 58 24981 0.2 1 24186 795 59 23876 0.2 1 23050 826 60 22847 0.2 1 22079 768 61 22415 0.2 1 21664 751 62 22875 0.2 1 22072 803 63 23285 0.2 1 22496 789 64 22734 0.2 1 21901 833 65 23845 0.2 1 22962 883 66 25087 0.2 1 24057 1030 67 35591 0.2 1 33120 2471 68 126559 0.2 1 123364 3195 69 43997 0.2 1 42424 1573 70 22246 0.2 1 21401 845 71 11570 0.2 1 11018 552 72 8449 0.2 1 8056 393 73 6060 0.2 1 5731 329 74 4726 0.2 1 4451 275 75 3975 0.2 1 3756 219 76 3537 0.2 1 3328 209 77 3006 0.2 1 2820 186 78 2630 0.2 1 2463 167 79 2316 0.2 1 2166 150 80 1793 0.2 1 1664 129 81 1543 0.2 1 1413 130 82 1323 0.2 1 1233 90 83 1091 0.2 1 1014 77 84 890 0.2 1 805 85 85 735 0.2 1 652 83 86 624 0.2 1 554 70 87 582 0.2 1 516 66 88 573 0.2 1 507 66 89 618 0.2 1 545 73 90 747 0.2 1 669 78 91 1031 0.2 1 903 128 92 1588 0.2 1 1390 198 93 3239 0.2 1 2906 333 94 9863 0.2 1 9009 854 95 16962 0.2 1 15606 1356 96 7512 0.2 1 6953 559 97 5477 0.2 1 5064 413 98 2182 0.2 1 2012 170 99 2280 0.2 1 2111 169 100 2715 0.2 1 2518 197 101 5543 0.2 1 5000 543 RUN STATISTICS FOR INPUT FILE: EPI-185_S19_L003_R2_001.fastq.gz ============================================= 11279672 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1383802 (12.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (322770) or CGA (106016) in total: 428786 (3.8%) Total number of sequences analysed for the sequence pair length validation: 11279672 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 274947 (2.44%)