SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-185_S19_L003_R1_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-185_S19_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 217.65 s (19 us/read; 3.11 M reads/minute). === Summary === Total reads processed: 11,279,672 Reads with adapters: 6,555,453 (58.1%) Reads written (passing filters): 11,279,672 (100.0%) Total basepairs processed: 1,131,855,398 bp Total written (filtered): 999,890,859 bp (88.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6555453 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.0% C: 12.7% G: 24.6% T: 38.2% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 2079993 2819918.0 0 2079993 2 472607 704979.5 0 472607 3 185020 176244.9 0 185020 4 133846 44061.2 0 133846 5 75348 11015.3 0 75348 6 73940 2753.8 0 73940 7 65716 688.5 0 65716 8 74495 172.1 0 74495 9 74702 43.0 0 74034 668 10 69878 10.8 1 66974 2904 11 71694 2.7 1 68283 3411 12 67751 0.7 1 64526 3225 13 65399 0.2 1 62386 3013 14 72865 0.2 1 67724 5141 15 69567 0.2 1 64535 5032 16 75688 0.2 1 69914 5774 17 72163 0.2 1 66528 5635 18 66926 0.2 1 62185 4741 19 71196 0.2 1 65280 5916 20 67701 0.2 1 62834 4867 21 72849 0.2 1 67158 5691 22 68477 0.2 1 63561 4916 23 67156 0.2 1 61994 5162 24 67031 0.2 1 61711 5320 25 63207 0.2 1 58462 4745 26 69967 0.2 1 64130 5837 27 64795 0.2 1 60947 3848 28 61063 0.2 1 57827 3236 29 67239 0.2 1 63448 3791 30 61174 0.2 1 57995 3179 31 68084 0.2 1 63837 4247 32 61817 0.2 1 58620 3197 33 65691 0.2 1 62094 3597 34 61956 0.2 1 58563 3393 35 58649 0.2 1 55641 3008 36 59164 0.2 1 56311 2853 37 60502 0.2 1 57667 2835 38 57519 0.2 1 54584 2935 39 56563 0.2 1 53729 2834 40 57464 0.2 1 54509 2955 41 75018 0.2 1 71767 3251 42 45017 0.2 1 42977 2040 43 33890 0.2 1 32152 1738 44 45800 0.2 1 43611 2189 45 44926 0.2 1 42982 1944 46 42507 0.2 1 40625 1882 47 45486 0.2 1 43246 2240 48 41233 0.2 1 39276 1957 49 43889 0.2 1 41765 2124 50 38165 0.2 1 36541 1624 51 37707 0.2 1 36036 1671 52 35818 0.2 1 34165 1653 53 33212 0.2 1 31866 1346 54 32821 0.2 1 31445 1376 55 33895 0.2 1 32530 1365 56 30944 0.2 1 29702 1242 57 28512 0.2 1 27342 1170 58 27697 0.2 1 26549 1148 59 26501 0.2 1 25408 1093 60 23736 0.2 1 22763 973 61 24233 0.2 1 23243 990 62 24367 0.2 1 23427 940 63 22288 0.2 1 21439 849 64 21311 0.2 1 20562 749 65 19731 0.2 1 19034 697 66 17699 0.2 1 16998 701 67 17067 0.2 1 16443 624 68 15710 0.2 1 15128 582 69 16379 0.2 1 15767 612 70 16187 0.2 1 15510 677 71 17657 0.2 1 16838 819 72 20115 0.2 1 19161 954 73 26313 0.2 1 24607 1706 74 65814 0.2 1 63327 2487 75 49467 0.2 1 47664 1803 76 28936 0.2 1 27827 1109 77 17580 0.2 1 16897 683 78 10749 0.2 1 10335 414 79 5812 0.2 1 5560 252 80 3769 0.2 1 3612 157 81 2388 0.2 1 2265 123 82 1643 0.2 1 1564 79 83 1242 0.2 1 1187 55 84 977 0.2 1 928 49 85 798 0.2 1 760 38 86 697 0.2 1 666 31 87 597 0.2 1 569 28 88 505 0.2 1 477 28 89 490 0.2 1 468 22 90 526 0.2 1 491 35 91 798 0.2 1 757 41 92 1317 0.2 1 1243 74 93 3208 0.2 1 3047 161 94 10060 0.2 1 9635 425 95 17879 0.2 1 17140 739 96 7919 0.2 1 7517 402 97 5771 0.2 1 5480 291 98 2470 0.2 1 2326 144 99 2508 0.2 1 2349 159 100 2852 0.2 1 2665 187 101 5988 0.2 1 5355 633 RUN STATISTICS FOR INPUT FILE: EPI-185_S19_L003_R1_001.fastq.gz ============================================= 11279672 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1254537 (11.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 6519651 (57.8%)