SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-184_S18_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-184_S18_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 401.65 s (19 us/read; 3.16 M reads/minute). === Summary === Total reads processed: 21,173,421 Reads with adapters: 14,240,527 (67.3%) Reads written (passing filters): 21,173,421 (100.0%) Total basepairs processed: 2,113,937,066 bp Total written (filtered): 1,843,277,693 bp (87.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14240527 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.8% C: 21.8% G: 9.5% T: 31.6% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 6171399 5293355.2 0 6171399 2 205716 1323338.8 0 205716 3 158475 330834.7 0 158475 4 138230 82708.7 0 138230 5 138904 20677.2 0 138904 6 138556 5169.3 0 138556 7 132635 1292.3 0 132635 8 138542 323.1 0 138542 9 135972 80.8 0 135408 564 10 134348 20.2 1 130333 4015 11 131133 5.0 1 126133 5000 12 133324 1.3 1 128392 4932 13 130480 0.3 1 125737 4743 14 140487 0.3 1 135266 5221 15 132939 0.3 1 127986 4953 16 136406 0.3 1 131437 4969 17 143248 0.3 1 138028 5220 18 128423 0.3 1 123764 4659 19 134642 0.3 1 129803 4839 20 134155 0.3 1 129130 5025 21 136652 0.3 1 131193 5459 22 139397 0.3 1 133995 5402 23 136614 0.3 1 131514 5100 24 143931 0.3 1 138388 5543 25 128363 0.3 1 123525 4838 26 132025 0.3 1 126442 5583 27 137489 0.3 1 130744 6745 28 140459 0.3 1 135083 5376 29 136708 0.3 1 130842 5866 30 148140 0.3 1 142850 5290 31 129358 0.3 1 124160 5198 32 133802 0.3 1 129270 4532 33 144946 0.3 1 139189 5757 34 146177 0.3 1 140037 6140 35 133655 0.3 1 129435 4220 36 132411 0.3 1 127314 5097 37 133027 0.3 1 128155 4872 38 118433 0.3 1 114132 4301 39 124811 0.3 1 120135 4676 40 123677 0.3 1 119083 4594 41 120128 0.3 1 116007 4121 42 116365 0.3 1 112855 3510 43 107968 0.3 1 104031 3937 44 107256 0.3 1 103583 3673 45 128268 0.3 1 124456 3812 46 104565 0.3 1 101007 3558 47 76840 0.3 1 74009 2831 48 101926 0.3 1 98999 2927 49 76836 0.3 1 74258 2578 50 79929 0.3 1 77153 2776 51 105039 0.3 1 102218 2821 52 67778 0.3 1 65430 2348 53 69751 0.3 1 67447 2304 54 61548 0.3 1 59538 2010 55 71942 0.3 1 69817 2125 56 68750 0.3 1 66505 2245 57 62435 0.3 1 60452 1983 58 59897 0.3 1 57943 1954 59 56832 0.3 1 54925 1907 60 55076 0.3 1 53244 1832 61 53984 0.3 1 52112 1872 62 54202 0.3 1 52272 1930 63 52162 0.3 1 50349 1813 64 50685 0.3 1 48814 1871 65 52489 0.3 1 50524 1965 66 55093 0.3 1 52899 2194 67 75502 0.3 1 70682 4820 68 255236 0.3 1 249018 6218 69 89724 0.3 1 86714 3010 70 43682 0.3 1 41945 1737 71 23850 0.3 1 22760 1090 72 16665 0.3 1 15827 838 73 12422 0.3 1 11756 666 74 10021 0.3 1 9457 564 75 8300 0.3 1 7818 482 76 7254 0.3 1 6803 451 77 6484 0.3 1 6087 397 78 5561 0.3 1 5238 323 79 4780 0.3 1 4484 296 80 3895 0.3 1 3640 255 81 3316 0.3 1 3116 200 82 2663 0.3 1 2490 173 83 2193 0.3 1 2018 175 84 1773 0.3 1 1624 149 85 1436 0.3 1 1304 132 86 1178 0.3 1 1053 125 87 1030 0.3 1 927 103 88 1042 0.3 1 911 131 89 1119 0.3 1 999 120 90 1382 0.3 1 1243 139 91 1982 0.3 1 1791 191 92 2788 0.3 1 2508 280 93 6029 0.3 1 5465 564 94 17720 0.3 1 16290 1430 95 30645 0.3 1 28386 2259 96 13511 0.3 1 12531 980 97 9408 0.3 1 8669 739 98 3843 0.3 1 3562 281 99 3814 0.3 1 3532 282 100 4529 0.3 1 4182 347 101 9917 0.3 1 9017 900 RUN STATISTICS FOR INPUT FILE: EPI-184_S18_L003_R2_001.fastq.gz ============================================= 21173421 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2564520 (12.1%) 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: 21173421 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 484273 (2.29%)