SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-200_S25_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 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-200_S25_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 525.64 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 27,883,056 Reads with adapters: 18,997,547 (68.1%) Reads written (passing filters): 27,883,056 (100.0%) Total basepairs processed: 2,769,872,436 bp Total written (filtered): 2,136,452,472 bp (77.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18997547 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.0% C: 16.5% G: 26.7% T: 34.5% none/other: 1.3% Overview of removed sequences length count expect max.err error counts 1 3875749 6970764.0 0 3875749 2 971023 1742691.0 0 971023 3 401329 435672.8 0 401329 4 277658 108918.2 0 277658 5 157883 27229.5 0 157883 6 155909 6807.4 0 155909 7 146539 1701.8 0 146539 8 167054 425.5 0 167054 9 157277 106.4 0 155990 1287 10 154803 26.6 1 148849 5954 11 154950 6.6 1 148122 6828 12 150739 1.7 1 144397 6342 13 145853 0.4 1 139680 6173 14 163057 0.4 1 152079 10978 15 156373 0.4 1 145473 10900 16 167808 0.4 1 155259 12549 17 163240 0.4 1 151712 11528 18 152051 0.4 1 142178 9873 19 168685 0.4 1 154880 13805 20 157005 0.4 1 146396 10609 21 177779 0.4 1 163864 13915 22 168308 0.4 1 156579 11729 23 159682 0.4 1 148221 11461 24 170638 0.4 1 158224 12414 25 162212 0.4 1 150823 11389 26 181402 0.4 1 166816 14586 27 169020 0.4 1 159509 9511 28 162595 0.4 1 154591 8004 29 179896 0.4 1 170381 9515 30 169096 0.4 1 160814 8282 31 186388 0.4 1 175900 10488 32 173727 0.4 1 165212 8515 33 184629 0.4 1 175247 9382 34 176516 0.4 1 167707 8809 35 173153 0.4 1 164773 8380 36 178446 0.4 1 170100 8346 37 183100 0.4 1 174300 8800 38 170925 0.4 1 163002 7923 39 185078 0.4 1 176093 8985 40 191170 0.4 1 181438 9732 41 254292 0.4 1 243252 11040 42 175998 0.4 1 168802 7196 43 96810 0.4 1 92181 4629 44 168507 0.4 1 161191 7316 45 166063 0.4 1 158947 7116 46 162580 0.4 1 155753 6827 47 175210 0.4 1 167209 8001 48 163083 0.4 1 155804 7279 49 172371 0.4 1 164282 8089 50 157487 0.4 1 150817 6670 51 156868 0.4 1 150417 6451 52 150978 0.4 1 144672 6306 53 147347 0.4 1 141892 5455 54 146839 0.4 1 141021 5818 55 152716 0.4 1 146741 5975 56 144442 0.4 1 138810 5632 57 138126 0.4 1 132562 5564 58 137383 0.4 1 132261 5122 59 133791 0.4 1 128606 5185 60 123543 0.4 1 119035 4508 61 126552 0.4 1 121931 4621 62 129203 0.4 1 124651 4552 63 119824 0.4 1 115669 4155 64 115386 0.4 1 111558 3828 65 109206 0.4 1 105617 3589 66 101741 0.4 1 98205 3536 67 101663 0.4 1 98158 3505 68 96873 0.4 1 93405 3468 69 102739 0.4 1 99228 3511 70 102358 0.4 1 98476 3882 71 103019 0.4 1 98868 4151 72 118962 0.4 1 113408 5554 73 192080 0.4 1 178776 13304 74 628369 0.4 1 607401 20968 75 502244 0.4 1 485489 16755 76 330378 0.4 1 319127 11251 77 212754 0.4 1 205445 7309 78 131112 0.4 1 126618 4494 79 74001 0.4 1 71423 2578 80 47419 0.4 1 45707 1712 81 28854 0.4 1 27622 1232 82 19832 0.4 1 18980 852 83 15621 0.4 1 14986 635 84 12611 0.4 1 12092 519 85 11058 0.4 1 10581 477 86 9894 0.4 1 9435 459 87 8262 0.4 1 7884 378 88 6789 0.4 1 6499 290 89 6855 0.4 1 6555 300 90 8469 0.4 1 8112 357 91 11090 0.4 1 10551 539 92 18310 0.4 1 17460 850 93 45497 0.4 1 43654 1843 94 131768 0.4 1 126670 5098 95 224748 0.4 1 216279 8469 96 99089 0.4 1 95074 4015 97 67286 0.4 1 64370 2916 98 29659 0.4 1 28235 1424 99 31016 0.4 1 29460 1556 100 33963 0.4 1 32056 1907 101 57814 0.4 1 52868 4946 RUN STATISTICS FOR INPUT FILE: EPI-200_S25_L003_R1_001.fastq.gz ============================================= 27883056 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4396452 (15.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 18403944 (66.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (217256) or CGA (160265) in total: 377521 (1.4%)