SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-221_S33_L004_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-221_S33_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 432.07 s (18 us/read; 3.36 M reads/minute). === Summary === Total reads processed: 24,207,549 Reads with adapters: 18,255,035 (75.4%) Reads written (passing filters): 24,207,549 (100.0%) Total basepairs processed: 2,331,632,532 bp Total written (filtered): 1,422,454,380 bp (61.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18255035 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.8% C: 31.9% G: 19.0% T: 27.7% none/other: 2.6% Overview of removed sequences length count expect max.err error counts 1 2651504 6051887.2 0 2651504 2 624818 1512971.8 0 624818 3 249103 378243.0 0 249103 4 168080 94560.7 0 168080 5 94579 23640.2 0 94579 6 90882 5910.0 0 90882 7 85760 1477.5 0 85760 8 96508 369.4 0 96508 9 95125 92.3 0 94276 849 10 91273 23.1 1 88158 3115 11 92103 5.8 1 88618 3485 12 87337 1.4 1 84078 3259 13 88948 0.4 1 85502 3446 14 94764 0.4 1 90666 4098 15 94236 0.4 1 90289 3947 16 99841 0.4 1 95368 4473 17 98251 0.4 1 94154 4097 18 90511 0.4 1 87121 3390 19 98049 0.4 1 93504 4545 20 94089 0.4 1 90499 3590 21 103862 0.4 1 98830 5032 22 98784 0.4 1 95037 3747 23 94317 0.4 1 90375 3942 24 98243 0.4 1 93598 4645 25 96536 0.4 1 92486 4050 26 102389 0.4 1 97673 4716 27 98282 0.4 1 93980 4302 28 97576 0.4 1 93495 4081 29 105290 0.4 1 100567 4723 30 99080 0.4 1 95107 3973 31 105358 0.4 1 100540 4818 32 102179 0.4 1 97894 4285 33 104954 0.4 1 100489 4465 34 102899 0.4 1 98602 4297 35 101785 0.4 1 97480 4305 36 103376 0.4 1 98855 4521 37 112001 0.4 1 106986 5015 38 108363 0.4 1 103387 4976 39 106227 0.4 1 101887 4340 40 110507 0.4 1 105201 5306 41 149987 0.4 1 143732 6255 42 104757 0.4 1 100838 3919 43 61428 0.4 1 58519 2909 44 100464 0.4 1 96320 4144 45 101875 0.4 1 97605 4270 46 98824 0.4 1 94756 4068 47 105551 0.4 1 100823 4728 48 102490 0.4 1 98012 4478 49 106507 0.4 1 101814 4693 50 97332 0.4 1 93479 3853 51 100622 0.4 1 96487 4135 52 99725 0.4 1 95569 4156 53 95375 0.4 1 91756 3619 54 96062 0.4 1 92193 3869 55 103090 0.4 1 99065 4025 56 97370 0.4 1 93722 3648 57 93327 0.4 1 89780 3547 58 97306 0.4 1 93692 3614 59 92899 0.4 1 89345 3554 60 85529 0.4 1 82393 3136 61 91269 0.4 1 87798 3471 62 92173 0.4 1 88889 3284 63 87355 0.4 1 84251 3104 64 83896 0.4 1 81156 2740 65 80428 0.4 1 77616 2812 66 76962 0.4 1 74219 2743 67 75989 0.4 1 73310 2679 68 72871 0.4 1 70306 2565 69 77314 0.4 1 74520 2794 70 76761 0.4 1 73773 2988 71 90646 0.4 1 86969 3677 72 112582 0.4 1 106976 5606 73 236798 0.4 1 215625 21173 74 1228481 0.4 1 1188433 40048 75 1222514 0.4 1 1183535 38979 76 981356 0.4 1 949240 32116 77 750750 0.4 1 726972 23778 78 496422 0.4 1 480602 15820 79 287017 0.4 1 277658 9359 80 176016 0.4 1 170370 5646 81 98885 0.4 1 95522 3363 82 60616 0.4 1 58384 2232 83 42745 0.4 1 41004 1741 84 35136 0.4 1 33768 1368 85 29874 0.4 1 28628 1246 86 27054 0.4 1 25981 1073 87 24216 0.4 1 23192 1024 88 21686 0.4 1 20758 928 89 21715 0.4 1 20807 908 90 27170 0.4 1 26040 1130 91 37930 0.4 1 36366 1564 92 61169 0.4 1 58676 2493 93 148021 0.4 1 142292 5729 94 444339 0.4 1 428205 16134 95 737767 0.4 1 711210 26557 96 310281 0.4 1 298080 12201 97 179831 0.4 1 172137 7694 98 70479 0.4 1 67360 3119 99 66754 0.4 1 63712 3042 100 67395 0.4 1 63871 3524 101 116083 0.4 1 107474 8609 RUN STATISTICS FOR INPUT FILE: EPI-221_S33_L004_R1_001.fastq.gz ============================================= 24207549 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7340129 (30.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 17294184 (71.4%) RRBS reads trimmed by 2 bp at the start when read started with CAA (206098) or CGA (163934) in total: 370032 (1.5%)