SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-215_S31_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-215_S31_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 441.93 s (18 us/read; 3.29 M reads/minute). === Summary === Total reads processed: 24,211,042 Reads with adapters: 16,353,054 (67.5%) Reads written (passing filters): 24,211,042 (100.0%) Total basepairs processed: 2,397,539,811 bp Total written (filtered): 1,824,564,077 bp (76.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16353054 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.7% C: 17.4% G: 26.1% T: 34.5% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 3440470 6052760.5 0 3440470 2 850370 1513190.1 0 850370 3 347707 378297.5 0 347707 4 232598 94574.4 0 232598 5 130973 23643.6 0 130973 6 126999 5910.9 0 126999 7 119965 1477.7 0 119965 8 139799 369.4 0 139799 9 132512 92.4 0 131366 1146 10 129931 23.1 1 125243 4688 11 126277 5.8 1 121187 5090 12 118890 1.4 1 114458 4432 13 120496 0.4 1 115697 4799 14 130764 0.4 1 124853 5911 15 129245 0.4 1 123770 5475 16 136741 0.4 1 130455 6286 17 131740 0.4 1 125757 5983 18 124260 0.4 1 119204 5056 19 130250 0.4 1 124176 6074 20 128046 0.4 1 122760 5286 21 136411 0.4 1 130006 6405 22 129295 0.4 1 124010 5285 23 128135 0.4 1 122564 5571 24 130079 0.4 1 123780 6299 25 129012 0.4 1 123479 5533 26 136257 0.4 1 129431 6826 27 129437 0.4 1 123800 5637 28 125670 0.4 1 120239 5431 29 137167 0.4 1 130662 6505 30 128212 0.4 1 123009 5203 31 137885 0.4 1 131041 6844 32 129723 0.4 1 123955 5768 33 134291 0.4 1 128109 6182 34 135054 0.4 1 128572 6482 35 127673 0.4 1 122422 5251 36 131144 0.4 1 125280 5864 37 138156 0.4 1 132341 5815 38 132282 0.4 1 126380 5902 39 130883 0.4 1 124730 6153 40 133756 0.4 1 127277 6479 41 176214 0.4 1 168659 7555 42 111423 0.4 1 106578 4845 43 96638 0.4 1 92166 4472 44 119577 0.4 1 114379 5198 45 123043 0.4 1 117604 5439 46 117720 0.4 1 112740 4980 47 126232 0.4 1 120292 5940 48 120666 0.4 1 115106 5560 49 127195 0.4 1 121296 5899 50 113967 0.4 1 109227 4740 51 117747 0.4 1 112597 5150 52 118860 0.4 1 113631 5229 53 110016 0.4 1 105566 4450 54 110627 0.4 1 105925 4702 55 121624 0.4 1 116645 4979 56 111984 0.4 1 107493 4491 57 108065 0.4 1 103638 4427 58 114833 0.4 1 110436 4397 59 107174 0.4 1 102919 4255 60 98824 0.4 1 94808 4016 61 106890 0.4 1 102659 4231 62 108163 0.4 1 104054 4109 63 100550 0.4 1 96719 3831 64 97437 0.4 1 94023 3414 65 94630 0.4 1 91199 3431 66 88842 0.4 1 85544 3298 67 89481 0.4 1 86154 3327 68 86471 0.4 1 83101 3370 69 90352 0.4 1 86989 3363 70 87806 0.4 1 84448 3358 71 97722 0.4 1 93795 3927 72 115522 0.4 1 110389 5133 73 166292 0.4 1 154242 12050 74 566225 0.4 1 546310 19915 75 550259 0.4 1 531610 18649 76 401875 0.4 1 387843 14032 77 286932 0.4 1 277190 9742 78 183607 0.4 1 177416 6191 79 103605 0.4 1 100045 3560 80 63667 0.4 1 61475 2192 81 36968 0.4 1 35612 1356 82 23409 0.4 1 22452 957 83 17430 0.4 1 16688 742 84 14522 0.4 1 13882 640 85 11939 0.4 1 11462 477 86 10115 0.4 1 9697 418 87 8444 0.4 1 8086 358 88 7477 0.4 1 7124 353 89 7624 0.4 1 7264 360 90 9924 0.4 1 9505 419 91 14840 0.4 1 14220 620 92 22857 0.4 1 21896 961 93 53062 0.4 1 50901 2161 94 159814 0.4 1 153603 6211 95 249272 0.4 1 239733 9539 96 101089 0.4 1 96837 4252 97 62884 0.4 1 60016 2868 98 27205 0.4 1 25892 1313 99 25310 0.4 1 24074 1236 100 28616 0.4 1 27018 1598 101 52941 0.4 1 48354 4587 RUN STATISTICS FOR INPUT FILE: EPI-215_S31_L004_R1_001.fastq.gz ============================================= 24211042 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4020215 (16.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 15801672 (65.3%) RRBS reads trimmed by 2 bp at the start when read started with CAA (194431) or CGA (166176) in total: 360607 (1.5%)