SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-143_S37_L005_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-143_S37_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 403.39 s (19 us/read; 3.17 M reads/minute). === Summary === Total reads processed: 21,282,370 Reads with adapters: 11,260,261 (52.9%) Reads written (passing filters): 21,282,370 (100.0%) Total basepairs processed: 2,140,435,130 bp Total written (filtered): 1,969,813,510 bp (92.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11260261 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.6% C: 6.9% G: 24.0% T: 42.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4482373 5320592.5 0 4482373 2 1024256 1330148.1 0 1024256 3 391385 332537.0 0 391385 4 255078 83134.3 0 255078 5 113489 20783.6 0 113489 6 115980 5195.9 0 115980 7 105271 1299.0 0 105271 8 129522 324.7 0 129522 9 110666 81.2 0 109633 1033 10 106179 20.3 1 99837 6342 11 110354 5.1 1 102703 7651 12 104385 1.3 1 97519 6866 13 96682 0.3 1 90386 6296 14 110539 0.3 1 102174 8365 15 101566 0.3 1 94805 6761 16 114572 0.3 1 105867 8705 17 104814 0.3 1 97519 7295 18 99457 0.3 1 92825 6632 19 103281 0.3 1 95631 7650 20 95227 0.3 1 88927 6300 21 105115 0.3 1 97526 7589 22 98193 0.3 1 91817 6376 23 96943 0.3 1 90261 6682 24 101318 0.3 1 93798 7520 25 91241 0.3 1 85210 6031 26 103285 0.3 1 95528 7757 27 90625 0.3 1 84591 6034 28 85545 0.3 1 79992 5553 29 94254 0.3 1 87786 6468 30 86674 0.3 1 81015 5659 31 99715 0.3 1 92348 7367 32 84200 0.3 1 78692 5508 33 90058 0.3 1 83829 6229 34 88235 0.3 1 82279 5956 35 82555 0.3 1 77106 5449 36 79032 0.3 1 74081 4951 37 81733 0.3 1 76571 5162 38 81929 0.3 1 76523 5406 39 78557 0.3 1 73203 5354 40 80037 0.3 1 74624 5413 41 114724 0.3 1 108177 6547 42 62833 0.3 1 59057 3776 43 41580 0.3 1 38612 2968 44 67438 0.3 1 63124 4314 45 65086 0.3 1 61098 3988 46 63531 0.3 1 59673 3858 47 67974 0.3 1 63592 4382 48 63836 0.3 1 59683 4153 49 63499 0.3 1 59282 4217 50 56634 0.3 1 53151 3483 51 53849 0.3 1 50620 3229 52 51340 0.3 1 48239 3101 53 49441 0.3 1 46531 2910 54 48590 0.3 1 45553 3037 55 50165 0.3 1 47250 2915 56 46742 0.3 1 43937 2805 57 45017 0.3 1 42419 2598 58 42362 0.3 1 40046 2316 59 40287 0.3 1 38063 2224 60 36944 0.3 1 34860 2084 61 37451 0.3 1 35520 1931 62 37410 0.3 1 35363 2047 63 35555 0.3 1 33682 1873 64 35152 0.3 1 33364 1788 65 31900 0.3 1 30175 1725 66 30171 0.3 1 28625 1546 67 28561 0.3 1 27044 1517 68 25844 0.3 1 24437 1407 69 25789 0.3 1 24415 1374 70 23432 0.3 1 22167 1265 71 22331 0.3 1 21152 1179 72 22086 0.3 1 20817 1269 73 22982 0.3 1 21410 1572 74 35894 0.3 1 34262 1632 75 15713 0.3 1 14960 753 76 6613 0.3 1 6252 361 77 3981 0.3 1 3763 218 78 2875 0.3 1 2733 142 79 1974 0.3 1 1842 132 80 1438 0.3 1 1346 92 81 1043 0.3 1 965 78 82 653 0.3 1 612 41 83 446 0.3 1 415 31 84 285 0.3 1 275 10 85 201 0.3 1 183 18 86 128 0.3 1 124 4 87 92 0.3 1 86 6 88 68 0.3 1 61 7 89 70 0.3 1 64 6 90 83 0.3 1 80 3 91 130 0.3 1 113 17 92 204 0.3 1 179 25 93 317 0.3 1 281 36 94 549 0.3 1 503 46 95 775 0.3 1 727 48 96 676 0.3 1 621 55 97 373 0.3 1 333 40 98 127 0.3 1 109 18 99 72 0.3 1 64 8 100 142 0.3 1 114 28 101 483 0.3 1 301 182 RUN STATISTICS FOR INPUT FILE: EPI-143_S37_L005_R1_001.fastq.gz ============================================= 21282370 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2281724 (10.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 11124407 (52.3%) RRBS reads trimmed by 2 bp at the start when read started with CAA (134968) or CGA (127968) in total: 262936 (1.2%)