SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-135_S35_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-135_S35_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 545.28 s (19 us/read; 3.19 M reads/minute). === Summary === Total reads processed: 28,955,967 Reads with adapters: 16,918,482 (58.4%) Reads written (passing filters): 28,955,967 (100.0%) Total basepairs processed: 2,911,650,789 bp Total written (filtered): 2,566,799,495 bp (88.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16918482 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.1% C: 7.9% G: 26.2% T: 40.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 5428543 7238991.8 0 5428543 2 1290338 1809747.9 0 1290338 3 515272 452437.0 0 515272 4 347053 113109.2 0 347053 5 169096 28277.3 0 169096 6 171664 7069.3 0 171664 7 161079 1767.3 0 161079 8 200034 441.8 0 200034 9 168076 110.5 0 166562 1514 10 160791 27.6 1 153792 6999 11 163873 6.9 1 155494 8379 12 159582 1.7 1 151837 7745 13 147870 0.4 1 140857 7013 14 170443 0.4 1 160715 9728 15 163034 0.4 1 154987 8047 16 175286 0.4 1 164943 10343 17 162040 0.4 1 153843 8197 18 150480 0.4 1 143218 7262 19 167101 0.4 1 157210 9891 20 155034 0.4 1 147927 7107 21 176265 0.4 1 165658 10607 22 164972 0.4 1 157002 7970 23 148517 0.4 1 140854 7663 24 159376 0.4 1 150398 8978 25 145410 0.4 1 138481 6929 26 165859 0.4 1 156308 9551 27 147453 0.4 1 140101 7352 28 140963 0.4 1 134308 6655 29 158516 0.4 1 150119 8397 30 146611 0.4 1 139727 6884 31 159589 0.4 1 150411 9178 32 142497 0.4 1 135686 6811 33 150448 0.4 1 142532 7916 34 141785 0.4 1 134909 6876 35 141080 0.4 1 134179 6901 36 141884 0.4 1 134682 7202 37 155716 0.4 1 147621 8095 38 136379 0.4 1 129949 6430 39 139061 0.4 1 131877 7184 40 148264 0.4 1 140515 7749 41 216332 0.4 1 207733 8599 42 117767 0.4 1 112933 4834 43 56334 0.4 1 52793 3541 44 125715 0.4 1 119688 6027 45 121953 0.4 1 116379 5574 46 122690 0.4 1 117073 5617 47 133187 0.4 1 126535 6652 48 125321 0.4 1 119309 6012 49 124393 0.4 1 117985 6408 50 113494 0.4 1 108278 5216 51 109913 0.4 1 104966 4947 52 104840 0.4 1 100229 4611 53 105571 0.4 1 101038 4533 54 105498 0.4 1 100725 4773 55 109384 0.4 1 104866 4518 56 105341 0.4 1 100708 4633 57 103448 0.4 1 99158 4290 58 96918 0.4 1 93426 3492 59 94925 0.4 1 91244 3681 60 88697 0.4 1 85302 3395 61 90666 0.4 1 87292 3374 62 97308 0.4 1 93711 3597 63 99049 0.4 1 95218 3831 64 103468 0.4 1 99781 3687 65 94368 0.4 1 90925 3443 66 90631 0.4 1 87290 3341 67 82973 0.4 1 79943 3030 68 70118 0.4 1 67507 2611 69 72946 0.4 1 70344 2602 70 67784 0.4 1 65310 2474 71 64306 0.4 1 61917 2389 72 65654 0.4 1 63003 2651 73 79697 0.4 1 75638 4059 74 140063 0.4 1 136002 4061 75 65158 0.4 1 62998 2160 76 30764 0.4 1 29569 1195 77 18668 0.4 1 17936 732 78 12681 0.4 1 12176 505 79 8732 0.4 1 8400 332 80 6313 0.4 1 6101 212 81 4391 0.4 1 4207 184 82 3076 0.4 1 2950 126 83 2246 0.4 1 2146 100 84 1443 0.4 1 1367 76 85 998 0.4 1 947 51 86 648 0.4 1 617 31 87 469 0.4 1 443 26 88 313 0.4 1 296 17 89 277 0.4 1 251 26 90 331 0.4 1 304 27 91 453 0.4 1 424 29 92 723 0.4 1 683 40 93 1690 0.4 1 1622 68 94 4123 0.4 1 3964 159 95 6446 0.4 1 6143 303 96 3311 0.4 1 3137 174 97 1898 0.4 1 1757 141 98 774 0.4 1 709 65 99 778 0.4 1 696 82 100 1026 0.4 1 872 154 101 2666 0.4 1 2062 604 RUN STATISTICS FOR INPUT FILE: EPI-135_S35_L005_R1_001.fastq.gz ============================================= 28955967 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3071325 (10.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 16705036 (57.7%) RRBS reads trimmed by 2 bp at the start when read started with CAA (191068) or CGA (170553) in total: 361621 (1.2%)