SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-227_S35_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-227_S35_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 291.54 s (18 us/read; 3.27 M reads/minute). === Summary === Total reads processed: 15,898,223 Reads with adapters: 10,496,391 (66.0%) Reads written (passing filters): 15,898,223 (100.0%) Total basepairs processed: 1,569,780,163 bp Total written (filtered): 1,203,924,385 bp (76.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10496391 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.3% C: 21.0% G: 23.0% T: 33.3% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 2402942 3974555.8 0 2402942 2 559375 993638.9 0 559375 3 221915 248409.7 0 221915 4 149103 62102.4 0 149103 5 82868 15525.6 0 82868 6 80713 3881.4 0 80713 7 75368 970.4 0 75368 8 83821 242.6 0 83821 9 82775 60.6 0 82018 757 10 79544 15.2 1 76628 2916 11 80685 3.8 1 77575 3110 12 76547 0.9 1 73643 2904 13 77448 0.2 1 74331 3117 14 83619 0.2 1 79978 3641 15 81763 0.2 1 78274 3489 16 85472 0.2 1 81641 3831 17 85460 0.2 1 81628 3832 18 78879 0.2 1 75832 3047 19 83937 0.2 1 79953 3984 20 79916 0.2 1 76837 3079 21 87729 0.2 1 83595 4134 22 81679 0.2 1 78474 3205 23 81403 0.2 1 77988 3415 24 82725 0.2 1 78778 3947 25 81093 0.2 1 77602 3491 26 85493 0.2 1 81410 4083 27 82223 0.2 1 78696 3527 28 79598 0.2 1 76293 3305 29 84962 0.2 1 81059 3903 30 81558 0.2 1 78293 3265 31 84973 0.2 1 81117 3856 32 81639 0.2 1 78185 3454 33 84275 0.2 1 80688 3587 34 80861 0.2 1 77389 3472 35 82191 0.2 1 78515 3676 36 82951 0.2 1 79260 3691 37 83513 0.2 1 80047 3466 38 83241 0.2 1 79748 3493 39 79149 0.2 1 75915 3234 40 79606 0.2 1 75906 3700 41 104665 0.2 1 100312 4353 42 71497 0.2 1 68586 2911 43 55192 0.2 1 52704 2488 44 71234 0.2 1 68308 2926 45 72806 0.2 1 69677 3129 46 68657 0.2 1 65858 2799 47 72666 0.2 1 69459 3207 48 68339 0.2 1 65286 3053 49 70637 0.2 1 67644 2993 50 65406 0.2 1 62810 2596 51 64775 0.2 1 62091 2684 52 64110 0.2 1 61477 2633 53 60337 0.2 1 58099 2238 54 59614 0.2 1 57168 2446 55 62855 0.2 1 60455 2400 56 57651 0.2 1 55512 2139 57 54333 0.2 1 52255 2078 58 55931 0.2 1 53796 2135 59 53209 0.2 1 51169 2040 60 48314 0.2 1 46464 1850 61 50937 0.2 1 49075 1862 62 50176 0.2 1 48334 1842 63 45927 0.2 1 44271 1656 64 43353 0.2 1 41839 1514 65 41065 0.2 1 39654 1411 66 38768 0.2 1 37374 1394 67 37392 0.2 1 36123 1269 68 35536 0.2 1 34318 1218 69 36376 0.2 1 35092 1284 70 34431 0.2 1 33152 1279 71 35970 0.2 1 34540 1430 72 43926 0.2 1 41683 2243 73 87101 0.2 1 79635 7466 74 401325 0.2 1 387668 13657 75 406211 0.2 1 393638 12573 76 285583 0.2 1 276152 9431 77 206238 0.2 1 199798 6440 78 129454 0.2 1 125251 4203 79 74865 0.2 1 72404 2461 80 46390 0.2 1 44839 1551 81 27343 0.2 1 26408 935 82 17304 0.2 1 16636 668 83 12602 0.2 1 12113 489 84 10628 0.2 1 10223 405 85 9142 0.2 1 8772 370 86 8012 0.2 1 7678 334 87 7375 0.2 1 7055 320 88 6550 0.2 1 6275 275 89 6612 0.2 1 6314 298 90 8191 0.2 1 7867 324 91 11551 0.2 1 11073 478 92 18369 0.2 1 17685 684 93 44311 0.2 1 42502 1809 94 130925 0.2 1 126105 4820 95 215056 0.2 1 207271 7785 96 90953 0.2 1 87257 3696 97 55275 0.2 1 52877 2398 98 22209 0.2 1 21258 951 99 21216 0.2 1 20251 965 100 21795 0.2 1 20644 1151 101 34708 0.2 1 32131 2577 RUN STATISTICS FOR INPUT FILE: EPI-227_S35_L004_R1_001.fastq.gz ============================================= 15898223 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2816948 (17.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 10126619 (63.7%) RRBS reads trimmed by 2 bp at the start when read started with CAA (142148) or CGA (102470) in total: 244618 (1.5%)