SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-128_S34_L005_R2_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 All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_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/20180516_geoduck_trimgalore_rrbs/EPI-128_S34_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 476.43 s (19 us/read; 3.11 M reads/minute). === Summary === Total reads processed: 24,692,504 Reads with adapters: 14,934,124 (60.5%) Reads written (passing filters): 24,692,504 (100.0%) Total basepairs processed: 2,468,847,949 bp Total written (filtered): 2,285,356,310 bp (92.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14934124 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.4% C: 25.0% G: 7.2% T: 28.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8886476 6173126.0 0 8886476 2 193460 1543281.5 0 193460 3 179484 385820.4 0 179484 4 134874 96455.1 0 134874 5 133712 24113.8 0 133712 6 134515 6028.4 0 134515 7 127750 1507.1 0 127750 8 166244 376.8 0 166244 9 122112 94.2 0 121553 559 10 122512 23.5 1 117969 4543 11 116330 5.9 1 110262 6068 12 116265 1.5 1 110704 5561 13 110775 0.4 1 105369 5406 14 124485 0.4 1 118609 5876 15 114058 0.4 1 108554 5504 16 113430 0.4 1 108022 5408 17 119352 0.4 1 113945 5407 18 100512 0.4 1 95684 4828 19 108406 0.4 1 103518 4888 20 105813 0.4 1 100683 5130 21 109719 0.4 1 103776 5943 22 113334 0.4 1 107588 5746 23 102874 0.4 1 97847 5027 24 110191 0.4 1 104739 5452 25 92793 0.4 1 88196 4597 26 98658 0.4 1 92965 5693 27 103155 0.4 1 96398 6757 28 103378 0.4 1 98463 4915 29 101158 0.4 1 94937 6221 30 110942 0.4 1 106184 4758 31 89269 0.4 1 84557 4712 32 94781 0.4 1 90977 3804 33 98519 0.4 1 93558 4961 34 102785 0.4 1 97006 5779 35 93779 0.4 1 90149 3630 36 88604 0.4 1 83931 4673 37 84310 0.4 1 80044 4266 38 76554 0.4 1 72589 3965 39 77847 0.4 1 73825 4022 40 79007 0.4 1 74897 4110 41 76518 0.4 1 73126 3392 42 81899 0.4 1 78766 3133 43 64197 0.4 1 60852 3345 44 71546 0.4 1 68325 3221 45 109426 0.4 1 105881 3545 46 64642 0.4 1 61709 2933 47 43337 0.4 1 40792 2545 48 73296 0.4 1 70734 2562 49 40234 0.4 1 38299 1935 50 46548 0.4 1 44197 2351 51 74127 0.4 1 71820 2307 52 35633 0.4 1 33811 1822 53 40766 0.4 1 38672 2094 54 35297 0.4 1 33499 1798 55 48128 0.4 1 46029 2099 56 46603 0.4 1 44236 2367 57 42105 0.4 1 40152 1953 58 41423 0.4 1 39594 1829 59 38118 0.4 1 36258 1860 60 39277 0.4 1 37297 1980 61 40458 0.4 1 38313 2145 62 44464 0.4 1 42249 2215 63 49723 0.4 1 47300 2423 64 51077 0.4 1 48624 2453 65 51974 0.4 1 49575 2399 66 51606 0.4 1 49329 2277 67 54310 0.4 1 51543 2767 68 104352 0.4 1 101629 2723 69 33627 0.4 1 32173 1454 70 16312 0.4 1 15351 961 71 10729 0.4 1 9966 763 72 8543 0.4 1 7930 613 73 7148 0.4 1 6560 588 74 6007 0.4 1 5526 481 75 5171 0.4 1 4774 397 76 4494 0.4 1 4153 341 77 3615 0.4 1 3343 272 78 2974 0.4 1 2733 241 79 2441 0.4 1 2266 175 80 1671 0.4 1 1550 121 81 1265 0.4 1 1170 95 82 989 0.4 1 918 71 83 603 0.4 1 564 39 84 381 0.4 1 352 29 85 238 0.4 1 215 23 86 134 0.4 1 124 10 87 91 0.4 1 79 12 88 56 0.4 1 49 7 89 65 0.4 1 57 8 90 73 0.4 1 62 11 91 111 0.4 1 96 15 92 189 0.4 1 176 13 93 337 0.4 1 290 47 94 778 0.4 1 695 83 95 1199 0.4 1 1087 112 96 699 0.4 1 635 64 97 343 0.4 1 304 39 98 97 0.4 1 92 5 99 75 0.4 1 66 9 100 93 0.4 1 84 9 101 270 0.4 1 236 34 RUN STATISTICS FOR INPUT FILE: EPI-128_S34_L005_R2_001.fastq.gz ============================================= 24692504 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2970017 (12.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 24692504 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 134701 (0.55%)