SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-119_S31_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-119_S31_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 567.83 s (20 us/read; 3.07 M reads/minute). === Summary === Total reads processed: 29,018,872 Reads with adapters: 17,577,477 (60.6%) Reads written (passing filters): 29,018,872 (100.0%) Total basepairs processed: 2,907,924,938 bp Total written (filtered): 2,698,026,759 bp (92.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17577477 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.0% C: 24.5% G: 6.6% T: 28.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10623426 7254718.0 0 10623426 2 204016 1813679.5 0 204016 3 191261 453419.9 0 191261 4 153503 113355.0 0 153503 5 152520 28338.7 0 152520 6 155382 7084.7 0 155382 7 149248 1771.2 0 149248 8 174564 442.8 0 174564 9 153649 110.7 0 153034 615 10 151900 27.7 1 146388 5512 11 141159 6.9 1 133903 7256 12 139912 1.7 1 133411 6501 13 134840 0.4 1 128432 6408 14 148227 0.4 1 141365 6862 15 134894 0.4 1 128378 6516 16 134361 0.4 1 127780 6581 17 140720 0.4 1 134221 6499 18 118306 0.4 1 112462 5844 19 126806 0.4 1 121075 5731 20 124632 0.4 1 118281 6351 21 131172 0.4 1 123910 7262 22 131727 0.4 1 125207 6520 23 120733 0.4 1 114960 5773 24 126875 0.4 1 120837 6038 25 108931 0.4 1 103424 5507 26 114888 0.4 1 108263 6625 27 120301 0.4 1 112508 7793 28 119100 0.4 1 113451 5649 29 117615 0.4 1 110388 7227 30 125958 0.4 1 120320 5638 31 105840 0.4 1 100158 5682 32 108168 0.4 1 103599 4569 33 115423 0.4 1 109408 6015 34 120487 0.4 1 113559 6928 35 105282 0.4 1 101153 4129 36 102375 0.4 1 96773 5602 37 98291 0.4 1 93339 4952 38 89382 0.4 1 84632 4750 39 91561 0.4 1 86681 4880 40 93391 0.4 1 88307 5084 41 88355 0.4 1 84549 3806 42 91995 0.4 1 88554 3441 43 75988 0.4 1 72029 3959 44 80847 0.4 1 77030 3817 45 116644 0.4 1 112674 3970 46 73021 0.4 1 69682 3339 47 50090 0.4 1 47168 2922 48 81729 0.4 1 78774 2955 49 48437 0.4 1 46180 2257 50 55225 0.4 1 52479 2746 51 84488 0.4 1 81817 2671 52 42339 0.4 1 40063 2276 53 47767 0.4 1 45221 2546 54 41242 0.4 1 39126 2116 55 55406 0.4 1 52946 2460 56 54559 0.4 1 51735 2824 57 48852 0.4 1 46482 2370 58 47863 0.4 1 45586 2277 59 45435 0.4 1 43157 2278 60 45171 0.4 1 42778 2393 61 46377 0.4 1 43945 2432 62 50934 0.4 1 48384 2550 63 54649 0.4 1 51861 2788 64 54951 0.4 1 52307 2644 65 55681 0.4 1 52999 2682 66 54806 0.4 1 52274 2532 67 57766 0.4 1 54825 2941 68 109731 0.4 1 106931 2800 69 35365 0.4 1 33787 1578 70 17204 0.4 1 16238 966 71 11271 0.4 1 10463 808 72 9032 0.4 1 8353 679 73 7490 0.4 1 6867 623 74 6420 0.4 1 5957 463 75 5411 0.4 1 5009 402 76 4653 0.4 1 4288 365 77 3737 0.4 1 3444 293 78 3042 0.4 1 2830 212 79 2385 0.4 1 2210 175 80 1669 0.4 1 1511 158 81 1270 0.4 1 1175 95 82 854 0.4 1 762 92 83 655 0.4 1 605 50 84 372 0.4 1 346 26 85 229 0.4 1 204 25 86 134 0.4 1 118 16 87 111 0.4 1 104 7 88 96 0.4 1 83 13 89 88 0.4 1 79 9 90 123 0.4 1 108 15 91 128 0.4 1 111 17 92 231 0.4 1 204 27 93 381 0.4 1 325 56 94 665 0.4 1 589 76 95 995 0.4 1 895 100 96 922 0.4 1 844 78 97 461 0.4 1 412 49 98 156 0.4 1 140 16 99 105 0.4 1 87 18 100 164 0.4 1 138 26 101 484 0.4 1 405 79 RUN STATISTICS FOR INPUT FILE: EPI-119_S31_L005_R2_001.fastq.gz ============================================= 29018872 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3325599 (11.5%) 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: 29018872 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 112889 (0.39%)