SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-181_S16_L003_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-181_S16_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 535.28 s (19 us/read; 3.09 M reads/minute). === Summary === Total reads processed: 27,579,953 Reads with adapters: 17,048,152 (61.8%) Reads written (passing filters): 27,579,953 (100.0%) Total basepairs processed: 2,762,247,024 bp Total written (filtered): 2,530,086,509 bp (91.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17048152 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.0% C: 23.8% G: 7.5% T: 29.5% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 9490090 6894988.2 0 9490090 2 237810 1723747.1 0 237810 3 208283 430936.8 0 208283 4 171129 107734.2 0 171129 5 168852 26933.5 0 168852 6 169554 6733.4 0 169554 7 164604 1683.3 0 164604 8 184878 420.8 0 184878 9 165614 105.2 0 164923 691 10 167569 26.3 1 163184 4385 11 150038 6.6 1 144806 5232 12 151490 1.6 1 146243 5247 13 146199 0.4 1 141169 5030 14 157823 0.4 1 152243 5580 15 148741 0.4 1 143620 5121 16 146557 0.4 1 141418 5139 17 149173 0.4 1 144051 5122 18 132553 0.4 1 128005 4548 19 139541 0.4 1 134842 4699 20 137787 0.4 1 132858 4929 21 139582 0.4 1 134288 5294 22 142267 0.4 1 137094 5173 23 132122 0.4 1 127340 4782 24 135373 0.4 1 130471 4902 25 123296 0.4 1 118883 4413 26 123073 0.4 1 117974 5099 27 124295 0.4 1 118643 5652 28 125684 0.4 1 121169 4515 29 120767 0.4 1 115793 4974 30 127845 0.4 1 123566 4279 31 110066 0.4 1 106088 3978 32 111132 0.4 1 107580 3552 33 117598 0.4 1 113116 4482 34 118077 0.4 1 113213 4864 35 107769 0.4 1 104442 3327 36 106148 0.4 1 102189 3959 37 103814 0.4 1 100130 3684 38 93479 0.4 1 90200 3279 39 96513 0.4 1 93096 3417 40 94314 0.4 1 90793 3521 41 92008 0.4 1 88861 3147 42 89683 0.4 1 86956 2727 43 81074 0.4 1 78131 2943 44 80683 0.4 1 78031 2652 45 98965 0.4 1 96110 2855 46 77401 0.4 1 74793 2608 47 57707 0.4 1 55587 2120 48 78102 0.4 1 75839 2263 49 57935 0.4 1 56130 1805 50 58863 0.4 1 56800 2063 51 80249 0.4 1 78105 2144 52 50139 0.4 1 48482 1657 53 51916 0.4 1 50338 1578 54 45180 0.4 1 43704 1476 55 55149 0.4 1 53576 1573 56 52603 0.4 1 50826 1777 57 48149 0.4 1 46722 1427 58 46650 0.4 1 45277 1373 59 44176 0.4 1 42786 1390 60 42360 0.4 1 40915 1445 61 42260 0.4 1 40786 1474 62 43132 0.4 1 41565 1567 63 44258 0.4 1 42768 1490 64 43780 0.4 1 42215 1565 65 45283 0.4 1 43618 1665 66 47458 0.4 1 45628 1830 67 63712 0.4 1 59641 4071 68 209670 0.4 1 204801 4869 69 73152 0.4 1 70795 2357 70 34449 0.4 1 33152 1297 71 18735 0.4 1 17831 904 72 13880 0.4 1 13165 715 73 10610 0.4 1 10011 599 74 8847 0.4 1 8348 499 75 7483 0.4 1 7021 462 76 6793 0.4 1 6406 387 77 6069 0.4 1 5732 337 78 5491 0.4 1 5169 322 79 4587 0.4 1 4324 263 80 3940 0.4 1 3710 230 81 3428 0.4 1 3218 210 82 2758 0.4 1 2581 177 83 2245 0.4 1 2092 153 84 1700 0.4 1 1559 141 85 1242 0.4 1 1139 103 86 902 0.4 1 819 83 87 850 0.4 1 779 71 88 733 0.4 1 645 88 89 769 0.4 1 684 85 90 932 0.4 1 848 84 91 1219 0.4 1 1100 119 92 1795 0.4 1 1622 173 93 3649 0.4 1 3312 337 94 10820 0.4 1 9966 854 95 18366 0.4 1 16986 1380 96 8287 0.4 1 7633 654 97 6285 0.4 1 5765 520 98 2664 0.4 1 2466 198 99 2767 0.4 1 2545 222 100 3686 0.4 1 3374 312 101 8975 0.4 1 8105 870 RUN STATISTICS FOR INPUT FILE: EPI-181_S16_L003_R2_001.fastq.gz ============================================= 27579953 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2698077 (9.8%) 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: 27579953 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 367035 (1.33%)