SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-159_S6_L002_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 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-159_S6_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 300.57 s (19 us/read; 3.19 M reads/minute). === Summary === Total reads processed: 15,964,870 Reads with adapters: 9,104,101 (57.0%) Reads written (passing filters): 15,964,870 (100.0%) Total basepairs processed: 1,601,164,936 bp Total written (filtered): 1,420,036,295 bp (88.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9104101 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.2% C: 11.4% G: 24.6% T: 39.3% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 3036072 3991217.5 0 3036072 2 718601 997804.4 0 718601 3 286515 249451.1 0 286515 4 193838 62362.8 0 193838 5 103261 15590.7 0 103261 6 103625 3897.7 0 103625 7 95838 974.4 0 95838 8 111825 243.6 0 111825 9 99403 60.9 0 98563 840 10 97139 15.2 1 93278 3861 11 95025 3.8 1 90952 4073 12 91257 1.0 1 87366 3891 13 88780 0.2 1 85068 3712 14 97668 0.2 1 92606 5062 15 93424 0.2 1 89144 4280 16 97513 0.2 1 92656 4857 17 92393 0.2 1 87822 4571 18 85195 0.2 1 81273 3922 19 93322 0.2 1 88079 5243 20 85547 0.2 1 81621 3926 21 95742 0.2 1 90208 5534 22 89978 0.2 1 85777 4201 23 82149 0.2 1 78283 3866 24 85152 0.2 1 80689 4463 25 81032 0.2 1 77298 3734 26 87413 0.2 1 82780 4633 27 80199 0.2 1 76530 3669 28 76736 0.2 1 73275 3461 29 81907 0.2 1 77949 3958 30 76778 0.2 1 73543 3235 31 79984 0.2 1 76099 3885 32 74249 0.2 1 71092 3157 33 78091 0.2 1 74571 3520 34 71891 0.2 1 68812 3079 35 70918 0.2 1 67781 3137 36 70245 0.2 1 67292 2953 37 73359 0.2 1 70009 3350 38 68133 0.2 1 65218 2915 39 67910 0.2 1 64908 3002 40 69154 0.2 1 65735 3419 41 98960 0.2 1 95015 3945 42 57604 0.2 1 55366 2238 43 27046 0.2 1 25526 1520 44 55845 0.2 1 53433 2412 45 53406 0.2 1 51071 2335 46 52794 0.2 1 50624 2170 47 55229 0.2 1 52798 2431 48 50959 0.2 1 48648 2311 49 51503 0.2 1 49131 2372 50 46729 0.2 1 44767 1962 51 45694 0.2 1 43755 1939 52 42773 0.2 1 40983 1790 53 40947 0.2 1 39411 1536 54 40419 0.2 1 38831 1588 55 41256 0.2 1 39676 1580 56 38527 0.2 1 37065 1462 57 35701 0.2 1 34344 1357 58 35155 0.2 1 33877 1278 59 33315 0.2 1 32060 1255 60 30461 0.2 1 29365 1096 61 30540 0.2 1 29426 1114 62 31015 0.2 1 29924 1091 63 28390 0.2 1 27433 957 64 28196 0.2 1 27331 865 65 25793 0.2 1 24878 915 66 23970 0.2 1 23121 849 67 23003 0.2 1 22195 808 68 21088 0.2 1 20343 745 69 22189 0.2 1 21386 803 70 20903 0.2 1 20127 776 71 22847 0.2 1 21953 894 72 24677 0.2 1 23587 1090 73 41395 0.2 1 38523 2872 74 134483 0.2 1 130027 4456 75 99020 0.2 1 95953 3067 76 52083 0.2 1 50273 1810 77 30114 0.2 1 29063 1051 78 17811 0.2 1 17203 608 79 10188 0.2 1 9820 368 80 6832 0.2 1 6560 272 81 4386 0.2 1 4210 176 82 3265 0.2 1 3148 117 83 2552 0.2 1 2443 109 84 2017 0.2 1 1918 99 85 1779 0.2 1 1695 84 86 1542 0.2 1 1484 58 87 1421 0.2 1 1362 59 88 1161 0.2 1 1095 66 89 1114 0.2 1 1068 46 90 1416 0.2 1 1341 75 91 1857 0.2 1 1769 88 92 3031 0.2 1 2865 166 93 7109 0.2 1 6804 305 94 21559 0.2 1 20720 839 95 36467 0.2 1 35005 1462 96 16468 0.2 1 15759 709 97 12083 0.2 1 11491 592 98 5319 0.2 1 5064 255 99 5608 0.2 1 5318 290 100 6433 0.2 1 6058 375 101 11393 0.2 1 10412 981 RUN STATISTICS FOR INPUT FILE: EPI-159_S6_L002_R1_001.fastq.gz ============================================= 15964870 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1698548 (10.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 9036230 (56.6%)