SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-168_S11_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-168_S11_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 444.72 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 23,309,550 Reads with adapters: 12,944,027 (55.5%) Reads written (passing filters): 23,309,550 (100.0%) Total basepairs processed: 2,339,674,044 bp Total written (filtered): 2,105,064,196 bp (90.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12944027 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.5% C: 10.2% G: 25.8% T: 40.2% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 4388270 5827387.5 0 4388270 2 1113160 1456846.9 0 1113160 3 426903 364211.7 0 426903 4 293056 91052.9 0 293056 5 154023 22763.2 0 154023 6 151496 5690.8 0 151496 7 143551 1422.7 0 143551 8 153510 355.7 0 153510 9 151312 88.9 0 149762 1550 10 148533 22.2 1 142648 5885 11 146629 5.6 1 140195 6434 12 141424 1.4 1 135358 6066 13 135490 0.3 1 129789 5701 14 148275 0.3 1 140772 7503 15 137595 0.3 1 131123 6472 16 146565 0.3 1 138958 7607 17 139262 0.3 1 132279 6983 18 130182 0.3 1 124246 5936 19 140790 0.3 1 133032 7758 20 129650 0.3 1 123659 5991 21 143012 0.3 1 134935 8077 22 131460 0.3 1 125264 6196 23 125080 0.3 1 118981 6099 24 128968 0.3 1 122268 6700 25 120534 0.3 1 114803 5731 26 130822 0.3 1 123888 6934 27 119017 0.3 1 113723 5294 28 111830 0.3 1 106987 4843 29 122512 0.3 1 116549 5963 30 113487 0.3 1 108882 4605 31 119423 0.3 1 113536 5887 32 109755 0.3 1 105129 4626 33 113683 0.3 1 108612 5071 34 106168 0.3 1 101699 4469 35 107364 0.3 1 102387 4977 36 104551 0.3 1 99692 4859 37 106416 0.3 1 101893 4523 38 99339 0.3 1 95166 4173 39 95443 0.3 1 91389 4054 40 93198 0.3 1 88549 4649 41 123288 0.3 1 118187 5101 42 81207 0.3 1 77808 3399 43 53662 0.3 1 51050 2612 44 77757 0.3 1 74339 3418 45 73684 0.3 1 70554 3130 46 70075 0.3 1 67121 2954 47 73313 0.3 1 70023 3290 48 66495 0.3 1 63504 2991 49 69357 0.3 1 66166 3191 50 61622 0.3 1 59025 2597 51 59049 0.3 1 56674 2375 52 54284 0.3 1 52049 2235 53 51339 0.3 1 49442 1897 54 49330 0.3 1 47311 2019 55 49154 0.3 1 47253 1901 56 45548 0.3 1 43827 1721 57 41639 0.3 1 39962 1677 58 39669 0.3 1 38244 1425 59 38146 0.3 1 36680 1466 60 33745 0.3 1 32504 1241 61 33757 0.3 1 32547 1210 62 33073 0.3 1 31942 1131 63 29364 0.3 1 28310 1054 64 27579 0.3 1 26645 934 65 24753 0.3 1 23934 819 66 22624 0.3 1 21832 792 67 21625 0.3 1 20795 830 68 19755 0.3 1 19007 748 69 20495 0.3 1 19772 723 70 18842 0.3 1 18136 706 71 19314 0.3 1 18508 806 72 24016 0.3 1 22705 1311 73 44840 0.3 1 41561 3279 74 147916 0.3 1 143047 4869 75 104214 0.3 1 100832 3382 76 58462 0.3 1 56488 1974 77 35133 0.3 1 33933 1200 78 21128 0.3 1 20413 715 79 11859 0.3 1 11433 426 80 7873 0.3 1 7586 287 81 5083 0.3 1 4874 209 82 3454 0.3 1 3311 143 83 2721 0.3 1 2611 110 84 2360 0.3 1 2275 85 85 2063 0.3 1 1974 89 86 1889 0.3 1 1801 88 87 1709 0.3 1 1639 70 88 1470 0.3 1 1407 63 89 1488 0.3 1 1405 83 90 1773 0.3 1 1691 82 91 2502 0.3 1 2357 145 92 4171 0.3 1 4006 165 93 9967 0.3 1 9541 426 94 28286 0.3 1 27121 1165 95 47920 0.3 1 46036 1884 96 22249 0.3 1 21275 974 97 14621 0.3 1 13883 738 98 6231 0.3 1 5914 317 99 6303 0.3 1 5981 322 100 6493 0.3 1 6111 382 101 10551 0.3 1 9605 946 RUN STATISTICS FOR INPUT FILE: EPI-168_S11_L002_R1_001.fastq.gz ============================================= 23309550 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2355317 (10.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 12879661 (55.3%)