SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-170_S13_L002_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-170_S13_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 536.17 s (19 us/read; 3.16 M reads/minute). === Summary === Total reads processed: 28,278,649 Reads with adapters: 20,140,271 (71.2%) Reads written (passing filters): 28,278,649 (100.0%) Total basepairs processed: 2,830,008,633 bp Total written (filtered): 2,391,773,628 bp (84.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20140271 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.1% C: 24.3% G: 8.9% T: 29.5% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 7426559 7069662.2 0 7426559 2 242817 1767415.6 0 242817 3 217006 441853.9 0 217006 4 190331 110463.5 0 190331 5 193841 27615.9 0 193841 6 196535 6904.0 0 196535 7 186554 1726.0 0 186554 8 200115 431.5 0 200115 9 192162 107.9 0 191320 842 10 193519 27.0 1 188194 5325 11 188339 6.7 1 181440 6899 12 192445 1.7 1 185770 6675 13 187664 0.4 1 181093 6571 14 204460 0.4 1 197134 7326 15 193344 0.4 1 186606 6738 16 193590 0.4 1 186941 6649 17 206476 0.4 1 199515 6961 18 186584 0.4 1 180218 6366 19 200880 0.4 1 194081 6799 20 199519 0.4 1 192417 7102 21 206739 0.4 1 198855 7884 22 213131 0.4 1 205305 7826 23 203186 0.4 1 195738 7448 24 215344 0.4 1 207374 7970 25 197072 0.4 1 189720 7352 26 203293 0.4 1 194806 8487 27 210766 0.4 1 200674 10092 28 217075 0.4 1 209168 7907 29 213544 0.4 1 204415 9129 30 232253 0.4 1 224447 7806 31 204229 0.4 1 196273 7956 32 212266 0.4 1 205399 6867 33 227812 0.4 1 219054 8758 34 236560 0.4 1 226758 9802 35 221485 0.4 1 214577 6908 36 217625 0.4 1 209421 8204 37 217943 0.4 1 210241 7702 38 197131 0.4 1 190208 6923 39 205706 0.4 1 198243 7463 40 206325 0.4 1 199183 7142 41 206432 0.4 1 200050 6382 42 202211 0.4 1 196507 5704 43 184050 0.4 1 177947 6103 44 189860 0.4 1 183885 5975 45 235581 0.4 1 229457 6124 46 185765 0.4 1 180256 5509 47 136735 0.4 1 132022 4713 48 190792 0.4 1 185649 5143 49 139330 0.4 1 135071 4259 50 145852 0.4 1 141190 4662 51 202056 0.4 1 197141 4915 52 126992 0.4 1 122998 3994 53 132869 0.4 1 128639 4230 54 117169 0.4 1 113313 3856 55 140672 0.4 1 136688 3984 56 136322 0.4 1 132076 4246 57 125438 0.4 1 121530 3908 58 120452 0.4 1 116820 3632 59 115520 0.4 1 111713 3807 60 111104 0.4 1 107595 3509 61 110656 0.4 1 106928 3728 62 113444 0.4 1 109695 3749 63 111859 0.4 1 108197 3662 64 110049 0.4 1 106344 3705 65 110845 0.4 1 107070 3775 66 111801 0.4 1 108034 3767 67 131280 0.4 1 124837 6443 68 341106 0.4 1 334400 6706 69 123117 0.4 1 119752 3365 70 54827 0.4 1 52810 2017 71 32394 0.4 1 30964 1430 72 25321 0.4 1 24156 1165 73 21010 0.4 1 19881 1129 74 17861 0.4 1 16953 908 75 15735 0.4 1 14925 810 76 13483 0.4 1 12757 726 77 12343 0.4 1 11681 662 78 10756 0.4 1 10211 545 79 8911 0.4 1 8466 445 80 7571 0.4 1 7176 395 81 6168 0.4 1 5858 310 82 4959 0.4 1 4734 225 83 3894 0.4 1 3699 195 84 3197 0.4 1 3038 159 85 2336 0.4 1 2203 133 86 1434 0.4 1 1362 72 87 1289 0.4 1 1216 73 88 714 0.4 1 672 42 89 663 0.4 1 611 52 90 843 0.4 1 789 54 91 869 0.4 1 798 71 92 1264 0.4 1 1137 127 93 1823 0.4 1 1674 149 94 4090 0.4 1 3709 381 95 6537 0.4 1 6003 534 96 5017 0.4 1 4696 321 97 3263 0.4 1 2989 274 98 1119 0.4 1 1010 109 99 812 0.4 1 729 83 100 1409 0.4 1 1240 169 101 6775 0.4 1 5897 878 RUN STATISTICS FOR INPUT FILE: EPI-170_S13_L002_R2_001.fastq.gz ============================================= 28278649 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3545451 (12.5%) 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: 28278649 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 282370 (1.00%)