SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-44_S41_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 File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_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/20180514_geoduck_trimgalore_rrbs/EPI-44_S41_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 673.14 s (17 us/read; 3.47 M reads/minute). === Summary === Total reads processed: 38,920,722 Reads with adapters: 34,034,770 (87.4%) Reads written (passing filters): 38,920,722 (100.0%) Total basepairs processed: 3,385,328,777 bp Total written (filtered): 1,354,648,320 bp (40.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34034770 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 17.6% C: 14.2% G: 34.1% T: 29.7% none/other: 4.3% Overview of removed sequences length count expect max.err error counts 1 4074995 9730180.5 0 4074995 2 150796 2432545.1 0 150796 3 110881 608136.3 0 110881 4 83450 152034.1 0 83450 5 83082 38008.5 0 83082 6 79646 9502.1 0 79646 7 78217 2375.5 0 78217 8 77680 593.9 0 77680 9 77380 148.5 0 76978 402 10 83506 37.1 1 78700 4806 11 78901 9.3 1 73026 5875 12 81137 2.3 1 75923 5214 13 77179 0.6 1 72351 4828 14 87387 0.6 1 81923 5464 15 79803 0.6 1 75067 4736 16 81714 0.6 1 76947 4767 17 86724 0.6 1 81883 4841 18 75824 0.6 1 71493 4331 19 83650 0.6 1 78954 4696 20 82847 0.6 1 77419 5428 21 87512 0.6 1 80925 6587 22 91237 0.6 1 85061 6176 23 88534 0.6 1 82881 5653 24 103701 0.6 1 96447 7254 25 83744 0.6 1 78383 5361 26 92879 0.6 1 85669 7210 27 100760 0.6 1 91537 9223 28 108001 0.6 1 100271 7730 29 102558 0.6 1 93709 8849 30 128198 0.6 1 119349 8849 31 112817 0.6 1 103247 9570 32 132316 0.6 1 123828 8488 33 144779 0.6 1 133305 11474 34 142120 0.6 1 130171 11949 35 140092 0.6 1 132254 7838 36 118156 0.6 1 109604 8552 37 120242 0.6 1 112078 8164 38 105370 0.6 1 97746 7624 39 121778 0.6 1 112914 8864 40 116337 0.6 1 107603 8734 41 122141 0.6 1 114885 7256 42 140778 0.6 1 133375 7403 43 99358 0.6 1 92625 6733 44 129719 0.6 1 121449 8270 45 313162 0.6 1 300483 12679 46 117442 0.6 1 110762 6680 47 72394 0.6 1 67542 4852 48 143808 0.6 1 136937 6871 49 72555 0.6 1 68459 4096 50 78978 0.6 1 74292 4686 51 155306 0.6 1 148690 6616 52 75507 0.6 1 71093 4414 53 73543 0.6 1 69310 4233 54 66577 0.6 1 62828 3749 55 86159 0.6 1 81639 4520 56 82189 0.6 1 77659 4530 57 81549 0.6 1 77255 4294 58 90865 0.6 1 85746 5119 59 82082 0.6 1 77095 4987 60 86598 0.6 1 81329 5269 61 101786 0.6 1 94987 6799 62 129752 0.6 1 120695 9057 63 170174 0.6 1 157607 12567 64 233751 0.6 1 216283 17468 65 361445 0.6 1 335467 25978 66 624351 0.6 1 578601 45750 67 1524642 0.6 1 1379473 145169 68 6886361 0.6 1 6624061 262300 69 2630499 0.6 1 2507064 123435 70 1469283 0.6 1 1397120 72163 71 739467 0.6 1 697053 42414 72 467157 0.6 1 438221 28936 73 294597 0.6 1 274344 20253 74 220175 0.6 1 203651 16524 75 170816 0.6 1 156939 13877 76 140106 0.6 1 128112 11994 77 121681 0.6 1 110866 10815 78 105286 0.6 1 95457 9829 79 93535 0.6 1 84288 9247 80 84606 0.6 1 76002 8604 81 76709 0.6 1 68755 7954 82 69613 0.6 1 62076 7537 83 65399 0.6 1 57958 7441 84 60054 0.6 1 52742 7312 85 56331 0.6 1 49321 7010 86 55226 0.6 1 48203 7023 87 55866 0.6 1 48622 7244 88 59152 0.6 1 51326 7826 89 66606 0.6 1 57713 8893 90 84135 0.6 1 73225 10910 91 119826 0.6 1 104730 15096 92 186555 0.6 1 163511 23044 93 427439 0.6 1 378694 48745 94 1285470 0.6 1 1156506 128964 95 2220079 0.6 1 2011361 208718 96 981495 0.6 1 892515 88980 97 564208 0.6 1 511482 52726 98 200736 0.6 1 181832 18904 99 192347 0.6 1 173735 18612 100 180192 0.6 1 162571 17621 101 331222 0.6 1 298161 33061 RUN STATISTICS FOR INPUT FILE: EPI-44_S41_L005_R2_001.fastq.gz ============================================= 38920722 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 21599141 (55.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (427761) or CGA (180955) in total: 608716 (1.6%) Total number of sequences analysed for the sequence pair length validation: 38920722 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 25156677 (64.64%)