SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-193_S22_L003_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-193_S22_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 609.75 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 32,584,046 Reads with adapters: 22,989,471 (70.6%) Reads written (passing filters): 32,584,046 (100.0%) Total basepairs processed: 3,198,771,046 bp Total written (filtered): 2,298,694,501 bp (71.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22989471 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.7% C: 22.8% G: 23.4% T: 31.7% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 4114120 8146011.5 0 4114120 2 1014987 2036502.9 0 1014987 3 410404 509125.7 0 410404 4 293426 127281.4 0 293426 5 167834 31820.4 0 167834 6 163106 7955.1 0 163106 7 150678 1988.8 0 150678 8 161873 497.2 0 161873 9 170056 124.3 0 168481 1575 10 158633 31.1 1 151933 6700 11 167203 7.8 1 159071 8132 12 162206 1.9 1 154769 7437 13 158263 0.5 1 150850 7413 14 174304 0.5 1 161629 12675 15 165898 0.5 1 153400 12498 16 181079 0.5 1 167028 14051 17 176291 0.5 1 162836 13455 18 163156 0.5 1 151676 11480 19 180838 0.5 1 165403 15435 20 168336 0.5 1 156051 12285 21 191837 0.5 1 175987 15850 22 179659 0.5 1 166340 13319 23 170922 0.5 1 157835 13087 24 182480 0.5 1 167980 14500 25 172853 0.5 1 159799 13054 26 192723 0.5 1 176654 16069 27 180793 0.5 1 169997 10796 28 172677 0.5 1 163369 9308 29 193767 0.5 1 182688 11079 30 182811 0.5 1 173219 9592 31 199064 0.5 1 186884 12180 32 189757 0.5 1 179550 10207 33 200107 0.5 1 188927 11180 34 192028 0.5 1 181467 10561 35 188964 0.5 1 178830 10134 36 187168 0.5 1 177436 9732 37 204378 0.5 1 193631 10747 38 185772 0.5 1 176262 9510 39 194396 0.5 1 184328 10068 40 204818 0.5 1 193673 11145 41 297124 0.5 1 284156 12968 42 181538 0.5 1 173900 7638 43 84282 0.5 1 78966 5316 44 178686 0.5 1 170112 8574 45 173680 0.5 1 165451 8229 46 171184 0.5 1 163195 7989 47 185654 0.5 1 176569 9085 48 171929 0.5 1 163431 8498 49 185142 0.5 1 175788 9354 50 169911 0.5 1 162002 7909 51 168437 0.5 1 160698 7739 52 161971 0.5 1 154372 7599 53 157037 0.5 1 150285 6752 54 156982 0.5 1 149975 7007 55 162098 0.5 1 155153 6945 56 152538 0.5 1 145892 6646 57 145749 0.5 1 139331 6418 58 143746 0.5 1 137772 5974 59 142847 0.5 1 136883 5964 60 132136 0.5 1 126597 5539 61 137438 0.5 1 131769 5669 62 139556 0.5 1 133939 5617 63 124776 0.5 1 119823 4953 64 121053 0.5 1 116542 4511 65 114334 0.5 1 110086 4248 66 107358 0.5 1 103171 4187 67 107678 0.5 1 103469 4209 68 103495 0.5 1 99343 4152 69 112069 0.5 1 107588 4481 70 110628 0.5 1 105793 4835 71 121383 0.5 1 115745 5638 72 160059 0.5 1 150839 9220 73 349653 0.5 1 321300 28353 74 1280574 0.5 1 1232651 47923 75 1157480 0.5 1 1118098 39382 76 642805 0.5 1 619639 23166 77 372807 0.5 1 359115 13692 78 211754 0.5 1 203963 7791 79 112796 0.5 1 108238 4558 80 71334 0.5 1 68534 2800 81 44308 0.5 1 42407 1901 82 29423 0.5 1 28075 1348 83 23533 0.5 1 22447 1086 84 19740 0.5 1 18780 960 85 17715 0.5 1 16805 910 86 16502 0.5 1 15642 860 87 14460 0.5 1 13741 719 88 13039 0.5 1 12354 685 89 12738 0.5 1 12079 659 90 16189 0.5 1 15334 855 91 22977 0.5 1 21814 1163 92 38071 0.5 1 36177 1894 93 97819 0.5 1 93304 4515 94 299813 0.5 1 286502 13311 95 522988 0.5 1 500374 22614 96 221161 0.5 1 210921 10240 97 124223 0.5 1 117939 6284 98 46957 0.5 1 44532 2425 99 44489 0.5 1 42151 2338 100 40639 0.5 1 38273 2366 101 71321 0.5 1 66082 5239 RUN STATISTICS FOR INPUT FILE: EPI-193_S22_L003_R1_001.fastq.gz ============================================= 32584046 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 6898762 (21.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 22550815 (69.2%)