SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-111_S29_L005_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.2 Cutadapt version: 1.12 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. Sequences with adapter contamination will be trimmed a further 2 bp to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Output file will be GZIP compressed This is cutadapt 1.12 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sean/Documents/Geoduck/trimmed-data/EPI-111_S29_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 544.91 s (20 us/read; 2.98 M reads/minute). === Summary === Total reads processed: 27,105,772 Reads with adapters: 14,982,353 (55.3%) Reads written (passing filters): 27,105,772 (100.0%) Total basepairs processed: 2,726,839,347 bp Total written (filtered): 2,481,800,627 bp (91.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14982353 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.8% C: 7.1% G: 24.3% T: 41.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5483972 6776443.0 0 5483972 2 1274250 1694110.8 0 1274250 3 512779 423527.7 0 512779 4 341820 105881.9 0 341820 5 164645 26470.5 0 164645 6 174313 6617.6 0 174313 7 160211 1654.4 0 160211 8 211425 413.6 0 211425 9 157792 103.4 0 156504 1288 10 148111 25.9 1 141574 6537 11 155336 6.5 1 147276 8060 12 147193 1.6 1 140126 7067 13 136226 0.4 1 129975 6251 14 157373 0.4 1 148257 9116 15 144686 0.4 1 137606 7080 16 161435 0.4 1 151860 9575 17 149652 0.4 1 142038 7614 18 139661 0.4 1 132766 6895 19 150743 0.4 1 141849 8894 20 135171 0.4 1 128911 6260 21 149597 0.4 1 141060 8537 22 139108 0.4 1 132453 6655 23 136887 0.4 1 129733 7154 24 142512 0.4 1 134191 8321 25 129883 0.4 1 123495 6388 26 145286 0.4 1 136818 8468 27 129347 0.4 1 123031 6316 28 123378 0.4 1 117520 5858 29 133640 0.4 1 126710 6930 30 126474 0.4 1 120518 5956 31 135306 0.4 1 127912 7394 32 120779 0.4 1 115146 5633 33 126665 0.4 1 120506 6159 34 115200 0.4 1 109936 5264 35 117247 0.4 1 111191 6056 36 121546 0.4 1 114784 6762 37 131297 0.4 1 124140 7157 38 116585 0.4 1 110787 5798 39 106975 0.4 1 101874 5101 40 108754 0.4 1 103350 5404 41 167236 0.4 1 160696 6540 42 87670 0.4 1 83719 3951 43 59983 0.4 1 56964 3019 44 98254 0.4 1 93641 4613 45 93948 0.4 1 89639 4309 46 91326 0.4 1 87241 4085 47 99509 0.4 1 94600 4909 48 91905 0.4 1 87395 4510 49 90827 0.4 1 86216 4611 50 81986 0.4 1 78288 3698 51 77745 0.4 1 74308 3437 52 73808 0.4 1 70498 3310 53 72750 0.4 1 69647 3103 54 71711 0.4 1 68460 3251 55 73188 0.4 1 70173 3015 56 69412 0.4 1 66464 2948 57 66606 0.4 1 63927 2679 58 62861 0.4 1 60536 2325 59 60202 0.4 1 57918 2284 60 55284 0.4 1 53296 1988 61 55670 0.4 1 53614 2056 62 57437 0.4 1 55398 2039 63 54602 0.4 1 52532 2070 64 54141 0.4 1 52296 1845 65 49744 0.4 1 47949 1795 66 46907 0.4 1 45215 1692 67 43987 0.4 1 42434 1553 68 39282 0.4 1 37871 1411 69 38064 0.4 1 36742 1322 70 34710 0.4 1 33450 1260 71 32109 0.4 1 30961 1148 72 29538 0.4 1 28469 1069 73 31344 0.4 1 29903 1441 74 50945 0.4 1 49580 1365 75 22262 0.4 1 21578 684 76 9931 0.4 1 9562 369 77 5935 0.4 1 5707 228 78 3974 0.4 1 3834 140 79 2839 0.4 1 2707 132 80 2018 0.4 1 1951 67 81 1309 0.4 1 1260 49 82 933 0.4 1 888 45 83 655 0.4 1 638 17 84 388 0.4 1 368 20 85 240 0.4 1 226 14 86 157 0.4 1 151 6 87 118 0.4 1 113 5 88 83 0.4 1 75 8 89 57 0.4 1 51 6 90 75 0.4 1 66 9 91 131 0.4 1 118 13 92 182 0.4 1 171 11 93 256 0.4 1 234 22 94 495 0.4 1 456 39 95 716 0.4 1 660 56 96 584 0.4 1 554 30 97 313 0.4 1 284 29 98 101 0.4 1 92 9 99 78 0.4 1 66 12 100 141 0.4 1 109 32 101 431 0.4 1 304 127 RUN STATISTICS FOR INPUT FILE: EPI-111_S29_L005_R1_001.fastq.gz ============================================= 27105772 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2777719 (10.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 14980376 (55.3%)