SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-199_S24_L003_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-199_S24_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 337.45 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 18,024,873 Reads with adapters: 12,800,216 (71.0%) Reads written (passing filters): 18,024,873 (100.0%) Total basepairs processed: 1,760,316,034 bp Total written (filtered): 1,394,026,623 bp (79.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12800216 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.6% C: 21.0% G: 15.8% T: 30.0% none/other: 1.5% Overview of removed sequences length count expect max.err error counts 1 4434426 4506218.2 0 4434426 2 163628 1126554.6 0 163628 3 117881 281638.6 0 117881 4 98347 70409.7 0 98347 5 98568 17602.4 0 98568 6 97723 4400.6 0 97723 7 93893 1100.2 0 93893 8 98433 275.0 0 98433 9 95773 68.8 0 95328 445 10 98315 17.2 1 94941 3374 11 93901 4.3 1 89831 4070 12 97422 1.1 1 93251 4171 13 95152 0.3 1 91269 3883 14 105018 0.3 1 100536 4482 15 96808 0.3 1 92821 3987 16 99372 0.3 1 95361 4011 17 104591 0.3 1 100291 4300 18 92412 0.3 1 88825 3587 19 100793 0.3 1 96711 4082 20 98350 0.3 1 94180 4170 21 101732 0.3 1 97087 4645 22 105546 0.3 1 100964 4582 23 100580 0.3 1 96125 4455 24 112214 0.3 1 107182 5032 25 97570 0.3 1 93421 4149 26 100570 0.3 1 95750 4820 27 103615 0.3 1 97872 5743 28 109943 0.3 1 105171 4772 29 105864 0.3 1 100426 5438 30 118109 0.3 1 113175 4934 31 101656 0.3 1 96840 4816 32 108090 0.3 1 103838 4252 33 115082 0.3 1 109761 5321 34 116860 0.3 1 111211 5649 35 114834 0.3 1 110582 4252 36 107301 0.3 1 102527 4774 37 110421 0.3 1 105925 4496 38 99226 0.3 1 95072 4154 39 104956 0.3 1 100448 4508 40 105778 0.3 1 101076 4702 41 106049 0.3 1 101891 4158 42 106146 0.3 1 102479 3667 43 92311 0.3 1 88485 3826 44 97900 0.3 1 93970 3930 45 137150 0.3 1 132601 4549 46 93568 0.3 1 89975 3593 47 68195 0.3 1 65374 2821 48 98439 0.3 1 95139 3300 49 71130 0.3 1 68541 2589 50 74117 0.3 1 71237 2880 51 106842 0.3 1 103674 3168 52 63430 0.3 1 60917 2513 53 66518 0.3 1 64088 2430 54 58692 0.3 1 56535 2157 55 72268 0.3 1 69918 2350 56 69649 0.3 1 67078 2571 57 64538 0.3 1 62164 2374 58 63896 0.3 1 61645 2251 59 61955 0.3 1 59524 2431 60 60723 0.3 1 58306 2417 61 61879 0.3 1 59390 2489 62 66089 0.3 1 63246 2843 63 69201 0.3 1 66057 3144 64 73430 0.3 1 70133 3297 65 85467 0.3 1 81415 4052 66 109233 0.3 1 103474 5759 67 199838 0.3 1 183350 16488 68 764787 0.3 1 743426 21361 69 251637 0.3 1 241588 10049 70 133818 0.3 1 128053 5765 71 68444 0.3 1 64865 3579 72 46387 0.3 1 43794 2593 73 32208 0.3 1 30170 2038 74 24977 0.3 1 23311 1666 75 20069 0.3 1 18719 1350 76 17559 0.3 1 16325 1234 77 15902 0.3 1 14733 1169 78 13735 0.3 1 12649 1086 79 12266 0.3 1 11319 947 80 10711 0.3 1 9856 855 81 9236 0.3 1 8500 736 82 8284 0.3 1 7535 749 83 7203 0.3 1 6500 703 84 6251 0.3 1 5684 567 85 5346 0.3 1 4829 517 86 4785 0.3 1 4264 521 87 4611 0.3 1 4075 536 88 4634 0.3 1 4084 550 89 5130 0.3 1 4563 567 90 6146 0.3 1 5396 750 91 8381 0.3 1 7372 1009 92 12243 0.3 1 10823 1420 93 27179 0.3 1 24260 2919 94 82853 0.3 1 75231 7622 95 155542 0.3 1 142268 13274 96 69313 0.3 1 63406 5907 97 48942 0.3 1 44834 4108 98 18995 0.3 1 17313 1682 99 20899 0.3 1 19101 1798 100 21512 0.3 1 19553 1959 101 40825 0.3 1 36614 4211 RUN STATISTICS FOR INPUT FILE: EPI-199_S24_L003_R2_001.fastq.gz ============================================= 18024873 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3678637 (20.4%) 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: 18024873 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2111804 (11.72%)