SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-193_S22_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-193_S22_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 606.52 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 32,584,046 Reads with adapters: 24,665,835 (75.7%) Reads written (passing filters): 32,584,046 (100.0%) Total basepairs processed: 3,149,934,795 bp Total written (filtered): 2,300,111,875 bp (73.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24665835 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.9% C: 19.5% G: 17.4% T: 31.0% none/other: 1.2% Overview of removed sequences length count expect max.err error counts 1 7108833 8146011.5 0 7108833 2 229860 2036502.9 0 229860 3 190805 509125.7 0 190805 4 165416 127281.4 0 165416 5 167956 31820.4 0 167956 6 168222 7955.1 0 168222 7 161982 1988.8 0 161982 8 168607 497.2 0 168607 9 167978 124.3 0 167296 682 10 167708 31.1 1 162434 5274 11 164939 7.8 1 158244 6695 12 169062 1.9 1 162636 6426 13 165829 0.5 1 159482 6347 14 178717 0.5 1 171738 6979 15 169374 0.5 1 162886 6488 16 172621 0.5 1 166060 6561 17 183498 0.5 1 176658 6840 18 164569 0.5 1 158526 6043 19 174927 0.5 1 168452 6475 20 175155 0.5 1 168271 6884 21 181141 0.5 1 173516 7625 22 185981 0.5 1 178402 7579 23 181528 0.5 1 174465 7063 24 194336 0.5 1 186513 7823 25 175624 0.5 1 168773 6851 26 182770 0.5 1 174549 8221 27 191240 0.5 1 181468 9772 28 197710 0.5 1 189720 7990 29 196033 0.5 1 186831 9202 30 213176 0.5 1 204951 8225 31 188679 0.5 1 180621 8058 32 198703 0.5 1 191490 7213 33 214535 0.5 1 205342 9193 34 222247 0.5 1 212032 10215 35 205531 0.5 1 198476 7055 36 203761 0.5 1 195283 8478 37 206081 0.5 1 198010 8071 38 188526 0.5 1 181167 7359 39 198878 0.5 1 190759 8119 40 201681 0.5 1 193466 8215 41 200228 0.5 1 192868 7360 42 199111 0.5 1 192417 6694 43 184465 0.5 1 177390 7075 44 189289 0.5 1 182312 6977 45 246542 0.5 1 238731 7811 46 188971 0.5 1 182396 6575 47 140150 0.5 1 134674 5476 48 194629 0.5 1 188450 6179 49 145652 0.5 1 140679 4973 50 152718 0.5 1 147255 5463 51 211066 0.5 1 205246 5820 52 135860 0.5 1 131090 4770 53 142948 0.5 1 138184 4764 54 126710 0.5 1 122376 4334 55 153472 0.5 1 148672 4800 56 147243 0.5 1 142128 5115 57 139168 0.5 1 134488 4680 58 136110 0.5 1 131548 4562 59 133114 0.5 1 128473 4641 60 130358 0.5 1 125517 4841 61 133894 0.5 1 128892 5002 62 140579 0.5 1 134934 5645 63 144796 0.5 1 138993 5803 64 153301 0.5 1 146876 6425 65 177421 0.5 1 169471 7950 66 227891 0.5 1 216827 11064 67 441266 0.5 1 404809 36457 68 2055325 0.5 1 2003050 52275 69 756796 0.5 1 730867 25929 70 404675 0.5 1 390208 14467 71 206228 0.5 1 197580 8648 72 133815 0.5 1 127772 6043 73 88072 0.5 1 83681 4391 74 67485 0.5 1 63916 3569 75 54081 0.5 1 50983 3098 76 46017 0.5 1 43360 2657 77 40797 0.5 1 38229 2568 78 36102 0.5 1 33752 2350 79 31745 0.5 1 29692 2053 80 27538 0.5 1 25700 1838 81 24522 0.5 1 22836 1686 82 21359 0.5 1 19878 1481 83 18784 0.5 1 17360 1424 84 16729 0.5 1 15445 1284 85 14737 0.5 1 13471 1266 86 14165 0.5 1 12962 1203 87 14015 0.5 1 12691 1324 88 14438 0.5 1 13063 1375 89 16781 0.5 1 15173 1608 90 20992 0.5 1 18980 2012 91 29020 0.5 1 26305 2715 92 43239 0.5 1 39436 3803 93 98138 0.5 1 90037 8101 94 290307 0.5 1 269408 20899 95 496937 0.5 1 463281 33656 96 211823 0.5 1 197753 14070 97 120183 0.5 1 111804 8379 98 43845 0.5 1 40724 3121 99 40884 0.5 1 37929 2955 100 37475 0.5 1 34743 2732 101 67615 0.5 1 62113 5502 RUN STATISTICS FOR INPUT FILE: EPI-193_S22_L003_R2_001.fastq.gz ============================================= 32584046 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7874385 (24.2%) 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: 32584046 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5813577 (17.84%)