SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-214_S30_L004_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-214_S30_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 566.50 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 30,640,077 Reads with adapters: 18,441,426 (60.2%) Reads written (passing filters): 30,640,077 (100.0%) Total basepairs processed: 3,061,380,032 bp Total written (filtered): 2,587,731,461 bp (84.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18441426 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.5% C: 13.8% G: 24.7% T: 37.4% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 5179468 7660019.2 0 5179468 2 1260918 1915004.8 0 1260918 3 497024 478751.2 0 497024 4 336137 119687.8 0 336137 5 188131 29922.0 0 188131 6 187227 7480.5 0 187227 7 173624 1870.1 0 173624 8 194715 467.5 0 194715 9 184665 116.9 0 183157 1508 10 176406 29.2 1 170385 6021 11 177674 7.3 1 171161 6513 12 169959 1.8 1 163715 6244 13 171286 0.5 1 164672 6614 14 178979 0.5 1 171389 7590 15 176966 0.5 1 169797 7169 16 181769 0.5 1 174190 7579 17 181421 0.5 1 173786 7635 18 167221 0.5 1 160894 6327 19 175512 0.5 1 167706 7806 20 169379 0.5 1 162907 6472 21 185265 0.5 1 176818 8447 22 172918 0.5 1 166410 6508 23 166722 0.5 1 160066 6656 24 168591 0.5 1 161187 7404 25 164475 0.5 1 157908 6567 26 168651 0.5 1 161226 7425 27 162432 0.5 1 155858 6574 28 159420 0.5 1 152895 6525 29 168210 0.5 1 161079 7131 30 161855 0.5 1 155582 6273 31 163640 0.5 1 156319 7321 32 162644 0.5 1 156010 6634 33 167055 0.5 1 160255 6800 34 156836 0.5 1 150380 6456 35 150607 0.5 1 144360 6247 36 151330 0.5 1 145185 6145 37 157288 0.5 1 150554 6734 38 146792 0.5 1 140964 5828 39 145476 0.5 1 139311 6165 40 148645 0.5 1 141593 7052 41 211274 0.5 1 203262 8012 42 129365 0.5 1 124690 4675 43 69857 0.5 1 66448 3409 44 124245 0.5 1 119329 4916 45 125279 0.5 1 120258 5021 46 120337 0.5 1 115807 4530 47 124316 0.5 1 119034 5282 48 117042 0.5 1 112033 5009 49 118670 0.5 1 113642 5028 50 109580 0.5 1 105397 4183 51 109058 0.5 1 104715 4343 52 106665 0.5 1 102309 4356 53 101910 0.5 1 98078 3832 54 100110 0.5 1 96201 3909 55 103822 0.5 1 99962 3860 56 96651 0.5 1 93169 3482 57 90532 0.5 1 87148 3384 58 91463 0.5 1 88131 3332 59 87557 0.5 1 84387 3170 60 80810 0.5 1 77865 2945 61 84173 0.5 1 81124 3049 62 83602 0.5 1 80558 3044 63 75296 0.5 1 72628 2668 64 73085 0.5 1 70671 2414 65 69216 0.5 1 66892 2324 66 64464 0.5 1 62219 2245 67 62047 0.5 1 59892 2155 68 57800 0.5 1 55822 1978 69 58168 0.5 1 56246 1922 70 54348 0.5 1 52495 1853 71 56219 0.5 1 54211 2008 72 57141 0.5 1 54734 2407 73 88636 0.5 1 82117 6519 74 354329 0.5 1 342407 11922 75 377243 0.5 1 365922 11321 76 253221 0.5 1 245036 8185 77 172926 0.5 1 167191 5735 78 105565 0.5 1 102145 3420 79 59328 0.5 1 57341 1987 80 37243 0.5 1 35974 1269 81 21793 0.5 1 21045 748 82 13536 0.5 1 13026 510 83 9839 0.5 1 9439 400 84 8208 0.5 1 7864 344 85 7109 0.5 1 6805 304 86 6470 0.5 1 6189 281 87 5668 0.5 1 5441 227 88 5205 0.5 1 4982 223 89 5275 0.5 1 5031 244 90 6886 0.5 1 6591 295 91 9961 0.5 1 9543 418 92 15848 0.5 1 15187 661 93 37612 0.5 1 36183 1429 94 113241 0.5 1 109143 4098 95 176405 0.5 1 169918 6487 96 70792 0.5 1 67915 2877 97 39731 0.5 1 38005 1726 98 15679 0.5 1 14988 691 99 14312 0.5 1 13673 639 100 14006 0.5 1 13310 696 101 23924 0.5 1 22238 1686 RUN STATISTICS FOR INPUT FILE: EPI-214_S30_L004_R1_001.fastq.gz ============================================= 30640077 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3470176 (11.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 18300371 (59.7%)