SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-230_S37_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-230_S37_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 596.01 s (18 us/read; 3.27 M reads/minute). === Summary === Total reads processed: 32,435,740 Reads with adapters: 21,365,396 (65.9%) Reads written (passing filters): 32,435,740 (100.0%) Total basepairs processed: 3,229,058,033 bp Total written (filtered): 2,566,732,115 bp (79.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21365396 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.8% C: 16.1% G: 26.3% T: 34.8% none/other: 1.0% Overview of removed sequences length count expect max.err error counts 1 4678659 8108935.0 0 4678659 2 1170265 2027233.8 0 1170265 3 471929 506808.4 0 471929 4 329431 126702.1 0 329431 5 199542 31675.5 0 199542 6 195155 7918.9 0 195155 7 184797 1979.7 0 184797 8 200246 494.9 0 200246 9 197929 123.7 0 196487 1442 10 190250 30.9 1 183966 6284 11 194674 7.7 1 187638 7036 12 188932 1.9 1 182205 6727 13 190921 0.5 1 184024 6897 14 201836 0.5 1 193771 8065 15 200196 0.5 1 192435 7761 16 206872 0.5 1 198457 8415 17 207387 0.5 1 199010 8377 18 191728 0.5 1 185070 6658 19 206071 0.5 1 196898 9173 20 198707 0.5 1 191478 7229 21 217790 0.5 1 208068 9722 22 204893 0.5 1 197313 7580 23 195954 0.5 1 188379 7575 24 202349 0.5 1 193803 8546 25 199619 0.5 1 191835 7784 26 210423 0.5 1 201134 9289 27 204961 0.5 1 196787 8174 28 199359 0.5 1 191664 7695 29 214628 0.5 1 205601 9027 30 205133 0.5 1 197545 7588 31 214427 0.5 1 204963 9464 32 211100 0.5 1 202871 8229 33 215495 0.5 1 206797 8698 34 207570 0.5 1 199069 8501 35 203501 0.5 1 195457 8044 36 203204 0.5 1 194967 8237 37 208565 0.5 1 200260 8305 38 192472 0.5 1 185518 6954 39 204941 0.5 1 196160 8781 40 210351 0.5 1 200766 9585 41 268782 0.5 1 258039 10743 42 188461 0.5 1 181664 6797 43 120495 0.5 1 115383 5112 44 177978 0.5 1 171080 6898 45 180752 0.5 1 173414 7338 46 169870 0.5 1 163467 6403 47 177687 0.5 1 170233 7454 48 168890 0.5 1 162013 6877 49 175123 0.5 1 167928 7195 50 160009 0.5 1 154023 5986 51 159140 0.5 1 152954 6186 52 154840 0.5 1 148760 6080 53 146827 0.5 1 141522 5305 54 144458 0.5 1 138977 5481 55 148938 0.5 1 143396 5542 56 139721 0.5 1 134725 4996 57 131264 0.5 1 126408 4856 58 129607 0.5 1 125053 4554 59 126497 0.5 1 121940 4557 60 115107 0.5 1 111218 3889 61 118239 0.5 1 114005 4234 62 119050 0.5 1 115012 4038 63 107951 0.5 1 104294 3657 64 100904 0.5 1 97645 3259 65 94959 0.5 1 91784 3175 66 87819 0.5 1 84867 2952 67 84827 0.5 1 81962 2865 68 79567 0.5 1 76880 2687 69 81259 0.5 1 78626 2633 70 77785 0.5 1 75092 2693 71 76131 0.5 1 73383 2748 72 82486 0.5 1 79054 3432 73 129739 0.5 1 120358 9381 74 499586 0.5 1 483512 16074 75 470293 0.5 1 455299 14994 76 374417 0.5 1 362288 12129 77 288555 0.5 1 279407 9148 78 193136 0.5 1 187236 5900 79 112571 0.5 1 108933 3638 80 69596 0.5 1 67364 2232 81 39883 0.5 1 38530 1353 82 25112 0.5 1 24209 903 83 18441 0.5 1 17687 754 84 15310 0.5 1 14707 603 85 12933 0.5 1 12449 484 86 11399 0.5 1 10928 471 87 9829 0.5 1 9415 414 88 8662 0.5 1 8328 334 89 8822 0.5 1 8445 377 90 10964 0.5 1 10517 447 91 14929 0.5 1 14342 587 92 23309 0.5 1 22406 903 93 54905 0.5 1 52949 1956 94 157339 0.5 1 151744 5595 95 256712 0.5 1 247895 8817 96 111706 0.5 1 107403 4303 97 71628 0.5 1 68607 3021 98 30822 0.5 1 29455 1367 99 30334 0.5 1 28963 1371 100 32364 0.5 1 30518 1846 101 54415 0.5 1 49640 4775 RUN STATISTICS FOR INPUT FILE: EPI-230_S37_L004_R1_001.fastq.gz ============================================= 32435740 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4285456 (13.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 21053669 (64.9%)