SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-199_S24_L003_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-199_S24_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 334.42 s (19 us/read; 3.23 M reads/minute). === Summary === Total reads processed: 18,024,873 Reads with adapters: 11,884,541 (65.9%) Reads written (passing filters): 18,024,873 (100.0%) Total basepairs processed: 1,783,767,890 bp Total written (filtered): 1,394,260,631 bp (78.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11884541 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.9% C: 19.1% G: 24.7% T: 33.6% none/other: 1.6% Overview of removed sequences length count expect max.err error counts 1 2718299 4506218.2 0 2718299 2 647702 1126554.6 0 647702 3 254635 281638.6 0 254635 4 177570 70409.7 0 177570 5 98679 17602.4 0 98679 6 94613 4400.6 0 94613 7 85034 1100.2 0 85034 8 95237 275.0 0 95237 9 97686 68.8 0 96684 1002 10 92836 17.2 1 88800 4036 11 97330 4.3 1 92403 4927 12 92406 1.1 1 88025 4381 13 90700 0.3 1 86193 4507 14 101424 0.3 1 94315 7109 15 94954 0.3 1 87633 7321 16 106173 0.3 1 97690 8483 17 99949 0.3 1 92068 7881 18 94896 0.3 1 87839 7057 19 101729 0.3 1 93077 8652 20 95734 0.3 1 88845 6889 21 104760 0.3 1 96351 8409 22 99020 0.3 1 91810 7210 23 97428 0.3 1 89816 7612 24 101981 0.3 1 93755 8226 25 97354 0.3 1 89996 7358 26 107860 0.3 1 98902 8958 27 99000 0.3 1 92938 6062 28 94919 0.3 1 89782 5137 29 106068 0.3 1 99938 6130 30 98393 0.3 1 93126 5267 31 111359 0.3 1 104371 6988 32 99030 0.3 1 93642 5388 33 105596 0.3 1 99778 5818 34 106930 0.3 1 100940 5990 35 101022 0.3 1 95715 5307 36 95944 0.3 1 91193 4751 37 105215 0.3 1 99992 5223 38 101839 0.3 1 96574 5265 39 100999 0.3 1 95873 5126 40 105348 0.3 1 99741 5607 41 149313 0.3 1 142824 6489 42 87579 0.3 1 83560 4019 43 59285 0.3 1 56131 3154 44 90930 0.3 1 86632 4298 45 89712 0.3 1 85597 4115 46 86385 0.3 1 82396 3989 47 92909 0.3 1 88216 4693 48 85402 0.3 1 81066 4336 49 92623 0.3 1 87972 4651 50 82771 0.3 1 79015 3756 51 82297 0.3 1 78502 3795 52 79993 0.3 1 76347 3646 53 75254 0.3 1 72203 3051 54 75077 0.3 1 71746 3331 55 78278 0.3 1 75031 3247 56 72563 0.3 1 69391 3172 57 67741 0.3 1 64858 2883 58 69430 0.3 1 66606 2824 59 67171 0.3 1 64360 2811 60 61459 0.3 1 58968 2491 61 64292 0.3 1 61718 2574 62 64990 0.3 1 62301 2689 63 58883 0.3 1 56494 2389 64 56389 0.3 1 54371 2018 65 52878 0.3 1 50900 1978 66 50005 0.3 1 48007 1998 67 51254 0.3 1 49288 1966 68 50536 0.3 1 48405 2131 69 54652 0.3 1 52493 2159 70 55655 0.3 1 53196 2459 71 66251 0.3 1 63035 3216 72 87900 0.3 1 83253 4647 73 150950 0.3 1 138448 12502 74 502356 0.3 1 482794 19562 75 436410 0.3 1 421877 14533 76 211660 0.3 1 203623 8037 77 118540 0.3 1 114012 4528 78 65954 0.3 1 63447 2507 79 36304 0.3 1 34812 1492 80 23005 0.3 1 22080 925 81 14850 0.3 1 14173 677 82 10255 0.3 1 9778 477 83 8236 0.3 1 7863 373 84 7143 0.3 1 6790 353 85 6194 0.3 1 5882 312 86 5431 0.3 1 5162 269 87 4808 0.3 1 4550 258 88 4052 0.3 1 3829 223 89 3939 0.3 1 3711 228 90 4860 0.3 1 4610 250 91 6466 0.3 1 6112 354 92 10409 0.3 1 9901 508 93 26147 0.3 1 24913 1234 94 86242 0.3 1 82412 3830 95 166719 0.3 1 159519 7200 96 73182 0.3 1 69752 3430 97 52056 0.3 1 49552 2504 98 20842 0.3 1 19723 1119 99 22766 0.3 1 21491 1275 100 23100 0.3 1 21656 1444 101 44157 0.3 1 40403 3754 RUN STATISTICS FOR INPUT FILE: EPI-199_S24_L003_R1_001.fastq.gz ============================================= 18024873 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3165588 (17.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 11615021 (64.4%)