SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-221_S33_L004_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-221_S33_L004_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 439.01 s (18 us/read; 3.31 M reads/minute). === Summary === Total reads processed: 24,207,549 Reads with adapters: 19,136,697 (79.1%) Reads written (passing filters): 24,207,549 (100.0%) Total basepairs processed: 2,277,987,168 bp Total written (filtered): 1,429,512,467 bp (62.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19136697 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.8% C: 18.5% G: 23.8% T: 29.4% none/other: 2.5% Overview of removed sequences length count expect max.err error counts 1 4409419 6051887.2 0 4409419 2 153474 1512971.8 0 153474 3 114813 378243.0 0 114813 4 94099 94560.7 0 94099 5 92581 23640.2 0 92581 6 93829 5910.0 0 93829 7 93406 1477.5 0 93406 8 99507 369.4 0 99507 9 93260 92.3 0 92827 433 10 96972 23.1 1 94325 2647 11 88819 5.8 1 85961 2858 12 93036 1.4 1 89895 3141 13 90680 0.4 1 87933 2747 14 98952 0.4 1 95614 3338 15 94219 0.4 1 91312 2907 16 96170 0.4 1 93321 2849 17 100745 0.4 1 97572 3173 18 91015 0.4 1 88222 2793 19 97539 0.4 1 94385 3154 20 96697 0.4 1 93652 3045 21 96694 0.4 1 93508 3186 22 102650 0.4 1 99093 3557 23 99261 0.4 1 96038 3223 24 106680 0.4 1 102733 3947 25 97673 0.4 1 94488 3185 26 98956 0.4 1 95279 3677 27 100348 0.4 1 96019 4329 28 107358 0.4 1 103588 3770 29 102952 0.4 1 99179 3773 30 113775 0.4 1 110080 3695 31 100483 0.4 1 96863 3620 32 106994 0.4 1 103492 3502 33 111968 0.4 1 107733 4235 34 113130 0.4 1 108565 4565 35 114127 0.4 1 110562 3565 36 110174 0.4 1 106200 3974 37 111196 0.4 1 107412 3784 38 103110 0.4 1 99575 3535 39 108109 0.4 1 104009 4100 40 107841 0.4 1 103865 3976 41 112722 0.4 1 108998 3724 42 112450 0.4 1 108781 3669 43 100830 0.4 1 97337 3493 44 108483 0.4 1 104520 3963 45 140922 0.4 1 136429 4493 46 107696 0.4 1 104045 3651 47 83938 0.4 1 80975 2963 48 118328 0.4 1 114663 3665 49 89267 0.4 1 86494 2773 50 91302 0.4 1 88153 3149 51 131587 0.4 1 127950 3637 52 86384 0.4 1 83760 2624 53 89129 0.4 1 86547 2582 54 80606 0.4 1 78050 2556 55 98970 0.4 1 96162 2808 56 95765 0.4 1 92874 2891 57 91903 0.4 1 89017 2886 58 92559 0.4 1 89691 2868 59 88172 0.4 1 85381 2791 60 85867 0.4 1 83110 2757 61 87874 0.4 1 84957 2917 62 91883 0.4 1 88640 3243 63 96730 0.4 1 93120 3610 64 102179 0.4 1 98020 4159 65 116425 0.4 1 111397 5028 66 151047 0.4 1 143212 7835 67 334314 0.4 1 294796 39518 68 2546479 0.4 1 2477056 69423 69 1226345 0.4 1 1185679 40666 70 689091 0.4 1 665555 23536 71 340000 0.4 1 326708 13292 72 200491 0.4 1 192222 8269 73 120303 0.4 1 114707 5596 74 84519 0.4 1 80217 4302 75 63496 0.4 1 60032 3464 76 50934 0.4 1 48091 2843 77 43788 0.4 1 41167 2621 78 37798 0.4 1 35439 2359 79 33543 0.4 1 31437 2106 80 29721 0.4 1 27742 1979 81 26363 0.4 1 24519 1844 82 23131 0.4 1 21477 1654 83 21211 0.4 1 19635 1576 84 19490 0.4 1 18019 1471 85 18205 0.4 1 16648 1557 86 17456 0.4 1 16045 1411 87 17869 0.4 1 16311 1558 88 19475 0.4 1 17786 1689 89 22389 0.4 1 20365 2024 90 28061 0.4 1 25626 2435 91 40297 0.4 1 36892 3405 92 60419 0.4 1 55268 5151 93 132953 0.4 1 122629 10324 94 403256 0.4 1 375672 27584 95 689495 0.4 1 645998 43497 96 286543 0.4 1 268319 18224 97 166684 0.4 1 155933 10751 98 62941 0.4 1 58892 4049 99 59020 0.4 1 55136 3884 100 57285 0.4 1 53367 3918 101 107603 0.4 1 98855 8748 RUN STATISTICS FOR INPUT FILE: EPI-221_S33_L004_R2_001.fastq.gz ============================================= 24207549 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7817177 (32.3%) 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: 24207549 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 7907175 (32.66%)