SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-151_S2_L002_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 File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_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/20180514_geoduck_trimgalore_rrbs/EPI-151_S2_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 548.40 s (19 us/read; 3.23 M reads/minute). === Summary === Total reads processed: 29,567,647 Reads with adapters: 18,416,542 (62.3%) Reads written (passing filters): 29,567,647 (100.0%) Total basepairs processed: 2,906,172,854 bp Total written (filtered): 2,292,566,276 bp (78.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18416542 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.8% C: 22.9% G: 21.9% T: 33.1% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 4808781 7391911.8 0 4808781 2 1212853 1847977.9 0 1212853 3 463533 461994.5 0 463533 4 319256 115498.6 0 319256 5 165093 28874.7 0 165093 6 156001 7218.7 0 156001 7 143328 1804.7 0 143328 8 155517 451.2 0 155517 9 159913 112.8 0 158563 1350 10 152530 28.2 1 146213 6317 11 158084 7.0 1 150482 7602 12 148882 1.8 1 142300 6582 13 140309 0.4 1 134135 6174 14 157523 0.4 1 148858 8665 15 146889 0.4 1 139695 7194 16 159217 0.4 1 150401 8816 17 147917 0.4 1 140180 7737 18 136955 0.4 1 130485 6470 19 149686 0.4 1 140875 8811 20 136498 0.4 1 129936 6562 21 150999 0.4 1 142074 8925 22 141518 0.4 1 134377 7141 23 131955 0.4 1 125198 6757 24 135639 0.4 1 127962 7677 25 126177 0.4 1 119913 6264 26 136775 0.4 1 129045 7730 27 125057 0.4 1 118958 6099 28 115713 0.4 1 110374 5339 29 128428 0.4 1 121782 6646 30 117667 0.4 1 112534 5133 31 125586 0.4 1 119280 6306 32 111179 0.4 1 106457 4722 33 127212 0.4 1 120558 6654 34 108383 0.4 1 103521 4862 35 109829 0.4 1 104424 5405 36 111812 0.4 1 106174 5638 37 105050 0.4 1 100393 4657 38 102270 0.4 1 97249 5021 39 101266 0.4 1 96426 4840 40 102186 0.4 1 97051 5135 41 142072 0.4 1 136225 5847 42 88018 0.4 1 84690 3328 43 36518 0.4 1 34400 2118 44 80713 0.4 1 77071 3642 45 76522 0.4 1 73025 3497 46 72944 0.4 1 69733 3211 47 78099 0.4 1 74409 3690 48 71724 0.4 1 68233 3491 49 76460 0.4 1 72806 3654 50 66016 0.4 1 63153 2863 51 64217 0.4 1 61414 2803 52 60330 0.4 1 57722 2608 53 54989 0.4 1 52838 2151 54 55495 0.4 1 53263 2232 55 55712 0.4 1 53477 2235 56 52318 0.4 1 50247 2071 57 49035 0.4 1 46963 2072 58 46948 0.4 1 45185 1763 59 46550 0.4 1 44771 1779 60 40797 0.4 1 39138 1659 61 42080 0.4 1 40520 1560 62 41323 0.4 1 39801 1522 63 37406 0.4 1 35991 1415 64 35831 0.4 1 34564 1267 65 32566 0.4 1 31348 1218 66 31260 0.4 1 30085 1175 67 31651 0.4 1 30420 1231 68 32262 0.4 1 30934 1328 69 37442 0.4 1 35808 1634 70 40171 0.4 1 38308 1863 71 55274 0.4 1 52565 2709 72 92338 0.4 1 87151 5187 73 234439 0.4 1 213590 20849 74 1194362 0.4 1 1155536 38826 75 861323 0.4 1 833151 28172 76 482119 0.4 1 465579 16540 77 283694 0.4 1 273994 9700 78 168410 0.4 1 162658 5752 79 93268 0.4 1 89858 3410 80 58008 0.4 1 55976 2032 81 35785 0.4 1 34466 1319 82 24314 0.4 1 23340 974 83 19592 0.4 1 18715 877 84 16407 0.4 1 15670 737 85 15394 0.4 1 14677 717 86 14642 0.4 1 13975 667 87 13030 0.4 1 12417 613 88 11843 0.4 1 11266 577 89 12239 0.4 1 11684 555 90 15502 0.4 1 14768 734 91 21299 0.4 1 20299 1000 92 35259 0.4 1 33608 1651 93 88883 0.4 1 85062 3821 94 271142 0.4 1 260096 11046 95 476679 0.4 1 457342 19337 96 212748 0.4 1 203349 9399 97 121193 0.4 1 115485 5708 98 42466 0.4 1 40380 2086 99 39387 0.4 1 37457 1930 100 34376 0.4 1 32562 1814 101 60192 0.4 1 56421 3771 RUN STATISTICS FOR INPUT FILE: EPI-151_S2_L002_R1_001.fastq.gz ============================================= 29567647 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 6071941 (20.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 17772423 (60.1%) RRBS reads trimmed by 2 bp at the start when read started with CAA (278655) or CGA (179871) in total: 458526 (1.6%)