SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-181_S16_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 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-181_S16_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 524.70 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 27,579,953 Reads with adapters: 14,601,620 (52.9%) Reads written (passing filters): 27,579,953 (100.0%) Total basepairs processed: 2,773,596,846 bp Total written (filtered): 2,535,163,738 bp (91.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14601620 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.6% C: 8.1% G: 25.7% T: 41.3% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 5449884 6894988.2 0 5449884 2 1336915 1723747.1 0 1336915 3 507747 430936.8 0 507747 4 344959 107734.2 0 344959 5 168076 26933.5 0 168076 6 165358 6733.4 0 165358 7 155633 1683.3 0 155633 8 178503 420.8 0 178503 9 166672 105.2 0 165204 1468 10 162140 26.3 1 155659 6481 11 154090 6.6 1 147095 6995 12 146933 1.6 1 140540 6393 13 140260 0.4 1 134185 6075 14 155420 0.4 1 144783 10637 15 146154 0.4 1 135814 10340 16 154336 0.4 1 142699 11637 17 143152 0.4 1 132622 10530 18 134507 0.4 1 125216 9291 19 144573 0.4 1 132889 11684 20 133870 0.4 1 124405 9465 21 144433 0.4 1 133216 11217 22 135621 0.4 1 126111 9510 23 130343 0.4 1 120599 9744 24 129292 0.4 1 119367 9925 25 123353 0.4 1 114362 8991 26 131468 0.4 1 120715 10753 27 120171 0.4 1 113190 6981 28 113943 0.4 1 108189 5754 29 120642 0.4 1 114031 6611 30 114079 0.4 1 108213 5866 31 119631 0.4 1 112649 6982 32 109286 0.4 1 103796 5490 33 112592 0.4 1 106732 5860 34 104087 0.4 1 98924 5163 35 102808 0.4 1 97342 5466 36 103306 0.4 1 97962 5344 37 110836 0.4 1 104819 6017 38 98981 0.4 1 93819 5162 39 92768 0.4 1 88583 4185 40 92964 0.4 1 88269 4695 41 135076 0.4 1 129452 5624 42 75644 0.4 1 72264 3380 43 54310 0.4 1 51631 2679 44 79310 0.4 1 75692 3618 45 76779 0.4 1 73347 3432 46 73905 0.4 1 70681 3224 47 77830 0.4 1 74078 3752 48 72029 0.4 1 68632 3397 49 74713 0.4 1 71066 3647 50 66463 0.4 1 63563 2900 51 65413 0.4 1 62587 2826 52 61746 0.4 1 58981 2765 53 58516 0.4 1 56112 2404 54 57112 0.4 1 54687 2425 55 59273 0.4 1 56833 2440 56 55284 0.4 1 52901 2383 57 51752 0.4 1 49463 2289 58 51151 0.4 1 49151 2000 59 48353 0.4 1 46358 1995 60 43816 0.4 1 42061 1755 61 45194 0.4 1 43482 1712 62 45721 0.4 1 43938 1783 63 42877 0.4 1 41326 1551 64 41417 0.4 1 39956 1461 65 38149 0.4 1 36844 1305 66 35306 0.4 1 34002 1304 67 33927 0.4 1 32739 1188 68 31253 0.4 1 30140 1113 69 32293 0.4 1 31167 1126 70 30150 0.4 1 28987 1163 71 29878 0.4 1 28738 1140 72 30458 0.4 1 28992 1466 73 41112 0.4 1 38235 2877 74 108669 0.4 1 104573 4096 75 87794 0.4 1 84866 2928 76 41563 0.4 1 40021 1542 77 23516 0.4 1 22572 944 78 14375 0.4 1 13813 562 79 8538 0.4 1 8197 341 80 6300 0.4 1 6029 271 81 4393 0.4 1 4209 184 82 3239 0.4 1 3073 166 83 2598 0.4 1 2487 111 84 2067 0.4 1 1958 109 85 1580 0.4 1 1485 95 86 1222 0.4 1 1149 73 87 946 0.4 1 890 56 88 732 0.4 1 695 37 89 729 0.4 1 691 38 90 852 0.4 1 806 46 91 1201 0.4 1 1132 69 92 1759 0.4 1 1663 96 93 4069 0.4 1 3863 206 94 12295 0.4 1 11735 560 95 20388 0.4 1 19539 849 96 9416 0.4 1 8955 461 97 6797 0.4 1 6441 356 98 3103 0.4 1 2918 185 99 3172 0.4 1 2968 204 100 4481 0.4 1 4124 357 101 9830 0.4 1 8796 1034 RUN STATISTICS FOR INPUT FILE: EPI-181_S16_L003_R1_001.fastq.gz ============================================= 27579953 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2583873 (9.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 14355512 (52.1%) RRBS reads trimmed by 2 bp at the start when read started with CAA (210030) or CGA (156484) in total: 366514 (1.3%)