SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-205_S26_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 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-205_S26_L004_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 463.66 s (17 us/read; 3.44 M reads/minute). === Summary === Total reads processed: 26,556,310 Reads with adapters: 21,963,819 (82.7%) Reads written (passing filters): 26,556,310 (100.0%) Total basepairs processed: 2,473,468,259 bp Total written (filtered): 1,417,741,514 bp (57.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21963819 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.4% C: 19.1% G: 24.6% T: 29.7% none/other: 2.2% Overview of removed sequences length count expect max.err error counts 1 4022861 6639077.5 0 4022861 2 145325 1659769.4 0 145325 3 121373 414942.3 0 121373 4 101357 103735.6 0 101357 5 101940 25933.9 0 101940 6 104532 6483.5 0 104532 7 103706 1620.9 0 103706 8 110368 405.2 0 110368 9 104948 101.3 0 104499 449 10 109570 25.3 1 106544 3026 11 99007 6.3 1 95749 3258 12 104359 1.6 1 100804 3555 13 101666 0.4 1 98491 3175 14 113085 0.4 1 109272 3813 15 108002 0.4 1 104587 3415 16 108641 0.4 1 105276 3365 17 113079 0.4 1 109425 3654 18 102836 0.4 1 99801 3035 19 109277 0.4 1 105697 3580 20 110305 0.4 1 106723 3582 21 111292 0.4 1 107579 3713 22 116961 0.4 1 112974 3987 23 112385 0.4 1 108471 3914 24 120220 0.4 1 115721 4499 25 110153 0.4 1 106569 3584 26 111251 0.4 1 107002 4249 27 115076 0.4 1 110141 4935 28 122264 0.4 1 117944 4320 29 116700 0.4 1 112219 4481 30 132041 0.4 1 127529 4512 31 114945 0.4 1 110725 4220 32 126637 0.4 1 122328 4309 33 131419 0.4 1 126274 5145 34 128960 0.4 1 123674 5286 35 130470 0.4 1 126246 4224 36 125003 0.4 1 120577 4426 37 125739 0.4 1 121281 4458 38 118231 0.4 1 113942 4289 39 122212 0.4 1 117493 4719 40 122367 0.4 1 117718 4649 41 128423 0.4 1 123896 4527 42 128363 0.4 1 124078 4285 43 114651 0.4 1 110433 4218 44 121500 0.4 1 116983 4517 45 164345 0.4 1 158722 5623 46 121900 0.4 1 117701 4199 47 94505 0.4 1 91086 3419 48 136524 0.4 1 132103 4421 49 103160 0.4 1 99798 3362 50 104616 0.4 1 100939 3677 51 153579 0.4 1 149245 4334 52 100819 0.4 1 97546 3273 53 102110 0.4 1 98949 3161 54 92382 0.4 1 89285 3097 55 115221 0.4 1 111615 3606 56 112070 0.4 1 108584 3486 57 108221 0.4 1 104727 3494 58 108112 0.4 1 104515 3597 59 104781 0.4 1 101252 3529 60 103613 0.4 1 100033 3580 61 107928 0.4 1 103913 4015 62 115463 0.4 1 111101 4362 63 124140 0.4 1 118990 5150 64 133037 0.4 1 127357 5680 65 156840 0.4 1 149418 7422 66 207467 0.4 1 196169 11298 67 461059 0.4 1 409937 51122 68 3322182 0.4 1 3230567 91615 69 1525539 0.4 1 1473955 51584 70 839445 0.4 1 809867 29578 71 412296 0.4 1 395748 16548 72 244380 0.4 1 233724 10656 73 149705 0.4 1 142412 7293 74 107049 0.4 1 101323 5726 75 82116 0.4 1 77531 4585 76 67015 0.4 1 63056 3959 77 59068 0.4 1 55446 3622 78 52035 0.4 1 48664 3371 79 46495 0.4 1 43443 3052 80 41159 0.4 1 38390 2769 81 36553 0.4 1 34022 2531 82 32255 0.4 1 29876 2379 83 29141 0.4 1 26941 2200 84 26196 0.4 1 24045 2151 85 24034 0.4 1 21949 2085 86 22927 0.4 1 20826 2101 87 23072 0.4 1 20934 2138 88 24790 0.4 1 22473 2317 89 29258 0.4 1 26497 2761 90 37288 0.4 1 33742 3546 91 53761 0.4 1 48788 4973 92 81324 0.4 1 74092 7232 93 181129 0.4 1 166056 15073 94 551154 0.4 1 510887 40267 95 884925 0.4 1 825037 59888 96 352010 0.4 1 328037 23973 97 193835 0.4 1 180673 13162 98 70757 0.4 1 66099 4658 99 61020 0.4 1 56728 4292 100 58021 0.4 1 54000 4021 101 106493 0.4 1 98497 7996 RUN STATISTICS FOR INPUT FILE: EPI-205_S26_L004_R2_001.fastq.gz ============================================= 26556310 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 9705346 (36.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (563274) or CGA (196079) in total: 759353 (2.9%) Total number of sequences analysed for the sequence pair length validation: 26556310 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 10013657 (37.71%)