SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-175_S14_L003_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-175_S14_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 481.19 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 25,152,012 Reads with adapters: 15,973,203 (63.5%) Reads written (passing filters): 25,152,012 (100.0%) Total basepairs processed: 2,514,906,748 bp Total written (filtered): 2,269,387,349 bp (90.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15973203 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.3% C: 22.7% G: 7.9% T: 30.8% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 8246232 6288003.0 0 8246232 2 222930 1572000.8 0 222930 3 189647 393000.2 0 189647 4 159970 98250.0 0 159970 5 160442 24562.5 0 160442 6 159960 6140.6 0 159960 7 152812 1535.2 0 152812 8 163469 383.8 0 163469 9 153368 95.9 0 152734 634 10 152918 24.0 1 148522 4396 11 145859 6.0 1 140572 5287 12 148358 1.5 1 142995 5363 13 143283 0.4 1 138284 4999 14 154164 0.4 1 148621 5543 15 143543 0.4 1 138342 5201 16 144544 0.4 1 139481 5063 17 151629 0.4 1 146440 5189 18 134145 0.4 1 129411 4734 19 140103 0.4 1 135235 4868 20 136822 0.4 1 131878 4944 21 140049 0.4 1 134613 5436 22 141043 0.4 1 135717 5326 23 135866 0.4 1 130927 4939 24 142734 0.4 1 137524 5210 25 126573 0.4 1 121918 4655 26 127546 0.4 1 122191 5355 27 129151 0.4 1 123052 6099 28 132859 0.4 1 128181 4678 29 126810 0.4 1 121487 5323 30 138056 0.4 1 133382 4674 31 118107 0.4 1 113616 4491 32 124204 0.4 1 120222 3982 33 129308 0.4 1 124400 4908 34 128066 0.4 1 122788 5278 35 119361 0.4 1 115666 3695 36 113941 0.4 1 109690 4251 37 111544 0.4 1 107478 4066 38 100444 0.4 1 96907 3537 39 104284 0.4 1 100437 3847 40 102062 0.4 1 98319 3743 41 100342 0.4 1 96872 3470 42 98645 0.4 1 95656 2989 43 87253 0.4 1 84135 3118 44 87874 0.4 1 84976 2898 45 108518 0.4 1 105416 3102 46 82139 0.4 1 79521 2618 47 59906 0.4 1 57641 2265 48 83997 0.4 1 81535 2462 49 60072 0.4 1 58035 2037 50 62104 0.4 1 60035 2069 51 84698 0.4 1 82367 2331 52 52531 0.4 1 50774 1757 53 54464 0.4 1 52678 1786 54 47540 0.4 1 45969 1571 55 56444 0.4 1 54801 1643 56 53915 0.4 1 52171 1744 57 49221 0.4 1 47707 1514 58 47318 0.4 1 45820 1498 59 44826 0.4 1 43336 1490 60 43265 0.4 1 41773 1492 61 42690 0.4 1 41217 1473 62 43362 0.4 1 41860 1502 63 42956 0.4 1 41410 1546 64 42423 0.4 1 40850 1573 65 44200 0.4 1 42553 1647 66 47614 0.4 1 45706 1908 67 69041 0.4 1 64489 4552 68 237975 0.4 1 232213 5762 69 83220 0.4 1 80535 2685 70 41822 0.4 1 40236 1586 71 22175 0.4 1 21149 1026 72 15678 0.4 1 14903 775 73 11541 0.4 1 10911 630 74 9355 0.4 1 8850 505 75 7705 0.4 1 7274 431 76 6748 0.4 1 6361 387 77 6068 0.4 1 5697 371 78 5338 0.4 1 5046 292 79 4605 0.4 1 4293 312 80 3917 0.4 1 3674 243 81 3264 0.4 1 3048 216 82 2666 0.4 1 2503 163 83 2267 0.4 1 2101 166 84 1912 0.4 1 1747 165 85 1462 0.4 1 1347 115 86 1259 0.4 1 1145 114 87 1052 0.4 1 972 80 88 1111 0.4 1 991 120 89 1220 0.4 1 1070 150 90 1540 0.4 1 1399 141 91 1996 0.4 1 1783 213 92 2913 0.4 1 2629 284 93 6518 0.4 1 5910 608 94 19521 0.4 1 17953 1568 95 31973 0.4 1 29615 2358 96 13367 0.4 1 12356 1011 97 9332 0.4 1 8667 665 98 3746 0.4 1 3461 285 99 3784 0.4 1 3521 263 100 4196 0.4 1 3865 331 101 8393 0.4 1 7664 729 RUN STATISTICS FOR INPUT FILE: EPI-175_S14_L003_R2_001.fastq.gz ============================================= 25152012 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2695273 (10.7%) 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 (811763) or CGA (269995) in total: 1081758 (4.3%) Total number of sequences analysed for the sequence pair length validation: 25152012 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 496086 (1.97%)