SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-226_S34_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-226_S34_L004_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 217.63 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 11,630,377 Reads with adapters: 7,404,920 (63.7%) Reads written (passing filters): 11,630,377 (100.0%) Total basepairs processed: 1,157,988,764 bp Total written (filtered): 1,024,770,860 bp (88.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7404920 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.2% C: 22.6% G: 10.0% T: 30.6% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 3628244 2907594.2 0 3628244 2 120931 726898.6 0 120931 3 92925 181724.6 0 92925 4 72328 45431.2 0 72328 5 70370 11357.8 0 70370 6 70694 2839.4 0 70694 7 69427 709.9 0 69427 8 76441 177.5 0 76441 9 68206 44.4 0 67861 345 10 72349 11.1 1 70585 1764 11 62688 2.8 1 60731 1957 12 64746 0.7 1 62680 2066 13 62122 0.2 1 60283 1839 14 68119 0.2 1 65892 2227 15 65737 0.2 1 63768 1969 16 64381 0.2 1 62446 1935 17 64370 0.2 1 62364 2006 18 57844 0.2 1 56132 1712 19 61618 0.2 1 59693 1925 20 61268 0.2 1 59368 1900 21 60009 0.2 1 58131 1878 22 62801 0.2 1 60761 2040 23 58177 0.2 1 56298 1879 24 61507 0.2 1 59444 2063 25 55765 0.2 1 53993 1772 26 54844 0.2 1 52879 1965 27 55293 0.2 1 53175 2118 28 57530 0.2 1 55591 1939 29 54181 0.2 1 52270 1911 30 58741 0.2 1 56865 1876 31 50389 0.2 1 48651 1738 32 52570 0.2 1 50852 1718 33 53501 0.2 1 51654 1847 34 52676 0.2 1 50620 2056 35 51627 0.2 1 50018 1609 36 49135 0.2 1 47483 1652 37 49239 0.2 1 47643 1596 38 45246 0.2 1 43742 1504 39 45295 0.2 1 43653 1642 40 44203 0.2 1 42669 1534 41 45183 0.2 1 43718 1465 42 43700 0.2 1 42298 1402 43 39488 0.2 1 38148 1340 44 40035 0.2 1 38675 1360 45 48040 0.2 1 46582 1458 46 38136 0.2 1 36861 1275 47 29595 0.2 1 28554 1041 48 39481 0.2 1 38170 1311 49 29605 0.2 1 28738 867 50 29615 0.2 1 28664 951 51 40575 0.2 1 39436 1139 52 26824 0.2 1 25981 843 53 26903 0.2 1 26043 860 54 23924 0.2 1 23171 753 55 28738 0.2 1 27904 834 56 27110 0.2 1 26251 859 57 25258 0.2 1 24424 834 58 24857 0.2 1 24048 809 59 22989 0.2 1 22220 769 60 21903 0.2 1 21151 752 61 21319 0.2 1 20583 736 62 21715 0.2 1 20975 740 63 22144 0.2 1 21328 816 64 21496 0.2 1 20727 769 65 22566 0.2 1 21672 894 66 23881 0.2 1 22865 1016 67 36382 0.2 1 33155 3227 68 188697 0.2 1 183703 4994 69 86290 0.2 1 83381 2909 70 46273 0.2 1 44559 1714 71 23319 0.2 1 22303 1016 72 14843 0.2 1 14121 722 73 9775 0.2 1 9298 477 74 7339 0.2 1 6955 384 75 5960 0.2 1 5640 320 76 4977 0.2 1 4684 293 77 4376 0.2 1 4104 272 78 3859 0.2 1 3608 251 79 3424 0.2 1 3221 203 80 2939 0.2 1 2730 209 81 2588 0.2 1 2411 177 82 2170 0.2 1 2027 143 83 1863 0.2 1 1706 157 84 1624 0.2 1 1487 137 85 1364 0.2 1 1245 119 86 1216 0.2 1 1113 103 87 1135 0.2 1 1032 103 88 1098 0.2 1 990 108 89 1376 0.2 1 1236 140 90 1628 0.2 1 1449 179 91 2181 0.2 1 1968 213 92 3263 0.2 1 2937 326 93 7057 0.2 1 6406 651 94 21207 0.2 1 19598 1609 95 35924 0.2 1 33314 2610 96 15537 0.2 1 14401 1136 97 10804 0.2 1 9985 819 98 4311 0.2 1 3979 332 99 4250 0.2 1 3906 344 100 4598 0.2 1 4239 359 101 8656 0.2 1 7846 810 RUN STATISTICS FOR INPUT FILE: EPI-226_S34_L004_R2_001.fastq.gz ============================================= 11630377 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1283059 (11.0%) 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 (332262) or CGA (119619) in total: 451881 (3.9%) Total number of sequences analysed for the sequence pair length validation: 11630377 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 496496 (4.27%)