SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-176_S15_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 All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_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/20180516_geoduck_trimgalore_rrbs/EPI-176_S15_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 713.29 s (20 us/read; 3.08 M reads/minute). === Summary === Total reads processed: 36,578,520 Reads with adapters: 23,445,651 (64.1%) Reads written (passing filters): 36,578,520 (100.0%) Total basepairs processed: 3,667,554,440 bp Total written (filtered): 3,336,054,540 bp (91.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23445651 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.3% C: 23.2% G: 7.2% T: 30.3% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 12217947 9144630.0 0 12217947 2 324404 2286157.5 0 324404 3 282059 571539.4 0 282059 4 246311 142884.8 0 246311 5 249013 35721.2 0 249013 6 247882 8930.3 0 247882 7 236185 2232.6 0 236185 8 244841 558.1 0 244841 9 236158 139.5 0 235185 973 10 231623 34.9 1 225444 6179 11 226889 8.7 1 218692 8197 12 230149 2.2 1 222141 8008 13 224426 0.5 1 216788 7638 14 238698 0.5 1 230300 8398 15 222836 0.5 1 215188 7648 16 222149 0.5 1 214369 7780 17 230724 0.5 1 222893 7831 18 205050 0.5 1 197973 7077 19 213128 0.5 1 205782 7346 20 212104 0.5 1 204469 7635 21 216677 0.5 1 208468 8209 22 215759 0.5 1 207682 8077 23 204021 0.5 1 196815 7206 24 211537 0.5 1 204022 7515 25 193292 0.5 1 186031 7261 26 195775 0.5 1 187569 8206 27 203077 0.5 1 193435 9642 28 200480 0.5 1 193497 6983 29 198916 0.5 1 190500 8416 30 210010 0.5 1 202904 7106 31 183961 0.5 1 176920 7041 32 190753 0.5 1 184732 6021 33 198894 0.5 1 191482 7412 34 198253 0.5 1 190129 8124 35 176551 0.5 1 171237 5314 36 176911 0.5 1 170538 6373 37 172582 0.5 1 166522 6060 38 155248 0.5 1 149879 5369 39 158356 0.5 1 152622 5734 40 157811 0.5 1 152184 5627 41 152637 0.5 1 147541 5096 42 146002 0.5 1 141608 4394 43 131757 0.5 1 127147 4610 44 131738 0.5 1 127360 4378 45 153838 0.5 1 149384 4454 46 124176 0.5 1 120139 4037 47 94204 0.5 1 90834 3370 48 122236 0.5 1 118769 3467 49 94646 0.5 1 91505 3141 50 96042 0.5 1 92849 3193 51 125167 0.5 1 121828 3339 52 80573 0.5 1 77843 2730 53 83017 0.5 1 80366 2651 54 71964 0.5 1 69634 2330 55 85099 0.5 1 82707 2392 56 80937 0.5 1 78422 2515 57 73970 0.5 1 71683 2287 58 69027 0.5 1 66967 2060 59 67467 0.5 1 65257 2210 60 63947 0.5 1 61895 2052 61 62988 0.5 1 60833 2155 62 63257 0.5 1 61101 2156 63 60394 0.5 1 58328 2066 64 58052 0.5 1 56052 2000 65 57393 0.5 1 55451 1942 66 58538 0.5 1 56416 2122 67 69422 0.5 1 65681 3741 68 186051 0.5 1 181784 4267 69 65784 0.5 1 63586 2198 70 29947 0.5 1 28798 1149 71 17294 0.5 1 16437 857 72 13176 0.5 1 12501 675 73 10746 0.5 1 10149 597 74 8954 0.5 1 8426 528 75 7587 0.5 1 7161 426 76 6765 0.5 1 6355 410 77 5857 0.5 1 5464 393 78 5058 0.5 1 4746 312 79 4111 0.5 1 3894 217 80 3427 0.5 1 3260 167 81 2811 0.5 1 2647 164 82 2126 0.5 1 1995 131 83 1575 0.5 1 1464 111 84 1183 0.5 1 1123 60 85 857 0.5 1 797 60 86 638 0.5 1 587 51 87 516 0.5 1 473 43 88 369 0.5 1 332 37 89 377 0.5 1 330 47 90 496 0.5 1 417 79 91 575 0.5 1 514 61 92 846 0.5 1 742 104 93 1592 0.5 1 1417 175 94 4227 0.5 1 3795 432 95 7276 0.5 1 6562 714 96 3815 0.5 1 3461 354 97 2631 0.5 1 2379 252 98 1010 0.5 1 919 91 99 943 0.5 1 841 102 100 1506 0.5 1 1349 157 101 5597 0.5 1 4927 670 RUN STATISTICS FOR INPUT FILE: EPI-176_S15_L003_R2_001.fastq.gz ============================================= 36578520 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3475253 (9.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 36578520 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 232965 (0.64%)