SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-161_S8_L002_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-161_S8_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 475.66 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 24,900,290 Reads with adapters: 17,398,074 (69.9%) Reads written (passing filters): 24,900,290 (100.0%) Total basepairs processed: 2,489,519,624 bp Total written (filtered): 2,142,972,575 bp (86.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17398074 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.6% C: 24.0% G: 9.6% T: 29.5% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 6703793 6225072.5 0 6703793 2 244709 1556268.1 0 244709 3 209763 389067.0 0 209763 4 182829 97266.8 0 182829 5 183471 24316.7 0 183471 6 187707 6079.2 0 187707 7 180286 1519.8 0 180286 8 191201 379.9 0 191201 9 182950 95.0 0 182198 752 10 184387 23.7 1 179253 5134 11 178112 5.9 1 171589 6523 12 183107 1.5 1 176580 6527 13 177804 0.4 1 171580 6224 14 195259 0.4 1 188155 7104 15 182445 0.4 1 175979 6466 16 181812 0.4 1 175450 6362 17 194215 0.4 1 187541 6674 18 174607 0.4 1 168637 5970 19 185895 0.4 1 179388 6507 20 185324 0.4 1 178725 6599 21 190060 0.4 1 182697 7363 22 194050 0.4 1 186481 7569 23 186230 0.4 1 179401 6829 24 200155 0.4 1 192719 7436 25 177972 0.4 1 171446 6526 26 183011 0.4 1 175297 7714 27 186201 0.4 1 177717 8484 28 193446 0.4 1 186449 6997 29 187337 0.4 1 179500 7837 30 202878 0.4 1 195959 6919 31 176708 0.4 1 169941 6767 32 185061 0.4 1 178996 6065 33 194774 0.4 1 187270 7504 34 199539 0.4 1 191311 8228 35 189338 0.4 1 183474 5864 36 180867 0.4 1 174150 6717 37 179680 0.4 1 173364 6316 38 162521 0.4 1 156738 5783 39 167889 0.4 1 161960 5929 40 166424 0.4 1 160651 5773 41 165019 0.4 1 159826 5193 42 162995 0.4 1 158402 4593 43 145292 0.4 1 140445 4847 44 149164 0.4 1 144338 4826 45 186759 0.4 1 181945 4814 46 141777 0.4 1 137474 4303 47 102199 0.4 1 98640 3559 48 144049 0.4 1 140149 3900 49 101445 0.4 1 98440 3005 50 106314 0.4 1 102808 3506 51 145929 0.4 1 142487 3442 52 91270 0.4 1 88333 2937 53 92756 0.4 1 89713 3043 54 80803 0.4 1 78114 2689 55 95836 0.4 1 93166 2670 56 90730 0.4 1 87804 2926 57 82315 0.4 1 79798 2517 58 79589 0.4 1 77207 2382 59 75168 0.4 1 72654 2514 60 72011 0.4 1 69581 2430 61 70634 0.4 1 68223 2411 62 70163 0.4 1 67846 2317 63 68564 0.4 1 66191 2373 64 66677 0.4 1 64280 2397 65 67712 0.4 1 65366 2346 66 70173 0.4 1 67676 2497 67 88785 0.4 1 83566 5219 68 257150 0.4 1 251571 5579 69 89495 0.4 1 86614 2881 70 41406 0.4 1 39895 1511 71 23481 0.4 1 22439 1042 72 17602 0.4 1 16760 842 73 13635 0.4 1 12935 700 74 11511 0.4 1 10887 624 75 9862 0.4 1 9297 565 76 8392 0.4 1 7936 456 77 7496 0.4 1 7084 412 78 6688 0.4 1 6295 393 79 5659 0.4 1 5348 311 80 4714 0.4 1 4479 235 81 3874 0.4 1 3663 211 82 3111 0.4 1 2927 184 83 2492 0.4 1 2333 159 84 1992 0.4 1 1858 134 85 1435 0.4 1 1343 92 86 1139 0.4 1 1066 73 87 968 0.4 1 875 93 88 761 0.4 1 703 58 89 881 0.4 1 787 94 90 1077 0.4 1 960 117 91 1343 0.4 1 1217 126 92 2060 0.4 1 1888 172 93 4034 0.4 1 3696 338 94 11331 0.4 1 10510 821 95 19616 0.4 1 18240 1376 96 10120 0.4 1 9381 739 97 7413 0.4 1 6817 596 98 2858 0.4 1 2623 235 99 2771 0.4 1 2551 220 100 3798 0.4 1 3475 323 101 9964 0.4 1 8997 967 RUN STATISTICS FOR INPUT FILE: EPI-161_S8_L002_R2_001.fastq.gz ============================================= 24900290 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3010801 (12.1%) 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: 24900290 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 389485 (1.56%)