SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-42_S39_L005_R1_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-42_S39_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 560.37 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 30,041,436 Reads with adapters: 19,010,654 (63.3%) Reads written (passing filters): 30,041,436 (100.0%) Total basepairs processed: 3,020,063,465 bp Total written (filtered): 2,544,526,180 bp (84.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19010654 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 22.2% C: 8.7% G: 30.2% T: 38.6% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 4839153 7510359.0 0 4839153 2 1230079 1877589.8 0 1230079 3 496881 469397.4 0 496881 4 332234 117349.4 0 332234 5 189945 29337.3 0 189945 6 178798 7334.3 0 178798 7 165879 1833.6 0 165879 8 178559 458.4 0 178559 9 182401 114.6 0 180844 1557 10 177130 28.6 1 169384 7746 11 181882 7.2 1 172935 8947 12 171867 1.8 1 163834 8033 13 171669 0.4 1 163202 8467 14 186645 0.4 1 176006 10639 15 183811 0.4 1 173927 9884 16 195217 0.4 1 183783 11434 17 190501 0.4 1 179966 10535 18 172141 0.4 1 163719 8422 19 188484 0.4 1 176755 11729 20 179359 0.4 1 170114 9245 21 205026 0.4 1 191543 13483 22 189461 0.4 1 179205 10256 23 178992 0.4 1 169034 9958 24 189011 0.4 1 177399 11612 25 182811 0.4 1 172905 9906 26 197467 0.4 1 184900 12567 27 187440 0.4 1 177488 9952 28 183510 0.4 1 174210 9300 29 200427 0.4 1 189396 11031 30 181551 0.4 1 172831 8720 31 198184 0.4 1 186977 11207 32 186477 0.4 1 177109 9368 33 203847 0.4 1 192280 11567 34 194540 0.4 1 184204 10336 35 188612 0.4 1 178870 9742 36 197121 0.4 1 187663 9458 37 196742 0.4 1 187217 9525 38 182243 0.4 1 173263 8980 39 177383 0.4 1 169016 8367 40 201535 0.4 1 189969 11566 41 273186 0.4 1 260772 12414 42 152641 0.4 1 144977 7664 43 121214 0.4 1 115030 6184 44 167704 0.4 1 159432 8272 45 173933 0.4 1 164821 9112 46 165905 0.4 1 157328 8577 47 180672 0.4 1 170644 10028 48 168762 0.4 1 159259 9503 49 179662 0.4 1 169466 10196 50 157445 0.4 1 149362 8083 51 162118 0.4 1 153422 8696 52 161449 0.4 1 152217 9232 53 151363 0.4 1 143476 7887 54 148470 0.4 1 140200 8270 55 164808 0.4 1 155888 8920 56 149600 0.4 1 141017 8583 57 139800 0.4 1 131748 8052 58 148378 0.4 1 140657 7721 59 142416 0.4 1 134970 7446 60 126969 0.4 1 120560 6409 61 139713 0.4 1 132655 7058 62 141541 0.4 1 134560 6981 63 129209 0.4 1 122589 6620 64 124623 0.4 1 118880 5743 65 117319 0.4 1 112279 5040 66 111548 0.4 1 106649 4899 67 112419 0.4 1 107493 4926 68 107295 0.4 1 102808 4487 69 113769 0.4 1 109068 4701 70 108044 0.4 1 103691 4353 71 103460 0.4 1 99169 4291 72 102749 0.4 1 98147 4602 73 126131 0.4 1 118629 7502 74 233092 0.4 1 225110 7982 75 130064 0.4 1 125412 4652 76 66306 0.4 1 63741 2565 77 40924 0.4 1 39253 1671 78 27651 0.4 1 26481 1170 79 17969 0.4 1 17114 855 80 14304 0.4 1 13686 618 81 10423 0.4 1 9985 438 82 7849 0.4 1 7528 321 83 6448 0.4 1 6188 260 84 4645 0.4 1 4448 197 85 3420 0.4 1 3264 156 86 2196 0.4 1 2076 120 87 1527 0.4 1 1441 86 88 887 0.4 1 833 54 89 713 0.4 1 660 53 90 794 0.4 1 746 48 91 909 0.4 1 849 60 92 1364 0.4 1 1260 104 93 2402 0.4 1 2259 143 94 5968 0.4 1 5617 351 95 9682 0.4 1 9197 485 96 6530 0.4 1 6147 383 97 4897 0.4 1 4556 341 98 1928 0.4 1 1781 147 99 1498 0.4 1 1333 165 100 2843 0.4 1 2468 375 101 14091 0.4 1 12101 1990 RUN STATISTICS FOR INPUT FILE: EPI-42_S39_L005_R1_001.fastq.gz ============================================= 30041436 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3528872 (11.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 18947734 (63.1%)