SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGCACACGTCTGAAC' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'AGATCGGAAGAGCGTCGTGTAGGGA' 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 /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -O 1 -a AGATCGGAAGAGCGTCGTGTAGGGA /gscratch/scrubbed/strigg/analyses/20200316/EPI-167_S10_L002_R2_001.fastq.gz_qual_trimmed.fastq Processing reads on 8 cores in single-end mode ... Finished in 85.41 s (3 us/read; 17.46 M reads/minute). === Summary === Total reads processed: 24,859,230 Reads with adapters: 15,363,536 (61.8%) Reads written (passing filters): 24,859,230 (100.0%) Total basepairs processed: 2,488,122,616 bp Total written (filtered): 2,293,251,313 bp (92.2%) === Adapter 1 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGA; Type: regular 3'; Length: 25; Trimmed: 15363536 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-25 bp: 2 Bases preceding removed adapters: A: 40.3% C: 20.3% G: 7.3% T: 32.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8554514 6214807.5 0 8554514 2 247131 1553701.9 0 247131 3 191193 388425.5 0 191193 4 164298 97106.4 0 164298 5 160566 24276.6 0 160566 6 159035 6069.1 0 159035 7 150319 1517.3 0 150319 8 152605 379.3 0 152605 9 152922 94.8 0 152285 637 10 151128 23.7 1 146689 4439 11 146920 5.9 1 141612 5308 12 148837 1.5 1 143363 5474 13 142341 0.4 1 137280 5061 14 151875 0.1 1 146116 5759 15 140621 0.0 1 135080 5541 16 140329 0.0 1 134360 5969 17 147590 0.0 1 141058 6532 18 131268 0.0 1 125180 5970 118 19 137242 0.0 1 130202 6888 152 20 134860 0.0 2 126296 7299 1265 21 136470 0.0 2 126594 8307 1569 22 137929 0.0 2 128046 8405 1478 23 132148 0.0 2 122951 7765 1432 24 137535 0.0 2 127293 8713 1529 25 121830 0.0 2 112500 7874 1456 26 122372 0.0 2 111493 9021 1858 27 122833 0.0 2 110779 9719 2335 28 125558 0.0 2 115435 8627 1496 29 121040 0.0 2 109875 9372 1793 30 127761 0.0 2 117798 8505 1458 31 110644 0.0 2 101253 7874 1517 32 113145 0.0 2 104687 7317 1141 33 117931 0.0 2 107886 8506 1539 34 119747 0.0 2 108853 9087 1807 35 109358 0.0 2 101564 6789 1005 36 102469 0.0 2 93985 7185 1299 37 101986 0.0 2 93931 6852 1203 38 88289 0.0 2 81349 5989 951 39 91384 0.0 2 83980 6298 1106 40 87968 0.0 2 81063 5902 1003 41 85810 0.0 2 79585 5436 789 42 82412 0.0 2 76871 4870 671 43 73026 0.0 2 67328 4920 778 44 72521 0.0 2 67133 4755 633 45 84963 0.0 2 79659 4649 655 46 65401 0.0 2 60883 3896 622 47 46340 0.0 2 42573 3316 451 48 62890 0.0 2 58972 3433 485 49 44178 0.0 2 41087 2712 379 50 45926 0.0 2 42356 3132 438 51 59803 0.0 2 56373 3012 418 52 36947 0.0 2 34103 2470 374 53 36693 0.0 2 33991 2310 392 54 32194 0.0 2 29695 2182 317 55 36861 0.0 2 34493 2101 267 56 34269 0.0 2 31729 2174 366 57 30720 0.0 2 28494 1961 265 58 28380 0.0 2 26339 1776 265 59 26631 0.0 2 24733 1671 227 60 25170 0.0 2 23184 1700 286 61 24593 0.0 2 22735 1596 262 62 24060 0.0 2 22223 1561 276 63 22601 0.0 2 20779 1597 225 64 21649 0.0 2 19897 1515 237 65 22204 0.0 2 20390 1572 242 66 24131 0.0 2 22040 1770 321 67 35937 0.0 2 31177 4455 305 68 129003 0.0 2 123606 5023 374 69 47313 0.0 2 44432 2606 275 70 24870 0.0 2 23330 1358 182 71 12976 0.0 2 11952 904 120 72 8650 0.0 2 7938 594 118 73 6006 0.0 2 5428 500 78 74 4673 0.0 2 4170 423 80 75 3587 0.0 2 3246 292 49 76 2967 0.0 2 2644 260 63 77 2595 0.0 2 2287 248 60 78 2277 0.0 2 1988 229 60 79 1974 0.0 2 1740 196 38 80 1588 0.0 2 1403 150 35 81 1399 0.0 2 1220 147 32 82 1178 0.0 2 1020 129 29 83 1067 0.0 2 929 111 27 84 908 0.0 2 767 111 30 85 844 0.0 2 702 108 34 86 765 0.0 2 629 110 26 87 784 0.0 2 659 101 24 88 797 0.0 2 673 96 28 89 913 0.0 2 759 123 31 90 1123 0.0 2 931 153 39 91 1402 0.0 2 1155 188 59 92 2147 0.0 2 1810 255 82 93 4579 0.0 2 3823 597 159 94 13431 0.0 2 11681 1388 362 95 23741 0.0 2 20778 2421 542 96 11598 0.0 2 10136 1204 258 97 8556 0.0 2 7512 866 178 98 3633 0.0 2 3223 345 65 99 3883 0.0 2 3382 409 92 100 4128 0.0 2 3619 404 105 101 7880 0.0 2 6828 858 194 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R2_001.fastq.gz ============================================= 24859230 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2502338 (10.1%) 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: 24859230 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 375991 (1.51%)