SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R1_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 AGATCGGAAGAGCACACGTCTGAAC /gscratch/scrubbed/strigg/analyses/20200316/EPI-167_S10_L002_R1_001.fastq.gz_qual_trimmed.fastq Processing reads on 8 cores in single-end mode ... Finished in 81.27 s (3 us/read; 18.35 M reads/minute). === Summary === Total reads processed: 24,859,230 Reads with adapters: 13,310,825 (53.5%) Reads written (passing filters): 24,859,230 (100.0%) Total basepairs processed: 2,499,293,998 bp Total written (filtered): 2,298,441,331 bp (92.0%) === Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAAC; Type: regular 3'; Length: 25; Trimmed: 13310825 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-25 bp: 2 Bases preceding removed adapters: A: 25.5% C: 9.5% G: 23.7% T: 41.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5079588 6214807.5 0 5079588 2 1202251 1553701.9 0 1202251 3 456300 388425.5 0 456300 4 315396 97106.4 0 315396 5 162023 24276.6 0 162023 6 154952 6069.1 0 154952 7 141317 1517.3 0 141317 8 147815 379.3 0 147815 9 156397 94.8 0 154875 1522 10 144818 23.7 1 138784 6034 11 151610 5.9 1 144610 7000 12 144234 1.5 1 137849 6385 13 138279 0.4 1 132093 6186 14 149582 0.1 1 141472 8110 15 139617 0.0 1 132371 7246 16 149533 0.0 1 140718 8815 17 143290 0.0 1 134911 8379 18 132507 0.0 1 123777 8159 571 19 143599 0.0 1 132190 10635 774 20 131755 0.0 2 122046 8589 1120 21 146494 0.0 2 132987 11445 2062 22 135126 0.0 2 124303 9630 1193 23 126194 0.0 2 115663 9314 1217 24 131857 0.0 2 119870 10387 1600 25 122353 0.0 2 112116 9190 1047 26 132356 0.0 2 119736 10869 1751 27 119873 0.0 2 109836 8721 1316 28 113147 0.0 2 103784 8301 1062 29 123716 0.0 2 112992 9263 1461 30 113300 0.0 2 103872 8363 1065 31 120517 0.0 2 109240 9537 1740 32 111072 0.0 2 102015 7969 1088 33 114305 0.0 2 104447 8569 1289 34 108779 0.0 2 99492 8120 1167 35 104061 0.0 2 95648 7427 986 36 99353 0.0 2 91169 7175 1009 37 105972 0.0 2 96779 8018 1175 38 92166 0.0 2 84732 6433 1001 39 93699 0.0 2 85639 6965 1095 40 94449 0.0 2 85795 7662 992 41 129224 0.0 2 119820 8107 1297 42 78034 0.0 2 72578 4766 690 43 35611 0.0 2 31892 3292 427 44 72241 0.0 2 66560 4941 740 45 66871 0.0 2 61637 4601 633 46 63480 0.0 2 58567 4379 534 47 65222 0.0 2 59962 4547 713 48 58338 0.0 2 53531 4197 610 49 59861 0.0 2 54840 4380 641 50 53802 0.0 2 49655 3678 469 51 50397 0.0 2 46525 3380 492 52 46801 0.0 2 43097 3252 452 53 42870 0.0 2 39683 2782 405 54 41405 0.0 2 38238 2746 421 55 40756 0.0 2 37782 2611 363 56 36903 0.0 2 34142 2423 338 57 33898 0.0 2 31227 2360 311 58 31239 0.0 2 28980 2027 232 59 30217 0.0 2 28005 1966 246 60 26732 0.0 2 24878 1668 186 61 26427 0.0 2 24460 1787 180 62 25361 0.0 2 23508 1647 206 63 21705 0.0 2 20154 1396 155 64 19937 0.0 2 18653 1152 132 65 17966 0.0 2 16711 1137 118 66 16513 0.0 2 15317 1088 108 67 15408 0.0 2 14252 1052 104 68 14019 0.0 2 12960 970 89 69 13548 0.0 2 12518 939 91 70 12389 0.0 2 11493 818 78 71 12247 0.0 2 11250 892 105 72 14140 0.0 2 12722 1193 225 73 24750 0.0 2 21535 2947 268 74 80751 0.0 2 75790 4690 271 75 62956 0.0 2 59263 3517 176 76 34298 0.0 2 32139 2050 109 77 19980 0.0 2 18745 1172 63 78 11508 0.0 2 10781 686 41 79 6171 0.0 2 5742 410 19 80 3991 0.0 2 3687 279 25 81 2402 0.0 2 2222 166 14 82 1642 0.0 2 1490 140 12 83 1273 0.0 2 1174 88 11 84 1130 0.0 2 1031 91 8 85 989 0.0 2 903 78 8 86 959 0.0 2 877 76 6 87 835 0.0 2 750 78 7 88 716 0.0 2 643 63 10 89 798 0.0 2 727 62 9 90 871 0.0 2 802 64 5 91 1229 0.0 2 1108 109 12 92 1963 0.0 2 1790 160 13 93 4579 0.0 2 4247 306 26 94 13773 0.0 2 12652 1011 110 95 24682 0.0 2 22814 1730 138 96 11975 0.0 2 11015 885 75 97 8863 0.0 2 8123 684 56 98 3854 0.0 2 3544 284 26 99 4127 0.0 2 3800 310 17 100 4411 0.0 2 4002 383 26 101 8135 0.0 2 7184 899 52 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R1_001.fastq.gz ============================================= 24859230 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2260450 (9.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 13261661 (53.3%)