SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 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 File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth5_R1_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 6887.26 s (24 us/read; 2.49 M reads/minute). === Summary === Total reads processed: 285,607,307 Reads with adapters: 229,365,416 (80.3%) Reads written (passing filters): 285,607,307 (100.0%) Total basepairs processed: 42,798,918,300 bp Total written (filtered): 30,082,664,292 bp (70.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 229365416 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.5% C: 2.8% G: 43.1% T: 5.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 37615404 71401826.8 0 37615404 2 3823272 17850456.7 0 3823272 3 1929705 4462614.2 0 1929705 4 8216086 1115653.5 0 8216086 5 874551 278913.4 0 874551 6 729732 69728.3 0 729732 7 719271 17432.1 0 719271 8 636616 4358.0 0 636616 9 610015 1089.5 0 601088 8927 10 897943 272.4 1 826202 71741 11 835081 68.1 1 758841 76240 12 732250 17.0 1 664625 67625 13 855682 4.3 1 768432 87250 14 934838 4.3 1 833256 101582 15 1237634 4.3 1 1110781 126853 16 1385243 4.3 1 1230937 154306 17 877314 4.3 1 779091 98223 18 908164 4.3 1 816927 91237 19 831362 4.3 1 745063 86299 20 1555687 4.3 1 1398148 157539 21 2741198 4.3 1 2465529 275669 22 1820876 4.3 1 1637482 183394 23 899390 4.3 1 803614 95776 24 918471 4.3 1 814304 104167 25 1671292 4.3 1 1502852 168440 26 867775 4.3 1 775720 92055 27 1324017 4.3 1 1180731 143286 28 4561981 4.3 1 4104006 457975 29 1146671 4.3 1 1017804 128867 30 1027972 4.3 1 924415 103557 31 1085728 4.3 1 972859 112869 32 1611448 4.3 1 1448791 162657 33 886562 4.3 1 789986 96576 34 1119780 4.3 1 1003394 116386 35 1031703 4.3 1 919280 112423 36 943899 4.3 1 846420 97479 37 1021879 4.3 1 914638 107241 38 1703806 4.3 1 1531207 172599 39 1123930 4.3 1 1003160 120770 40 1482557 4.3 1 1327082 155475 41 1692413 4.3 1 1520244 172169 42 1153325 4.3 1 1033386 119939 43 1672983 4.3 1 1496297 176686 44 1714346 4.3 1 1528267 186079 45 1935829 4.3 1 1747015 188814 46 768909 4.3 1 685312 83597 47 896871 4.3 1 802485 94386 48 1053398 4.3 1 944221 109177 49 1302932 4.3 1 1168808 134124 50 885825 4.3 1 788797 97028 51 1010152 4.3 1 899387 110765 52 1404553 4.3 1 1260893 143660 53 930746 4.3 1 831140 99606 54 1129444 4.3 1 1007089 122355 55 1433735 4.3 1 1282800 150935 56 1194201 4.3 1 1067503 126698 57 1324099 4.3 1 1183222 140877 58 2002838 4.3 1 1793889 208949 59 1371764 4.3 1 1224247 147517 60 2124403 4.3 1 1907764 216639 61 2020633 4.3 1 1811014 209619 62 1081769 4.3 1 965189 116580 63 1231632 4.3 1 1101342 130290 64 1763384 4.3 1 1582772 180612 65 1092017 4.3 1 973871 118146 66 1470910 4.3 1 1313554 157356 67 1593438 4.3 1 1422138 171300 68 1348060 4.3 1 1201756 146304 69 1376068 4.3 1 1200593 175475 70 3341550 4.3 1 3030992 310558 71 249878 4.3 1 218574 31304 72 104243 4.3 1 85095 19148 73 534650 4.3 1 469177 65473 74 1018477 4.3 1 907342 111135 75 1252802 4.3 1 1117960 134842 76 2034078 4.3 1 1819042 215036 77 1298399 4.3 1 1156782 141617 78 1009250 4.3 1 898957 110293 79 1326076 4.3 1 1182564 143512 80 1241862 4.3 1 1105651 136211 81 1246431 4.3 1 1107915 138516 82 1860293 4.3 1 1632119 228174 83 1544206 4.3 1 1361468 182738 84 1473965 4.3 1 1309253 164712 85 1514414 4.3 1 1347322 167092 86 1131141 4.3 1 1004718 126423 87 1457872 4.3 1 1296908 160964 88 1729833 4.3 1 1539759 190074 89 1706854 4.3 1 1517143 189711 90 2084838 4.3 1 1854550 230288 91 1887471 4.3 1 1675495 211976 92 2101576 4.3 1 1863429 238147 93 2084969 4.3 1 1849308 235661 94 2336410 4.3 1 2066675 269735 95 1590695 4.3 1 1407361 183334 96 2684007 4.3 1 2384074 299933 97 2256733 4.3 1 1998241 258492 98 2219956 4.3 1 1964200 255756 99 1737602 4.3 1 1536908 200694 100 1881866 4.3 1 1664340 217526 101 1686004 4.3 1 1489669 196335 102 1364518 4.3 1 1204809 159709 103 2414501 4.3 1 2136096 278405 104 1521021 4.3 1 1339449 181572 105 1471000 4.3 1 1296875 174125 106 1849669 4.3 1 1632079 217590 107 1356605 4.3 1 1193999 162606 108 2158876 4.3 1 1902708 256168 109 1684151 4.3 1 1477712 206439 110 1457010 4.3 1 1280244 176766 111 1398943 4.3 1 1228355 170588 112 2115042 4.3 1 1858382 256660 113 1446018 4.3 1 1267467 178551 114 2191531 4.3 1 1920127 271404 115 2230740 4.3 1 1957130 273610 116 1344965 4.3 1 1176649 168316 117 1386741 4.3 1 1214186 172555 118 1947265 4.3 1 1704881 242384 119 2807501 4.3 1 2458055 349446 120 1145668 4.3 1 999495 146173 121 1344777 4.3 1 1174737 170040 122 1151281 4.3 1 1004528 146753 123 1360292 4.3 1 1188619 171673 124 1273651 4.3 1 1112417 161234 125 736748 4.3 1 642212 94536 126 739344 4.3 1 644508 94836 127 1094512 4.3 1 954291 140221 128 424513 4.3 1 369000 55513 129 295771 4.3 1 257526 38245 130 264580 4.3 1 230384 34196 131 367593 4.3 1 319865 47728 132 135721 4.3 1 117681 18040 133 54134 4.3 1 47126 7008 134 10091 4.3 1 8754 1337 135 2902 4.3 1 2533 369 136 7458 4.3 1 6469 989 137 264 4.3 1 206 58 138 56 4.3 1 39 17 139 40 4.3 1 36 4 140 24 4.3 1 16 8 141 18 4.3 1 16 2 142 15 4.3 1 7 8 143 2 4.3 1 2 144 10 4.3 1 3 7 145 3 4.3 1 2 1 146 1 4.3 1 1 147 8 4.3 1 5 3 148 193 4.3 1 164 29 149 207 4.3 1 190 17 150 3579 4.3 1 3140 439 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R1_001.fastq.gz ============================================= 285607307 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 12455645 (4.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 108911143 (38.1%) RRBS reads trimmed by 2 bp at the start when read started with CAA (3181836) or CGA (143429518) in total: 146611354 (51.3%)