SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R2_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_R2_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 7144.92 s (25 us/read; 2.40 M reads/minute). === Summary === Total reads processed: 285,607,307 Reads with adapters: 225,585,200 (79.0%) Reads written (passing filters): 285,607,307 (100.0%) Total basepairs processed: 42,516,646,914 bp Total written (filtered): 30,155,326,446 bp (70.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 225585200 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 2.4% G: 45.8% T: 6.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 37550958 71401826.8 0 37550958 2 3999282 17850456.7 0 3999282 3 2189402 4462614.2 0 2189402 4 8119262 1115653.5 0 8119262 5 873671 278913.4 0 873671 6 709476 69728.3 0 709476 7 656407 17432.1 0 656407 8 637060 4358.0 0 637060 9 590881 1089.5 0 586446 4435 10 862637 272.4 1 804753 57884 11 824942 68.1 1 751663 73279 12 800616 17.0 1 733556 67060 13 776504 4.3 1 694301 82203 14 914479 4.3 1 818113 96366 15 1168832 4.3 1 1050977 117855 16 1375438 4.3 1 1219584 155854 17 821395 4.3 1 736617 84778 18 836446 4.3 1 756621 79825 19 883523 4.3 1 796330 87193 20 1661465 4.3 1 1500619 160846 21 2530193 4.3 1 2289437 240756 22 1790993 4.3 1 1630887 160106 23 816304 4.3 1 739867 76437 24 910457 4.3 1 821999 88458 25 1742369 4.3 1 1582488 159881 26 775650 4.3 1 695991 79659 27 1392418 4.3 1 1223561 168857 28 4306874 4.3 1 3932359 374515 29 1126540 4.3 1 1016211 110329 30 998742 4.3 1 909760 88982 31 1089490 4.3 1 985790 103700 32 1541836 4.3 1 1407132 134704 33 886377 4.3 1 802233 84144 34 1142805 4.3 1 1028498 114307 35 1013539 4.3 1 920862 92677 36 873015 4.3 1 797615 75400 37 1020651 4.3 1 927408 93243 38 1610806 4.3 1 1464903 145903 39 1178072 4.3 1 1067170 110902 40 1452147 4.3 1 1315194 136953 41 1658733 4.3 1 1514018 144715 42 1128479 4.3 1 1028781 99698 43 1542277 4.3 1 1405387 136890 44 1725407 4.3 1 1575400 150007 45 1474146 4.3 1 1339373 134773 46 1343257 4.3 1 1217202 126055 47 1088504 4.3 1 998241 90263 48 902566 4.3 1 820574 81992 49 1156175 4.3 1 1052588 103587 50 904523 4.3 1 824983 79540 51 844725 4.3 1 767457 77268 52 1414166 4.3 1 1290004 124162 53 932731 4.3 1 850233 82498 54 1439177 4.3 1 1317857 121320 55 962029 4.3 1 873407 88622 56 1249213 4.3 1 1129428 119785 57 2495058 4.3 1 2280619 214439 58 1082649 4.3 1 978738 103911 59 1196960 4.3 1 1086582 110378 60 2655580 4.3 1 2434981 220599 61 1878629 4.3 1 1715325 163304 62 955590 4.3 1 850632 104958 63 4125480 4.3 1 3793647 331833 64 1156038 4.3 1 1052382 103656 65 633976 4.3 1 576567 57409 66 827307 4.3 1 747215 80092 67 2040729 4.3 1 1870475 170254 68 1138467 4.3 1 1037794 100673 69 953600 4.3 1 868744 84856 70 1330080 4.3 1 1216756 113324 71 1065370 4.3 1 973142 92228 72 910235 4.3 1 828615 81620 73 1301346 4.3 1 1187735 113611 74 1212881 4.3 1 1103622 109259 75 1426499 4.3 1 1299462 127037 76 1442267 4.3 1 1318503 123764 77 616653 4.3 1 556610 60043 78 796348 4.3 1 724140 72208 79 1173497 4.3 1 1069659 103838 80 1147825 4.3 1 1043683 104142 81 1190242 4.3 1 1078511 111731 82 1766597 4.3 1 1579901 186696 83 1596348 4.3 1 1436533 159815 84 1469557 4.3 1 1333989 135568 85 1611221 4.3 1 1464960 146261 86 1178902 4.3 1 1070210 108692 87 1436923 4.3 1 1305971 130952 88 1674824 4.3 1 1523974 150850 89 1637483 4.3 1 1488217 149266 90 1988478 4.3 1 1809837 178641 91 1795727 4.3 1 1630997 164730 92 1986686 4.3 1 1803966 182720 93 1981772 4.3 1 1800991 180781 94 2188078 4.3 1 1982590 205488 95 1515832 4.3 1 1374456 141376 96 2527317 4.3 1 2299131 228186 97 2154423 4.3 1 1958347 196076 98 2140234 4.3 1 1945322 194912 99 1721542 4.3 1 1563192 158350 100 1854808 4.3 1 1684175 170633 101 1626385 4.3 1 1475357 151028 102 1311137 4.3 1 1188590 122547 103 2263843 4.3 1 2054809 209034 104 1424019 4.3 1 1289898 134121 105 1393582 4.3 1 1262542 131040 106 1734960 4.3 1 1571195 163765 107 1291706 4.3 1 1169023 122683 108 2035934 4.3 1 1842451 193483 109 1576095 4.3 1 1422638 153457 110 1373934 4.3 1 1241688 132246 111 1325579 4.3 1 1196575 129004 112 2004815 4.3 1 1811963 192852 113 1416896 4.3 1 1279101 137795 114 2124004 4.3 1 1916759 207245 115 2170659 4.3 1 1958563 212096 116 1324252 4.3 1 1193624 130628 117 1343993 4.3 1 1211034 132959 118 1904040 4.3 1 1716333 187707 119 2690112 4.3 1 2423928 266184 120 1115731 4.3 1 1003786 111945 121 1300134 4.3 1 1169857 130277 122 1101233 4.3 1 990008 111225 123 1307813 4.3 1 1176141 131672 124 1219643 4.3 1 1097092 122551 125 720809 4.3 1 648163 72646 126 725237 4.3 1 651779 73458 127 1052435 4.3 1 944640 107795 128 411841 4.3 1 369359 42482 129 284093 4.3 1 255062 29031 130 256111 4.3 1 229972 26139 131 350724 4.3 1 314098 36626 132 129417 4.3 1 116452 12965 133 51882 4.3 1 46490 5392 134 9690 4.3 1 8650 1040 135 2831 4.3 1 2512 319 136 7300 4.3 1 6487 813 137 246 4.3 1 222 24 138 52 4.3 1 47 5 139 39 4.3 1 34 5 140 20 4.3 1 19 1 141 19 4.3 1 14 5 142 13 4.3 1 9 4 143 9 4.3 1 3 6 144 13 4.3 1 5 8 145 3 4.3 1 2 1 146 2 4.3 1 0 2 147 12 4.3 1 9 3 148 189 4.3 1 163 26 149 221 4.3 1 197 24 150 3373 4.3 1 3088 285 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R2_001.fastq.gz ============================================= 285607307 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 29966360 (10.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (2851016) or CGA (127749902) in total: 130600918 (45.7%) Total number of sequences analysed for the sequence pair length validation: 285607307 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1490937 (0.52%)