SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040875_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.2 Cutadapt version: 2.6 Number of cores used for trimming: 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 1 sequences will be trimmed by 3 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Output file will be GZIP compressed This is cutadapt 2.6 with Python 3.6.7 Command line parameters: -j 1 -e 0.1 -O 1 -a AGATCGGAAGAGC /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/test_analysis/tmp/77c42ccc-d1de-11eb-b5c3-6c92bfc1303a/trimmed/RRBS20A040875_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 4087.95 s (36 us/read; 1.66 M reads/minute). === Summary === Total reads processed: 113,389,968 Reads with adapters: 42,925,263 (37.9%) Reads written (passing filters): 113,389,968 (100.0%) Total basepairs processed: 9,675,057,466 bp Total written (filtered): 8,849,515,392 bp (91.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 42925263 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 8.4% C: 81.8% G: 7.5% T: 2.3% none/other: 0.0% WARNING: The adapter is preceded by "C" extremely often. The provided adapter sequence could be incomplete at its 3' end. Overview of removed sequences length count expect max.err error counts 1 36906771 28347492.0 0 36906771 2 120063 7086873.0 0 120063 3 30412 1771718.2 0 30412 4 38951 442929.6 0 38951 5 7704 110732.4 0 7704 6 3237 27683.1 0 3237 7 3350 6920.8 0 3350 8 3787 1730.2 0 3787 9 3496 432.5 0 3328 168 10 9540 108.1 1 2867 6673 11 1093 27.0 1 202 891 12 2278 6.8 1 570 1708 13 2154 1.7 1 202 1952 14 2431 1.7 1 244 2187 15 899 1.7 1 82 817 16 2061 1.7 1 209 1852 17 2359 1.7 1 206 2153 18 971 1.7 1 81 890 19 2477 1.7 1 228 2249 20 2273 1.7 1 237 2036 21 221 1.7 1 72 149 22 706 1.7 1 58 648 23 2131 1.7 1 162 1969 24 4423 1.7 1 386 4037 25 2412 1.7 1 175 2237 26 3790 1.7 1 309 3481 27 3206 1.7 1 270 2936 28 1978 1.7 1 231 1747 29 385 1.7 1 32 353 30 778 1.7 1 65 713 31 860 1.7 1 80 780 32 2241 1.7 1 192 2049 33 5007 1.7 1 399 4608 34 1772 1.7 1 155 1617 35 1378 1.7 1 139 1239 36 462 1.7 1 28 434 37 2845 1.7 1 255 2590 38 880 1.7 1 88 792 39 1159 1.7 1 132 1027 40 1206 1.7 1 120 1086 41 2675 1.7 1 93 2582 42 1836 1.7 1 149 1687 43 1088 1.7 1 99 989 44 1509 1.7 1 116 1393 45 3323 1.7 1 254 3069 46 1500 1.7 1 140 1360 47 682 1.7 1 67 615 48 1978 1.7 1 167 1811 49 1208 1.7 1 117 1091 50 1744 1.7 1 130 1614 51 2131 1.7 1 199 1932 52 1697 1.7 1 125 1572 53 284 1.7 1 25 259 54 1203 1.7 1 119 1084 55 1263 1.7 1 102 1161 56 253 1.7 1 20 233 57 1051 1.7 1 94 957 58 1559 1.7 1 144 1415 59 1249 1.7 1 120 1129 60 1841 1.7 1 198 1643 61 2243 1.7 1 260 1983 62 3353 1.7 1 577 2776 63 3136 1.7 1 747 2389 64 1136 1.7 1 147 989 65 842 1.7 1 106 736 66 2151 1.7 1 258 1893 67 1543 1.7 1 156 1387 68 1560 1.7 1 128 1432 69 1206 1.7 1 109 1097 70 1613 1.7 1 127 1486 71 1840 1.7 1 191 1649 72 1873 1.7 1 216 1657 73 1402 1.7 1 169 1233 74 1422 1.7 1 155 1267 75 2128 1.7 1 191 1937 76 2909 1.7 1 182 2727 77 932 1.7 1 56 876 78 1090 1.7 1 76 1014 79 1065 1.7 1 85 980 80 1058 1.7 1 76 982 81 930 1.7 1 60 870 82 748 1.7 1 60 688 83 1225 1.7 1 78 1147 84 1207 1.7 1 102 1105 85 1043 1.7 1 91 952 86 839 1.7 1 79 760 87 629 1.7 1 45 584 88 605 1.7 1 58 547 89 631 1.7 1 42 589 90 501 1.7 1 32 469 91 521 1.7 1 46 475 92 539 1.7 1 43 496 93 622 1.7 1 57 565 94 638 1.7 1 47 591 95 361 1.7 1 22 339 96 407 1.7 1 37 370 97 361 1.7 1 24 337 98 342 1.7 1 30 312 99 431 1.7 1 27 404 100 303 1.7 1 29 274 101 244 1.7 1 16 228 102 373 1.7 1 24 349 103 233 1.7 1 26 207 104 204 1.7 1 16 188 105 179 1.7 1 9 170 106 126 1.7 1 5 121 107 97 1.7 1 16 81 108 134 1.7 1 20 114 109 401 1.7 1 35 366 110 131 1.7 1 13 118 111 68 1.7 1 11 57 112 26 1.7 1 4 22 113 13 1.7 1 9 4 114 40 1.7 1 21 19 115 39 1.7 1 34 5 116 23 1.7 1 19 4 117 38 1.7 1 29 9 118 23 1.7 1 17 6 119 23 1.7 1 18 5 120 14 1.7 1 14 121 16 1.7 1 10 6 122 19 1.7 1 17 2 123 19 1.7 1 19 124 23 1.7 1 19 4 125 29 1.7 1 28 1 126 31 1.7 1 28 3 127 71 1.7 1 70 1 128 136 1.7 1 132 4 129 123 1.7 1 117 6 130 140 1.7 1 136 4 131 136 1.7 1 130 6 132 138 1.7 1 129 9 133 246 1.7 1 231 15 134 248 1.7 1 230 18 135 726 1.7 1 702 24 136 912 1.7 1 847 65 137 36224 1.7 1 35530 694 138 5621990 1.7 1 5553957 68033 139 1 1.7 1 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040875_val_2.fq.gz ============================================= 113389968 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4205823 (3.7%) 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: 113389968 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 6208543 (5.48%)