SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041594_val_1.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 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) All Read 1 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases 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/cup/BS_workflow/20201104_20201106/tmp/6029eba2-48bc-11eb-ab4d-6c92bfc12b7e/trimmed/RRBS20A041594_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 377.53 s (21 us/read; 2.82 M reads/minute). === Summary === Total reads processed: 17,728,246 Reads with adapters: 7,634,189 (43.1%) Reads written (passing filters): 17,728,246 (100.0%) Total basepairs processed: 1,799,229,967 bp Total written (filtered): 1,770,327,458 bp (98.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7634189 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 0.5% G: 21.1% T: 48.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5500609 4432061.5 0 5500609 2 1496120 1108015.4 0 1496120 3 352569 277003.8 0 352569 4 80015 69251.0 0 80015 5 5348 17312.7 0 5348 6 2366 4328.2 0 2366 7 1343 1082.0 0 1343 8 1619 270.5 0 1619 9 2371 67.6 0 2130 241 10 2181 16.9 1 843 1338 11 2225 4.2 1 246 1979 12 624 1.1 1 71 553 13 732 0.3 1 116 616 14 1468 0.3 1 171 1297 15 1236 0.3 1 161 1075 16 2566 0.3 1 385 2181 17 4166 0.3 1 813 3353 18 2446 0.3 1 1179 1267 19 68 0.3 1 6 62 20 844 0.3 1 149 695 21 69 0.3 1 5 64 22 103 0.3 1 12 91 23 617 0.3 1 77 540 24 2146 0.3 1 302 1844 25 1001 0.3 1 155 846 26 380 0.3 1 42 338 27 861 0.3 1 114 747 28 2002 0.3 1 350 1652 29 2042 0.3 1 324 1718 30 443 0.3 1 56 387 31 104 0.3 1 13 91 32 909 0.3 1 187 722 33 1378 0.3 1 202 1176 34 1704 0.3 1 260 1444 35 528 0.3 1 81 447 36 996 0.3 1 153 843 37 1274 0.3 1 232 1042 38 1579 0.3 1 373 1206 39 352 0.3 1 41 311 40 1010 0.3 1 142 868 41 2006 0.3 1 306 1700 42 238 0.3 1 30 208 43 3012 0.3 1 402 2610 44 401 0.3 1 55 346 45 1017 0.3 1 138 879 46 268 0.3 1 30 238 47 707 0.3 1 94 613 48 1859 0.3 1 276 1583 49 154 0.3 1 16 138 50 1145 0.3 1 153 992 51 307 0.3 1 29 278 52 177 0.3 1 17 160 53 762 0.3 1 124 638 54 2488 0.3 1 350 2138 55 1156 0.3 1 160 996 56 593 0.3 1 71 522 57 1155 0.3 1 197 958 58 545 0.3 1 65 480 59 299 0.3 1 35 264 60 566 0.3 1 103 463 61 739 0.3 1 111 628 62 2077 0.3 1 364 1713 63 622 0.3 1 98 524 64 58 0.3 1 12 46 65 47 0.3 1 5 42 66 209 0.3 1 31 178 67 261 0.3 1 38 223 68 1076 0.3 1 166 910 69 1105 0.3 1 147 958 70 2107 0.3 1 313 1794 71 936 0.3 1 117 819 72 383 0.3 1 47 336 73 299 0.3 1 39 260 74 362 0.3 1 66 296 75 490 0.3 1 86 404 76 578 0.3 1 107 471 77 633 0.3 1 109 524 78 503 0.3 1 76 427 79 480 0.3 1 74 406 80 592 0.3 1 60 532 81 445 0.3 1 71 374 82 644 0.3 1 80 564 83 646 0.3 1 85 561 84 463 0.3 1 45 418 85 549 0.3 1 79 470 86 519 0.3 1 71 448 87 369 0.3 1 61 308 88 339 0.3 1 52 287 89 338 0.3 1 57 281 90 347 0.3 1 59 288 91 230 0.3 1 22 208 92 246 0.3 1 17 229 93 1366 0.3 1 165 1201 94 1893 0.3 1 170 1723 95 456 0.3 1 57 399 96 280 0.3 1 35 245 97 1367 0.3 1 128 1239 98 229 0.3 1 39 190 99 148 0.3 1 17 131 100 169 0.3 1 17 152 101 126 0.3 1 20 106 102 284 0.3 1 41 243 103 105 0.3 1 12 93 104 52 0.3 1 9 43 105 52 0.3 1 7 45 106 70 0.3 1 11 59 107 51 0.3 1 10 41 108 12 0.3 1 0 12 109 28 0.3 1 11 17 110 59 0.3 1 5 54 111 5 0.3 1 0 5 112 3 0.3 1 0 3 113 3 0.3 1 0 3 114 6 0.3 1 3 3 115 1 0.3 1 0 1 116 5 0.3 1 1 4 117 1 0.3 1 0 1 118 1 0.3 1 0 1 119 1 0.3 1 0 1 121 2 0.3 1 2 125 2 0.3 1 2 126 4 0.3 1 3 1 127 1 0.3 1 1 128 4 0.3 1 3 1 129 4 0.3 1 4 130 8 0.3 1 7 1 131 7 0.3 1 7 132 3 0.3 1 2 1 133 31 0.3 1 16 15 134 21 0.3 1 17 4 135 46 0.3 1 42 4 136 57 0.3 1 49 8 137 6683 0.3 1 6528 155 138 102577 0.3 1 100649 1928 140 5 0.3 1 0 5 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041594_val_1.fq.gz ============================================= 17728246 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 577145 (3.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 7634187 (43.1%)