SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041691_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/20201120/tmp/a7d87d3e-5572-11eb-abb3-6c92bfc12890/trimmed/RRBS20A041691_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 392.17 s (22 us/read; 2.72 M reads/minute). === Summary === Total reads processed: 17,789,570 Reads with adapters: 7,695,077 (43.3%) Reads written (passing filters): 17,789,570 (100.0%) Total basepairs processed: 1,846,419,022 bp Total written (filtered): 1,678,632,672 bp (90.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7695077 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.5% C: 0.5% G: 17.5% T: 56.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4803854 4447392.5 0 4803854 2 1315221 1111848.1 0 1315221 3 316064 277962.0 0 316064 4 69465 69490.5 0 69465 5 3644 17372.6 0 3644 6 1440 4343.2 0 1440 7 1337 1085.8 0 1337 8 546 271.4 0 546 9 929 67.9 0 754 175 10 1480 17.0 1 268 1212 11 1101 4.2 1 96 1005 12 431 1.1 1 38 393 13 425 0.3 1 30 395 14 801 0.3 1 71 730 15 541 0.3 1 46 495 16 1453 0.3 1 118 1335 17 1721 0.3 1 172 1549 18 1604 0.3 1 730 874 19 70 0.3 1 7 63 20 376 0.3 1 47 329 21 80 0.3 1 7 73 22 101 0.3 1 28 73 23 425 0.3 1 27 398 24 1311 0.3 1 139 1172 25 533 0.3 1 48 485 26 259 0.3 1 40 219 27 537 0.3 1 48 489 28 1063 0.3 1 94 969 29 1141 0.3 1 110 1031 30 287 0.3 1 40 247 31 60 0.3 1 9 51 32 418 0.3 1 39 379 33 870 0.3 1 66 804 34 684 0.3 1 59 625 35 1170 0.3 1 113 1057 36 525 0.3 1 54 471 37 243 0.3 1 29 214 38 782 0.3 1 75 707 39 313 0.3 1 27 286 40 929 0.3 1 94 835 41 682 0.3 1 55 627 42 767 0.3 1 63 704 43 1086 0.3 1 81 1005 44 209 0.3 1 15 194 45 533 0.3 1 55 478 46 190 0.3 1 22 168 47 317 0.3 1 25 292 48 1130 0.3 1 120 1010 49 126 0.3 1 17 109 50 469 0.3 1 52 417 51 196 0.3 1 22 174 52 116 0.3 1 14 102 53 280 0.3 1 25 255 54 1090 0.3 1 146 944 55 688 0.3 1 67 621 56 428 0.3 1 45 383 57 449 0.3 1 56 393 58 319 0.3 1 31 288 59 187 0.3 1 13 174 60 314 0.3 1 28 286 61 488 0.3 1 58 430 62 1168 0.3 1 161 1007 63 327 0.3 1 44 283 64 67 0.3 1 7 60 65 43 0.3 1 2 41 66 223 0.3 1 30 193 67 142 0.3 1 15 127 68 468 0.3 1 54 414 69 573 0.3 1 67 506 70 1070 0.3 1 129 941 71 492 0.3 1 45 447 72 190 0.3 1 21 169 73 260 0.3 1 18 242 74 238 0.3 1 18 220 75 211 0.3 1 13 198 76 261 0.3 1 26 235 77 285 0.3 1 22 263 78 240 0.3 1 21 219 79 226 0.3 1 22 204 80 363 0.3 1 28 335 81 209 0.3 1 18 191 82 272 0.3 1 15 257 83 332 0.3 1 39 293 84 266 0.3 1 24 242 85 465 0.3 1 41 424 86 232 0.3 1 24 208 87 181 0.3 1 12 169 88 194 0.3 1 16 178 89 231 0.3 1 22 209 90 224 0.3 1 27 197 91 159 0.3 1 22 137 92 157 0.3 1 13 144 93 474 0.3 1 38 436 94 510 0.3 1 39 471 95 195 0.3 1 14 181 96 153 0.3 1 13 140 97 524 0.3 1 26 498 98 132 0.3 1 18 114 99 80 0.3 1 6 74 100 84 0.3 1 6 78 101 111 0.3 1 9 102 102 198 0.3 1 15 183 103 66 0.3 1 10 56 104 49 0.3 1 9 40 105 44 0.3 1 5 39 106 46 0.3 1 2 44 107 23 0.3 1 1 22 108 4 0.3 1 2 2 109 15 0.3 1 3 12 110 16 0.3 1 1 15 111 9 0.3 1 4 5 113 3 0.3 1 3 114 6 0.3 1 3 3 115 1 0.3 1 0 1 117 7 0.3 1 6 1 118 2 0.3 1 0 2 119 6 0.3 1 5 1 120 6 0.3 1 5 1 121 6 0.3 1 5 1 122 6 0.3 1 4 2 123 10 0.3 1 7 3 124 8 0.3 1 7 1 125 5 0.3 1 3 2 126 12 0.3 1 11 1 127 21 0.3 1 12 9 128 23 0.3 1 16 7 129 26 0.3 1 20 6 130 27 0.3 1 21 6 131 46 0.3 1 37 9 132 85 0.3 1 65 20 133 174 0.3 1 132 42 134 254 0.3 1 211 43 135 338 0.3 1 279 59 136 607 0.3 1 508 99 137 9766 0.3 1 9107 659 138 1126828 0.3 1 1100197 26631 139 1 0.3 1 1 140 2 0.3 1 0 2 141 1 0.3 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041691_val_1.fq.gz ============================================= 17789570 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 677144 (3.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 7695077 (43.3%)