SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041597_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/a7204e8a-5572-11eb-9350-6c92bfc12e8a/trimmed/RRBS20A041597_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 262.21 s (23 us/read; 2.64 M reads/minute). === Summary === Total reads processed: 11,553,983 Reads with adapters: 4,759,518 (41.2%) Reads written (passing filters): 11,553,983 (100.0%) Total basepairs processed: 1,175,393,184 bp Total written (filtered): 1,141,069,324 bp (97.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4759518 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.6% C: 0.7% G: 24.8% T: 46.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3295462 2888495.8 0 3295462 2 943076 722123.9 0 943076 3 222078 180531.0 0 222078 4 52119 45132.7 0 52119 5 2549 11283.2 0 2549 6 1583 2820.8 0 1583 7 1179 705.2 0 1179 8 888 176.3 0 888 9 1449 44.1 0 1313 136 10 1452 11.0 1 558 894 11 1013 2.8 1 185 828 12 461 0.7 1 80 381 13 568 0.2 1 97 471 14 908 0.2 1 157 751 15 690 0.2 1 122 568 16 1642 0.2 1 301 1341 17 2150 0.2 1 461 1689 18 1378 0.2 1 525 853 19 67 0.2 1 13 54 20 499 0.2 1 111 388 21 70 0.2 1 13 57 22 94 0.2 1 18 76 23 473 0.2 1 81 392 24 1438 0.2 1 311 1127 25 597 0.2 1 120 477 26 241 0.2 1 38 203 27 667 0.2 1 121 546 28 1393 0.2 1 283 1110 29 1266 0.2 1 222 1044 30 326 0.2 1 50 276 31 46 0.2 1 3 43 32 510 0.2 1 76 434 33 809 0.2 1 140 669 34 832 0.2 1 145 687 35 1345 0.2 1 241 1104 36 598 0.2 1 102 496 37 280 0.2 1 55 225 38 871 0.2 1 148 723 39 398 0.2 1 74 324 40 1168 0.2 1 210 958 41 891 0.2 1 183 708 42 931 0.2 1 196 735 43 1399 0.2 1 298 1101 44 233 0.2 1 36 197 45 730 0.2 1 157 573 46 278 0.2 1 38 240 47 470 0.2 1 92 378 48 1420 0.2 1 276 1144 49 151 0.2 1 26 125 50 588 0.2 1 91 497 51 211 0.2 1 34 177 52 167 0.2 1 28 139 53 406 0.2 1 82 324 54 1444 0.2 1 316 1128 55 805 0.2 1 134 671 56 441 0.2 1 76 365 57 637 0.2 1 131 506 58 360 0.2 1 68 292 59 187 0.2 1 39 148 60 314 0.2 1 45 269 61 480 0.2 1 71 409 62 1128 0.2 1 230 898 63 391 0.2 1 70 321 64 71 0.2 1 10 61 65 31 0.2 1 3 28 66 172 0.2 1 36 136 67 155 0.2 1 31 124 68 638 0.2 1 133 505 69 601 0.2 1 123 478 70 1271 0.2 1 227 1044 71 601 0.2 1 112 489 72 200 0.2 1 40 160 73 274 0.2 1 57 217 74 270 0.2 1 66 204 75 300 0.2 1 73 227 76 293 0.2 1 52 241 77 373 0.2 1 73 300 78 362 0.2 1 82 280 79 304 0.2 1 66 238 80 530 0.2 1 117 413 81 378 0.2 1 99 279 82 407 0.2 1 110 297 83 420 0.2 1 107 313 84 323 0.2 1 62 261 85 399 0.2 1 87 312 86 325 0.2 1 84 241 87 258 0.2 1 66 192 88 234 0.2 1 46 188 89 246 0.2 1 58 188 90 242 0.2 1 54 188 91 213 0.2 1 59 154 92 222 0.2 1 59 163 93 543 0.2 1 135 408 94 847 0.2 1 180 667 95 340 0.2 1 73 267 96 208 0.2 1 43 165 97 956 0.2 1 238 718 98 172 0.2 1 38 134 99 122 0.2 1 36 86 100 127 0.2 1 34 93 101 127 0.2 1 35 92 102 208 0.2 1 41 167 103 99 0.2 1 25 74 104 73 0.2 1 15 58 105 42 0.2 1 9 33 106 55 0.2 1 15 40 107 26 0.2 1 6 20 108 12 0.2 1 4 8 109 11 0.2 1 1 10 110 13 0.2 1 3 10 111 3 0.2 1 1 2 112 2 0.2 1 1 1 113 1 0.2 1 0 1 114 1 0.2 1 0 1 115 4 0.2 1 2 2 116 7 0.2 1 0 7 118 1 0.2 1 1 120 1 0.2 1 1 121 1 0.2 1 0 1 122 1 0.2 1 0 1 124 2 0.2 1 1 1 125 1 0.2 1 1 126 3 0.2 1 3 127 4 0.2 1 2 2 128 4 0.2 1 3 1 129 11 0.2 1 8 3 130 8 0.2 1 6 2 131 7 0.2 1 6 1 132 10 0.2 1 9 1 133 34 0.2 1 22 12 134 58 0.2 1 50 8 135 72 0.2 1 60 12 136 178 0.2 1 153 25 137 15752 0.2 1 15307 445 138 170558 0.2 1 166047 4511 139 1 0.2 1 0 1 140 4 0.2 1 0 4 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041597_val_1.fq.gz ============================================= 11553983 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 437463 (3.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 4759517 (41.2%)