SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041521_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 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/a6fb391a-5572-11eb-a954-6c92bfc12788/trimmed/RRBS20A041521_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 512.01 s (25 us/read; 2.44 M reads/minute). === Summary === Total reads processed: 20,854,664 Reads with adapters: 7,871,204 (37.7%) Reads written (passing filters): 20,854,664 (100.0%) Total basepairs processed: 2,097,083,184 bp Total written (filtered): 2,045,766,826 bp (97.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7871204 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.0% C: 66.6% G: 5.0% T: 7.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7407805 5213666.0 0 7407805 2 102156 1303416.5 0 102156 3 10295 325854.1 0 10295 4 6169 81463.5 0 6169 5 1788 20365.9 0 1788 6 920 5091.5 0 920 7 1428 1272.9 0 1428 8 552 318.2 0 552 9 279 79.6 0 227 52 10 3205 19.9 1 676 2529 11 108 5.0 1 5 103 12 2311 1.2 1 395 1916 13 532 0.3 1 46 486 14 817 0.3 1 65 752 15 257 0.3 1 17 240 16 369 0.3 1 29 340 17 638 0.3 1 40 598 18 249 0.3 1 14 235 19 646 0.3 1 52 594 20 416 0.3 1 31 385 21 46 0.3 1 12 34 22 337 0.3 1 21 316 23 566 0.3 1 44 522 24 1398 0.3 1 78 1320 25 368 0.3 1 14 354 26 577 0.3 1 42 535 27 198 0.3 1 12 186 28 525 0.3 1 57 468 29 52 0.3 1 2 50 30 409 0.3 1 24 385 31 386 0.3 1 36 350 32 494 0.3 1 42 452 33 984 0.3 1 70 914 34 252 0.3 1 21 231 35 486 0.3 1 45 441 36 92 0.3 1 7 85 37 511 0.3 1 43 468 38 163 0.3 1 17 146 39 211 0.3 1 14 197 40 148 0.3 1 7 141 41 305 0.3 1 15 290 42 402 0.3 1 25 377 43 213 0.3 1 7 206 44 333 0.3 1 22 311 45 702 0.3 1 47 655 46 311 0.3 1 25 286 47 152 0.3 1 7 145 48 554 0.3 1 61 493 49 301 0.3 1 25 276 50 519 0.3 1 39 480 51 683 0.3 1 52 631 52 587 0.3 1 54 533 53 94 0.3 1 16 78 54 304 0.3 1 28 276 55 286 0.3 1 17 269 56 70 0.3 1 3 67 57 248 0.3 1 25 223 58 506 0.3 1 47 459 59 243 0.3 1 13 230 60 338 0.3 1 41 297 61 380 0.3 1 60 320 62 477 0.3 1 116 361 63 425 0.3 1 91 334 64 185 0.3 1 24 161 65 254 0.3 1 40 214 66 689 0.3 1 54 635 67 321 0.3 1 25 296 68 296 0.3 1 19 277 69 228 0.3 1 20 208 70 251 0.3 1 18 233 71 241 0.3 1 29 212 72 217 0.3 1 19 198 73 200 0.3 1 23 177 74 186 0.3 1 15 171 75 445 0.3 1 37 408 76 377 0.3 1 32 345 77 264 0.3 1 12 252 78 165 0.3 1 19 146 79 195 0.3 1 20 175 80 227 0.3 1 21 206 81 211 0.3 1 15 196 82 195 0.3 1 13 182 83 212 0.3 1 23 189 84 237 0.3 1 20 217 85 243 0.3 1 16 227 86 143 0.3 1 9 134 87 126 0.3 1 11 115 88 128 0.3 1 8 120 89 143 0.3 1 6 137 90 101 0.3 1 5 96 91 86 0.3 1 7 79 92 106 0.3 1 6 100 93 124 0.3 1 12 112 94 113 0.3 1 9 104 95 82 0.3 1 7 75 96 64 0.3 1 5 59 97 85 0.3 1 8 77 98 81 0.3 1 8 73 99 117 0.3 1 16 101 100 76 0.3 1 7 69 101 50 0.3 1 1 49 102 80 0.3 1 5 75 103 34 0.3 1 2 32 104 20 0.3 1 4 16 105 13 0.3 1 1 12 106 15 0.3 1 0 15 107 14 0.3 1 3 11 108 13 0.3 1 1 12 109 6 0.3 1 0 6 110 19 0.3 1 1 18 111 8 0.3 1 0 8 112 1 0.3 1 1 114 2 0.3 1 0 2 115 2 0.3 1 1 1 116 2 0.3 1 1 1 117 3 0.3 1 3 118 1 0.3 1 1 119 1 0.3 1 1 120 1 0.3 1 1 121 2 0.3 1 2 122 2 0.3 1 2 123 2 0.3 1 2 124 5 0.3 1 5 125 6 0.3 1 5 1 126 4 0.3 1 4 127 8 0.3 1 8 128 18 0.3 1 18 129 17 0.3 1 17 130 16 0.3 1 14 2 131 17 0.3 1 15 2 132 23 0.3 1 22 1 133 30 0.3 1 29 1 134 43 0.3 1 39 4 135 118 0.3 1 113 5 136 300 0.3 1 272 28 137 7518 0.3 1 7325 193 138 297800 0.3 1 292647 5153 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041521_val_2.fq.gz ============================================= 20854664 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1061328 (5.1%) 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: 20854664 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 358191 (1.72%)