SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041691_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/a7d87d3e-5572-11eb-abb3-6c92bfc12890/trimmed/RRBS20A041691_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 446.97 s (25 us/read; 2.39 M reads/minute). === Summary === Total reads processed: 17,789,570 Reads with adapters: 6,974,399 (39.2%) Reads written (passing filters): 17,789,570 (100.0%) Total basepairs processed: 1,827,041,666 bp Total written (filtered): 1,663,129,396 bp (91.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6974399 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 14.8% C: 63.1% G: 0.8% T: 21.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5746049 4447392.5 0 5746049 2 39276 1111848.1 0 39276 3 8603 277962.0 0 8603 4 8422 69490.5 0 8422 5 1972 17372.6 0 1972 6 954 4343.2 0 954 7 1169 1085.8 0 1169 8 896 271.4 0 896 9 486 67.9 0 462 24 10 2452 17.0 1 487 1965 11 220 4.2 1 27 193 12 541 1.1 1 45 496 13 638 0.3 1 77 561 14 738 0.3 1 78 660 15 235 0.3 1 20 215 16 521 0.3 1 42 479 17 627 0.3 1 68 559 18 240 0.3 1 18 222 19 768 0.3 1 88 680 20 653 0.3 1 94 559 21 90 0.3 1 37 53 22 128 0.3 1 16 112 23 572 0.3 1 55 517 24 1350 0.3 1 136 1214 25 532 0.3 1 60 472 26 876 0.3 1 96 780 27 622 0.3 1 69 553 28 547 0.3 1 85 462 29 63 0.3 1 4 59 30 141 0.3 1 13 128 31 105 0.3 1 8 97 32 605 0.3 1 65 540 33 1081 0.3 1 99 982 34 327 0.3 1 31 296 35 298 0.3 1 43 255 36 71 0.3 1 6 65 37 576 0.3 1 54 522 38 201 0.3 1 22 179 39 249 0.3 1 25 224 40 281 0.3 1 20 261 41 263 0.3 1 27 236 42 424 0.3 1 35 389 43 237 0.3 1 30 207 44 306 0.3 1 32 274 45 647 0.3 1 72 575 46 330 0.3 1 26 304 47 149 0.3 1 21 128 48 391 0.3 1 50 341 49 306 0.3 1 27 279 50 433 0.3 1 59 374 51 554 0.3 1 53 501 52 495 0.3 1 52 443 53 75 0.3 1 9 66 54 234 0.3 1 15 219 55 357 0.3 1 45 312 56 70 0.3 1 8 62 57 214 0.3 1 20 194 58 391 0.3 1 28 363 59 211 0.3 1 33 178 60 335 0.3 1 59 276 61 436 0.3 1 87 349 62 621 0.3 1 171 450 63 587 0.3 1 140 447 64 194 0.3 1 26 168 65 167 0.3 1 25 142 66 517 0.3 1 51 466 67 232 0.3 1 25 207 68 204 0.3 1 20 184 69 178 0.3 1 20 158 70 218 0.3 1 17 201 71 204 0.3 1 26 178 72 210 0.3 1 18 192 73 220 0.3 1 33 187 74 206 0.3 1 27 179 75 411 0.3 1 51 360 76 397 0.3 1 33 364 77 219 0.3 1 18 201 78 158 0.3 1 9 149 79 149 0.3 1 8 141 80 169 0.3 1 16 153 81 141 0.3 1 11 130 82 186 0.3 1 20 166 83 207 0.3 1 22 185 84 209 0.3 1 30 179 85 213 0.3 1 27 186 86 155 0.3 1 11 144 87 116 0.3 1 14 102 88 102 0.3 1 7 95 89 104 0.3 1 8 96 90 117 0.3 1 15 102 91 87 0.3 1 12 75 92 108 0.3 1 12 96 93 104 0.3 1 7 97 94 121 0.3 1 6 115 95 52 0.3 1 5 47 96 90 0.3 1 7 83 97 95 0.3 1 10 85 98 91 0.3 1 11 80 99 67 0.3 1 7 60 100 54 0.3 1 4 50 101 48 0.3 1 2 46 102 75 0.3 1 5 70 103 47 0.3 1 3 44 104 26 0.3 1 4 22 105 25 0.3 1 3 22 106 11 0.3 1 0 11 107 20 0.3 1 4 16 108 11 0.3 1 0 11 109 19 0.3 1 2 17 110 18 0.3 1 1 17 111 4 0.3 1 2 2 112 3 0.3 1 3 113 4 0.3 1 4 114 10 0.3 1 5 5 115 5 0.3 1 4 1 116 1 0.3 1 1 117 3 0.3 1 3 118 2 0.3 1 2 119 3 0.3 1 2 1 120 4 0.3 1 3 1 121 4 0.3 1 4 122 4 0.3 1 3 1 123 7 0.3 1 7 124 10 0.3 1 9 1 125 9 0.3 1 8 1 126 8 0.3 1 6 2 127 18 0.3 1 15 3 128 23 0.3 1 23 129 20 0.3 1 19 1 130 21 0.3 1 20 1 131 28 0.3 1 24 4 132 31 0.3 1 26 5 133 64 0.3 1 54 10 134 81 0.3 1 72 9 135 213 0.3 1 186 27 136 569 0.3 1 511 58 137 7600 0.3 1 7159 441 138 1126637 0.3 1 1105961 20676 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041691_val_2.fq.gz ============================================= 17789570 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 913023 (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: 17789570 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1193580 (6.71%)