SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041589_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/a5a585f2-5572-11eb-a546-6c92bfc12f0e/trimmed/RRBS20A041589_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 418.53 s (23 us/read; 2.59 M reads/minute). === Summary === Total reads processed: 18,087,775 Reads with adapters: 5,907,283 (32.7%) Reads written (passing filters): 18,087,775 (100.0%) Total basepairs processed: 1,823,305,017 bp Total written (filtered): 1,763,908,177 bp (96.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5907283 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.0% C: 68.2% G: 0.8% T: 13.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5429533 4521943.8 0 5429533 2 44534 1130485.9 0 44534 3 9164 282621.5 0 9164 4 8718 70655.4 0 8718 5 1896 17663.8 0 1896 6 886 4416.0 0 886 7 1156 1104.0 0 1156 8 714 276.0 0 714 9 473 69.0 0 450 23 10 2301 17.2 1 436 1865 11 220 4.3 1 28 192 12 504 1.1 1 56 448 13 538 0.3 1 57 481 14 667 0.3 1 66 601 15 249 0.3 1 23 226 16 438 0.3 1 49 389 17 542 0.3 1 56 486 18 204 0.3 1 19 185 19 697 0.3 1 72 625 20 532 0.3 1 56 476 21 59 0.3 1 11 48 22 88 0.3 1 6 82 23 544 0.3 1 55 489 24 1292 0.3 1 139 1153 25 513 0.3 1 51 462 26 792 0.3 1 82 710 27 570 0.3 1 65 505 28 523 0.3 1 93 430 29 66 0.3 1 12 54 30 129 0.3 1 19 110 31 92 0.3 1 7 85 32 512 0.3 1 56 456 33 1062 0.3 1 107 955 34 303 0.3 1 29 274 35 274 0.3 1 33 241 36 56 0.3 1 6 50 37 527 0.3 1 56 471 38 206 0.3 1 26 180 39 222 0.3 1 16 206 40 267 0.3 1 30 237 41 265 0.3 1 24 241 42 414 0.3 1 51 363 43 219 0.3 1 29 190 44 314 0.3 1 33 281 45 635 0.3 1 60 575 46 260 0.3 1 23 237 47 149 0.3 1 17 132 48 360 0.3 1 38 322 49 332 0.3 1 31 301 50 501 0.3 1 52 449 51 551 0.3 1 71 480 52 481 0.3 1 53 428 53 68 0.3 1 11 57 54 251 0.3 1 22 229 55 386 0.3 1 48 338 56 55 0.3 1 6 49 57 204 0.3 1 20 184 58 385 0.3 1 27 358 59 237 0.3 1 27 210 60 333 0.3 1 38 295 61 479 0.3 1 57 422 62 543 0.3 1 114 429 63 439 0.3 1 72 367 64 189 0.3 1 28 161 65 164 0.3 1 16 148 66 602 0.3 1 60 542 67 260 0.3 1 22 238 68 214 0.3 1 25 189 69 195 0.3 1 23 172 70 210 0.3 1 16 194 71 227 0.3 1 28 199 72 229 0.3 1 24 205 73 234 0.3 1 26 208 74 233 0.3 1 30 203 75 483 0.3 1 72 411 76 338 0.3 1 37 301 77 235 0.3 1 26 209 78 156 0.3 1 16 140 79 175 0.3 1 14 161 80 197 0.3 1 19 178 81 157 0.3 1 17 140 82 176 0.3 1 13 163 83 187 0.3 1 21 166 84 204 0.3 1 23 181 85 203 0.3 1 17 186 86 140 0.3 1 23 117 87 128 0.3 1 12 116 88 118 0.3 1 11 107 89 121 0.3 1 4 117 90 92 0.3 1 7 85 91 57 0.3 1 4 53 92 91 0.3 1 7 84 93 105 0.3 1 8 97 94 110 0.3 1 11 99 95 75 0.3 1 9 66 96 67 0.3 1 5 62 97 91 0.3 1 14 77 98 66 0.3 1 9 57 99 78 0.3 1 8 70 100 80 0.3 1 11 69 101 53 0.3 1 3 50 102 77 0.3 1 12 65 103 36 0.3 1 1 35 104 25 0.3 1 5 20 105 16 0.3 1 1 15 106 17 0.3 1 2 15 107 6 0.3 1 0 6 108 10 0.3 1 1 9 109 26 0.3 1 2 24 110 13 0.3 1 3 10 111 4 0.3 1 1 3 112 1 0.3 1 0 1 114 2 0.3 1 2 115 5 0.3 1 4 1 116 1 0.3 1 1 117 1 0.3 1 0 1 119 1 0.3 1 1 121 1 0.3 1 1 123 2 0.3 1 2 124 3 0.3 1 3 125 4 0.3 1 3 1 126 8 0.3 1 6 2 127 7 0.3 1 6 1 128 6 0.3 1 4 2 129 9 0.3 1 6 3 130 4 0.3 1 4 131 11 0.3 1 5 6 132 7 0.3 1 6 1 133 22 0.3 1 19 3 134 39 0.3 1 33 6 135 75 0.3 1 67 8 136 177 0.3 1 167 10 137 2375 0.3 1 2252 123 138 377628 0.3 1 371293 6335 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041589_val_2.fq.gz ============================================= 18087775 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 950080 (5.3%) 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: 18087775 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 428227 (2.37%)