SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041588_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/raw_data/cup/BS_workflow/20201115/tmp/44fb8ac6-3e8e-11eb-b4e4-6c92bfc12f0e/trimmed/RRBS20A041588_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 720.69 s (31 us/read; 1.92 M reads/minute). === Summary === Total reads processed: 23,052,481 Reads with adapters: 8,297,399 (36.0%) Reads written (passing filters): 23,052,481 (100.0%) Total basepairs processed: 2,426,515,991 bp Total written (filtered): 2,203,124,407 bp (90.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8297399 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.9% C: 73.8% G: 0.6% T: 6.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6659565 5763120.2 0 6659565 2 37385 1440780.1 0 37385 3 4083 360195.0 0 4083 4 5648 90048.8 0 5648 5 1596 22512.2 0 1596 6 662 5628.0 0 662 7 1080 1407.0 0 1080 8 1051 351.8 0 1051 9 335 87.9 0 322 13 10 1539 22.0 1 234 1305 11 101 5.5 1 16 85 12 242 1.4 1 21 221 13 385 0.3 1 20 365 14 479 0.3 1 28 451 15 255 0.3 1 20 235 16 324 0.3 1 27 297 17 425 0.3 1 25 400 18 219 0.3 1 9 210 19 513 0.3 1 28 485 20 458 0.3 1 29 429 21 39 0.3 1 12 27 22 94 0.3 1 3 91 23 430 0.3 1 12 418 24 1026 0.3 1 57 969 25 366 0.3 1 23 343 26 904 0.3 1 45 859 27 191 0.3 1 9 182 28 192 0.3 1 10 182 29 38 0.3 1 4 34 30 89 0.3 1 4 85 31 349 0.3 1 22 327 32 461 0.3 1 28 433 33 1159 0.3 1 58 1101 34 88 0.3 1 1 87 35 82 0.3 1 0 82 36 54 0.3 1 1 53 37 456 0.3 1 20 436 38 122 0.3 1 6 116 39 229 0.3 1 13 216 40 197 0.3 1 6 191 41 200 0.3 1 8 192 42 314 0.3 1 9 305 43 180 0.3 1 9 171 44 282 0.3 1 10 272 45 592 0.3 1 35 557 46 326 0.3 1 8 318 47 128 0.3 1 4 124 48 360 0.3 1 17 343 49 244 0.3 1 13 231 50 335 0.3 1 8 327 51 343 0.3 1 20 323 52 444 0.3 1 23 421 53 41 0.3 1 2 39 54 220 0.3 1 9 211 55 218 0.3 1 14 204 56 49 0.3 1 2 47 57 163 0.3 1 5 158 58 372 0.3 1 24 348 59 149 0.3 1 12 137 60 297 0.3 1 30 267 61 348 0.3 1 46 302 62 539 0.3 1 141 398 63 552 0.3 1 121 431 64 201 0.3 1 23 178 65 128 0.3 1 13 115 66 349 0.3 1 36 313 67 230 0.3 1 12 218 68 211 0.3 1 17 194 69 190 0.3 1 19 171 70 176 0.3 1 11 165 71 184 0.3 1 10 174 72 182 0.3 1 12 170 73 183 0.3 1 12 171 74 182 0.3 1 21 161 75 260 0.3 1 12 248 76 291 0.3 1 19 272 77 216 0.3 1 9 207 78 193 0.3 1 13 180 79 165 0.3 1 10 155 80 160 0.3 1 12 148 81 133 0.3 1 14 119 82 156 0.3 1 9 147 83 193 0.3 1 12 181 84 241 0.3 1 11 230 85 222 0.3 1 14 208 86 143 0.3 1 7 136 87 132 0.3 1 9 123 88 131 0.3 1 13 118 89 91 0.3 1 2 89 90 82 0.3 1 6 76 91 62 0.3 1 3 59 92 79 0.3 1 3 76 93 95 0.3 1 4 91 94 103 0.3 1 9 94 95 54 0.3 1 6 48 96 100 0.3 1 11 89 97 63 0.3 1 2 61 98 50 0.3 1 4 46 99 95 0.3 1 13 82 100 101 0.3 1 7 94 101 59 0.3 1 3 56 102 82 0.3 1 8 74 103 46 0.3 1 5 41 104 23 0.3 1 2 21 105 15 0.3 1 3 12 106 14 0.3 1 2 12 107 13 0.3 1 3 10 108 20 0.3 1 3 17 109 17 0.3 1 2 15 110 11 0.3 1 2 9 111 16 0.3 1 2 14 112 3 0.3 1 1 2 113 7 0.3 1 5 2 114 18 0.3 1 11 7 115 9 0.3 1 7 2 116 8 0.3 1 6 2 117 10 0.3 1 5 5 118 7 0.3 1 5 2 119 5 0.3 1 3 2 120 10 0.3 1 6 4 121 3 0.3 1 2 1 122 7 0.3 1 7 123 10 0.3 1 9 1 124 7 0.3 1 5 2 125 14 0.3 1 10 4 126 17 0.3 1 14 3 127 33 0.3 1 29 4 128 40 0.3 1 37 3 129 47 0.3 1 42 5 130 48 0.3 1 42 6 131 50 0.3 1 45 5 132 54 0.3 1 45 9 133 73 0.3 1 66 7 134 101 0.3 1 90 11 135 321 0.3 1 288 33 136 890 0.3 1 832 58 137 14388 0.3 1 13865 523 138 1545468 0.3 1 1523164 22304 139 1 0.3 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041588_val_2.fq.gz ============================================= 23052481 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1052209 (4.6%) 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: 23052481 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1618770 (7.02%)