SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040873_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 1 sequences will be trimmed by 3 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) 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/test_BSworkflow/test_analysis/tmp/8c68ee60-d1de-11eb-886d-f8f21e2f3ee9/trimmed/RRBS20A040873_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 140.18 s (17 us/read; 3.56 M reads/minute). === Summary === Total reads processed: 8,314,304 Reads with adapters: 3,860,081 (46.4%) Reads written (passing filters): 8,314,304 (100.0%) Total basepairs processed: 707,292,707 bp Total written (filtered): 544,273,865 bp (77.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3860081 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.1% C: 30.8% G: 16.8% T: 28.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1990673 2078576.0 0 1990673 2 509066 519644.0 0 509066 3 137634 129911.0 0 137634 4 43349 32477.8 0 43349 5 851 8119.4 0 851 6 529 2029.9 0 529 7 750 507.5 0 750 8 377 126.9 0 377 9 686 31.7 0 622 64 10 461 7.9 1 234 227 11 500 2.0 1 73 427 12 118 0.5 1 24 94 13 130 0.1 1 18 112 14 429 0.1 1 67 362 15 271 0.1 1 42 229 16 1055 0.1 1 188 867 17 1198 0.1 1 196 1002 18 318 0.1 1 86 232 19 30 0.1 1 1 29 20 153 0.1 1 34 119 21 21 0.1 1 1 20 22 37 0.1 1 5 32 23 234 0.1 1 48 186 24 948 0.1 1 190 758 25 332 0.1 1 54 278 26 83 0.1 1 15 68 27 287 0.1 1 36 251 28 576 0.1 1 91 485 29 654 0.1 1 107 547 30 75 0.1 1 16 59 31 18 0.1 1 3 15 32 224 0.1 1 44 180 33 809 0.1 1 152 657 34 674 0.1 1 105 569 35 92 0.1 1 14 78 36 474 0.1 1 67 407 37 94 0.1 1 11 83 38 1257 0.1 1 204 1053 39 709 0.1 1 95 614 40 147 0.1 1 22 125 41 979 0.1 1 172 807 42 89 0.1 1 10 79 43 1511 0.1 1 258 1253 44 264 0.1 1 40 224 45 456 0.1 1 71 385 46 165 0.1 1 19 146 47 347 0.1 1 66 281 48 789 0.1 1 133 656 49 110 0.1 1 22 88 50 367 0.1 1 55 312 51 270 0.1 1 42 228 52 134 0.1 1 19 115 53 307 0.1 1 48 259 54 665 0.1 1 118 547 55 374 0.1 1 70 304 56 369 0.1 1 63 306 57 280 0.1 1 44 236 58 352 0.1 1 73 279 59 269 0.1 1 53 216 60 255 0.1 1 35 220 61 546 0.1 1 90 456 62 1139 0.1 1 205 934 63 210 0.1 1 31 179 64 27 0.1 1 4 23 65 35 0.1 1 2 33 66 162 0.1 1 22 140 67 132 0.1 1 14 118 68 640 0.1 1 133 507 69 707 0.1 1 130 577 70 1234 0.1 1 189 1045 71 349 0.1 1 49 300 72 141 0.1 1 19 122 73 111 0.1 1 9 102 74 169 0.1 1 18 151 75 219 0.1 1 25 194 76 251 0.1 1 33 218 77 369 0.1 1 22 347 78 354 0.1 1 42 312 79 219 0.1 1 13 206 80 228 0.1 1 23 205 81 209 0.1 1 12 197 82 345 0.1 1 37 308 83 309 0.1 1 40 269 84 291 0.1 1 25 266 85 481 0.1 1 63 418 86 253 0.1 1 17 236 87 180 0.1 1 14 166 88 229 0.1 1 17 212 89 207 0.1 1 15 192 90 173 0.1 1 14 159 91 203 0.1 1 23 180 92 182 0.1 1 19 163 93 293 0.1 1 27 266 94 425 0.1 1 46 379 95 209 0.1 1 23 186 96 165 0.1 1 22 143 97 309 0.1 1 43 266 98 137 0.1 1 24 113 99 122 0.1 1 18 104 100 132 0.1 1 10 122 101 124 0.1 1 28 96 102 143 0.1 1 34 109 103 99 0.1 1 9 90 104 57 0.1 1 12 45 105 37 0.1 1 9 28 106 38 0.1 1 7 31 107 31 0.1 1 4 27 108 21 0.1 1 3 18 109 16 0.1 1 1 15 110 28 0.1 1 8 20 111 24 0.1 1 9 15 112 8 0.1 1 4 4 113 6 0.1 1 2 4 114 7 0.1 1 4 3 115 5 0.1 1 4 1 116 11 0.1 1 10 1 117 6 0.1 1 5 1 118 6 0.1 1 4 2 119 3 0.1 1 2 1 120 5 0.1 1 3 2 121 6 0.1 1 5 1 122 8 0.1 1 7 1 123 9 0.1 1 8 1 124 20 0.1 1 17 3 125 10 0.1 1 9 1 126 22 0.1 1 17 5 127 25 0.1 1 24 1 128 25 0.1 1 20 5 129 33 0.1 1 28 5 130 38 0.1 1 34 4 131 40 0.1 1 36 4 132 82 0.1 1 69 13 133 135 0.1 1 117 18 134 195 0.1 1 175 20 135 340 0.1 1 309 31 136 695 0.1 1 611 84 137 7734 0.1 1 7343 391 138 1133211 0.1 1 1110612 22599 140 7 0.1 1 0 7 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040873_val_1.fq.gz ============================================= 8314304 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 204170 (2.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 3860081 (46.4%)