SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041690_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/20201121/tmp/c309dc1a-3f65-11eb-a3a2-6c92bfc12bba/trimmed/RRBS20A041690_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 297.52 s (24 us/read; 2.46 M reads/minute). === Summary === Total reads processed: 12,178,016 Reads with adapters: 5,240,075 (43.0%) Reads written (passing filters): 12,178,016 (100.0%) Total basepairs processed: 1,246,024,927 bp Total written (filtered): 1,036,837,279 bp (83.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5240075 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 14.2% C: 80.3% G: 0.7% T: 4.8% none/other: 0.0% WARNING: The adapter is preceded by "C" extremely often. The provided adapter sequence could be incomplete at its 3' end. Overview of removed sequences length count expect max.err error counts 1 3692781 3044504.0 0 3692781 2 33028 761126.0 0 33028 3 5423 190281.5 0 5423 4 2851 47570.4 0 2851 5 880 11892.6 0 880 6 396 2973.1 0 396 7 603 743.3 0 603 8 373 185.8 0 373 9 133 46.5 0 112 21 10 1538 11.6 1 391 1147 11 53 2.9 1 9 44 12 1154 0.7 1 255 899 13 392 0.2 1 53 339 14 450 0.2 1 71 379 15 162 0.2 1 21 141 16 142 0.2 1 12 130 17 361 0.2 1 42 319 18 153 0.2 1 16 137 19 482 0.2 1 131 351 20 315 0.2 1 48 267 21 51 0.2 1 29 22 22 369 0.2 1 83 286 23 539 0.2 1 128 411 24 824 0.2 1 85 739 25 375 0.2 1 34 341 26 481 0.2 1 56 425 27 163 0.2 1 27 136 28 365 0.2 1 53 312 29 23 0.2 1 3 20 30 285 0.2 1 34 251 31 305 0.2 1 41 264 32 265 0.2 1 32 233 33 786 0.2 1 110 676 34 214 0.2 1 31 183 35 346 0.2 1 42 304 36 65 0.2 1 7 58 37 349 0.2 1 50 299 38 81 0.2 1 15 66 39 122 0.2 1 18 104 40 108 0.2 1 19 89 41 232 0.2 1 30 202 42 288 0.2 1 37 251 43 144 0.2 1 14 130 44 193 0.2 1 29 164 45 422 0.2 1 41 381 46 199 0.2 1 18 181 47 59 0.2 1 5 54 48 236 0.2 1 25 211 49 174 0.2 1 20 154 50 240 0.2 1 30 210 51 346 0.2 1 55 291 52 277 0.2 1 36 241 53 50 0.2 1 5 45 54 169 0.2 1 14 155 55 99 0.2 1 13 86 56 29 0.2 1 4 25 57 173 0.2 1 24 149 58 262 0.2 1 39 223 59 191 0.2 1 47 144 60 260 0.2 1 57 203 61 374 0.2 1 125 249 62 572 0.2 1 231 341 63 391 0.2 1 132 259 64 122 0.2 1 22 100 65 98 0.2 1 13 85 66 213 0.2 1 21 192 67 160 0.2 1 26 134 68 177 0.2 1 25 152 69 124 0.2 1 18 106 70 136 0.2 1 26 110 71 152 0.2 1 15 137 72 147 0.2 1 11 136 73 129 0.2 1 14 115 74 144 0.2 1 16 128 75 198 0.2 1 18 180 76 163 0.2 1 14 149 77 118 0.2 1 11 107 78 106 0.2 1 8 98 79 120 0.2 1 24 96 80 124 0.2 1 13 111 81 101 0.2 1 10 91 82 117 0.2 1 11 106 83 144 0.2 1 21 123 84 106 0.2 1 10 96 85 150 0.2 1 12 138 86 91 0.2 1 11 80 87 75 0.2 1 15 60 88 90 0.2 1 7 83 89 65 0.2 1 8 57 90 48 0.2 1 2 46 91 55 0.2 1 8 47 92 50 0.2 1 3 47 93 55 0.2 1 6 49 94 52 0.2 1 4 48 95 39 0.2 1 1 38 96 55 0.2 1 8 47 97 46 0.2 1 3 43 98 47 0.2 1 3 44 99 50 0.2 1 4 46 100 56 0.2 1 4 52 101 36 0.2 1 3 33 102 56 0.2 1 9 47 103 24 0.2 1 1 23 104 20 0.2 1 1 19 105 15 0.2 1 1 14 106 13 0.2 1 1 12 107 11 0.2 1 3 8 108 5 0.2 1 0 5 109 13 0.2 1 0 13 110 18 0.2 1 2 16 111 5 0.2 1 1 4 112 3 0.2 1 2 1 113 2 0.2 1 2 114 18 0.2 1 2 16 115 8 0.2 1 5 3 116 6 0.2 1 6 117 9 0.2 1 6 3 118 5 0.2 1 4 1 119 6 0.2 1 6 120 4 0.2 1 4 121 2 0.2 1 1 1 122 5 0.2 1 3 2 123 9 0.2 1 6 3 124 14 0.2 1 12 2 125 14 0.2 1 13 1 126 24 0.2 1 22 2 127 40 0.2 1 38 2 128 40 0.2 1 39 1 129 59 0.2 1 55 4 130 42 0.2 1 36 6 131 57 0.2 1 55 2 132 76 0.2 1 64 12 133 104 0.2 1 98 6 134 180 0.2 1 159 21 135 596 0.2 1 536 60 136 2055 0.2 1 1938 117 137 86136 0.2 1 84533 1603 138 1393255 0.2 1 1375890 17365 139 1 0.2 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041690_val_2.fq.gz ============================================= 12178016 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 503165 (4.1%) 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: 12178016 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1526821 (12.54%)