SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041606_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/20201118/tmp/68a4493e-5592-11eb-92b6-6c92bfc12f0e/trimmed/RRBS20A041606_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 167.76 s (23 us/read; 2.57 M reads/minute). === Summary === Total reads processed: 7,181,082 Reads with adapters: 2,747,598 (38.3%) Reads written (passing filters): 7,181,082 (100.0%) Total basepairs processed: 781,678,965 bp Total written (filtered): 767,384,151 bp (98.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2747598 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.6% C: 66.7% G: 4.1% T: 7.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2616406 1795270.5 0 2616406 2 33278 448817.6 0 33278 3 3036 112204.4 0 3036 4 1697 28051.1 0 1697 5 481 7012.8 0 481 6 248 1753.2 0 248 7 467 438.3 0 467 8 262 109.6 0 262 9 127 27.4 0 115 12 10 1106 6.8 1 224 882 11 34 1.7 1 9 25 12 843 0.4 1 170 673 13 163 0.1 1 19 144 14 286 0.1 1 21 265 15 92 0.1 1 8 84 16 115 0.1 1 15 100 17 276 0.1 1 22 254 18 76 0.1 1 4 72 19 286 0.1 1 16 270 20 169 0.1 1 5 164 21 18 0.1 1 10 8 22 156 0.1 1 6 150 23 197 0.1 1 16 181 24 537 0.1 1 39 498 25 179 0.1 1 8 171 26 238 0.1 1 9 229 27 65 0.1 1 4 61 28 219 0.1 1 15 204 29 15 0.1 1 0 15 30 175 0.1 1 8 167 31 162 0.1 1 7 155 32 187 0.1 1 21 166 33 359 0.1 1 25 334 34 104 0.1 1 9 95 35 191 0.1 1 14 177 36 30 0.1 1 1 29 37 178 0.1 1 13 165 38 37 0.1 1 0 37 39 55 0.1 1 4 51 40 36 0.1 1 1 35 41 92 0.1 1 5 87 42 167 0.1 1 9 158 43 44 0.1 1 2 42 44 89 0.1 1 3 86 45 253 0.1 1 12 241 46 105 0.1 1 10 95 47 19 0.1 1 1 18 48 173 0.1 1 10 163 49 56 0.1 1 3 53 50 121 0.1 1 12 109 51 160 0.1 1 15 145 52 166 0.1 1 14 152 53 21 0.1 1 0 21 54 75 0.1 1 4 71 55 46 0.1 1 2 44 56 8 0.1 1 1 7 57 58 0.1 1 2 56 58 138 0.1 1 10 128 59 62 0.1 1 5 57 60 71 0.1 1 7 64 61 96 0.1 1 14 82 62 106 0.1 1 17 89 63 109 0.1 1 15 94 64 36 0.1 1 6 30 65 46 0.1 1 5 41 66 99 0.1 1 13 86 67 50 0.1 1 4 46 68 76 0.1 1 5 71 69 44 0.1 1 6 38 70 39 0.1 1 1 38 71 57 0.1 1 1 56 72 50 0.1 1 3 47 73 35 0.1 1 5 30 74 42 0.1 1 3 39 75 102 0.1 1 9 93 76 70 0.1 1 5 65 77 56 0.1 1 6 50 78 19 0.1 1 0 19 79 36 0.1 1 4 32 80 45 0.1 1 0 45 81 39 0.1 1 2 37 82 38 0.1 1 3 35 83 58 0.1 1 4 54 84 49 0.1 1 3 46 85 40 0.1 1 4 36 86 35 0.1 1 5 30 87 30 0.1 1 2 28 88 21 0.1 1 1 20 89 23 0.1 1 0 23 90 21 0.1 1 3 18 91 12 0.1 1 1 11 92 14 0.1 1 0 14 93 33 0.1 1 3 30 94 22 0.1 1 1 21 95 14 0.1 1 0 14 96 24 0.1 1 2 22 97 9 0.1 1 1 8 98 11 0.1 1 2 9 99 24 0.1 1 4 20 100 11 0.1 1 1 10 101 8 0.1 1 1 7 102 18 0.1 1 2 16 103 5 0.1 1 0 5 104 4 0.1 1 0 4 105 2 0.1 1 0 2 106 1 0.1 1 0 1 107 1 0.1 1 0 1 108 2 0.1 1 1 1 109 4 0.1 1 1 3 110 3 0.1 1 0 3 111 2 0.1 1 1 1 115 1 0.1 1 1 123 1 0.1 1 0 1 126 2 0.1 1 2 127 3 0.1 1 3 128 3 0.1 1 3 129 2 0.1 1 2 130 1 0.1 1 1 133 10 0.1 1 10 134 5 0.1 1 5 135 20 0.1 1 17 3 136 45 0.1 1 42 3 137 698 0.1 1 676 22 138 80506 0.1 1 78990 1516 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041606_val_2.fq.gz ============================================= 7181082 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 319490 (4.4%) 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: 7181082 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 92222 (1.28%)