SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041689_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/20201110/tmp/cd67b24a-5581-11eb-85e4-6c92bfc12bba/trimmed/RRBS20A041689_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 175.34 s (23 us/read; 2.56 M reads/minute). === Summary === Total reads processed: 7,481,333 Reads with adapters: 2,841,550 (38.0%) Reads written (passing filters): 7,481,333 (100.0%) Total basepairs processed: 762,224,735 bp Total written (filtered): 724,819,547 bp (95.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2841550 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 14.5% C: 80.1% G: 0.6% 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 2571163 1870333.2 0 2571163 2 9199 467583.3 0 9199 3 1029 116895.8 0 1029 4 1476 29224.0 0 1476 5 350 7306.0 0 350 6 173 1826.5 0 173 7 303 456.6 0 303 8 296 114.2 0 296 9 89 28.5 0 84 5 10 478 7.1 1 115 363 11 27 1.8 1 6 21 12 93 0.4 1 11 82 13 121 0.1 1 9 112 14 167 0.1 1 14 153 15 77 0.1 1 6 71 16 87 0.1 1 7 80 17 163 0.1 1 5 158 18 55 0.1 1 3 52 19 197 0.1 1 11 186 20 122 0.1 1 3 119 21 9 0.1 1 0 9 22 27 0.1 1 1 26 23 106 0.1 1 4 102 24 362 0.1 1 23 339 25 124 0.1 1 5 119 26 272 0.1 1 13 259 27 55 0.1 1 2 53 28 54 0.1 1 5 49 29 19 0.1 1 0 19 30 50 0.1 1 0 50 31 99 0.1 1 8 91 32 144 0.1 1 7 137 33 295 0.1 1 12 283 34 35 0.1 1 1 34 35 38 0.1 1 1 37 36 44 0.1 1 0 44 37 128 0.1 1 8 120 38 52 0.1 1 2 50 39 57 0.1 1 7 50 40 44 0.1 1 4 40 41 66 0.1 1 4 62 42 113 0.1 1 2 111 43 51 0.1 1 5 46 44 88 0.1 1 4 84 45 198 0.1 1 6 192 46 96 0.1 1 5 91 47 45 0.1 1 3 42 48 149 0.1 1 7 142 49 79 0.1 1 5 74 50 83 0.1 1 3 80 51 97 0.1 1 4 93 52 135 0.1 1 6 129 53 51 0.1 1 3 48 54 85 0.1 1 6 79 55 72 0.1 1 1 71 56 36 0.1 1 0 36 57 71 0.1 1 2 69 58 124 0.1 1 3 121 59 67 0.1 1 5 62 60 74 0.1 1 8 66 61 111 0.1 1 15 96 62 159 0.1 1 28 131 63 171 0.1 1 31 140 64 48 0.1 1 6 42 65 53 0.1 1 2 51 66 136 0.1 1 10 126 67 66 0.1 1 3 63 68 56 0.1 1 7 49 69 63 0.1 1 3 60 70 38 0.1 1 3 35 71 59 0.1 1 2 57 72 64 0.1 1 4 60 73 39 0.1 1 2 37 74 55 0.1 1 5 50 75 129 0.1 1 5 124 76 124 0.1 1 12 112 77 110 0.1 1 1 109 78 69 0.1 1 5 64 79 41 0.1 1 2 39 80 43 0.1 1 4 39 81 49 0.1 1 5 44 82 36 0.1 1 4 32 83 47 0.1 1 2 45 84 80 0.1 1 4 76 85 61 0.1 1 5 56 86 46 0.1 1 2 44 87 34 0.1 1 2 32 88 26 0.1 1 2 24 89 36 0.1 1 0 36 90 29 0.1 1 0 29 91 12 0.1 1 2 10 92 24 0.1 1 1 23 93 27 0.1 1 1 26 94 35 0.1 1 5 30 95 11 0.1 1 1 10 96 21 0.1 1 2 19 97 16 0.1 1 2 14 98 14 0.1 1 1 13 99 19 0.1 1 1 18 100 27 0.1 1 3 24 101 21 0.1 1 0 21 102 26 0.1 1 2 24 103 12 0.1 1 1 11 104 4 0.1 1 0 4 105 4 0.1 1 0 4 106 8 0.1 1 0 8 107 8 0.1 1 1 7 108 3 0.1 1 0 3 109 7 0.1 1 0 7 110 6 0.1 1 0 6 111 2 0.1 1 1 1 112 2 0.1 1 1 1 114 4 0.1 1 1 3 115 1 0.1 1 1 116 1 0.1 1 1 117 2 0.1 1 2 118 1 0.1 1 1 120 2 0.1 1 2 122 1 0.1 1 1 123 1 0.1 1 1 125 3 0.1 1 3 126 4 0.1 1 3 1 127 10 0.1 1 9 1 128 14 0.1 1 14 129 10 0.1 1 10 130 8 0.1 1 7 1 131 10 0.1 1 10 132 7 0.1 1 5 2 133 12 0.1 1 10 2 134 32 0.1 1 29 3 135 56 0.1 1 49 7 136 182 0.1 1 172 10 137 11563 0.1 1 11335 228 138 237780 0.1 1 234519 3261 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/processing/cup/20201110/RRBS20A041689_val_2.fq.gz ============================================= 7481333 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 316470 (4.2%) 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: 7481333 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 275009 (3.68%)