SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040873_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 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_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 155.65 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 8,314,304 Reads with adapters: 4,762,704 (57.3%) Reads written (passing filters): 8,314,304 (100.0%) Total basepairs processed: 700,284,001 bp Total written (filtered): 538,587,075 bp (76.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4762704 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 4.3% C: 94.7% G: 0.2% T: 0.9% 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 3603681 2078576.0 0 3603681 2 4418 519644.0 0 4418 3 1952 129911.0 0 1952 4 1768 32477.8 0 1768 5 307 8119.4 0 307 6 99 2029.9 0 99 7 92 507.5 0 92 8 172 126.9 0 172 9 180 31.7 0 165 15 10 353 7.9 1 108 245 11 52 2.0 1 8 44 12 43 0.5 1 5 38 13 75 0.1 1 4 71 14 85 0.1 1 5 80 15 45 0.1 1 4 41 16 87 0.1 1 6 81 17 78 0.1 1 5 73 18 36 0.1 1 0 36 19 94 0.1 1 8 86 20 97 0.1 1 6 91 21 18 0.1 1 4 14 22 10 0.1 1 0 10 23 88 0.1 1 5 83 24 165 0.1 1 17 148 25 111 0.1 1 9 102 26 185 0.1 1 7 178 27 163 0.1 1 13 150 28 79 0.1 1 3 76 29 17 0.1 1 1 16 30 25 0.1 1 3 22 31 20 0.1 1 2 18 32 110 0.1 1 7 103 33 238 0.1 1 15 223 34 84 0.1 1 8 76 35 45 0.1 1 2 43 36 22 0.1 1 0 22 37 128 0.1 1 11 117 38 39 0.1 1 9 30 39 60 0.1 1 6 54 40 57 0.1 1 4 53 41 111 0.1 1 2 109 42 64 0.1 1 2 62 43 69 0.1 1 6 63 44 73 0.1 1 5 68 45 159 0.1 1 7 152 46 94 0.1 1 6 88 47 39 0.1 1 3 36 48 84 0.1 1 4 80 49 62 0.1 1 1 61 50 84 0.1 1 2 82 51 67 0.1 1 3 64 52 77 0.1 1 6 71 53 15 0.1 1 0 15 54 70 0.1 1 6 64 55 57 0.1 1 4 53 56 12 0.1 1 1 11 57 64 0.1 1 5 59 58 73 0.1 1 4 69 59 54 0.1 1 5 49 60 85 0.1 1 6 79 61 130 0.1 1 25 105 62 207 0.1 1 49 158 63 273 0.1 1 84 189 64 121 0.1 1 17 104 65 57 0.1 1 5 52 66 94 0.1 1 15 79 67 52 0.1 1 9 43 68 50 0.1 1 4 46 69 73 0.1 1 5 68 70 107 0.1 1 6 101 71 104 0.1 1 8 96 72 73 0.1 1 5 68 73 71 0.1 1 7 64 74 63 0.1 1 10 53 75 87 0.1 1 3 84 76 87 0.1 1 5 82 77 79 0.1 1 2 77 78 60 0.1 1 3 57 79 66 0.1 1 4 62 80 87 0.1 1 7 80 81 113 0.1 1 8 105 82 98 0.1 1 7 91 83 129 0.1 1 8 121 84 98 0.1 1 1 97 85 104 0.1 1 6 98 86 69 0.1 1 6 63 87 80 0.1 1 5 75 88 101 0.1 1 10 91 89 85 0.1 1 6 79 90 25 0.1 1 1 24 91 54 0.1 1 5 49 92 29 0.1 1 2 27 93 30 0.1 1 2 28 94 32 0.1 1 3 29 95 14 0.1 1 0 14 96 25 0.1 1 1 24 97 17 0.1 1 1 16 98 16 0.1 1 0 16 99 22 0.1 1 2 20 100 14 0.1 1 1 13 101 21 0.1 1 4 17 102 18 0.1 1 2 16 103 13 0.1 1 1 12 104 7 0.1 1 0 7 105 12 0.1 1 1 11 106 8 0.1 1 2 6 107 8 0.1 1 1 7 108 13 0.1 1 0 13 109 16 0.1 1 2 14 110 10 0.1 1 0 10 111 2 0.1 1 1 1 112 2 0.1 1 2 115 3 0.1 1 2 1 117 6 0.1 1 6 118 3 0.1 1 2 1 120 1 0.1 1 1 121 2 0.1 1 2 122 5 0.1 1 5 123 4 0.1 1 4 124 3 0.1 1 2 1 125 5 0.1 1 5 126 6 0.1 1 6 127 8 0.1 1 8 128 19 0.1 1 19 129 13 0.1 1 13 130 15 0.1 1 15 131 13 0.1 1 13 132 21 0.1 1 16 5 133 40 0.1 1 38 2 134 37 0.1 1 36 1 135 113 0.1 1 104 9 136 119 0.1 1 112 7 137 5148 0.1 1 5045 103 138 1137103 0.1 1 1125689 11414 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/test_BSworkflow/merged_raw_data/RRBS20A040873_val_2.fq.gz ============================================= 8314304 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 243793 (2.9%) 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: 8314304 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1175853 (14.14%)