SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041592_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/20201120/tmp/a5a0f398-5572-11eb-97c5-6c92bfc12b7e/trimmed/RRBS20A041592_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 143.97 s (22 us/read; 2.69 M reads/minute). === Summary === Total reads processed: 6,449,350 Reads with adapters: 2,682,985 (41.6%) Reads written (passing filters): 6,449,350 (100.0%) Total basepairs processed: 679,120,058 bp Total written (filtered): 602,535,125 bp (88.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2682985 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 14.9% C: 80.1% G: 0.5% T: 4.5% 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 2121123 1612337.5 0 2121123 2 11293 403084.4 0 11293 3 1454 100771.1 0 1454 4 2087 25192.8 0 2087 5 649 6298.2 0 649 6 271 1574.5 0 271 7 389 393.6 0 389 8 294 98.4 0 294 9 112 24.6 0 109 3 10 492 6.2 1 69 423 11 42 1.5 1 4 38 12 118 0.4 1 11 107 13 162 0.1 1 12 150 14 181 0.1 1 14 167 15 115 0.1 1 5 110 16 154 0.1 1 8 146 17 276 0.1 1 17 259 18 77 0.1 1 7 70 19 186 0.1 1 17 169 20 198 0.1 1 11 187 21 14 0.1 1 4 10 22 37 0.1 1 1 36 23 142 0.1 1 7 135 24 326 0.1 1 19 307 25 119 0.1 1 6 113 26 305 0.1 1 22 283 27 69 0.1 1 0 69 28 76 0.1 1 8 68 29 23 0.1 1 1 22 30 37 0.1 1 2 35 31 119 0.1 1 7 112 32 164 0.1 1 11 153 33 361 0.1 1 16 345 34 25 0.1 1 0 25 35 27 0.1 1 0 27 36 16 0.1 1 0 16 37 155 0.1 1 8 147 38 54 0.1 1 2 52 39 86 0.1 1 3 83 40 87 0.1 1 6 81 41 73 0.1 1 2 71 42 118 0.1 1 6 112 43 86 0.1 1 3 83 44 72 0.1 1 4 68 45 167 0.1 1 10 157 46 93 0.1 1 5 88 47 45 0.1 1 0 45 48 119 0.1 1 5 114 49 66 0.1 1 6 60 50 131 0.1 1 4 127 51 148 0.1 1 9 139 52 139 0.1 1 12 127 53 23 0.1 1 3 20 54 82 0.1 1 4 78 55 85 0.1 1 6 79 56 14 0.1 1 2 12 57 62 0.1 1 4 58 58 153 0.1 1 4 149 59 68 0.1 1 6 62 60 102 0.1 1 12 90 61 116 0.1 1 32 84 62 229 0.1 1 93 136 63 236 0.1 1 114 122 64 73 0.1 1 21 52 65 69 0.1 1 13 56 66 195 0.1 1 19 176 67 75 0.1 1 6 69 68 79 0.1 1 6 73 69 63 0.1 1 5 58 70 63 0.1 1 7 56 71 68 0.1 1 6 62 72 55 0.1 1 8 47 73 57 0.1 1 8 49 74 60 0.1 1 4 56 75 88 0.1 1 6 82 76 73 0.1 1 8 65 77 52 0.1 1 5 47 78 55 0.1 1 1 54 79 57 0.1 1 7 50 80 63 0.1 1 2 61 81 45 0.1 1 1 44 82 57 0.1 1 2 55 83 77 0.1 1 6 71 84 80 0.1 1 4 76 85 117 0.1 1 6 111 86 52 0.1 1 3 49 87 45 0.1 1 0 45 88 33 0.1 1 1 32 89 39 0.1 1 1 38 90 22 0.1 1 2 20 91 32 0.1 1 1 31 92 28 0.1 1 1 27 93 36 0.1 1 4 32 94 45 0.1 1 2 43 95 21 0.1 1 0 21 96 20 0.1 1 0 20 97 21 0.1 1 0 21 98 28 0.1 1 2 26 99 26 0.1 1 1 25 100 23 0.1 1 2 21 101 14 0.1 1 0 14 102 35 0.1 1 3 32 103 18 0.1 1 2 16 104 9 0.1 1 1 8 105 9 0.1 1 0 9 106 5 0.1 1 1 4 107 6 0.1 1 2 4 108 1 0.1 1 0 1 109 2 0.1 1 0 2 110 3 0.1 1 0 3 111 2 0.1 1 0 2 112 1 0.1 1 1 113 6 0.1 1 5 1 114 3 0.1 1 1 2 115 4 0.1 1 4 116 2 0.1 1 2 117 2 0.1 1 0 2 118 3 0.1 1 3 119 3 0.1 1 3 120 1 0.1 1 1 121 3 0.1 1 3 122 2 0.1 1 2 123 2 0.1 1 1 1 124 1 0.1 1 1 125 7 0.1 1 7 126 11 0.1 1 10 1 127 8 0.1 1 7 1 128 21 0.1 1 18 3 129 20 0.1 1 19 1 130 17 0.1 1 16 1 131 22 0.1 1 21 1 132 27 0.1 1 25 2 133 34 0.1 1 31 3 134 62 0.1 1 57 5 135 154 0.1 1 136 18 136 367 0.1 1 349 18 137 7443 0.1 1 7269 174 138 528221 0.1 1 520407 7814 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/20201120/RRBS20A041592_val_2.fq.gz ============================================= 6449350 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 334169 (5.2%) 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: 6449350 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 555914 (8.62%)