SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040876_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/797f3174-d1de-11eb-864a-6c92bfa0ec38/trimmed/RRBS20A040876_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 321.05 s (14 us/read; 4.33 M reads/minute). === Summary === Total reads processed: 23,169,318 Reads with adapters: 22,767,883 (98.3%) Reads written (passing filters): 23,169,318 (100.0%) Total basepairs processed: 3,183,472,820 bp Total written (filtered): 67,820,786 bp (2.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22767883 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.3% C: 0.5% G: 0.0% T: 99.2% none/other: 0.0% WARNING: The adapter is preceded by "T" 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 177111 5792329.5 0 177111 2 1524 1448082.4 0 1524 3 295 362020.6 0 295 4 221 90505.1 0 221 5 22 22626.3 0 22 6 17 5656.6 0 17 7 16 1414.1 0 16 8 14 353.5 0 14 9 14 88.4 0 13 1 10 41 22.1 1 15 26 11 11 5.5 1 2 9 12 60 1.4 1 15 45 13 8 0.3 1 1 7 14 16 0.3 1 4 12 15 8 0.3 1 1 7 16 4 0.3 1 2 2 17 23 0.3 1 2 21 18 6 0.3 1 2 4 19 87 0.3 1 45 42 20 504 0.3 1 386 118 21 1970 0.3 1 1775 195 22 34 0.3 1 24 10 23 22 0.3 1 7 15 24 46 0.3 1 10 36 25 23 0.3 1 6 17 26 50 0.3 1 18 32 27 70 0.3 1 30 40 28 30 0.3 1 13 17 29 4 0.3 1 0 4 30 28 0.3 1 7 21 31 26 0.3 1 8 18 32 29 0.3 1 4 25 33 59 0.3 1 5 54 34 82 0.3 1 53 29 35 51 0.3 1 30 21 36 27 0.3 1 4 23 37 80 0.3 1 31 49 38 55 0.3 1 25 30 39 87 0.3 1 23 64 40 296 0.3 1 23 273 41 3657 0.3 1 17 3640 42 37 0.3 1 4 33 43 17 0.3 1 11 6 44 16 0.3 1 4 12 45 46 0.3 1 11 35 46 16 0.3 1 3 13 47 8 0.3 1 4 4 48 18 0.3 1 5 13 49 13 0.3 1 2 11 50 14 0.3 1 5 9 51 24 0.3 1 5 19 52 17 0.3 1 4 13 53 5 0.3 1 1 4 54 15 0.3 1 7 8 55 28 0.3 1 18 10 56 5 0.3 1 0 5 57 25 0.3 1 13 12 58 37 0.3 1 19 18 59 57 0.3 1 42 15 60 176 0.3 1 143 33 61 614 0.3 1 551 63 62 2503 0.3 1 2338 165 63 3926 0.3 1 3729 197 64 331 0.3 1 286 45 65 282 0.3 1 246 36 66 234 0.3 1 195 39 67 132 0.3 1 112 20 68 144 0.3 1 121 23 69 129 0.3 1 113 16 70 196 0.3 1 172 24 71 289 0.3 1 268 21 72 185 0.3 1 158 27 73 231 0.3 1 213 18 74 150 0.3 1 127 23 75 79 0.3 1 60 19 76 45 0.3 1 28 17 77 35 0.3 1 18 17 78 36 0.3 1 23 13 79 19 0.3 1 9 10 80 20 0.3 1 11 9 81 16 0.3 1 6 10 82 12 0.3 1 3 9 83 22 0.3 1 12 10 84 39 0.3 1 7 32 85 21 0.3 1 6 15 86 25 0.3 1 14 11 87 31 0.3 1 21 10 88 20 0.3 1 15 5 89 14 0.3 1 5 9 90 32 0.3 1 15 17 91 14 0.3 1 5 9 92 17 0.3 1 8 9 93 9 0.3 1 7 2 94 11 0.3 1 4 7 95 12 0.3 1 8 4 96 15 0.3 1 13 2 97 22 0.3 1 14 8 98 13 0.3 1 5 8 99 15 0.3 1 6 9 100 10 0.3 1 5 5 101 8 0.3 1 5 3 102 16 0.3 1 11 5 103 16 0.3 1 13 3 104 14 0.3 1 9 5 105 16 0.3 1 12 4 106 21 0.3 1 12 9 107 27 0.3 1 22 5 108 58 0.3 1 29 29 109 50 0.3 1 35 15 110 28 0.3 1 27 1 111 28 0.3 1 28 112 30 0.3 1 26 4 113 83 0.3 1 75 8 114 176 0.3 1 143 33 115 131 0.3 1 122 9 116 206 0.3 1 189 17 117 248 0.3 1 229 19 118 110 0.3 1 100 10 119 93 0.3 1 82 11 120 116 0.3 1 103 13 121 99 0.3 1 83 16 122 112 0.3 1 94 18 123 169 0.3 1 145 24 124 190 0.3 1 160 30 125 223 0.3 1 202 21 126 402 0.3 1 379 23 127 627 0.3 1 596 31 128 1055 0.3 1 1013 42 129 942 0.3 1 897 45 130 972 0.3 1 919 53 131 960 0.3 1 906 54 132 990 0.3 1 929 61 133 1704 0.3 1 1601 103 134 1954 0.3 1 1874 80 135 5767 0.3 1 5540 227 136 5320 0.3 1 5055 265 137 58569 0.3 1 56801 1768 138 22489098 0.3 1 22153264 335834 139 3 0.3 1 1 2 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/RRBS20A040876_val_2.fq.gz ============================================= 23169318 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 21910 (0.1%) 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: 23169318 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 22633745 (97.69%)