SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040876_val_1.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_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 251.39 s (11 us/read; 5.53 M reads/minute). === Summary === Total reads processed: 23,169,318 Reads with adapters: 22,855,892 (98.6%) Reads written (passing filters): 23,169,318 (100.0%) Total basepairs processed: 3,275,470,731 bp Total written (filtered): 158,271,079 bp (4.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22855892 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.4% C: 0.0% G: 0.2% T: 99.3% 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 177798 5792329.5 0 177798 2 41233 1448082.4 0 41233 3 12428 362020.6 0 12428 4 3666 90505.1 0 3666 5 195 22626.3 0 195 6 94 5656.6 0 94 7 146 1414.1 0 146 8 87 353.5 0 87 9 145 88.4 0 143 2 10 128 22.1 1 96 32 11 55 5.5 1 8 47 12 19 1.4 1 1 18 13 27 0.3 1 2 25 14 57 0.3 1 7 50 15 86 0.3 1 31 55 16 474 0.3 1 226 248 17 3431 0.3 1 1743 1688 18 24279 0.3 1 21531 2748 19 110 0.3 1 73 37 20 70 0.3 1 30 40 21 58 0.3 1 46 12 22 170 0.3 1 145 25 23 40 0.3 1 9 31 24 110 0.3 1 13 97 25 52 0.3 1 8 44 26 10 0.3 1 3 7 27 70 0.3 1 12 58 28 330 0.3 1 189 141 29 210 0.3 1 23 187 30 18 0.3 1 4 14 31 8 0.3 1 2 6 32 40 0.3 1 5 35 33 108 0.3 1 14 94 34 111 0.3 1 14 97 35 18 0.3 1 6 12 36 147 0.3 1 25 122 37 307 0.3 1 62 245 38 3628 0.3 1 537 3091 39 137 0.3 1 29 108 40 32 0.3 1 10 22 41 167 0.3 1 41 126 42 14 0.3 1 6 8 43 247 0.3 1 67 180 44 36 0.3 1 16 20 45 89 0.3 1 26 63 46 38 0.3 1 18 20 47 99 0.3 1 36 63 48 184 0.3 1 53 131 49 31 0.3 1 10 21 50 118 0.3 1 52 66 51 63 0.3 1 19 44 52 31 0.3 1 13 18 53 64 0.3 1 26 38 54 132 0.3 1 43 89 55 81 0.3 1 30 51 56 105 0.3 1 33 72 57 72 0.3 1 30 42 58 111 0.3 1 45 66 59 72 0.3 1 16 56 60 76 0.3 1 31 45 61 143 0.3 1 46 97 62 303 0.3 1 93 210 63 59 0.3 1 17 42 64 8 0.3 1 3 5 65 9 0.3 1 3 6 66 73 0.3 1 35 38 67 36 0.3 1 9 27 68 152 0.3 1 71 81 69 198 0.3 1 101 97 70 494 0.3 1 289 205 71 217 0.3 1 143 74 72 123 0.3 1 89 34 73 64 0.3 1 40 24 74 58 0.3 1 29 29 75 73 0.3 1 38 35 76 71 0.3 1 33 38 77 80 0.3 1 23 57 78 93 0.3 1 33 60 79 85 0.3 1 29 56 80 65 0.3 1 24 41 81 58 0.3 1 21 37 82 86 0.3 1 32 54 83 87 0.3 1 34 53 84 79 0.3 1 31 48 85 115 0.3 1 46 69 86 79 0.3 1 28 51 87 50 0.3 1 15 35 88 57 0.3 1 17 40 89 63 0.3 1 30 33 90 180 0.3 1 93 87 91 73 0.3 1 36 37 92 56 0.3 1 24 32 93 86 0.3 1 39 47 94 62 0.3 1 28 34 95 77 0.3 1 30 47 96 70 0.3 1 45 25 97 86 0.3 1 34 52 98 75 0.3 1 34 41 99 66 0.3 1 41 25 100 81 0.3 1 45 36 101 59 0.3 1 30 29 102 64 0.3 1 39 25 103 59 0.3 1 36 23 104 58 0.3 1 42 16 105 63 0.3 1 41 22 106 56 0.3 1 43 13 107 60 0.3 1 46 14 108 65 0.3 1 55 10 109 58 0.3 1 40 18 110 178 0.3 1 80 98 111 93 0.3 1 61 32 112 76 0.3 1 63 13 113 67 0.3 1 54 13 114 141 0.3 1 71 70 115 87 0.3 1 78 9 116 141 0.3 1 122 19 117 130 0.3 1 109 21 118 102 0.3 1 82 20 119 87 0.3 1 67 20 120 79 0.3 1 58 21 121 133 0.3 1 110 23 122 141 0.3 1 112 29 123 164 0.3 1 135 29 124 220 0.3 1 185 35 125 309 0.3 1 270 39 126 313 0.3 1 270 43 127 430 0.3 1 367 63 128 541 0.3 1 454 87 129 779 0.3 1 675 104 130 808 0.3 1 685 123 131 969 0.3 1 843 126 132 1544 0.3 1 1328 216 133 2878 0.3 1 2473 405 134 4228 0.3 1 3698 530 135 7311 0.3 1 6531 780 136 14041 0.3 1 12697 1344 137 76358 0.3 1 70972 5386 138 22467034 0.3 1 22000958 466076 139 11 0.3 1 2 9 140 1 0.3 1 1 141 3 0.3 1 2 1 143 1 0.3 1 0 1 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_1.fq.gz ============================================= 23169318 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 24162 (0.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 22855888 (98.6%)