SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040784_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/8c4d1e2e-d1de-11eb-8629-f8f21e2f3ee9/trimmed/RRBS20A040784_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 562.01 s (16 us/read; 3.67 M reads/minute). === Summary === Total reads processed: 34,341,869 Reads with adapters: 34,197,742 (99.6%) Reads written (passing filters): 34,341,869 (100.0%) Total basepairs processed: 4,696,523,740 bp Total written (filtered): 59,285,864 bp (1.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34197742 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 99.6% C: 0.4% G: 0.0% T: 0.0% none/other: 0.0% WARNING: The adapter is preceded by "A" 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 130219 8585467.2 0 130219 2 839 2146366.8 0 839 3 243 536591.7 0 243 4 346 134147.9 0 346 5 73 33537.0 0 73 6 6 8384.2 0 6 7 10 2096.1 0 10 8 18 524.0 0 18 9 3 131.0 0 3 10 11 32.8 1 2 9 11 3 8.2 1 2 1 12 2 2.0 1 0 2 13 1 0.5 1 1 14 2 0.5 1 1 1 15 11 0.5 1 3 8 16 10 0.5 1 1 9 17 12 0.5 1 4 8 18 11 0.5 1 2 9 19 16 0.5 1 8 8 20 59 0.5 1 45 14 21 262 0.5 1 208 54 22 5 0.5 1 1 4 23 16 0.5 1 10 6 24 29 0.5 1 14 15 25 86 0.5 1 72 14 26 291 0.5 1 229 62 27 10 0.5 1 5 5 28 8 0.5 1 5 3 29 31 0.5 1 23 8 30 16 0.5 1 13 3 31 81 0.5 1 61 20 32 42 0.5 1 25 17 33 195 0.5 1 149 46 34 20 0.5 1 6 14 35 14 0.5 1 4 10 36 14 0.5 1 3 11 37 97 0.5 1 58 39 38 134 0.5 1 84 50 39 172 0.5 1 94 78 40 675 0.5 1 115 560 41 13764 0.5 1 68 13696 42 187 0.5 1 20 167 43 60 0.5 1 45 15 44 51 0.5 1 39 12 45 49 0.5 1 28 21 46 35 0.5 1 18 17 47 35 0.5 1 25 10 48 34 0.5 1 17 17 49 36 0.5 1 28 8 50 42 0.5 1 30 12 51 62 0.5 1 46 16 52 97 0.5 1 74 23 53 7 0.5 1 3 4 54 64 0.5 1 47 17 55 242 0.5 1 206 36 56 28 0.5 1 17 11 57 211 0.5 1 150 61 58 776 0.5 1 663 113 59 1320 0.5 1 949 371 60 3913 0.5 1 3147 766 61 12414 0.5 1 10352 2062 62 23681 0.5 1 22664 1017 63 95024 0.5 1 92690 2334 64 519924 0.5 1 514511 5413 65 83375 0.5 1 81945 1430 66 5221 0.5 1 5014 207 67 4763 0.5 1 4603 160 68 2739 0.5 1 2599 140 69 2218 0.5 1 2114 104 70 1206 0.5 1 1123 83 71 1131 0.5 1 1069 62 72 675 0.5 1 630 45 73 697 0.5 1 654 43 74 667 0.5 1 621 46 75 476 0.5 1 442 34 76 312 0.5 1 296 16 77 300 0.5 1 275 25 78 253 0.5 1 227 26 79 292 0.5 1 274 18 80 241 0.5 1 223 18 81 228 0.5 1 215 13 82 240 0.5 1 211 29 83 207 0.5 1 191 16 84 224 0.5 1 206 18 85 388 0.5 1 363 25 86 677 0.5 1 647 30 87 937 0.5 1 898 39 88 1180 0.5 1 1139 41 89 950 0.5 1 901 49 90 751 0.5 1 614 137 91 483 0.5 1 459 24 92 475 0.5 1 445 30 93 357 0.5 1 329 28 94 512 0.5 1 491 21 95 432 0.5 1 407 25 96 499 0.5 1 468 31 97 504 0.5 1 471 33 98 553 0.5 1 513 40 99 560 0.5 1 532 28 100 550 0.5 1 518 32 101 515 0.5 1 476 39 102 653 0.5 1 608 45 103 751 0.5 1 697 54 104 1089 0.5 1 1030 59 105 1491 0.5 1 1438 53 106 2710 0.5 1 2616 94 107 2481 0.5 1 2394 87 108 2318 0.5 1 2230 88 109 2803 0.5 1 2684 119 110 1766 0.5 1 1686 80 111 2736 0.5 1 2649 87 112 3358 0.5 1 3232 126 113 5836 0.5 1 5696 140 114 6163 0.5 1 6031 132 115 7549 0.5 1 7410 139 116 8201 0.5 1 8063 138 117 6081 0.5 1 5900 181 118 4318 0.5 1 4181 137 119 3740 0.5 1 3583 157 120 4703 0.5 1 4545 158 121 5383 0.5 1 5198 185 122 5861 0.5 1 5630 231 123 8113 0.5 1 7817 296 124 7966 0.5 1 7642 324 125 15171 0.5 1 14755 416 126 22660 0.5 1 22145 515 127 35112 0.5 1 34549 563 128 44122 0.5 1 43413 709 129 28277 0.5 1 27695 582 130 20201 0.5 1 19651 550 131 16236 0.5 1 15774 462 132 16094 0.5 1 15583 511 133 23756 0.5 1 22933 823 134 23088 0.5 1 22226 862 135 84144 0.5 1 81811 2333 136 95739 0.5 1 92675 3064 137 736234 0.5 1 717557 18677 138 32018893 0.5 1 31467409 551484 139 8 0.5 1 4 4 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/RRBS20A040784_val_2.fq.gz ============================================= 34341869 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 84247 (0.2%) 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: 34341869 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 34116899 (99.34%)