SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041608_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/20201118/tmp/66177452-5592-11eb-8b6f-6c92bfc13046/trimmed/RRBS20A041608_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1754.39 s (47 us/read; 1.27 M reads/minute). === Summary === Total reads processed: 37,199,102 Reads with adapters: 12,171,389 (32.7%) Reads written (passing filters): 37,199,102 (100.0%) Total basepairs processed: 3,989,973,079 bp Total written (filtered): 3,970,162,811 bp (99.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12171389 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.9% C: 73.2% G: 0.9% T: 6.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11967568 9299775.5 0 11967568 2 65362 2324943.9 0 65362 3 16501 581236.0 0 16501 4 16007 145309.0 0 16007 5 3390 36327.2 0 3390 6 1802 9081.8 0 1802 7 2803 2270.5 0 2803 8 1889 567.6 0 1889 9 1325 141.9 0 1279 46 10 4930 35.5 1 982 3948 11 515 8.9 1 90 425 12 986 2.2 1 135 851 13 1111 0.6 1 157 954 14 1715 0.6 1 223 1492 15 606 0.6 1 61 545 16 781 0.6 1 95 686 17 1342 0.6 1 168 1174 18 644 0.6 1 76 568 19 1909 0.6 1 252 1657 20 1334 0.6 1 147 1187 21 53 0.6 1 10 43 22 256 0.6 1 23 233 23 1189 0.6 1 115 1074 24 3324 0.6 1 357 2967 25 1056 0.6 1 83 973 26 2088 0.6 1 213 1875 27 1318 0.6 1 141 1177 28 1077 0.6 1 133 944 29 104 0.6 1 12 92 30 320 0.6 1 47 273 31 276 0.6 1 32 244 32 1481 0.6 1 158 1323 33 2622 0.6 1 312 2310 34 524 0.6 1 42 482 35 607 0.6 1 55 552 36 154 0.6 1 13 141 37 1103 0.6 1 123 980 38 282 0.6 1 33 249 39 415 0.6 1 42 373 40 344 0.6 1 35 309 41 455 0.6 1 44 411 42 834 0.6 1 89 745 43 395 0.6 1 33 362 44 600 0.6 1 57 543 45 1288 0.6 1 130 1158 46 596 0.6 1 54 542 47 194 0.6 1 23 171 48 789 0.6 1 75 714 49 451 0.6 1 40 411 50 626 0.6 1 62 564 51 849 0.6 1 89 760 52 977 0.6 1 107 870 53 102 0.6 1 7 95 54 393 0.6 1 45 348 55 412 0.6 1 37 375 56 89 0.6 1 11 78 57 331 0.6 1 19 312 58 542 0.6 1 35 507 59 337 0.6 1 30 307 60 500 0.6 1 46 454 61 607 0.6 1 63 544 62 744 0.6 1 50 694 63 658 0.6 1 70 588 64 252 0.6 1 26 226 65 228 0.6 1 15 213 66 503 0.6 1 46 457 67 289 0.6 1 34 255 68 245 0.6 1 21 224 69 221 0.6 1 15 206 70 248 0.6 1 31 217 71 246 0.6 1 17 229 72 224 0.6 1 23 201 73 273 0.6 1 31 242 74 260 0.6 1 31 229 75 361 0.6 1 29 332 76 415 0.6 1 49 366 77 340 0.6 1 36 304 78 178 0.6 1 8 170 79 190 0.6 1 22 168 80 189 0.6 1 13 176 81 187 0.6 1 8 179 82 227 0.6 1 26 201 83 269 0.6 1 35 234 84 250 0.6 1 28 222 85 271 0.6 1 25 246 86 176 0.6 1 18 158 87 116 0.6 1 11 105 88 127 0.6 1 11 116 89 154 0.6 1 12 142 90 105 0.6 1 12 93 91 82 0.6 1 4 78 92 96 0.6 1 5 91 93 122 0.6 1 13 109 94 101 0.6 1 12 89 95 64 0.6 1 4 60 96 86 0.6 1 5 81 97 63 0.6 1 8 55 98 60 0.6 1 9 51 99 85 0.6 1 7 78 100 59 0.6 1 5 54 101 50 0.6 1 2 48 102 58 0.6 1 7 51 103 39 0.6 1 2 37 104 24 0.6 1 1 23 105 21 0.6 1 6 15 106 20 0.6 1 2 18 107 12 0.6 1 1 11 108 13 0.6 1 2 11 109 12 0.6 1 0 12 110 10 0.6 1 1 9 111 3 0.6 1 0 3 112 1 0.6 1 0 1 113 1 0.6 1 0 1 117 4 0.6 1 1 3 118 1 0.6 1 0 1 125 2 0.6 1 2 127 1 0.6 1 1 131 2 0.6 1 1 1 133 3 0.6 1 3 134 4 0.6 1 4 135 5 0.6 1 5 136 21 0.6 1 18 3 137 238 0.6 1 213 25 138 39600 0.6 1 38891 709 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041608_val_2.fq.gz ============================================= 37199102 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1768617 (4.8%) 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: 37199102 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 95353 (0.26%)