SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040795_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/8ccac9be-d1de-11eb-8791-f8f21e2f3ee9/trimmed/RRBS20A040795_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 695.53 s (22 us/read; 2.67 M reads/minute). === Summary === Total reads processed: 30,942,064 Reads with adapters: 25,939,988 (83.8%) Reads written (passing filters): 30,942,064 (100.0%) Total basepairs processed: 3,697,602,416 bp Total written (filtered): 919,571,368 bp (24.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25939988 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 1.6% C: 20.6% G: 55.2% T: 22.3% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 5739780 7735516.0 0 5739780 2 15753 1933879.0 0 15753 3 4725 483469.8 0 4725 4 3362 120867.4 0 3362 5 837 30216.9 0 837 6 386 7554.2 0 386 7 461 1888.6 0 461 8 532 472.1 0 532 9 498 118.0 0 480 18 10 970 29.5 1 215 755 11 130 7.4 1 21 109 12 112 1.8 1 20 92 13 57 0.5 1 5 52 14 311 0.5 1 21 290 15 134 0.5 1 13 121 16 223 0.5 1 19 204 17 303 0.5 1 36 267 18 135 0.5 1 21 114 19 332 0.5 1 38 294 20 393 0.5 1 79 314 21 212 0.5 1 162 50 22 83 0.5 1 14 69 23 363 0.5 1 25 338 24 744 0.5 1 59 685 25 375 0.5 1 41 334 26 695 0.5 1 76 619 27 465 0.5 1 74 391 28 192 0.5 1 33 159 29 49 0.5 1 7 42 30 71 0.5 1 9 62 31 269 0.5 1 18 251 32 298 0.5 1 23 275 33 877 0.5 1 82 795 34 302 0.5 1 46 256 35 155 0.5 1 19 136 36 89 0.5 1 5 84 37 383 0.5 1 36 347 38 140 0.5 1 25 115 39 175 0.5 1 21 154 40 250 0.5 1 30 220 41 1214 0.5 1 20 1194 42 422 0.5 1 32 390 43 138 0.5 1 8 130 44 223 0.5 1 15 208 45 530 0.5 1 50 480 46 268 0.5 1 26 242 47 73 0.5 1 5 68 48 232 0.5 1 15 217 49 150 0.5 1 18 132 50 291 0.5 1 28 263 51 354 0.5 1 41 313 52 221 0.5 1 27 194 53 32 0.5 1 3 29 54 145 0.5 1 18 127 55 150 0.5 1 45 105 56 28 0.5 1 4 24 57 160 0.5 1 26 134 58 327 0.5 1 77 250 59 312 0.5 1 115 197 60 716 0.5 1 381 335 61 1958 0.5 1 1367 591 62 3956 0.5 1 3362 594 63 14266 0.5 1 13488 778 64 81094 0.5 1 79979 1115 65 14747 0.5 1 14388 359 66 885 0.5 1 662 223 67 682 0.5 1 455 227 68 454 0.5 1 254 200 69 451 0.5 1 212 239 70 489 0.5 1 146 343 71 510 0.5 1 149 361 72 416 0.5 1 98 318 73 432 0.5 1 117 315 74 300 0.5 1 97 203 75 361 0.5 1 105 256 76 296 0.5 1 51 245 77 201 0.5 1 38 163 78 236 0.5 1 41 195 79 271 0.5 1 61 210 80 186 0.5 1 31 155 81 174 0.5 1 34 140 82 167 0.5 1 38 129 83 151 0.5 1 43 108 84 208 0.5 1 52 156 85 132 0.5 1 53 79 86 202 0.5 1 71 131 87 164 0.5 1 77 87 88 172 0.5 1 75 97 89 178 0.5 1 100 78 90 271 0.5 1 90 181 91 144 0.5 1 63 81 92 157 0.5 1 75 82 93 150 0.5 1 48 102 94 152 0.5 1 83 69 95 92 0.5 1 39 53 96 115 0.5 1 51 64 97 152 0.5 1 69 83 98 151 0.5 1 93 58 99 145 0.5 1 75 70 100 139 0.5 1 70 69 101 99 0.5 1 60 39 102 151 0.5 1 96 55 103 149 0.5 1 95 54 104 149 0.5 1 112 37 105 221 0.5 1 182 39 106 247 0.5 1 221 26 107 281 0.5 1 220 61 108 274 0.5 1 225 49 109 320 0.5 1 266 54 110 227 0.5 1 190 37 111 323 0.5 1 293 30 112 336 0.5 1 307 29 113 464 0.5 1 431 33 114 515 0.5 1 477 38 115 599 0.5 1 571 28 116 587 0.5 1 559 28 117 560 0.5 1 527 33 118 437 0.5 1 410 27 119 436 0.5 1 403 33 120 500 0.5 1 471 29 121 603 0.5 1 572 31 122 660 0.5 1 609 51 123 949 0.5 1 896 53 124 892 0.5 1 826 66 125 1361 0.5 1 1304 57 126 1650 0.5 1 1574 76 127 2385 0.5 1 2292 93 128 5210 0.5 1 5042 168 129 2849 0.5 1 2736 113 130 1938 0.5 1 1823 115 131 1601 0.5 1 1495 106 132 1747 0.5 1 1617 130 133 2937 0.5 1 2729 208 134 3340 0.5 1 3095 245 135 10600 0.5 1 10001 599 136 15374 0.5 1 14374 1000 137 1060373 0.5 1 1035184 25189 138 18362130 0.5 1 18122055 240075 139 549500 0.5 1 12 549488 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040795_val_2.fq.gz ============================================= 30942064 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 440399 (1.4%) 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: 30942064 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 20332367 (65.71%)