SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040795_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/8ccac9be-d1de-11eb-8791-f8f21e2f3ee9/trimmed/RRBS20A040795_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 391.30 s (13 us/read; 4.74 M reads/minute). === Summary === Total reads processed: 30,942,064 Reads with adapters: 24,304,058 (78.5%) Reads written (passing filters): 30,942,064 (100.0%) Total basepairs processed: 3,800,042,562 bp Total written (filtered): 1,002,130,507 bp (26.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24304058 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 5.3% C: 0.1% G: 64.2% T: 30.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2991239 7735516.0 0 2991239 2 757383 1933879.0 0 757383 3 179093 483469.8 0 179093 4 52230 120867.4 0 52230 5 2243 30216.9 0 2243 6 1431 7554.2 0 1431 7 1514 1888.6 0 1514 8 1286 472.1 0 1286 9 1745 118.0 0 1600 145 10 2097 29.5 1 790 1307 11 1011 7.4 1 142 869 12 484 1.8 1 79 405 13 475 0.5 1 67 408 14 892 0.5 1 122 770 15 804 0.5 1 87 717 16 3793 0.5 1 333 3460 17 8189 0.5 1 1074 7115 18 23687 0.5 1 5435 18252 19 237 0.5 1 37 200 20 663 0.5 1 85 578 21 395 0.5 1 54 341 22 1045 0.5 1 252 793 23 581 0.5 1 77 504 24 1652 0.5 1 254 1398 25 723 0.5 1 119 604 26 192 0.5 1 22 170 27 880 0.5 1 215 665 28 1184 0.5 1 169 1015 29 1468 0.5 1 240 1228 30 417 0.5 1 69 348 31 79 0.5 1 4 75 32 627 0.5 1 79 548 33 1339 0.5 1 193 1146 34 1125 0.5 1 168 957 35 2102 0.5 1 309 1793 36 515 0.5 1 54 461 37 1577 0.5 1 264 1313 38 201 0.5 1 28 173 39 847 0.5 1 142 705 40 231 0.5 1 44 187 41 1878 0.5 1 268 1610 42 785 0.5 1 110 675 43 2503 0.5 1 401 2102 44 588 0.5 1 65 523 45 1157 0.5 1 160 997 46 378 0.5 1 60 318 47 753 0.5 1 93 660 48 1555 0.5 1 274 1281 49 175 0.5 1 20 155 50 913 0.5 1 160 753 51 354 0.5 1 72 282 52 247 0.5 1 38 209 53 917 0.5 1 139 778 54 1639 0.5 1 275 1364 55 1490 0.5 1 249 1241 56 817 0.5 1 170 647 57 1161 0.5 1 204 957 58 1069 0.5 1 204 865 59 539 0.5 1 110 429 60 856 0.5 1 150 706 61 1489 0.5 1 327 1162 62 3917 0.5 1 785 3132 63 833 0.5 1 171 662 64 77 0.5 1 15 62 65 66 0.5 1 8 58 66 703 0.5 1 124 579 67 378 0.5 1 58 320 68 1529 0.5 1 295 1234 69 1591 0.5 1 301 1290 70 2486 0.5 1 568 1918 71 818 0.5 1 288 530 72 587 0.5 1 302 285 73 587 0.5 1 239 348 74 561 0.5 1 128 433 75 628 0.5 1 114 514 76 526 0.5 1 108 418 77 848 0.5 1 150 698 78 708 0.5 1 129 579 79 726 0.5 1 114 612 80 681 0.5 1 141 540 81 476 0.5 1 106 370 82 699 0.5 1 100 599 83 511 0.5 1 93 418 84 428 0.5 1 66 362 85 624 0.5 1 113 511 86 402 0.5 1 83 319 87 427 0.5 1 72 355 88 374 0.5 1 71 303 89 485 0.5 1 99 386 90 585 0.5 1 138 447 91 414 0.5 1 83 331 92 355 0.5 1 86 269 93 471 0.5 1 102 369 94 934 0.5 1 171 763 95 353 0.5 1 72 281 96 327 0.5 1 91 236 97 741 0.5 1 126 615 98 344 0.5 1 98 246 99 214 0.5 1 82 132 100 216 0.5 1 70 146 101 232 0.5 1 64 168 102 299 0.5 1 82 217 103 234 0.5 1 96 138 104 194 0.5 1 76 118 105 188 0.5 1 94 94 106 321 0.5 1 140 181 107 442 0.5 1 199 243 108 731 0.5 1 135 596 109 822 0.5 1 130 692 110 870 0.5 1 190 680 111 468 0.5 1 127 341 112 263 0.5 1 113 150 113 136 0.5 1 117 19 114 216 0.5 1 170 46 115 192 0.5 1 169 23 116 262 0.5 1 224 38 117 248 0.5 1 218 30 118 241 0.5 1 213 28 119 182 0.5 1 148 34 120 222 0.5 1 177 45 121 324 0.5 1 276 48 122 385 0.5 1 343 42 123 473 0.5 1 413 60 124 572 0.5 1 492 80 125 580 0.5 1 506 74 126 587 0.5 1 502 85 127 771 0.5 1 674 97 128 1001 0.5 1 857 144 129 1149 0.5 1 992 157 130 1169 0.5 1 971 198 131 1592 0.5 1 1343 249 132 2272 0.5 1 1914 358 133 4758 0.5 1 4075 683 134 7384 0.5 1 6302 1082 135 13870 0.5 1 12054 1816 136 28145 0.5 1 24510 3635 137 1127190 0.5 1 989637 137553 138 18447774 0.5 1 16740928 1706846 139 2171 0.5 1 1707 464 140 558525 0.5 1 469820 88705 141 23 0.5 1 15 8 142 5 0.5 1 2 3 143 6 0.5 1 0 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040795_val_1.fq.gz ============================================= 30942064 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 527438 (1.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 24303962 (78.5%)