SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2//RRBS21T000221_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) 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_2/tmp/428f7790-e7c4-11eb-a920-6c92bfc12ff2/trimmed/RRBS21T000221_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1223.93 s (14 us/read; 4.14 M reads/minute). === Summary === Total reads processed: 84,439,684 Reads with adapters: 41,979,149 (49.7%) Reads written (passing filters): 84,439,684 (100.0%) Total basepairs processed: 6,622,485,355 bp Total written (filtered): 5,733,361,801 bp (86.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 41979149 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 2.8% C: 96.6% G: 0.1% T: 0.5% none/other: 0.0% WARNING: The adapter is preceded by "C" 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 35571765 21109921.0 0 35571765 2 29761 5277480.2 0 29761 3 16176 1319370.1 0 16176 4 5194 329842.5 0 5194 5 2829 82460.6 0 2829 6 2869 20615.2 0 2869 7 6544 5153.8 0 6544 8 4978 1288.4 0 4978 9 1008 322.1 0 960 48 10 5134 80.5 1 1367 3767 11 353 20.1 1 69 284 12 1591 5.0 1 265 1326 13 5523 1.3 1 888 4635 14 3897 1.3 1 622 3275 15 1167 1.3 1 157 1010 16 1795 1.3 1 256 1539 17 3920 1.3 1 593 3327 18 1335 1.3 1 198 1137 19 5504 1.3 1 857 4647 20 3051 1.3 1 437 2614 21 795 1.3 1 530 265 22 850 1.3 1 95 755 23 3800 1.3 1 528 3272 24 15355 1.3 1 2605 12750 25 3252 1.3 1 475 2777 26 5643 1.3 1 984 4659 27 843 1.3 1 134 709 28 2171 1.3 1 338 1833 29 755 1.3 1 99 656 30 3496 1.3 1 573 2923 31 2316 1.3 1 376 1940 32 6612 1.3 1 1029 5583 33 4538 1.3 1 770 3768 34 1693 1.3 1 243 1450 35 4007 1.3 1 612 3395 36 3112 1.3 1 403 2709 37 2301 1.3 1 335 1966 38 2324 1.3 1 331 1993 39 2145 1.3 1 309 1836 40 2152 1.3 1 329 1823 41 2860 1.3 1 372 2488 42 3404 1.3 1 517 2887 43 2427 1.3 1 320 2107 44 2706 1.3 1 387 2319 45 3931 1.3 1 588 3343 46 2544 1.3 1 369 2175 47 2398 1.3 1 426 1972 48 4591 1.3 1 745 3846 49 3400 1.3 1 555 2845 50 1738 1.3 1 260 1478 51 4002 1.3 1 593 3409 52 6000 1.3 1 906 5094 53 4496 1.3 1 690 3806 54 3370 1.3 1 460 2910 55 3600 1.3 1 577 3023 56 2331 1.3 1 362 1969 57 3465 1.3 1 511 2954 58 2730 1.3 1 390 2340 59 1969 1.3 1 270 1699 60 1551 1.3 1 227 1324 61 1224 1.3 1 185 1039 62 1089 1.3 1 135 954 63 1107 1.3 1 173 934 64 1457 1.3 1 234 1223 65 2023 1.3 1 298 1725 66 3367 1.3 1 501 2866 67 2568 1.3 1 404 2164 68 2015 1.3 1 299 1716 69 2515 1.3 1 350 2165 70 2258 1.3 1 359 1899 71 2124 1.3 1 354 1770 72 2233 1.3 1 369 1864 73 2125 1.3 1 359 1766 74 1873 1.3 1 350 1523 75 4001 1.3 1 649 3352 76 7180 1.3 1 1185 5995 77 2542 1.3 1 402 2140 78 1587 1.3 1 195 1392 79 1858 1.3 1 261 1597 80 1485 1.3 1 170 1315 81 1677 1.3 1 233 1444 82 1513 1.3 1 231 1282 83 1582 1.3 1 253 1329 84 1537 1.3 1 226 1311 85 1899 1.3 1 306 1593 86 1597 1.3 1 223 1374 87 1129 1.3 1 161 968 88 1009 1.3 1 164 845 89 1172 1.3 1 140 1032 90 1243 1.3 1 187 1056 91 1023 1.3 1 177 846 92 771 1.3 1 105 666 93 1160 1.3 1 176 984 94 772 1.3 1 132 640 95 607 1.3 1 70 537 96 649 1.3 1 78 571 97 629 1.3 1 113 516 98 461 1.3 1 64 397 99 604 1.3 1 80 524 100 429 1.3 1 82 347 101 368 1.3 1 55 313 102 496 1.3 1 89 407 103 365 1.3 1 56 309 104 392 1.3 1 49 343 105 272 1.3 1 51 221 106 262 1.3 1 42 220 107 138 1.3 1 18 120 108 192 1.3 1 22 170 109 259 1.3 1 32 227 110 170 1.3 1 21 149 111 67 1.3 1 15 52 112 30 1.3 1 8 22 113 16 1.3 1 9 7 114 48 1.3 1 13 35 115 13 1.3 1 9 4 116 17 1.3 1 11 6 117 6 1.3 1 4 2 118 7 1.3 1 5 2 119 4 1.3 1 2 2 120 5 1.3 1 2 3 121 2 1.3 1 2 122 7 1.3 1 5 2 123 2 1.3 1 2 124 6 1.3 1 4 2 125 6 1.3 1 5 1 126 11 1.3 1 9 2 127 27 1.3 1 24 3 128 33 1.3 1 30 3 129 39 1.3 1 37 2 130 38 1.3 1 35 3 131 41 1.3 1 37 4 132 44 1.3 1 39 5 133 51 1.3 1 42 9 134 81 1.3 1 77 4 135 280 1.3 1 267 13 136 627 1.3 1 594 33 137 28402 1.3 1 27900 502 138 6072164 1.3 1 6023188 48976 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/clean_data_2//RRBS21T000221_val_2.fq.gz ============================================= 84439684 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1647054 (2.0%) 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: 84439684 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 6340096 (7.51%)