SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000234_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 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_20210722/tmp/f9776294-1990-11ec-b146-6c92bfc12eb4/trimmed/RRBS21T000234_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 651.39 s (18 us/read; 3.34 M reads/minute). === Summary === Total reads processed: 36,279,302 Reads with adapters: 17,862,090 (49.2%) Reads written (passing filters): 36,279,302 (100.0%) Total basepairs processed: 3,472,675,729 bp Total written (filtered): 2,366,812,376 bp (68.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17862090 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 17.6% C: 45.6% G: 13.1% T: 23.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7171751 9069825.5 0 7171751 2 1956088 2267456.4 0 1956088 3 489374 566864.1 0 489374 4 153118 141716.0 0 153118 5 7432 35429.0 0 7432 6 5566 8857.3 0 5566 7 6338 2214.3 0 6338 8 5180 553.6 0 5180 9 6888 138.4 0 6599 289 10 6192 34.6 1 3728 2464 11 4225 8.6 1 827 3398 12 1644 2.2 1 364 1280 13 1526 0.5 1 308 1218 14 4225 0.5 1 785 3440 15 2178 0.5 1 453 1725 16 10851 0.5 1 1787 9064 17 8772 0.5 1 1522 7250 18 3315 0.5 1 766 2549 19 161 0.5 1 19 142 20 1490 0.5 1 270 1220 21 142 0.5 1 19 123 22 282 0.5 1 39 243 23 1620 0.5 1 299 1321 24 6840 0.5 1 1293 5547 25 2212 0.5 1 417 1795 26 501 0.5 1 62 439 27 2069 0.5 1 379 1690 28 3808 0.5 1 728 3080 29 5417 0.5 1 930 4487 30 1091 0.5 1 242 849 31 155 0.5 1 16 139 32 1622 0.5 1 322 1300 33 4270 0.5 1 802 3468 34 3360 0.5 1 623 2737 35 6736 0.5 1 1232 5504 36 1452 0.5 1 268 1184 37 8992 0.5 1 1492 7500 38 5810 0.5 1 1223 4587 39 5425 0.5 1 974 4451 40 7256 0.5 1 1291 5965 41 2487 0.5 1 493 1994 42 1031 0.5 1 162 869 43 2276 0.5 1 403 1873 44 1631 0.5 1 279 1352 45 2919 0.5 1 553 2366 46 893 0.5 1 144 749 47 1590 0.5 1 261 1329 48 6442 0.5 1 1273 5169 49 581 0.5 1 87 494 50 2348 0.5 1 402 1946 51 1070 0.5 1 166 904 52 755 0.5 1 132 623 53 1568 0.5 1 285 1283 54 3273 0.5 1 583 2690 55 3959 0.5 1 839 3120 56 1695 0.5 1 307 1388 57 1827 0.5 1 324 1503 58 1327 0.5 1 265 1062 59 707 0.5 1 89 618 60 1194 0.5 1 190 1004 61 1530 0.5 1 223 1307 62 6458 0.5 1 1113 5345 63 1127 0.5 1 189 938 64 178 0.5 1 32 146 65 126 0.5 1 22 104 66 1507 0.5 1 265 1242 67 549 0.5 1 70 479 68 3101 0.5 1 655 2446 69 3587 0.5 1 711 2876 70 4157 0.5 1 723 3434 71 940 0.5 1 161 779 72 478 0.5 1 83 395 73 805 0.5 1 118 687 74 1253 0.5 1 222 1031 75 1663 0.5 1 225 1438 76 1542 0.5 1 205 1337 77 1932 0.5 1 300 1632 78 1791 0.5 1 296 1495 79 1599 0.5 1 175 1424 80 1213 0.5 1 112 1101 81 1060 0.5 1 130 930 82 1459 0.5 1 190 1269 83 1350 0.5 1 163 1187 84 1210 0.5 1 122 1088 85 1821 0.5 1 246 1575 86 964 0.5 1 109 855 87 962 0.5 1 129 833 88 918 0.5 1 109 809 89 904 0.5 1 109 795 90 733 0.5 1 78 655 91 926 0.5 1 94 832 92 691 0.5 1 70 621 93 879 0.5 1 128 751 94 1908 0.5 1 244 1664 95 782 0.5 1 94 688 96 680 0.5 1 117 563 97 1109 0.5 1 209 900 98 561 0.5 1 81 480 99 396 0.5 1 66 330 100 414 0.5 1 49 365 101 382 0.5 1 70 312 102 509 0.5 1 93 416 103 297 0.5 1 67 230 104 225 0.5 1 33 192 105 229 0.5 1 47 182 106 194 0.5 1 27 167 107 130 0.5 1 30 100 108 92 0.5 1 19 73 109 103 0.5 1 25 78 110 236 0.5 1 43 193 111 62 0.5 1 15 47 112 39 0.5 1 13 26 113 21 0.5 1 13 8 114 9 0.5 1 6 3 115 22 0.5 1 16 6 116 22 0.5 1 17 5 117 21 0.5 1 15 6 118 28 0.5 1 23 5 119 34 0.5 1 23 11 120 19 0.5 1 12 7 121 32 0.5 1 24 8 122 49 0.5 1 38 11 123 63 0.5 1 43 20 124 61 0.5 1 50 11 125 37 0.5 1 30 7 126 82 0.5 1 63 19 127 133 0.5 1 104 29 128 143 0.5 1 108 35 129 173 0.5 1 138 35 130 246 0.5 1 195 51 131 311 0.5 1 238 73 132 492 0.5 1 399 93 133 1068 0.5 1 877 191 134 2285 0.5 1 1939 346 135 3024 0.5 1 2652 372 136 5752 0.5 1 5105 647 137 95968 0.5 1 91339 4629 138 7739245 0.5 1 7568201 171044 139 11 0.5 1 8 3 140 25 0.5 1 1 24 143 6 0.5 1 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000234_val_1.fq.gz ============================================= 36279302 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1058338 (2.9%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 17862079 (49.2%)