SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000236_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/f93fdf04-1990-11ec-8507-6c92bfc12faa/trimmed/RRBS21T000236_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 576.66 s (14 us/read; 4.18 M reads/minute). === Summary === Total reads processed: 40,219,190 Reads with adapters: 23,964,208 (59.6%) Reads written (passing filters): 40,219,190 (100.0%) Total basepairs processed: 4,168,031,594 bp Total written (filtered): 2,154,420,157 bp (51.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23964208 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 74.5% C: 0.7% G: 9.0% T: 15.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6827005 10054797.5 0 6827005 2 1791052 2513699.4 0 1791052 3 461553 628424.8 0 461553 4 137145 157106.2 0 137145 5 7179 39276.6 0 7179 6 3652 9819.1 0 3652 7 4532 2454.8 0 4532 8 3482 613.7 0 3482 9 5408 153.4 0 5122 286 10 4760 38.4 1 2543 2217 11 4464 9.6 1 618 3846 12 1317 2.4 1 186 1131 13 1482 0.6 1 225 1257 14 3839 0.6 1 611 3228 15 2503 0.6 1 477 2026 16 13000 0.6 1 2851 10149 17 23113 0.6 1 12587 10526 18 49506 0.6 1 42564 6942 19 632 0.6 1 306 326 20 1950 0.6 1 588 1362 21 127 0.6 1 37 90 22 225 0.6 1 57 168 23 1453 0.6 1 183 1270 24 6700 0.6 1 1040 5660 25 2215 0.6 1 307 1908 26 493 0.6 1 60 433 27 1838 0.6 1 270 1568 28 3733 0.6 1 625 3108 29 5564 0.6 1 832 4732 30 957 0.6 1 160 797 31 143 0.6 1 18 125 32 1617 0.6 1 262 1355 33 4260 0.6 1 714 3546 34 3388 0.6 1 537 2851 35 6996 0.6 1 1223 5773 36 1374 0.6 1 232 1142 37 11866 0.6 1 1938 9928 38 5851 0.6 1 1080 4771 39 5627 0.6 1 1043 4584 40 11133 0.6 1 1986 9147 41 3243 0.6 1 540 2703 42 1324 0.6 1 282 1042 43 3396 0.6 1 578 2818 44 2965 0.6 1 565 2400 45 3966 0.6 1 752 3214 46 1062 0.6 1 172 890 47 1850 0.6 1 283 1567 48 8681 0.6 1 1630 7051 49 819 0.6 1 138 681 50 3653 0.6 1 595 3058 51 1973 0.6 1 366 1607 52 862 0.6 1 169 693 53 1824 0.6 1 300 1524 54 4863 0.6 1 829 4034 55 5045 0.6 1 1045 4000 56 2457 0.6 1 390 2067 57 2649 0.6 1 451 2198 58 1547 0.6 1 258 1289 59 1218 0.6 1 244 974 60 1481 0.6 1 245 1236 61 2062 0.6 1 298 1764 62 11962 0.6 1 2719 9243 63 1708 0.6 1 296 1412 64 177 0.6 1 30 147 65 122 0.6 1 13 109 66 1956 0.6 1 498 1458 67 721 0.6 1 97 624 68 3432 0.6 1 668 2764 69 3887 0.6 1 570 3317 70 6358 0.6 1 842 5516 71 1526 0.6 1 228 1298 72 532 0.6 1 86 446 73 965 0.6 1 131 834 74 1127 0.6 1 158 969 75 1337 0.6 1 124 1213 76 2064 0.6 1 185 1879 77 1821 0.6 1 202 1619 78 1914 0.6 1 202 1712 79 1573 0.6 1 128 1445 80 1469 0.6 1 131 1338 81 1409 0.6 1 146 1263 82 1949 0.6 1 153 1796 83 1723 0.6 1 190 1533 84 1198 0.6 1 96 1102 85 2870 0.6 1 447 2423 86 1304 0.6 1 147 1157 87 1004 0.6 1 96 908 88 1039 0.6 1 136 903 89 1083 0.6 1 143 940 90 1117 0.6 1 123 994 91 1126 0.6 1 125 1001 92 849 0.6 1 99 750 93 1297 0.6 1 221 1076 94 2564 0.6 1 327 2237 95 923 0.6 1 148 775 96 852 0.6 1 142 710 97 1701 0.6 1 295 1406 98 897 0.6 1 126 771 99 502 0.6 1 78 424 100 548 0.6 1 69 479 101 516 0.6 1 86 430 102 732 0.6 1 128 604 103 446 0.6 1 67 379 104 356 0.6 1 84 272 105 307 0.6 1 56 251 106 296 0.6 1 42 254 107 210 0.6 1 45 165 108 150 0.6 1 28 122 109 145 0.6 1 35 110 110 314 0.6 1 76 238 111 138 0.6 1 39 99 112 123 0.6 1 41 82 113 41 0.6 1 31 10 114 107 0.6 1 24 83 115 58 0.6 1 25 33 116 169 0.6 1 66 103 117 33 0.6 1 17 16 118 35 0.6 1 24 11 119 51 0.6 1 35 16 120 39 0.6 1 30 9 121 64 0.6 1 47 17 122 71 0.6 1 54 17 123 83 0.6 1 59 24 124 85 0.6 1 68 17 125 123 0.6 1 93 30 126 139 0.6 1 103 36 127 200 0.6 1 144 56 128 252 0.6 1 186 66 129 267 0.6 1 202 65 130 424 0.6 1 311 113 131 672 0.6 1 526 146 132 925 0.6 1 722 203 133 2254 0.6 1 1773 481 134 5049 0.6 1 4142 907 135 6079 0.6 1 5073 1006 136 12352 0.6 1 10415 1937 137 303939 0.6 1 288807 15132 138 14076236 0.6 1 13722888 353348 139 27 0.6 1 3 24 140 10 0.6 1 2 8 141 11 0.6 1 0 11 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000236_val_1.fq.gz ============================================= 40219190 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 970604 (2.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 23964198 (59.6%)