SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000238_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_20210722/tmp/f977676c-1990-11ec-a78a-6c92bfc12eb4/trimmed/RRBS21T000238_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1039.70 s (27 us/read; 2.19 M reads/minute). === Summary === Total reads processed: 37,986,056 Reads with adapters: 22,659,137 (59.7%) Reads written (passing filters): 37,986,056 (100.0%) Total basepairs processed: 3,085,872,587 bp Total written (filtered): 2,871,967,882 bp (93.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22659137 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 4.0% C: 88.7% G: 0.3% T: 7.0% 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 21150950 9496514.0 0 21150950 2 28490 2374128.5 0 28490 3 12139 593532.1 0 12139 4 6165 148383.0 0 6165 5 1725 37095.8 0 1725 6 1285 9273.9 0 1285 7 2636 2318.5 0 2636 8 1655 579.6 0 1655 9 1148 144.9 0 1086 62 10 4844 36.2 1 981 3863 11 524 9.1 1 94 430 12 972 2.3 1 146 826 13 1418 0.6 1 167 1251 14 1819 0.6 1 166 1653 15 607 0.6 1 64 543 16 983 0.6 1 114 869 17 1612 0.6 1 181 1431 18 634 0.6 1 74 560 19 2044 0.6 1 173 1871 20 1174 0.6 1 140 1034 21 210 0.6 1 52 158 22 467 0.6 1 45 422 23 1188 0.6 1 98 1090 24 3759 0.6 1 346 3413 25 1419 0.6 1 112 1307 26 1063 0.6 1 105 958 27 544 0.6 1 76 468 28 676 0.6 1 69 607 29 259 0.6 1 17 242 30 801 0.6 1 72 729 31 672 0.6 1 76 596 32 1669 0.6 1 188 1481 33 1298 0.6 1 145 1153 34 704 0.6 1 71 633 35 1411 0.6 1 120 1291 36 1234 0.6 1 123 1111 37 931 0.6 1 116 815 38 806 0.6 1 72 734 39 783 0.6 1 80 703 40 695 0.6 1 65 630 41 994 0.6 1 98 896 42 1094 0.6 1 100 994 43 907 0.6 1 92 815 44 932 0.6 1 79 853 45 1405 0.6 1 147 1258 46 860 0.6 1 71 789 47 922 0.6 1 91 831 48 1754 0.6 1 165 1589 49 1139 0.6 1 100 1039 50 675 0.6 1 55 620 51 1387 0.6 1 142 1245 52 1974 0.6 1 171 1803 53 1550 0.6 1 137 1413 54 1218 0.6 1 112 1106 55 1050 0.6 1 93 957 56 908 0.6 1 72 836 57 1017 0.6 1 86 931 58 875 0.6 1 87 788 59 730 0.6 1 57 673 60 600 0.6 1 57 543 61 529 0.6 1 53 476 62 475 0.6 1 38 437 63 525 0.6 1 50 475 64 525 0.6 1 56 469 65 625 0.6 1 63 562 66 1114 0.6 1 90 1024 67 944 0.6 1 79 865 68 878 0.6 1 70 808 69 908 0.6 1 100 808 70 1013 0.6 1 107 906 71 1023 0.6 1 108 915 72 1301 0.6 1 133 1168 73 1052 0.6 1 120 932 74 979 0.6 1 133 846 75 2075 0.6 1 279 1796 76 2322 0.6 1 311 2011 77 1308 0.6 1 120 1188 78 700 0.6 1 59 641 79 627 0.6 1 45 582 80 753 0.6 1 44 709 81 623 0.6 1 58 565 82 432 0.6 1 27 405 83 355 0.6 1 28 327 84 434 0.6 1 26 408 85 372 0.6 1 24 348 86 354 0.6 1 21 333 87 211 0.6 1 15 196 88 228 0.6 1 11 217 89 211 0.6 1 15 196 90 205 0.6 1 18 187 91 305 0.6 1 28 277 92 271 0.6 1 20 251 93 307 0.6 1 24 283 94 317 0.6 1 23 294 95 308 0.6 1 18 290 96 470 0.6 1 43 427 97 406 0.6 1 45 361 98 248 0.6 1 25 223 99 417 0.6 1 56 361 100 176 0.6 1 18 158 101 100 0.6 1 9 91 102 322 0.6 1 42 280 103 110 0.6 1 8 102 104 165 0.6 1 14 151 105 85 0.6 1 12 73 106 57 0.6 1 2 55 107 80 0.6 1 7 73 108 81 0.6 1 5 76 109 187 0.6 1 28 159 110 43 0.6 1 4 39 111 18 0.6 1 1 17 112 8 0.6 1 1 7 113 3 0.6 1 1 2 114 7 0.6 1 0 7 115 2 0.6 1 2 116 5 0.6 1 5 117 4 0.6 1 1 3 118 1 0.6 1 1 119 1 0.6 1 1 121 2 0.6 1 2 122 2 0.6 1 2 123 2 0.6 1 2 124 2 0.6 1 2 125 4 0.6 1 4 126 8 0.6 1 7 1 127 9 0.6 1 8 1 128 9 0.6 1 8 1 129 18 0.6 1 18 130 9 0.6 1 7 2 131 16 0.6 1 14 2 132 24 0.6 1 21 3 133 33 0.6 1 30 3 134 69 0.6 1 66 3 135 191 0.6 1 178 13 136 531 0.6 1 500 31 137 47699 0.6 1 46403 1296 138 1317499 0.6 1 1289523 27976 139 1 0.6 1 1 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_20210722/clean_data/RRBS21T000238_val_2.fq.gz ============================================= 37986056 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1279848 (3.4%) 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: 37986056 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1471256 (3.87%)