SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000222_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/f94f81c0-1990-11ec-9fe6-6c92bfc12faa/trimmed/RRBS21T000222_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 3249.32 s (35 us/read; 1.72 M reads/minute). === Summary === Total reads processed: 93,300,644 Reads with adapters: 65,261,904 (69.9%) Reads written (passing filters): 93,300,644 (100.0%) Total basepairs processed: 8,845,757,207 bp Total written (filtered): 3,920,778,569 bp (44.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 65261904 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 4.3% C: 40.5% G: 48.0% T: 7.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29638181 23325161.0 0 29638181 2 56911 5831290.2 0 56911 3 9438 1457822.6 0 9438 4 3640 364455.6 0 3640 5 1388 91113.9 0 1388 6 988 22778.5 0 988 7 2064 5694.6 0 2064 8 1013 1423.7 0 1013 9 684 355.9 0 637 47 10 3503 89.0 1 812 2691 11 258 22.2 1 57 201 12 2098 5.6 1 498 1600 13 815 1.4 1 87 728 14 1158 1.4 1 133 1025 15 384 1.4 1 40 344 16 529 1.4 1 62 467 17 975 1.4 1 110 865 18 435 1.4 1 42 393 19 1440 1.4 1 218 1222 20 1174 1.4 1 297 877 21 2689 1.4 1 2158 531 22 512 1.4 1 99 413 23 943 1.4 1 92 851 24 3036 1.4 1 270 2766 25 862 1.4 1 123 739 26 917 1.4 1 197 720 27 615 1.4 1 234 381 28 769 1.4 1 209 560 29 206 1.4 1 30 176 30 886 1.4 1 210 676 31 648 1.4 1 207 441 32 1277 1.4 1 201 1076 33 1220 1.4 1 293 927 34 671 1.4 1 105 566 35 1226 1.4 1 241 985 36 768 1.4 1 80 688 37 785 1.4 1 190 595 38 724 1.4 1 117 607 39 707 1.4 1 120 587 40 902 1.4 1 90 812 41 4359 1.4 1 94 4265 42 1516 1.4 1 173 1343 43 854 1.4 1 132 722 44 915 1.4 1 121 794 45 1313 1.4 1 233 1080 46 838 1.4 1 124 714 47 838 1.4 1 94 744 48 1651 1.4 1 228 1423 49 1057 1.4 1 112 945 50 712 1.4 1 77 635 51 1428 1.4 1 205 1223 52 2002 1.4 1 212 1790 53 1586 1.4 1 150 1436 54 1311 1.4 1 147 1164 55 1327 1.4 1 154 1173 56 969 1.4 1 93 876 57 1190 1.4 1 128 1062 58 1237 1.4 1 155 1082 59 1070 1.4 1 128 942 60 815 1.4 1 111 704 61 820 1.4 1 143 677 62 749 1.4 1 185 564 63 811 1.4 1 221 590 64 990 1.4 1 248 742 65 976 1.4 1 173 803 66 1299 1.4 1 247 1052 67 1350 1.4 1 179 1171 68 1439 1.4 1 233 1206 69 1613 1.4 1 221 1392 70 1557 1.4 1 241 1316 71 1942 1.4 1 428 1514 72 1956 1.4 1 395 1561 73 2266 1.4 1 575 1691 74 1864 1.4 1 357 1507 75 2273 1.4 1 322 1951 76 2769 1.4 1 298 2471 77 1670 1.4 1 166 1504 78 1458 1.4 1 161 1297 79 1411 1.4 1 137 1274 80 1263 1.4 1 116 1147 81 1144 1.4 1 129 1015 82 1306 1.4 1 129 1177 83 976 1.4 1 96 880 84 960 1.4 1 87 873 85 897 1.4 1 82 815 86 1018 1.4 1 103 915 87 995 1.4 1 111 884 88 937 1.4 1 100 837 89 707 1.4 1 65 642 90 775 1.4 1 71 704 91 794 1.4 1 50 744 92 758 1.4 1 54 704 93 743 1.4 1 61 682 94 735 1.4 1 56 679 95 732 1.4 1 54 678 96 673 1.4 1 58 615 97 670 1.4 1 107 563 98 838 1.4 1 129 709 99 824 1.4 1 85 739 100 1193 1.4 1 175 1018 101 670 1.4 1 84 586 102 547 1.4 1 59 488 103 289 1.4 1 30 259 104 396 1.4 1 45 351 105 257 1.4 1 40 217 106 348 1.4 1 64 284 107 444 1.4 1 74 370 108 483 1.4 1 73 410 109 539 1.4 1 87 452 110 324 1.4 1 53 271 111 111 1.4 1 24 87 112 101 1.4 1 31 70 113 99 1.4 1 47 52 114 325 1.4 1 82 243 115 99 1.4 1 74 25 116 259 1.4 1 88 171 117 70 1.4 1 56 14 118 62 1.4 1 52 10 119 49 1.4 1 43 6 120 47 1.4 1 39 8 121 64 1.4 1 59 5 122 52 1.4 1 49 3 123 45 1.4 1 44 1 124 84 1.4 1 77 7 125 112 1.4 1 101 11 126 222 1.4 1 204 18 127 299 1.4 1 292 7 128 547 1.4 1 534 13 129 886 1.4 1 853 33 130 748 1.4 1 720 28 131 928 1.4 1 895 33 132 948 1.4 1 909 39 133 1305 1.4 1 1227 78 134 2133 1.4 1 2026 107 135 6243 1.4 1 5938 305 136 16300 1.4 1 15697 603 137 1088516 1.4 1 1067407 21109 138 34314336 1.4 1 33779595 534741 139 39 1.4 1 28 11 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000222_val_2.fq.gz ============================================= 93300644 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1526869 (1.6%) 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: 93300644 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 36242061 (38.84%)