SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000238_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/f977676c-1990-11ec-a78a-6c92bfc12eb4/trimmed/RRBS21T000238_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 784.36 s (21 us/read; 2.91 M reads/minute). === Summary === Total reads processed: 37,986,056 Reads with adapters: 14,064,684 (37.0%) Reads written (passing filters): 37,986,056 (100.0%) Total basepairs processed: 3,118,863,695 bp Total written (filtered): 2,902,531,955 bp (93.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14064684 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.9% C: 1.0% G: 23.9% T: 48.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9153851 9496514.0 0 9153851 2 2319327 2374128.5 0 2319327 3 770501 593532.1 0 770501 4 200172 148383.0 0 200172 5 6908 37095.8 0 6908 6 4073 9273.9 0 4073 7 4313 2318.5 0 4313 8 3132 579.6 0 3132 9 4936 144.9 0 4568 368 10 5833 36.2 1 2413 3420 11 4341 9.1 1 406 3935 12 1430 2.3 1 178 1252 13 1189 0.6 1 124 1065 14 3884 0.6 1 392 3492 15 1927 0.6 1 241 1686 16 10386 0.6 1 924 9462 17 8123 0.6 1 916 7207 18 3834 0.6 1 1293 2541 19 194 0.6 1 22 172 20 1306 0.6 1 147 1159 21 119 0.6 1 11 108 22 237 0.6 1 60 177 23 1425 0.6 1 138 1287 24 6247 0.6 1 655 5592 25 2138 0.6 1 245 1893 26 677 0.6 1 80 597 27 1792 0.6 1 220 1572 28 3395 0.6 1 380 3015 29 5380 0.6 1 577 4803 30 929 0.6 1 117 812 31 193 0.6 1 7 186 32 1474 0.6 1 157 1317 33 4530 0.6 1 508 4022 34 3345 0.6 1 345 3000 35 7614 0.6 1 879 6735 36 1357 0.6 1 140 1217 37 10810 0.6 1 1052 9758 38 5628 0.6 1 727 4901 39 6150 0.6 1 718 5432 40 9140 0.6 1 1044 8096 41 2581 0.6 1 328 2253 42 1461 0.6 1 203 1258 43 2750 0.6 1 321 2429 44 2223 0.6 1 289 1934 45 3162 0.6 1 391 2771 46 921 0.6 1 104 817 47 1550 0.6 1 169 1381 48 6857 0.6 1 851 6006 49 649 0.6 1 66 583 50 2556 0.6 1 245 2311 51 1173 0.6 1 127 1046 52 798 0.6 1 95 703 53 1622 0.6 1 180 1442 54 3482 0.6 1 372 3110 55 4194 0.6 1 569 3625 56 1882 0.6 1 241 1641 57 1988 0.6 1 235 1753 58 1542 0.6 1 205 1337 59 889 0.6 1 109 780 60 1336 0.6 1 148 1188 61 1921 0.6 1 216 1705 62 11856 0.6 1 1927 9929 63 1543 0.6 1 216 1327 64 338 0.6 1 35 303 65 209 0.6 1 24 185 66 3006 0.6 1 581 2425 67 854 0.6 1 92 762 68 3562 0.6 1 443 3119 69 4465 0.6 1 532 3933 70 5668 0.6 1 654 5014 71 1405 0.6 1 139 1266 72 712 0.6 1 82 630 73 819 0.6 1 85 734 74 1444 0.6 1 144 1300 75 1671 0.6 1 160 1511 76 1641 0.6 1 121 1520 77 2160 0.6 1 206 1954 78 1681 0.6 1 146 1535 79 1423 0.6 1 110 1313 80 1431 0.6 1 128 1303 81 939 0.6 1 60 879 82 1349 0.6 1 94 1255 83 1568 0.6 1 154 1414 84 1291 0.6 1 83 1208 85 2048 0.6 1 197 1851 86 1286 0.6 1 89 1197 87 1190 0.6 1 100 1090 88 1071 0.6 1 98 973 89 1013 0.6 1 71 942 90 1000 0.6 1 70 930 91 1048 0.6 1 78 970 92 919 0.6 1 82 837 93 1175 0.6 1 96 1079 94 1126 0.6 1 93 1033 95 849 0.6 1 64 785 96 803 0.6 1 76 727 97 1008 0.6 1 105 903 98 825 0.6 1 73 752 99 570 0.6 1 56 514 100 585 0.6 1 61 524 101 447 0.6 1 46 401 102 636 0.6 1 77 559 103 456 0.6 1 44 412 104 283 0.6 1 21 262 105 286 0.6 1 28 258 106 182 0.6 1 15 167 107 166 0.6 1 25 141 108 104 0.6 1 9 95 109 100 0.6 1 13 87 110 138 0.6 1 17 121 111 48 0.6 1 6 42 112 23 0.6 1 2 21 113 2 0.6 1 0 2 114 9 0.6 1 2 7 115 2 0.6 1 2 116 1 0.6 1 0 1 117 3 0.6 1 1 2 118 3 0.6 1 2 1 119 5 0.6 1 4 1 120 6 0.6 1 3 3 121 5 0.6 1 3 2 122 5 0.6 1 3 2 123 8 0.6 1 5 3 124 8 0.6 1 4 4 125 10 0.6 1 8 2 126 8 0.6 1 6 2 127 19 0.6 1 12 7 128 16 0.6 1 10 6 129 17 0.6 1 14 3 130 33 0.6 1 21 12 131 48 0.6 1 39 9 132 69 0.6 1 52 17 133 166 0.6 1 123 43 134 405 0.6 1 333 72 135 461 0.6 1 387 74 136 1172 0.6 1 952 220 137 51238 0.6 1 48952 2286 138 1312760 0.6 1 1263751 49009 139 4 0.6 1 3 1 140 3 0.6 1 1 2 141 1 0.6 1 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000238_val_1.fq.gz ============================================= 37986056 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1532751 (4.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 14064682 (37.0%)