SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2//RRBS21T000219_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/test_analysis_2/tmp/4287720c-e7c4-11eb-b332-6c92bfc12f0e/trimmed/RRBS21T000219_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1148.48 s (19 us/read; 3.13 M reads/minute). === Summary === Total reads processed: 59,821,506 Reads with adapters: 31,094,681 (52.0%) Reads written (passing filters): 59,821,506 (100.0%) Total basepairs processed: 5,656,572,244 bp Total written (filtered): 5,224,182,211 bp (92.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 31094681 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 10.2% C: 76.8% G: 0.4% T: 12.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 27877206 14955376.5 0 27877206 2 118439 3738844.1 0 118439 3 22119 934711.0 0 22119 4 16487 233677.8 0 16487 5 4057 58419.4 0 4057 6 3876 14604.9 0 3876 7 8043 3651.2 0 8043 8 2788 912.8 0 2788 9 1254 228.2 0 1081 173 10 12219 57.1 1 3158 9061 11 386 14.3 1 60 326 12 9180 3.6 1 2214 6966 13 2314 0.9 1 277 2037 14 4396 0.9 1 496 3900 15 1256 0.9 1 137 1119 16 1373 0.9 1 171 1202 17 4174 0.9 1 462 3712 18 1260 0.9 1 125 1135 19 4582 0.9 1 539 4043 20 2119 0.9 1 282 1837 21 219 0.9 1 91 128 22 2157 0.9 1 231 1926 23 3539 0.9 1 391 3148 24 11874 0.9 1 1339 10535 25 2210 0.9 1 240 1970 26 2101 0.9 1 235 1866 27 659 0.9 1 87 572 28 3075 0.9 1 348 2727 29 556 0.9 1 67 489 30 3511 0.9 1 421 3090 31 1591 0.9 1 191 1400 32 4188 0.9 1 485 3703 33 3002 0.9 1 308 2694 34 1284 0.9 1 150 1134 35 3128 0.9 1 400 2728 36 2348 0.9 1 277 2071 37 1717 0.9 1 229 1488 38 1640 0.9 1 183 1457 39 1358 0.9 1 140 1218 40 1349 0.9 1 135 1214 41 2085 0.9 1 197 1888 42 2131 0.9 1 177 1954 43 1490 0.9 1 148 1342 44 1675 0.9 1 143 1532 45 2101 0.9 1 200 1901 46 1498 0.9 1 126 1372 47 1324 0.9 1 109 1215 48 2371 0.9 1 258 2113 49 1752 0.9 1 181 1571 50 1023 0.9 1 94 929 51 1814 0.9 1 162 1652 52 2514 0.9 1 242 2272 53 2015 0.9 1 172 1843 54 1509 0.9 1 141 1368 55 1537 0.9 1 132 1405 56 1263 0.9 1 112 1151 57 1570 0.9 1 147 1423 58 1276 0.9 1 130 1146 59 944 0.9 1 88 856 60 734 0.9 1 70 664 61 533 0.9 1 42 491 62 545 0.9 1 67 478 63 602 0.9 1 77 525 64 729 0.9 1 90 639 65 933 0.9 1 88 845 66 1348 0.9 1 142 1206 67 1046 0.9 1 108 938 68 926 0.9 1 84 842 69 908 0.9 1 78 830 70 810 0.9 1 72 738 71 825 0.9 1 88 737 72 902 0.9 1 91 811 73 870 0.9 1 104 766 74 754 0.9 1 71 683 75 917 0.9 1 86 831 76 1655 0.9 1 185 1470 77 790 0.9 1 72 718 78 686 0.9 1 56 630 79 678 0.9 1 57 621 80 701 0.9 1 64 637 81 644 0.9 1 38 606 82 607 0.9 1 52 555 83 632 0.9 1 56 576 84 567 0.9 1 52 515 85 777 0.9 1 90 687 86 766 0.9 1 94 672 87 545 0.9 1 49 496 88 403 0.9 1 36 367 89 490 0.9 1 45 445 90 414 0.9 1 35 379 91 406 0.9 1 35 371 92 323 0.9 1 29 294 93 379 0.9 1 35 344 94 337 0.9 1 31 306 95 293 0.9 1 28 265 96 247 0.9 1 13 234 97 293 0.9 1 33 260 98 242 0.9 1 29 213 99 245 0.9 1 19 226 100 172 0.9 1 24 148 101 138 0.9 1 10 128 102 175 0.9 1 16 159 103 147 0.9 1 16 131 104 144 0.9 1 24 120 105 101 0.9 1 13 88 106 96 0.9 1 14 82 107 66 0.9 1 6 60 108 77 0.9 1 14 63 109 130 0.9 1 25 105 110 58 0.9 1 8 50 111 19 0.9 1 5 14 112 10 0.9 1 2 8 113 13 0.9 1 5 8 114 54 0.9 1 13 41 115 14 0.9 1 6 8 116 132 0.9 1 32 100 117 10 0.9 1 3 7 118 9 0.9 1 6 3 119 2 0.9 1 2 120 4 0.9 1 4 121 1 0.9 1 1 122 4 0.9 1 4 123 5 0.9 1 5 124 5 0.9 1 4 1 125 9 0.9 1 9 126 21 0.9 1 21 127 31 0.9 1 28 3 128 56 0.9 1 53 3 129 65 0.9 1 64 1 130 32 0.9 1 30 2 131 53 0.9 1 52 1 132 58 0.9 1 51 7 133 71 0.9 1 65 6 134 112 0.9 1 106 6 135 361 0.9 1 338 23 136 813 0.9 1 783 30 137 65213 0.9 1 64051 1162 138 2818770 0.9 1 2775938 42832 139 2 0.9 1 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2//RRBS21T000219_val_2.fq.gz ============================================= 59821506 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2081721 (3.5%) 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: 59821506 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2962401 (4.95%)