SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040874_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 1 sequences will be trimmed by 3 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 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/tmp/8ca7969c-d1de-11eb-8a1c-f8f21e2f3ee9/trimmed/RRBS20A040874_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 874.14 s (24 us/read; 2.54 M reads/minute). === Summary === Total reads processed: 37,064,926 Reads with adapters: 13,155,800 (35.5%) Reads written (passing filters): 37,064,926 (100.0%) Total basepairs processed: 2,817,259,499 bp Total written (filtered): 2,747,465,006 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13155800 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.1% C: 3.5% G: 23.9% T: 41.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9239142 9266231.5 0 9239142 2 2514879 2316557.9 0 2514879 3 658097 579139.5 0 658097 4 207018 144784.9 0 207018 5 4120 36196.2 0 4120 6 2294 9049.1 0 2294 7 2416 2262.3 0 2416 8 2237 565.6 0 2237 9 3693 141.4 0 3459 234 10 2257 35.3 1 1117 1140 11 2879 8.8 1 409 2470 12 634 2.2 1 120 514 13 794 0.6 1 135 659 14 2464 0.6 1 412 2052 15 1474 0.6 1 240 1234 16 5910 0.6 1 984 4926 17 6312 0.6 1 1140 5172 18 1295 0.6 1 268 1027 19 91 0.6 1 11 80 20 1074 0.6 1 197 877 21 126 0.6 1 11 115 22 130 0.6 1 22 108 23 1390 0.6 1 236 1154 24 5313 0.6 1 870 4443 25 2050 0.6 1 389 1661 26 534 0.6 1 81 453 27 1633 0.6 1 230 1403 28 3155 0.6 1 591 2564 29 3703 0.6 1 642 3061 30 542 0.6 1 105 437 31 138 0.6 1 22 116 32 1282 0.6 1 222 1060 33 4572 0.6 1 774 3798 34 4045 0.6 1 769 3276 35 419 0.6 1 60 359 36 2909 0.6 1 519 2390 37 432 0.6 1 55 377 38 7421 0.6 1 1365 6056 39 4161 0.6 1 773 3388 40 763 0.6 1 118 645 41 6528 0.6 1 1199 5329 42 595 0.6 1 89 506 43 10838 0.6 1 2157 8681 44 1932 0.6 1 362 1570 45 3583 0.6 1 731 2852 46 1060 0.6 1 174 886 47 2755 0.6 1 498 2257 48 5830 0.6 1 1157 4673 49 1039 0.6 1 205 834 50 3526 0.6 1 668 2858 51 2082 0.6 1 448 1634 52 888 0.6 1 153 735 53 2214 0.6 1 406 1808 54 6509 0.6 1 1442 5067 55 2697 0.6 1 615 2082 56 3172 0.6 1 667 2505 57 2718 0.6 1 610 2108 58 2604 0.6 1 571 2033 59 2037 0.6 1 506 1531 60 1982 0.6 1 405 1577 61 3691 0.6 1 827 2864 62 7180 0.6 1 1929 5251 63 1526 0.6 1 366 1160 64 181 0.6 1 36 145 65 175 0.6 1 25 150 66 807 0.6 1 177 630 67 1174 0.6 1 237 937 68 5125 0.6 1 1152 3973 69 6236 0.6 1 1297 4939 70 10963 0.6 1 2290 8673 71 3461 0.6 1 610 2851 72 1171 0.6 1 176 995 73 492 0.6 1 73 419 74 1225 0.6 1 211 1014 75 1457 0.6 1 239 1218 76 2211 0.6 1 235 1976 77 2888 0.6 1 469 2419 78 2151 0.6 1 278 1873 79 1756 0.6 1 206 1550 80 2003 0.6 1 272 1731 81 1509 0.6 1 196 1313 82 2917 0.6 1 472 2445 83 2805 0.6 1 420 2385 84 1949 0.6 1 205 1744 85 2487 0.6 1 349 2138 86 2322 0.6 1 319 2003 87 1708 0.6 1 170 1538 88 1953 0.6 1 289 1664 89 1643 0.6 1 187 1456 90 1870 0.6 1 253 1617 91 1525 0.6 1 165 1360 92 1441 0.6 1 162 1279 93 2227 0.6 1 404 1823 94 2602 0.6 1 366 2236 95 1777 0.6 1 323 1454 96 1468 0.6 1 298 1170 97 2199 0.6 1 459 1740 98 1853 0.6 1 467 1386 99 833 0.6 1 168 665 100 954 0.6 1 179 775 101 907 0.6 1 173 734 102 1264 0.6 1 280 984 103 715 0.6 1 109 606 104 464 0.6 1 95 369 105 420 0.6 1 81 339 106 274 0.6 1 76 198 107 222 0.6 1 36 186 108 141 0.6 1 28 113 109 117 0.6 1 27 90 110 98 0.6 1 17 81 111 60 0.6 1 15 45 112 34 0.6 1 11 23 113 2 0.6 1 1 1 114 5 0.6 1 2 3 115 1 0.6 1 0 1 116 6 0.6 1 1 5 118 2 0.6 1 1 1 121 3 0.6 1 3 122 2 0.6 1 2 124 3 0.6 1 3 126 5 0.6 1 4 1 127 3 0.6 1 3 128 3 0.6 1 3 129 5 0.6 1 4 1 130 7 0.6 1 6 1 131 15 0.6 1 13 2 132 19 0.6 1 14 5 133 31 0.6 1 30 1 134 42 0.6 1 37 5 135 93 0.6 1 80 13 136 155 0.6 1 137 18 137 7646 0.6 1 7448 198 138 280719 0.6 1 274719 6000 140 14 0.6 1 3 11 141 1 0.6 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040874_val_1.fq.gz ============================================= 37064926 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 996060 (2.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 13155795 (35.5%)