SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041585_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) All Read 1 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases 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/cup/BS_workflow/20201110/tmp/caf4347a-5581-11eb-a01e-6c92bfc13316/trimmed/RRBS20A041585_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 649.72 s (24 us/read; 2.54 M reads/minute). === Summary === Total reads processed: 27,551,916 Reads with adapters: 11,744,473 (42.6%) Reads written (passing filters): 27,551,916 (100.0%) Total basepairs processed: 2,809,936,981 bp Total written (filtered): 2,712,551,484 bp (96.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11744473 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 0.8% G: 23.8% T: 46.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8200576 6887979.0 0 8200576 2 2203814 1721994.8 0 2203814 3 507216 430498.7 0 507216 4 118292 107624.7 0 118292 5 8381 26906.2 0 8381 6 3306 6726.5 0 3306 7 2317 1681.6 0 2317 8 2297 420.4 0 2297 9 3815 105.1 0 3557 258 10 2920 26.3 1 1261 1659 11 3409 6.6 1 351 3058 12 756 1.6 1 105 651 13 1214 0.4 1 168 1046 14 2376 0.4 1 267 2109 15 1712 0.4 1 194 1518 16 6100 0.4 1 801 5299 17 6830 0.4 1 1592 5238 18 6350 0.4 1 4646 1704 19 154 0.4 1 34 120 20 1358 0.4 1 216 1142 21 74 0.4 1 7 67 22 139 0.4 1 31 108 23 1341 0.4 1 145 1196 24 4468 0.4 1 593 3875 25 1648 0.4 1 214 1434 26 451 0.4 1 50 401 27 1458 0.4 1 186 1272 28 3477 0.4 1 675 2802 29 3924 0.4 1 524 3400 30 431 0.4 1 69 362 31 115 0.4 1 15 100 32 1049 0.4 1 145 904 33 2161 0.4 1 282 1879 34 1968 0.4 1 239 1729 35 4267 0.4 1 666 3601 36 1697 0.4 1 230 1467 37 472 0.4 1 79 393 38 3868 0.4 1 853 3015 39 607 0.4 1 83 524 40 4833 0.4 1 593 4240 41 2019 0.4 1 292 1727 42 2112 0.4 1 303 1809 43 3848 0.4 1 572 3276 44 945 0.4 1 137 808 45 2273 0.4 1 300 1973 46 711 0.4 1 91 620 47 1492 0.4 1 196 1296 48 3383 0.4 1 464 2919 49 794 0.4 1 94 700 50 2028 0.4 1 335 1693 51 732 0.4 1 91 641 52 464 0.4 1 62 402 53 1107 0.4 1 136 971 54 4037 0.4 1 577 3460 55 1280 0.4 1 211 1069 56 1232 0.4 1 168 1064 57 1441 0.4 1 224 1217 58 821 0.4 1 123 698 59 700 0.4 1 111 589 60 895 0.4 1 122 773 61 1188 0.4 1 160 1028 62 2429 0.4 1 400 2029 63 817 0.4 1 133 684 64 100 0.4 1 12 88 65 64 0.4 1 10 54 66 307 0.4 1 43 264 67 448 0.4 1 62 386 68 1649 0.4 1 252 1397 69 1678 0.4 1 234 1444 70 3259 0.4 1 429 2830 71 1075 0.4 1 137 938 72 295 0.4 1 27 268 73 203 0.4 1 16 187 74 221 0.4 1 31 190 75 450 0.4 1 72 378 76 702 0.4 1 111 591 77 741 0.4 1 98 643 78 775 0.4 1 103 672 79 775 0.4 1 106 669 80 1005 0.4 1 130 875 81 830 0.4 1 141 689 82 937 0.4 1 129 808 83 1093 0.4 1 165 928 84 755 0.4 1 100 655 85 867 0.4 1 126 741 86 825 0.4 1 95 730 87 607 0.4 1 99 508 88 519 0.4 1 60 459 89 520 0.4 1 72 448 90 466 0.4 1 57 409 91 406 0.4 1 52 354 92 444 0.4 1 64 380 93 1515 0.4 1 208 1307 94 3381 0.4 1 448 2933 95 710 0.4 1 95 615 96 359 0.4 1 60 299 97 2399 0.4 1 297 2102 98 420 0.4 1 70 350 99 289 0.4 1 53 236 100 246 0.4 1 31 215 101 263 0.4 1 35 228 102 519 0.4 1 98 421 103 179 0.4 1 36 143 104 89 0.4 1 12 77 105 98 0.4 1 14 84 106 90 0.4 1 15 75 107 78 0.4 1 7 71 108 25 0.4 1 3 22 109 31 0.4 1 6 25 110 87 0.4 1 13 74 111 16 0.4 1 2 14 112 5 0.4 1 2 3 113 2 0.4 1 1 1 114 6 0.4 1 2 4 115 3 0.4 1 2 1 116 3 0.4 1 2 1 117 4 0.4 1 2 2 118 2 0.4 1 2 119 1 0.4 1 1 120 4 0.4 1 4 121 6 0.4 1 3 3 122 3 0.4 1 3 123 8 0.4 1 7 1 124 13 0.4 1 11 2 125 7 0.4 1 4 3 126 4 0.4 1 3 1 127 7 0.4 1 5 2 128 23 0.4 1 20 3 129 25 0.4 1 18 7 130 26 0.4 1 24 2 131 43 0.4 1 37 6 132 51 0.4 1 38 13 133 115 0.4 1 87 28 134 196 0.4 1 160 36 135 198 0.4 1 175 23 136 402 0.4 1 340 62 137 32374 0.4 1 31555 819 138 519736 0.4 1 508114 11622 139 1 0.4 1 0 1 140 6 0.4 1 2 4 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041585_val_1.fq.gz ============================================= 27551916 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 924520 (3.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 11744469 (42.6%)