SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2/RRBS21T000221_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/test_analysis_2/tmp/428f7790-e7c4-11eb-a920-6c92bfc12ff2/trimmed/RRBS21T000221_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1283.92 s (15 us/read; 3.95 M reads/minute). === Summary === Total reads processed: 84,439,684 Reads with adapters: 38,072,481 (45.1%) Reads written (passing filters): 84,439,684 (100.0%) Total basepairs processed: 6,698,001,323 bp Total written (filtered): 5,777,212,331 bp (86.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 38072481 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.0% C: 17.2% G: 21.1% T: 29.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 23406074 21109921.0 0 23406074 2 5243066 5277480.2 0 5243066 3 1976315 1319370.1 0 1976315 4 560931 329842.5 0 560931 5 19839 82460.6 0 19839 6 10389 20615.2 0 10389 7 13237 5153.8 0 13237 8 7329 1288.4 0 7329 9 11985 322.1 0 11083 902 10 11160 80.5 1 5159 6001 11 9893 20.1 1 1867 8026 12 3535 5.0 1 764 2771 13 3608 1.3 1 705 2903 14 10295 1.3 1 2203 8092 15 5830 1.3 1 1191 4639 16 22046 1.3 1 3960 18086 17 21984 1.3 1 4168 17816 18 7947 1.3 1 1832 6115 19 425 1.3 1 39 386 20 4052 1.3 1 878 3174 21 620 1.3 1 52 568 22 1084 1.3 1 232 852 23 3945 1.3 1 767 3178 24 20864 1.3 1 4301 16563 25 8271 1.3 1 1774 6497 26 1769 1.3 1 298 1471 27 5528 1.3 1 1106 4422 28 12878 1.3 1 2621 10257 29 15249 1.3 1 2913 12336 30 3906 1.3 1 780 3126 31 553 1.3 1 80 473 32 5173 1.3 1 1018 4155 33 10474 1.3 1 1973 8501 34 12728 1.3 1 2412 10316 35 26689 1.3 1 5411 21278 36 5789 1.3 1 1177 4612 37 2211 1.3 1 394 1817 38 14792 1.3 1 2933 11859 39 13348 1.3 1 2913 10435 40 2112 1.3 1 301 1811 41 34798 1.3 1 7189 27609 42 4973 1.3 1 955 4018 43 33177 1.3 1 6918 26259 44 6066 1.3 1 1196 4870 45 9018 1.3 1 1778 7240 46 2426 1.3 1 446 1980 47 4336 1.3 1 649 3687 48 21431 1.3 1 4659 16772 49 1954 1.3 1 347 1607 50 8965 1.3 1 1757 7208 51 3973 1.3 1 832 3141 52 2212 1.3 1 394 1818 53 5868 1.3 1 1163 4705 54 16202 1.3 1 3389 12813 55 17042 1.3 1 3962 13080 56 7310 1.3 1 1412 5898 57 7864 1.3 1 1755 6109 58 3745 1.3 1 703 3042 59 3049 1.3 1 600 2449 60 4386 1.3 1 823 3563 61 5405 1.3 1 853 4552 62 39363 1.3 1 9476 29887 63 5566 1.3 1 1104 4462 64 709 1.3 1 135 574 65 392 1.3 1 66 326 66 6214 1.3 1 1442 4772 67 2169 1.3 1 326 1843 68 9198 1.3 1 2079 7119 69 10705 1.3 1 2280 8425 70 16762 1.3 1 3774 12988 71 3862 1.3 1 729 3133 72 1477 1.3 1 267 1210 73 3886 1.3 1 663 3223 74 5207 1.3 1 1173 4034 75 5286 1.3 1 1227 4059 76 6062 1.3 1 1297 4765 77 7099 1.3 1 1701 5398 78 7754 1.3 1 1523 6231 79 6528 1.3 1 1351 5177 80 5693 1.3 1 1216 4477 81 5783 1.3 1 1114 4669 82 5877 1.3 1 1066 4811 83 6222 1.3 1 1235 4987 84 5509 1.3 1 1105 4404 85 7241 1.3 1 1514 5727 86 5391 1.3 1 1193 4198 87 4967 1.3 1 1037 3930 88 4146 1.3 1 919 3227 89 4042 1.3 1 813 3229 90 3759 1.3 1 824 2935 91 4370 1.3 1 996 3374 92 3653 1.3 1 683 2970 93 4372 1.3 1 852 3520 94 7790 1.3 1 1673 6117 95 3834 1.3 1 815 3019 96 2771 1.3 1 556 2215 97 4158 1.3 1 966 3192 98 3184 1.3 1 780 2404 99 2116 1.3 1 466 1650 100 2033 1.3 1 482 1551 101 1703 1.3 1 382 1321 102 2006 1.3 1 453 1553 103 1677 1.3 1 374 1303 104 1159 1.3 1 265 894 105 1103 1.3 1 198 905 106 832 1.3 1 203 629 107 608 1.3 1 145 463 108 458 1.3 1 97 361 109 429 1.3 1 106 323 110 707 1.3 1 172 535 111 367 1.3 1 81 286 112 186 1.3 1 44 142 113 7 1.3 1 1 6 114 37 1.3 1 7 30 115 8 1.3 1 4 4 116 6 1.3 1 5 1 117 5 1.3 1 3 2 118 15 1.3 1 7 8 119 7 1.3 1 5 2 120 5 1.3 1 2 3 121 13 1.3 1 7 6 122 6 1.3 1 6 123 8 1.3 1 8 124 13 1.3 1 11 2 125 16 1.3 1 12 4 126 16 1.3 1 10 6 127 18 1.3 1 12 6 128 24 1.3 1 15 9 129 24 1.3 1 21 3 130 58 1.3 1 38 20 131 81 1.3 1 63 18 132 142 1.3 1 118 24 133 273 1.3 1 217 56 134 709 1.3 1 604 105 135 781 1.3 1 659 122 136 1596 1.3 1 1357 239 137 37533 1.3 1 35536 1997 138 6062381 1.3 1 5886042 176339 139 36 1.3 1 16 20 140 144 1.3 1 13 131 141 11 1.3 1 9 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2/RRBS21T000221_val_1.fq.gz ============================================= 84439684 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2136410 (2.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 38072457 (45.1%)