SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2//RRBS21T000220_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/429273a0-e7c4-11eb-ad2f-6c92bfc12dd0/trimmed/RRBS21T000220_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1478.43 s (17 us/read; 3.58 M reads/minute). === Summary === Total reads processed: 88,179,496 Reads with adapters: 45,543,314 (51.6%) Reads written (passing filters): 88,179,496 (100.0%) Total basepairs processed: 7,174,751,291 bp Total written (filtered): 6,888,367,842 bp (96.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 45543314 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 4.5% C: 89.8% G: 4.5% T: 1.2% none/other: 0.0% WARNING: The adapter is preceded by "C" extremely often. The provided adapter sequence could be incomplete at its 3' end. Overview of removed sequences length count expect max.err error counts 1 43479615 22044874.0 0 43479615 2 118825 5511218.5 0 118825 3 13988 1377804.6 0 13988 4 7779 344451.2 0 7779 5 4255 86112.8 0 4255 6 4164 21528.2 0 4164 7 8505 5382.0 0 8505 8 2945 1345.5 0 2945 9 1563 336.4 0 1394 169 10 12555 84.1 1 3496 9059 11 432 21.0 1 50 382 12 8828 5.3 1 2279 6549 13 2910 1.3 1 325 2585 14 4397 1.3 1 438 3959 15 1232 1.3 1 122 1110 16 1832 1.3 1 188 1644 17 4601 1.3 1 408 4193 18 1250 1.3 1 131 1119 19 4935 1.3 1 423 4512 20 2366 1.3 1 222 2144 21 305 1.3 1 144 161 22 2051 1.3 1 185 1866 23 3496 1.3 1 302 3194 24 12964 1.3 1 1166 11798 25 2467 1.3 1 207 2260 26 2966 1.3 1 317 2649 27 916 1.3 1 87 829 28 3937 1.3 1 441 3496 29 582 1.3 1 46 536 30 4207 1.3 1 360 3847 31 2001 1.3 1 157 1844 32 5397 1.3 1 500 4897 33 3870 1.3 1 373 3497 34 1501 1.3 1 132 1369 35 4260 1.3 1 407 3853 36 3392 1.3 1 256 3136 37 2168 1.3 1 177 1991 38 2151 1.3 1 196 1955 39 2069 1.3 1 174 1895 40 1576 1.3 1 153 1423 41 3056 1.3 1 246 2810 42 2734 1.3 1 255 2479 43 2194 1.3 1 190 2004 44 2184 1.3 1 229 1955 45 3316 1.3 1 319 2997 46 2147 1.3 1 216 1931 47 2235 1.3 1 254 1981 48 4000 1.3 1 414 3586 49 3022 1.3 1 317 2705 50 1499 1.3 1 139 1360 51 2611 1.3 1 226 2385 52 4140 1.3 1 396 3744 53 3468 1.3 1 347 3121 54 2964 1.3 1 312 2652 55 2714 1.3 1 282 2432 56 1845 1.3 1 203 1642 57 2338 1.3 1 230 2108 58 1886 1.3 1 182 1704 59 1488 1.3 1 162 1326 60 1121 1.3 1 108 1013 61 925 1.3 1 90 835 62 857 1.3 1 75 782 63 873 1.3 1 75 798 64 1053 1.3 1 107 946 65 1337 1.3 1 130 1207 66 2762 1.3 1 283 2479 67 1628 1.3 1 178 1450 68 1552 1.3 1 164 1388 69 1993 1.3 1 200 1793 70 1393 1.3 1 152 1241 71 1321 1.3 1 135 1186 72 1331 1.3 1 131 1200 73 1279 1.3 1 144 1135 74 973 1.3 1 111 862 75 1886 1.3 1 184 1702 76 11668 1.3 1 1816 9852 77 1848 1.3 1 167 1681 78 1079 1.3 1 139 940 79 1156 1.3 1 138 1018 80 942 1.3 1 91 851 81 914 1.3 1 80 834 82 886 1.3 1 89 797 83 880 1.3 1 99 781 84 720 1.3 1 70 650 85 915 1.3 1 102 813 86 792 1.3 1 87 705 87 595 1.3 1 69 526 88 600 1.3 1 65 535 89 526 1.3 1 42 484 90 515 1.3 1 48 467 91 355 1.3 1 34 321 92 355 1.3 1 52 303 93 500 1.3 1 56 444 94 357 1.3 1 30 327 95 274 1.3 1 29 245 96 266 1.3 1 26 240 97 190 1.3 1 22 168 98 230 1.3 1 21 209 99 215 1.3 1 23 192 100 198 1.3 1 23 175 101 157 1.3 1 16 141 102 157 1.3 1 13 144 103 136 1.3 1 18 118 104 113 1.3 1 12 101 105 108 1.3 1 11 97 106 99 1.3 1 8 91 107 57 1.3 1 9 48 108 154 1.3 1 25 129 109 241 1.3 1 36 205 110 77 1.3 1 8 69 111 20 1.3 1 4 16 112 6 1.3 1 0 6 113 6 1.3 1 3 3 114 39 1.3 1 8 31 115 6 1.3 1 3 3 116 28 1.3 1 8 20 117 3 1.3 1 2 1 118 2 1.3 1 2 119 3 1.3 1 0 3 121 1 1.3 1 1 122 8 1.3 1 8 123 5 1.3 1 1 4 124 1 1.3 1 1 125 7 1.3 1 5 2 126 5 1.3 1 5 127 5 1.3 1 5 128 29 1.3 1 28 1 129 32 1.3 1 32 130 15 1.3 1 13 2 131 20 1.3 1 19 1 132 25 1.3 1 22 3 133 32 1.3 1 31 1 134 63 1.3 1 61 2 135 148 1.3 1 140 8 136 429 1.3 1 417 12 137 52964 1.3 1 52268 696 138 1639759 1.3 1 1619173 20586 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2//RRBS21T000220_val_2.fq.gz ============================================= 88179496 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2140623 (2.4%) 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: 88179496 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1806738 (2.05%)