SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040773_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 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/7739f4e4-d1de-11eb-badf-6c92bfc12bba/trimmed/RRBS20A040773_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1912.59 s (17 us/read; 3.50 M reads/minute). === Summary === Total reads processed: 111,598,811 Reads with adapters: 106,474,533 (95.4%) Reads written (passing filters): 111,598,811 (100.0%) Total basepairs processed: 14,877,168,133 bp Total written (filtered): 739,553,285 bp (5.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 106474533 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.4% C: 2.4% G: 96.9% T: 0.1% none/other: 0.1% WARNING: The adapter is preceded by "G" 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 2954095 27899702.8 0 2954095 2 56063 6974925.7 0 56063 3 5318 1743731.4 0 5318 4 5522 435932.9 0 5522 5 1415 108983.2 0 1415 6 220 27245.8 0 220 7 87 6811.5 0 87 8 382 1702.9 0 382 9 426 425.7 0 415 11 10 741 106.4 1 118 623 11 148 26.6 1 25 123 12 59 6.7 1 6 53 13 25 1.7 1 1 24 14 99 1.7 1 11 88 15 160 1.7 1 25 135 16 230 1.7 1 20 210 17 106 1.7 1 15 91 18 211 1.7 1 26 185 19 268 1.7 1 113 155 20 1778 1.7 1 1051 727 21 3662 1.7 1 3106 556 22 85 1.7 1 15 70 23 142 1.7 1 22 120 24 241 1.7 1 35 206 25 351 1.7 1 90 261 26 423 1.7 1 98 325 27 487 1.7 1 156 331 28 235 1.7 1 88 147 29 27 1.7 1 6 21 30 58 1.7 1 12 46 31 302 1.7 1 49 253 32 207 1.7 1 24 183 33 543 1.7 1 82 461 34 389 1.7 1 144 245 35 331 1.7 1 111 220 36 95 1.7 1 23 72 37 472 1.7 1 92 380 38 287 1.7 1 107 180 39 374 1.7 1 109 265 40 541 1.7 1 145 396 41 3713 1.7 1 56 3657 42 155 1.7 1 34 121 43 260 1.7 1 48 212 44 209 1.7 1 42 167 45 208 1.7 1 44 164 46 361 1.7 1 40 321 47 205 1.7 1 43 162 48 139 1.7 1 30 109 49 240 1.7 1 54 186 50 298 1.7 1 78 220 51 260 1.7 1 99 161 52 431 1.7 1 120 311 53 51 1.7 1 15 36 54 391 1.7 1 82 309 55 890 1.7 1 535 355 56 117 1.7 1 40 77 57 650 1.7 1 325 325 58 1605 1.7 1 899 706 59 2355 1.7 1 1466 889 60 7600 1.7 1 5375 2225 61 23312 1.7 1 19732 3580 62 65892 1.7 1 60976 4916 63 269102 1.7 1 264716 4386 64 933047 1.7 1 927443 5604 65 298791 1.7 1 295352 3439 66 36849 1.7 1 34251 2598 67 12057 1.7 1 10863 1194 68 7052 1.7 1 6042 1010 69 6086 1.7 1 5362 724 70 3156 1.7 1 2719 437 71 3377 1.7 1 2857 520 72 2563 1.7 1 2041 522 73 2214 1.7 1 1814 400 74 2460 1.7 1 2034 426 75 1903 1.7 1 1580 323 76 1303 1.7 1 1080 223 77 1135 1.7 1 919 216 78 987 1.7 1 771 216 79 1100 1.7 1 877 223 80 944 1.7 1 783 161 81 1157 1.7 1 887 270 82 1019 1.7 1 868 151 83 963 1.7 1 778 185 84 1030 1.7 1 774 256 85 1250 1.7 1 1082 168 86 1682 1.7 1 1465 217 87 1761 1.7 1 1557 204 88 2215 1.7 1 2028 187 89 2019 1.7 1 1813 206 90 1551 1.7 1 1320 231 91 1527 1.7 1 1366 161 92 2955 1.7 1 2810 145 93 1086 1.7 1 896 190 94 4014 1.7 1 3856 158 95 1185 1.7 1 1032 153 96 1126 1.7 1 976 150 97 1325 1.7 1 1172 153 98 1349 1.7 1 1207 142 99 1329 1.7 1 1179 150 100 1464 1.7 1 1277 187 101 1207 1.7 1 1059 148 102 1703 1.7 1 1529 174 103 1825 1.7 1 1641 184 104 2575 1.7 1 2405 170 105 3192 1.7 1 2986 206 106 5234 1.7 1 4974 260 107 4898 1.7 1 4578 320 108 4688 1.7 1 4371 317 109 6251 1.7 1 5952 299 110 4604 1.7 1 4319 285 111 6167 1.7 1 5910 257 112 7280 1.7 1 6945 335 113 11289 1.7 1 10936 353 114 12553 1.7 1 12152 401 115 15826 1.7 1 15418 408 116 16193 1.7 1 15821 372 117 13598 1.7 1 13221 377 118 10287 1.7 1 9961 326 119 9117 1.7 1 8746 371 120 11090 1.7 1 10661 429 121 13579 1.7 1 13081 498 122 13828 1.7 1 13173 655 123 17826 1.7 1 16979 847 124 18168 1.7 1 17323 845 125 34213 1.7 1 33216 997 126 45887 1.7 1 44523 1364 127 64993 1.7 1 63528 1465 128 113161 1.7 1 111525 1636 129 49488 1.7 1 48110 1378 130 45489 1.7 1 44247 1242 131 37796 1.7 1 36521 1275 132 43308 1.7 1 41864 1444 133 64895 1.7 1 62730 2165 134 86007 1.7 1 83208 2799 135 255738 1.7 1 249311 6427 136 360631 1.7 1 351216 9415 137 2799866 1.7 1 2744811 55055 138 97171899 1.7 1 96445689 726210 139 326104 1.7 1 6 326098 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/merged_raw_data/RRBS20A040773_val_2.fq.gz ============================================= 111598811 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1072240 (1.0%) 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: 111598811 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 103766398 (92.98%)