SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040784_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/8c4d1e2e-d1de-11eb-8629-f8f21e2f3ee9/trimmed/RRBS20A040784_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 343.59 s (10 us/read; 6.00 M reads/minute). === Summary === Total reads processed: 34,341,869 Reads with adapters: 34,190,065 (99.6%) Reads written (passing filters): 34,341,869 (100.0%) Total basepairs processed: 4,894,018,869 bp Total written (filtered): 192,515,449 bp (3.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34190065 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 99.8% C: 0.0% G: 0.1% T: 0.1% none/other: 0.0% WARNING: The adapter is preceded by "A" 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 67517 8585467.2 0 67517 2 18094 2146366.8 0 18094 3 5758 536591.7 0 5758 4 1755 134147.9 0 1755 5 66 33537.0 0 66 6 28 8384.2 0 28 7 21 2096.1 0 21 8 24 524.0 0 24 9 26 131.0 0 22 4 10 17 32.8 1 10 7 11 10 8.2 1 1 9 12 13 2.0 1 7 6 13 15 0.5 1 9 6 14 7 0.5 1 0 7 15 13 0.5 1 5 8 16 47 0.5 1 19 28 17 214 0.5 1 50 164 18 952 0.5 1 587 365 19 47 0.5 1 8 39 20 8 0.5 1 3 5 21 14 0.5 1 5 9 22 28 0.5 1 15 13 23 14 0.5 1 6 8 24 16 0.5 1 7 9 25 7 0.5 1 3 4 26 20 0.5 1 7 13 27 196 0.5 1 135 61 28 648 0.5 1 436 212 29 355 0.5 1 75 280 30 91 0.5 1 8 83 31 29 0.5 1 17 12 32 48 0.5 1 32 16 33 38 0.5 1 15 23 34 19 0.5 1 3 16 35 88 0.5 1 20 68 36 267 0.5 1 53 214 37 3182 0.5 1 918 2264 38 10022 0.5 1 1643 8379 39 28 0.5 1 7 21 40 91 0.5 1 54 37 41 21 0.5 1 11 10 42 13 0.5 1 9 4 43 87 0.5 1 59 28 44 9 0.5 1 3 6 45 26 0.5 1 16 10 46 22 0.5 1 13 9 47 46 0.5 1 33 13 48 72 0.5 1 44 28 49 4 0.5 1 1 3 50 48 0.5 1 32 16 51 16 0.5 1 9 7 52 18 0.5 1 6 12 53 32 0.5 1 15 17 54 85 0.5 1 49 36 55 56 0.5 1 34 22 56 47 0.5 1 27 20 57 51 0.5 1 25 26 58 164 0.5 1 121 43 59 27 0.5 1 15 12 60 80 0.5 1 45 35 61 147 0.5 1 83 64 62 124 0.5 1 58 66 63 61 0.5 1 46 15 64 7 0.5 1 3 4 65 8 0.5 1 7 1 66 55 0.5 1 24 31 67 37 0.5 1 16 21 68 228 0.5 1 133 95 69 397 0.5 1 307 90 70 868 0.5 1 682 186 71 813 0.5 1 653 160 72 1157 0.5 1 932 225 73 859 0.5 1 714 145 74 211 0.5 1 170 41 75 268 0.5 1 215 53 76 313 0.5 1 244 69 77 306 0.5 1 241 65 78 297 0.5 1 248 49 79 325 0.5 1 268 57 80 335 0.5 1 289 46 81 366 0.5 1 305 61 82 336 0.5 1 266 70 83 224 0.5 1 188 36 84 267 0.5 1 227 40 85 290 0.5 1 235 55 86 353 0.5 1 283 70 87 259 0.5 1 212 47 88 206 0.5 1 159 47 89 376 0.5 1 291 85 90 874 0.5 1 378 496 91 320 0.5 1 259 61 92 361 0.5 1 298 63 93 293 0.5 1 251 42 94 264 0.5 1 230 34 95 236 0.5 1 194 42 96 335 0.5 1 275 60 97 223 0.5 1 187 36 98 313 0.5 1 219 94 99 384 0.5 1 340 44 100 311 0.5 1 274 37 101 257 0.5 1 212 45 102 292 0.5 1 245 47 103 365 0.5 1 325 40 104 310 0.5 1 271 39 105 397 0.5 1 362 35 106 393 0.5 1 359 34 107 458 0.5 1 400 58 108 360 0.5 1 330 30 109 399 0.5 1 350 49 110 404 0.5 1 350 54 111 425 0.5 1 387 38 112 471 0.5 1 438 33 113 602 0.5 1 543 59 114 790 0.5 1 660 130 115 887 0.5 1 813 74 116 1147 0.5 1 1062 85 117 1098 0.5 1 1015 83 118 1156 0.5 1 1065 91 119 729 0.5 1 650 79 120 819 0.5 1 731 88 121 1571 0.5 1 1458 113 122 1773 0.5 1 1634 139 123 1961 0.5 1 1809 152 124 2139 0.5 1 1991 148 125 2239 0.5 1 2058 181 126 2252 0.5 1 2056 196 127 2667 0.5 1 2440 227 128 3394 0.5 1 3130 264 129 4010 0.5 1 3687 323 130 3974 0.5 1 3611 363 131 4468 0.5 1 4080 388 132 5950 0.5 1 5405 545 133 13073 0.5 1 12028 1045 134 17119 0.5 1 15795 1324 135 38528 0.5 1 36207 2321 136 67851 0.5 1 64253 3598 137 392369 0.5 1 375677 16692 138 33488764 0.5 1 32630208 858556 139 30 0.5 1 11 19 140 8 0.5 1 2 6 142 1 0.5 1 1 143 1 0.5 1 0 1 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/RRBS20A040784_val_1.fq.gz ============================================= 34341869 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 19974 (0.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 34190058 (99.6%)