SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 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; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 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 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28 Output file will be GZIP compressed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4267.50 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 150,811,300 Reads with adapters: 55,622,993 (36.9%) Reads written (passing filters): 150,811,300 (100.0%) Total basepairs processed: 17,546,903,399 bp Quality-trimmed: 4,282,115 bp (0.0%) Total written (filtered): 17,469,617,103 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55622993 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.5% C: 9.7% G: 7.7% T: 39.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 46232463 37702825.0 0 46232463 2 6383119 9425706.2 0 6383119 3 1263005 2356426.6 0 1263005 4 1119159 589106.6 0 1119159 5 357925 147276.7 0 357925 6 86321 36819.2 0 86321 7 58304 9204.8 0 58304 8 36108 2301.2 0 36108 9 6434 575.3 0 4845 1589 10 54733 143.8 1 51602 3131 11 574 36.0 1 108 466 12 304 9.0 1 201 103 13 181 2.2 1 158 23 14 76 2.2 1 64 12 15 169 2.2 1 156 13 16 78 2.2 1 63 15 17 55 2.2 1 43 12 18 130 2.2 1 104 26 19 135 2.2 1 115 20 20 171 2.2 1 149 22 21 92 2.2 1 83 9 22 107 2.2 1 84 23 23 166 2.2 1 148 18 24 110 2.2 1 97 13 25 110 2.2 1 102 8 26 111 2.2 1 97 14 27 96 2.2 1 81 15 28 109 2.2 1 94 15 29 107 2.2 1 97 10 30 94 2.2 1 84 10 31 102 2.2 1 94 8 32 89 2.2 1 79 10 33 112 2.2 1 102 10 34 116 2.2 1 105 11 35 128 2.2 1 110 18 36 126 2.2 1 111 15 37 118 2.2 1 105 13 38 115 2.2 1 101 14 39 101 2.2 1 86 15 40 128 2.2 1 108 20 41 127 2.2 1 117 10 42 147 2.2 1 120 27 43 123 2.2 1 109 14 44 129 2.2 1 115 14 45 123 2.2 1 110 13 46 96 2.2 1 93 3 47 136 2.2 1 117 19 48 140 2.2 1 133 7 49 138 2.2 1 120 18 50 162 2.2 1 146 16 51 116 2.2 1 97 19 52 151 2.2 1 133 18 53 141 2.2 1 131 10 54 143 2.2 1 128 15 55 150 2.2 1 135 15 56 128 2.2 1 120 8 57 174 2.2 1 152 22 58 172 2.2 1 156 16 59 170 2.2 1 159 11 60 166 2.2 1 148 18 61 146 2.2 1 136 10 62 166 2.2 1 146 20 63 167 2.2 1 152 15 64 156 2.2 1 140 16 65 203 2.2 1 187 16 66 147 2.2 1 133 14 67 171 2.2 1 158 13 68 192 2.2 1 176 16 69 161 2.2 1 142 19 70 206 2.2 1 185 21 71 262 2.2 1 240 22 72 212 2.2 1 185 27 73 228 2.2 1 195 33 74 197 2.2 1 179 18 75 194 2.2 1 173 21 76 214 2.2 1 196 18 77 214 2.2 1 190 24 78 186 2.2 1 160 26 79 213 2.2 1 197 16 80 252 2.2 1 220 32 81 209 2.2 1 191 18 82 192 2.2 1 174 18 83 226 2.2 1 197 29 84 187 2.2 1 164 23 85 214 2.2 1 194 20 86 235 2.2 1 192 43 87 222 2.2 1 198 24 88 249 2.2 1 214 35 89 256 2.2 1 224 32 90 221 2.2 1 196 25 91 265 2.2 1 235 30 92 227 2.2 1 210 17 93 220 2.2 1 201 19 94 226 2.2 1 199 27 95 210 2.2 1 185 25 96 277 2.2 1 236 41 97 227 2.2 1 204 23 98 244 2.2 1 207 37 99 230 2.2 1 199 31 100 246 2.2 1 215 31 101 225 2.2 1 202 23 102 272 2.2 1 235 37 103 236 2.2 1 217 19 104 221 2.2 1 191 30 105 207 2.2 1 181 26 106 194 2.2 1 162 32 107 239 2.2 1 202 37 108 281 2.2 1 242 39 109 282 2.2 1 239 43 110 271 2.2 1 238 33 111 239 2.2 1 207 32 112 239 2.2 1 215 24 113 242 2.2 1 215 27 114 251 2.2 1 223 28 115 234 2.2 1 212 22 116 257 2.2 1 224 33 117 307 2.2 1 272 35 118 246 2.2 1 226 20 119 288 2.2 1 267 21 120 278 2.2 1 249 29 121 302 2.2 1 266 36 122 284 2.2 1 260 24 123 296 2.2 1 263 33 124 258 2.2 1 229 29 125 312 2.2 1 265 47 126 274 2.2 1 237 37 127 321 2.2 1 273 48 128 309 2.2 1 261 48 129 338 2.2 1 302 36 130 392 2.2 1 352 40 131 320 2.2 1 272 48 132 334 2.2 1 285 49 133 373 2.2 1 313 60 134 397 2.2 1 294 103 135 491 2.2 1 219 272 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R2.fq.gz ============================================= 150811300 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 150811300 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1589275 (1.05%)