SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R1.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_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4204.58 s (28 µs/read; 2.15 M reads/minute). === Summary === Total reads processed: 150,811,300 Reads with adapters: 55,728,162 (37.0%) Reads written (passing filters): 150,811,300 (100.0%) Total basepairs processed: 17,548,799,698 bp Quality-trimmed: 4,591,455 bp (0.0%) Total written (filtered): 17,470,764,290 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55728162 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.1% C: 9.6% G: 7.9% T: 39.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 46056625 37702825.0 0 46056625 2 6594663 9425706.2 0 6594663 3 1319173 2356426.6 0 1319173 4 1125771 589106.6 0 1125771 5 361289 147276.7 0 361289 6 88158 36819.2 0 88158 7 58900 9204.8 0 58900 8 35648 2301.2 0 35648 9 6354 575.3 0 4742 1612 10 56808 143.8 1 53528 3280 11 645 36.0 1 128 517 12 237 9.0 1 143 94 13 77 2.2 1 54 23 14 68 2.2 1 52 16 15 168 2.2 1 153 15 16 38 2.2 1 28 10 17 72 2.2 1 56 16 18 105 2.2 1 94 11 19 133 2.2 1 108 25 20 149 2.2 1 134 15 21 119 2.2 1 111 8 22 92 2.2 1 78 14 23 167 2.2 1 156 11 24 88 2.2 1 76 12 25 97 2.2 1 90 7 26 74 2.2 1 64 10 27 109 2.2 1 96 13 28 99 2.2 1 92 7 29 118 2.2 1 108 10 30 82 2.2 1 74 8 31 119 2.2 1 105 14 32 108 2.2 1 101 7 33 97 2.2 1 90 7 34 135 2.2 1 125 10 35 111 2.2 1 90 21 36 103 2.2 1 96 7 37 115 2.2 1 101 14 38 129 2.2 1 108 21 39 114 2.2 1 97 17 40 136 2.2 1 116 20 41 144 2.2 1 131 13 42 157 2.2 1 137 20 43 128 2.2 1 115 13 44 102 2.2 1 99 3 45 114 2.2 1 102 12 46 134 2.2 1 122 12 47 140 2.2 1 131 9 48 157 2.2 1 147 10 49 128 2.2 1 117 11 50 139 2.2 1 127 12 51 133 2.2 1 117 16 52 155 2.2 1 144 11 53 158 2.2 1 147 11 54 130 2.2 1 116 14 55 177 2.2 1 151 26 56 138 2.2 1 127 11 57 168 2.2 1 139 29 58 147 2.2 1 129 18 59 170 2.2 1 152 18 60 179 2.2 1 156 23 61 169 2.2 1 154 15 62 134 2.2 1 122 12 63 183 2.2 1 170 13 64 164 2.2 1 145 19 65 175 2.2 1 149 26 66 175 2.2 1 155 20 67 190 2.2 1 168 22 68 221 2.2 1 212 9 69 178 2.2 1 162 16 70 182 2.2 1 170 12 71 205 2.2 1 181 24 72 207 2.2 1 180 27 73 212 2.2 1 191 21 74 209 2.2 1 186 23 75 174 2.2 1 158 16 76 182 2.2 1 170 12 77 213 2.2 1 194 19 78 205 2.2 1 175 30 79 207 2.2 1 186 21 80 217 2.2 1 189 28 81 205 2.2 1 181 24 82 226 2.2 1 202 24 83 222 2.2 1 197 25 84 184 2.2 1 165 19 85 183 2.2 1 169 14 86 185 2.2 1 157 28 87 207 2.2 1 174 33 88 221 2.2 1 208 13 89 239 2.2 1 210 29 90 231 2.2 1 215 16 91 212 2.2 1 195 17 92 245 2.2 1 216 29 93 237 2.2 1 213 24 94 217 2.2 1 187 30 95 199 2.2 1 179 20 96 228 2.2 1 198 30 97 214 2.2 1 191 23 98 224 2.2 1 197 27 99 240 2.2 1 209 31 100 240 2.2 1 209 31 101 255 2.2 1 226 29 102 235 2.2 1 215 20 103 237 2.2 1 210 27 104 201 2.2 1 178 23 105 264 2.2 1 235 29 106 211 2.2 1 175 36 107 232 2.2 1 201 31 108 221 2.2 1 187 34 109 304 2.2 1 277 27 110 237 2.2 1 210 27 111 245 2.2 1 218 27 112 219 2.2 1 184 35 113 225 2.2 1 187 38 114 233 2.2 1 195 38 115 231 2.2 1 215 16 116 223 2.2 1 191 32 117 249 2.2 1 228 21 118 285 2.2 1 254 31 119 297 2.2 1 252 45 120 284 2.2 1 257 27 121 289 2.2 1 252 37 122 286 2.2 1 251 35 123 274 2.2 1 249 25 124 267 2.2 1 223 44 125 269 2.2 1 250 19 126 287 2.2 1 249 38 127 278 2.2 1 252 26 128 313 2.2 1 263 50 129 355 2.2 1 324 31 130 376 2.2 1 338 38 131 332 2.2 1 290 42 132 339 2.2 1 294 45 133 388 2.2 1 314 74 134 358 2.2 1 247 111 135 511 2.2 1 205 306 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R1.fq.gz ============================================= 150811300 sequences processed in total