SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_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_6_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5262.54 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 197,572,800 Reads with adapters: 70,057,307 (35.5%) Reads written (passing filters): 197,572,800 (100.0%) Total basepairs processed: 22,544,053,643 bp Quality-trimmed: 5,055,245 bp (0.0%) Total written (filtered): 22,445,212,917 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 70057307 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.3% C: 9.4% G: 8.1% T: 39.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 57214116 49393200.0 0 57214116 2 8670692 12348300.0 0 8670692 3 1627836 3087075.0 0 1627836 4 1538525 771768.8 0 1538525 5 568835 192942.2 0 568835 6 141297 48235.5 0 141297 7 99862 12058.9 0 99862 8 63665 3014.7 0 63665 9 10903 753.7 0 8510 2393 10 94034 188.4 1 89381 4653 11 956 47.1 1 191 765 12 350 11.8 1 210 140 13 222 2.9 1 187 35 14 73 2.9 1 49 24 15 186 2.9 1 159 27 16 40 2.9 1 35 5 17 56 2.9 1 43 13 18 145 2.9 1 128 17 19 137 2.9 1 126 11 20 207 2.9 1 182 25 21 135 2.9 1 119 16 22 70 2.9 1 56 14 23 154 2.9 1 149 5 24 101 2.9 1 89 12 25 123 2.9 1 114 9 26 113 2.9 1 103 10 27 129 2.9 1 119 10 28 116 2.9 1 106 10 29 114 2.9 1 98 16 30 102 2.9 1 85 17 31 117 2.9 1 104 13 32 88 2.9 1 75 13 33 107 2.9 1 97 10 34 103 2.9 1 87 16 35 125 2.9 1 112 13 36 118 2.9 1 102 16 37 134 2.9 1 117 17 38 131 2.9 1 109 22 39 107 2.9 1 98 9 40 161 2.9 1 140 21 41 141 2.9 1 128 13 42 130 2.9 1 118 12 43 152 2.9 1 138 14 44 123 2.9 1 108 15 45 136 2.9 1 123 13 46 155 2.9 1 139 16 47 155 2.9 1 141 14 48 168 2.9 1 147 21 49 150 2.9 1 133 17 50 181 2.9 1 159 22 51 160 2.9 1 145 15 52 134 2.9 1 120 14 53 183 2.9 1 161 22 54 160 2.9 1 143 17 55 180 2.9 1 170 10 56 174 2.9 1 154 20 57 196 2.9 1 177 19 58 157 2.9 1 138 19 59 207 2.9 1 184 23 60 184 2.9 1 165 19 61 175 2.9 1 155 20 62 185 2.9 1 175 10 63 209 2.9 1 189 20 64 190 2.9 1 163 27 65 200 2.9 1 180 20 66 196 2.9 1 170 26 67 210 2.9 1 190 20 68 212 2.9 1 188 24 69 205 2.9 1 197 8 70 194 2.9 1 175 19 71 234 2.9 1 214 20 72 202 2.9 1 182 20 73 227 2.9 1 202 25 74 202 2.9 1 180 22 75 242 2.9 1 213 29 76 242 2.9 1 215 27 77 247 2.9 1 220 27 78 288 2.9 1 251 37 79 267 2.9 1 234 33 80 259 2.9 1 243 16 81 229 2.9 1 202 27 82 235 2.9 1 215 20 83 248 2.9 1 224 24 84 227 2.9 1 210 17 85 251 2.9 1 223 28 86 225 2.9 1 208 17 87 255 2.9 1 221 34 88 273 2.9 1 241 32 89 271 2.9 1 243 28 90 278 2.9 1 249 29 91 250 2.9 1 225 25 92 224 2.9 1 195 29 93 227 2.9 1 200 27 94 261 2.9 1 227 34 95 259 2.9 1 228 31 96 246 2.9 1 208 38 97 212 2.9 1 178 34 98 262 2.9 1 232 30 99 270 2.9 1 236 34 100 260 2.9 1 234 26 101 262 2.9 1 238 24 102 253 2.9 1 231 22 103 258 2.9 1 219 39 104 253 2.9 1 231 22 105 258 2.9 1 228 30 106 269 2.9 1 245 24 107 276 2.9 1 242 34 108 218 2.9 1 191 27 109 268 2.9 1 237 31 110 259 2.9 1 215 44 111 298 2.9 1 266 32 112 272 2.9 1 234 38 113 255 2.9 1 225 30 114 244 2.9 1 222 22 115 290 2.9 1 251 39 116 278 2.9 1 244 34 117 289 2.9 1 251 38 118 282 2.9 1 252 30 119 276 2.9 1 231 45 120 287 2.9 1 261 26 121 279 2.9 1 248 31 122 303 2.9 1 275 28 123 262 2.9 1 238 24 124 283 2.9 1 249 34 125 256 2.9 1 220 36 126 297 2.9 1 268 29 127 308 2.9 1 262 46 128 292 2.9 1 246 46 129 324 2.9 1 277 47 130 340 2.9 1 296 44 131 330 2.9 1 292 38 132 338 2.9 1 289 49 133 393 2.9 1 299 94 134 368 2.9 1 273 95 135 529 2.9 1 227 302 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R2.fq.gz ============================================= 197572800 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 197572800 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2541198 (1.29%)