SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_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_6_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5409.37 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 197,572,800 Reads with adapters: 70,288,569 (35.6%) Reads written (passing filters): 197,572,800 (100.0%) Total basepairs processed: 22,541,948,875 bp Quality-trimmed: 5,531,625 bp (0.0%) Total written (filtered): 22,442,009,492 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 70288569 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 42.9% C: 9.7% G: 8.3% T: 39.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 57128669 49393200.0 0 57128669 2 8853172 12348300.0 0 8853172 3 1746170 3087075.0 0 1746170 4 1549392 771768.8 0 1549392 5 570617 192942.2 0 570617 6 143035 48235.5 0 143035 7 99889 12058.9 0 99889 8 63778 3014.7 0 63778 9 11204 753.7 0 8840 2364 10 96284 188.4 1 91445 4839 11 970 47.1 1 181 789 12 301 11.8 1 124 177 13 97 2.9 1 67 30 14 78 2.9 1 57 21 15 164 2.9 1 137 27 16 57 2.9 1 46 11 17 62 2.9 1 46 16 18 130 2.9 1 106 24 19 146 2.9 1 126 20 20 204 2.9 1 179 25 21 102 2.9 1 86 16 22 66 2.9 1 60 6 23 171 2.9 1 159 12 24 117 2.9 1 102 15 25 129 2.9 1 121 8 26 90 2.9 1 74 16 27 124 2.9 1 103 21 28 110 2.9 1 88 22 29 85 2.9 1 77 8 30 104 2.9 1 91 13 31 104 2.9 1 92 12 32 96 2.9 1 82 14 33 79 2.9 1 75 4 34 128 2.9 1 107 21 35 128 2.9 1 113 15 36 144 2.9 1 126 18 37 144 2.9 1 134 10 38 119 2.9 1 105 14 39 134 2.9 1 118 16 40 139 2.9 1 127 12 41 138 2.9 1 121 17 42 165 2.9 1 149 16 43 134 2.9 1 127 7 44 115 2.9 1 100 15 45 143 2.9 1 134 9 46 163 2.9 1 142 21 47 174 2.9 1 159 15 48 181 2.9 1 164 17 49 185 2.9 1 170 15 50 150 2.9 1 135 15 51 164 2.9 1 150 14 52 153 2.9 1 135 18 53 149 2.9 1 136 13 54 171 2.9 1 159 12 55 159 2.9 1 142 17 56 189 2.9 1 166 23 57 180 2.9 1 155 25 58 196 2.9 1 177 19 59 200 2.9 1 183 17 60 149 2.9 1 134 15 61 177 2.9 1 149 28 62 188 2.9 1 165 23 63 209 2.9 1 186 23 64 187 2.9 1 163 24 65 157 2.9 1 142 15 66 192 2.9 1 170 22 67 209 2.9 1 186 23 68 164 2.9 1 150 14 69 175 2.9 1 159 16 70 250 2.9 1 227 23 71 210 2.9 1 189 21 72 226 2.9 1 207 19 73 233 2.9 1 218 15 74 201 2.9 1 189 12 75 248 2.9 1 227 21 76 230 2.9 1 203 27 77 208 2.9 1 176 32 78 256 2.9 1 229 27 79 242 2.9 1 210 32 80 277 2.9 1 246 31 81 224 2.9 1 202 22 82 256 2.9 1 236 20 83 219 2.9 1 193 26 84 223 2.9 1 194 29 85 255 2.9 1 228 27 86 190 2.9 1 172 18 87 209 2.9 1 186 23 88 222 2.9 1 196 26 89 190 2.9 1 175 15 90 231 2.9 1 204 27 91 216 2.9 1 192 24 92 240 2.9 1 225 15 93 246 2.9 1 220 26 94 232 2.9 1 202 30 95 232 2.9 1 210 22 96 250 2.9 1 227 23 97 254 2.9 1 230 24 98 250 2.9 1 217 33 99 244 2.9 1 211 33 100 235 2.9 1 209 26 101 233 2.9 1 205 28 102 242 2.9 1 219 23 103 210 2.9 1 187 23 104 240 2.9 1 210 30 105 241 2.9 1 208 33 106 229 2.9 1 206 23 107 224 2.9 1 195 29 108 247 2.9 1 205 42 109 218 2.9 1 194 24 110 235 2.9 1 209 26 111 262 2.9 1 234 28 112 234 2.9 1 213 21 113 234 2.9 1 209 25 114 236 2.9 1 211 25 115 240 2.9 1 210 30 116 240 2.9 1 223 17 117 267 2.9 1 228 39 118 260 2.9 1 236 24 119 296 2.9 1 266 30 120 290 2.9 1 246 44 121 253 2.9 1 224 29 122 254 2.9 1 227 27 123 270 2.9 1 243 27 124 293 2.9 1 268 25 125 276 2.9 1 246 30 126 279 2.9 1 247 32 127 278 2.9 1 241 37 128 356 2.9 1 315 41 129 329 2.9 1 275 54 130 295 2.9 1 268 27 131 376 2.9 1 336 40 132 353 2.9 1 309 44 133 330 2.9 1 270 60 134 368 2.9 1 261 107 135 534 2.9 1 237 297 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R1.fq.gz ============================================= 197572800 sequences processed in total