SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/20181211_metagenomics_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2750.95 s (33 us/read; 1.79 M reads/minute). === Summary === Total reads processed: 82,206,331 Reads with adapters: 32,831,180 (39.9%) Reads written (passing filters): 82,206,331 (100.0%) Total basepairs processed: 10,973,171,706 bp Quality-trimmed: 6,128,036 bp (0.1%) Total written (filtered): 10,921,172,993 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 32831180 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 35.1% C: 8.2% G: 16.7% T: 40.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 25154314 20551582.8 0 25154314 2 5441389 5137895.7 0 5441389 3 1658348 1284473.9 0 1658348 4 309694 321118.5 0 309694 5 167405 80279.6 0 167405 6 49246 20069.9 0 49246 7 14287 5017.5 0 14287 8 1584 1254.4 0 1584 9 689 313.6 0 81 608 10 1972 78.4 1 56 1916 11 1428 19.6 1 16 1412 12 318 4.9 1 4 314 13 244 4.9 1 1 243 14 247 4.9 1 3 244 15 245 4.9 1 0 245 16 212 4.9 1 0 212 17 220 4.9 1 1 219 18 235 4.9 1 5 230 19 247 4.9 1 1 246 20 263 4.9 1 10 253 21 219 4.9 1 0 219 22 214 4.9 1 4 210 23 301 4.9 1 2 299 24 304 4.9 1 1 303 25 319 4.9 1 3 316 26 260 4.9 1 2 258 27 274 4.9 1 0 274 28 247 4.9 1 6 241 29 284 4.9 1 0 284 30 209 4.9 1 6 203 31 257 4.9 1 1 256 32 308 4.9 1 5 303 33 254 4.9 1 0 254 34 229 4.9 1 2 227 35 286 4.9 1 7 279 36 232 4.9 1 3 229 37 242 4.9 1 6 236 38 268 4.9 1 1 267 39 252 4.9 1 2 250 40 242 4.9 1 1 241 41 267 4.9 1 3 264 42 242 4.9 1 5 237 43 266 4.9 1 1 265 44 250 4.9 1 3 247 45 227 4.9 1 0 227 46 261 4.9 1 6 255 47 218 4.9 1 0 218 48 248 4.9 1 2 246 49 225 4.9 1 0 225 50 283 4.9 1 1 282 51 253 4.9 1 2 251 52 198 4.9 1 5 193 53 234 4.9 1 1 233 54 273 4.9 1 0 273 55 277 4.9 1 5 272 56 284 4.9 1 2 282 57 254 4.9 1 0 254 58 206 4.9 1 1 205 59 253 4.9 1 0 253 60 185 4.9 1 4 181 61 245 4.9 1 0 245 62 245 4.9 1 0 245 63 243 4.9 1 2 241 64 216 4.9 1 1 215 65 236 4.9 1 5 231 66 259 4.9 1 2 257 67 241 4.9 1 0 241 68 257 4.9 1 4 253 69 221 4.9 1 4 217 70 229 4.9 1 1 228 71 232 4.9 1 3 229 72 240 4.9 1 0 240 73 238 4.9 1 1 237 74 227 4.9 1 5 222 75 253 4.9 1 1 252 76 243 4.9 1 2 241 77 212 4.9 1 1 211 78 210 4.9 1 3 207 79 183 4.9 1 0 183 80 241 4.9 1 5 236 81 177 4.9 1 1 176 82 201 4.9 1 1 200 83 238 4.9 1 7 231 84 238 4.9 1 0 238 85 215 4.9 1 0 215 86 203 4.9 1 1 202 87 221 4.9 1 5 216 88 228 4.9 1 2 226 89 224 4.9 1 1 223 90 201 4.9 1 0 201 91 234 4.9 1 3 231 92 247 4.9 1 1 246 93 235 4.9 1 3 232 94 173 4.9 1 4 169 95 236 4.9 1 2 234 96 214 4.9 1 3 211 97 186 4.9 1 4 182 98 218 4.9 1 2 216 99 242 4.9 1 6 236 100 187 4.9 1 2 185 101 222 4.9 1 2 220 102 197 4.9 1 3 194 103 237 4.9 1 3 234 104 236 4.9 1 1 235 105 200 4.9 1 0 200 106 220 4.9 1 0 220 107 240 4.9 1 5 235 108 212 4.9 1 1 211 109 219 4.9 1 2 217 110 239 4.9 1 1 238 111 184 4.9 1 4 180 112 154 4.9 1 0 154 113 210 4.9 1 0 210 114 249 4.9 1 2 247 115 200 4.9 1 0 200 116 180 4.9 1 5 175 117 200 4.9 1 1 199 118 196 4.9 1 1 195 119 193 4.9 1 0 193 120 176 4.9 1 1 175 121 214 4.9 1 0 214 122 288 4.9 1 0 288 123 183 4.9 1 0 183 124 214 4.9 1 0 214 125 166 4.9 1 0 166 126 198 4.9 1 2 196 127 198 4.9 1 3 195 128 255 4.9 1 1 254 129 214 4.9 1 0 214 130 170 4.9 1 0 170 131 213 4.9 1 3 210 132 184 4.9 1 1 183 133 182 4.9 1 1 181 134 214 4.9 1 0 214 135 153 4.9 1 1 152 136 178 4.9 1 1 177 137 193 4.9 1 3 190 138 250 4.9 1 2 248 139 202 4.9 1 3 199 140 206 4.9 1 7 199 141 130 4.9 1 0 130 142 119 4.9 1 1 118 143 116 4.9 1 1 115 144 96 4.9 1 0 96 145 130 4.9 1 3 127 146 123 4.9 1 1 122 147 192 4.9 1 1 191 148 170 4.9 1 1 169 149 87 4.9 1 0 87 150 95 4.9 1 0 95 151 2 4.9 1 0 2 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz ============================================= 82206331 sequences processed in total