SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_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_7_S2_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 2941.23 s (33 us/read; 1.80 M reads/minute). === Summary === Total reads processed: 88,036,439 Reads with adapters: 35,638,015 (40.5%) Reads written (passing filters): 88,036,439 (100.0%) Total basepairs processed: 11,754,350,316 bp Quality-trimmed: 4,836,285 bp (0.0%) Total written (filtered): 11,699,753,699 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 35638015 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 35.7% C: 8.2% G: 15.7% T: 40.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 27394243 22009109.8 0 27394243 2 5797880 5502277.4 0 5797880 3 1805026 1375569.4 0 1805026 4 337285 343892.3 0 337285 5 188941 85973.1 0 188941 6 57639 21493.3 0 57639 7 16581 5373.3 0 16581 8 2106 1343.3 0 2106 9 717 335.8 0 104 613 10 2296 84.0 1 60 2236 11 1692 21.0 1 13 1679 12 376 5.2 1 4 372 13 247 5.2 1 0 247 14 286 5.2 1 4 282 15 280 5.2 1 2 278 16 223 5.2 1 1 222 17 217 5.2 1 1 216 18 260 5.2 1 8 252 19 227 5.2 1 3 224 20 325 5.2 1 2 323 21 248 5.2 1 0 248 22 255 5.2 1 4 251 23 340 5.2 1 0 340 24 362 5.2 1 0 362 25 321 5.2 1 1 320 26 323 5.2 1 2 321 27 270 5.2 1 2 268 28 278 5.2 1 4 274 29 329 5.2 1 9 320 30 260 5.2 1 5 255 31 258 5.2 1 3 255 32 317 5.2 1 5 312 33 281 5.2 1 6 275 34 257 5.2 1 1 256 35 270 5.2 1 3 267 36 279 5.2 1 2 277 37 282 5.2 1 5 277 38 265 5.2 1 3 262 39 295 5.2 1 1 294 40 314 5.2 1 0 314 41 278 5.2 1 6 272 42 222 5.2 1 6 216 43 281 5.2 1 3 278 44 292 5.2 1 6 286 45 229 5.2 1 4 225 46 312 5.2 1 2 310 47 287 5.2 1 5 282 48 256 5.2 1 1 255 49 247 5.2 1 1 246 50 267 5.2 1 0 267 51 226 5.2 1 2 224 52 254 5.2 1 2 252 53 258 5.2 1 1 257 54 268 5.2 1 5 263 55 270 5.2 1 2 268 56 262 5.2 1 8 254 57 286 5.2 1 0 286 58 279 5.2 1 1 278 59 268 5.2 1 0 268 60 238 5.2 1 2 236 61 246 5.2 1 5 241 62 266 5.2 1 1 265 63 240 5.2 1 0 240 64 235 5.2 1 3 232 65 286 5.2 1 2 284 66 239 5.2 1 1 238 67 295 5.2 1 4 291 68 229 5.2 1 3 226 69 216 5.2 1 1 215 70 256 5.2 1 0 256 71 257 5.2 1 2 255 72 260 5.2 1 1 259 73 242 5.2 1 1 241 74 250 5.2 1 0 250 75 248 5.2 1 5 243 76 238 5.2 1 6 232 77 268 5.2 1 3 265 78 242 5.2 1 2 240 79 261 5.2 1 2 259 80 236 5.2 1 0 236 81 240 5.2 1 2 238 82 220 5.2 1 1 219 83 258 5.2 1 5 253 84 234 5.2 1 0 234 85 265 5.2 1 2 263 86 255 5.2 1 4 251 87 239 5.2 1 2 237 88 246 5.2 1 1 245 89 284 5.2 1 1 283 90 184 5.2 1 0 184 91 232 5.2 1 0 232 92 217 5.2 1 4 213 93 242 5.2 1 2 240 94 206 5.2 1 2 204 95 246 5.2 1 2 244 96 215 5.2 1 7 208 97 213 5.2 1 3 210 98 230 5.2 1 0 230 99 264 5.2 1 3 261 100 220 5.2 1 4 216 101 290 5.2 1 2 288 102 228 5.2 1 6 222 103 243 5.2 1 4 239 104 246 5.2 1 0 246 105 192 5.2 1 0 192 106 226 5.2 1 0 226 107 288 5.2 1 3 285 108 232 5.2 1 1 231 109 238 5.2 1 1 237 110 288 5.2 1 1 287 111 248 5.2 1 1 247 112 156 5.2 1 6 150 113 252 5.2 1 1 251 114 258 5.2 1 1 257 115 252 5.2 1 4 248 116 221 5.2 1 5 216 117 193 5.2 1 5 188 118 250 5.2 1 3 247 119 258 5.2 1 0 258 120 213 5.2 1 1 212 121 247 5.2 1 1 246 122 256 5.2 1 0 256 123 220 5.2 1 1 219 124 205 5.2 1 2 203 125 217 5.2 1 1 216 126 228 5.2 1 4 224 127 230 5.2 1 12 218 128 266 5.2 1 1 265 129 236 5.2 1 1 235 130 187 5.2 1 1 186 131 213 5.2 1 0 213 132 197 5.2 1 2 195 133 162 5.2 1 2 160 134 193 5.2 1 4 189 135 195 5.2 1 0 195 136 207 5.2 1 4 203 137 181 5.2 1 5 176 138 251 5.2 1 2 249 139 203 5.2 1 0 203 140 224 5.2 1 0 224 141 120 5.2 1 0 120 142 121 5.2 1 1 120 143 89 5.2 1 0 89 144 109 5.2 1 1 108 145 129 5.2 1 3 126 146 114 5.2 1 0 114 147 250 5.2 1 3 247 148 130 5.2 1 2 128 149 83 5.2 1 0 83 150 127 5.2 1 1 126 151 2 5.2 1 0 2 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz ============================================= 88036439 sequences processed in total