SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_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_1_S3_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 2879.23 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 83,250,751 Reads with adapters: 31,902,917 (38.3%) Reads written (passing filters): 83,250,751 (100.0%) Total basepairs processed: 11,301,487,423 bp Quality-trimmed: 7,592,579 bp (0.1%) Total written (filtered): 11,249,045,252 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 31902917 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 33.7% C: 8.8% G: 17.6% T: 39.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24138260 20812687.8 0 24138260 2 5462884 5203171.9 0 5462884 3 1774135 1300793.0 0 1774135 4 289598 325198.2 0 289598 5 150336 81299.6 0 150336 6 41866 20324.9 0 41866 7 12564 5081.2 0 12564 8 1209 1270.3 0 1209 9 534 317.6 0 79 455 10 1672 79.4 1 35 1637 11 1239 19.8 1 21 1218 12 292 5.0 1 6 286 13 237 5.0 1 0 237 14 204 5.0 1 0 204 15 168 5.0 1 2 166 16 200 5.0 1 3 197 17 193 5.0 1 0 193 18 227 5.0 1 3 224 19 181 5.0 1 4 177 20 225 5.0 1 2 223 21 202 5.0 1 0 202 22 203 5.0 1 1 202 23 283 5.0 1 4 279 24 290 5.0 1 3 287 25 256 5.0 1 2 254 26 210 5.0 1 4 206 27 235 5.0 1 0 235 28 231 5.0 1 3 228 29 284 5.0 1 7 277 30 214 5.0 1 1 213 31 260 5.0 1 1 259 32 224 5.0 1 0 224 33 241 5.0 1 1 240 34 257 5.0 1 1 256 35 243 5.0 1 6 237 36 225 5.0 1 4 221 37 256 5.0 1 2 254 38 256 5.0 1 2 254 39 248 5.0 1 1 247 40 197 5.0 1 3 194 41 197 5.0 1 4 193 42 208 5.0 1 6 202 43 241 5.0 1 2 239 44 201 5.0 1 2 199 45 209 5.0 1 2 207 46 233 5.0 1 1 232 47 204 5.0 1 4 200 48 196 5.0 1 0 196 49 221 5.0 1 4 217 50 266 5.0 1 1 265 51 219 5.0 1 0 219 52 259 5.0 1 0 259 53 239 5.0 1 1 238 54 238 5.0 1 3 235 55 273 5.0 1 4 269 56 235 5.0 1 3 232 57 266 5.0 1 3 263 58 258 5.0 1 3 255 59 269 5.0 1 2 267 60 200 5.0 1 0 200 61 213 5.0 1 3 210 62 216 5.0 1 4 212 63 200 5.0 1 3 197 64 266 5.0 1 2 264 65 232 5.0 1 0 232 66 223 5.0 1 1 222 67 238 5.0 1 3 235 68 233 5.0 1 0 233 69 187 5.0 1 2 185 70 250 5.0 1 5 245 71 230 5.0 1 0 230 72 230 5.0 1 3 227 73 181 5.0 1 2 179 74 199 5.0 1 2 197 75 212 5.0 1 2 210 76 271 5.0 1 1 270 77 217 5.0 1 4 213 78 209 5.0 1 1 208 79 198 5.0 1 0 198 80 222 5.0 1 4 218 81 209 5.0 1 0 209 82 203 5.0 1 1 202 83 168 5.0 1 1 167 84 253 5.0 1 1 252 85 222 5.0 1 0 222 86 224 5.0 1 4 220 87 221 5.0 1 1 220 88 245 5.0 1 9 236 89 213 5.0 1 2 211 90 189 5.0 1 0 189 91 166 5.0 1 1 165 92 237 5.0 1 3 234 93 201 5.0 1 4 197 94 160 5.0 1 5 155 95 232 5.0 1 2 230 96 225 5.0 1 2 223 97 225 5.0 1 0 225 98 172 5.0 1 2 170 99 235 5.0 1 6 229 100 168 5.0 1 1 167 101 246 5.0 1 3 243 102 191 5.0 1 4 187 103 237 5.0 1 3 234 104 206 5.0 1 0 206 105 186 5.0 1 0 186 106 165 5.0 1 0 165 107 214 5.0 1 5 209 108 188 5.0 1 2 186 109 178 5.0 1 1 177 110 193 5.0 1 3 190 111 181 5.0 1 2 179 112 190 5.0 1 3 187 113 248 5.0 1 1 247 114 211 5.0 1 3 208 115 182 5.0 1 2 180 116 162 5.0 1 3 159 117 165 5.0 1 1 164 118 188 5.0 1 1 187 119 205 5.0 1 2 203 120 156 5.0 1 2 154 121 207 5.0 1 3 204 122 179 5.0 1 1 178 123 200 5.0 1 2 198 124 178 5.0 1 1 177 125 168 5.0 1 1 167 126 199 5.0 1 1 198 127 150 5.0 1 2 148 128 188 5.0 1 0 188 129 172 5.0 1 1 171 130 166 5.0 1 2 164 131 188 5.0 1 0 188 132 155 5.0 1 0 155 133 187 5.0 1 4 183 134 157 5.0 1 0 157 135 171 5.0 1 1 170 136 166 5.0 1 2 164 137 160 5.0 1 1 159 138 186 5.0 1 3 183 139 187 5.0 1 1 186 140 184 5.0 1 0 184 141 132 5.0 1 0 132 142 101 5.0 1 2 99 143 88 5.0 1 3 85 144 75 5.0 1 0 75 145 123 5.0 1 2 121 146 104 5.0 1 1 103 147 207 5.0 1 0 207 148 158 5.0 1 1 157 149 81 5.0 1 0 81 150 140 5.0 1 1 139 151 2 5.0 1 0 2 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz ============================================= 83250751 sequences processed in total