SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_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_3_S1_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 2677.82 s (30 us/read; 1.99 M reads/minute). === Summary === Total reads processed: 88,647,204 Reads with adapters: 34,402,376 (38.8%) Reads written (passing filters): 88,647,204 (100.0%) Total basepairs processed: 10,786,340,239 bp Quality-trimmed: 8,243,040 bp (0.1%) Total written (filtered): 10,730,992,217 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 34402376 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 36.6% C: 8.7% G: 18.2% T: 36.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 26415990 22161801.0 0 26415990 2 5891012 5540450.2 0 5891012 3 1599136 1385112.6 0 1599136 4 265923 346278.1 0 265923 5 140882 86569.5 0 140882 6 46671 21642.4 0 46671 7 10088 5410.6 0 10088 8 1910 1352.6 0 1910 9 990 338.2 0 90 900 10 2093 84.5 1 33 2060 11 1509 21.1 1 14 1495 12 269 5.3 1 2 267 13 253 5.3 1 0 253 14 195 5.3 1 7 188 15 166 5.3 1 2 164 16 198 5.3 1 7 191 17 148 5.3 1 0 148 18 225 5.3 1 6 219 19 186 5.3 1 1 185 20 303 5.3 1 2 301 21 237 5.3 1 1 236 22 227 5.3 1 3 224 23 290 5.3 1 4 286 24 268 5.3 1 1 267 25 258 5.3 1 2 256 26 250 5.3 1 1 249 27 238 5.3 1 4 234 28 256 5.3 1 7 249 29 234 5.3 1 0 234 30 214 5.3 1 6 208 31 229 5.3 1 1 228 32 233 5.3 1 1 232 33 211 5.3 1 0 211 34 230 5.3 1 1 229 35 256 5.3 1 4 252 36 248 5.3 1 4 244 37 196 5.3 1 3 193 38 210 5.3 1 3 207 39 228 5.3 1 8 220 40 223 5.3 1 13 210 41 200 5.3 1 2 198 42 231 5.3 1 4 227 43 232 5.3 1 4 228 44 225 5.3 1 7 218 45 202 5.3 1 11 191 46 225 5.3 1 3 222 47 219 5.3 1 2 217 48 235 5.3 1 0 235 49 211 5.3 1 8 203 50 244 5.3 1 1 243 51 223 5.3 1 0 223 52 210 5.3 1 8 202 53 235 5.3 1 1 234 54 237 5.3 1 11 226 55 232 5.3 1 6 226 56 240 5.3 1 4 236 57 192 5.3 1 4 188 58 217 5.3 1 0 217 59 220 5.3 1 1 219 60 173 5.3 1 1 172 61 166 5.3 1 2 164 62 164 5.3 1 3 161 63 199 5.3 1 2 197 64 201 5.3 1 5 196 65 177 5.3 1 4 173 66 193 5.3 1 4 189 67 171 5.3 1 4 167 68 187 5.3 1 3 184 69 186 5.3 1 1 185 70 205 5.3 1 1 204 71 201 5.3 1 2 199 72 221 5.3 1 4 217 73 185 5.3 1 0 185 74 205 5.3 1 1 204 75 198 5.3 1 1 197 76 190 5.3 1 0 190 77 218 5.3 1 1 217 78 238 5.3 1 1 237 79 199 5.3 1 2 197 80 186 5.3 1 1 185 81 164 5.3 1 0 164 82 182 5.3 1 1 181 83 203 5.3 1 7 196 84 189 5.3 1 0 189 85 197 5.3 1 1 196 86 212 5.3 1 0 212 87 152 5.3 1 0 152 88 161 5.3 1 1 160 89 197 5.3 1 2 195 90 183 5.3 1 4 179 91 178 5.3 1 5 173 92 178 5.3 1 3 175 93 175 5.3 1 4 171 94 189 5.3 1 3 186 95 194 5.3 1 2 192 96 195 5.3 1 2 193 97 210 5.3 1 3 207 98 182 5.3 1 2 180 99 180 5.3 1 0 180 100 153 5.3 1 0 153 101 201 5.3 1 2 199 102 196 5.3 1 0 196 103 185 5.3 1 0 185 104 187 5.3 1 3 184 105 180 5.3 1 2 178 106 165 5.3 1 1 164 107 189 5.3 1 0 189 108 190 5.3 1 1 189 109 158 5.3 1 3 155 110 180 5.3 1 0 180 111 165 5.3 1 2 163 112 140 5.3 1 1 139 113 205 5.3 1 3 202 114 158 5.3 1 2 156 115 150 5.3 1 0 150 116 149 5.3 1 2 147 117 156 5.3 1 2 154 118 152 5.3 1 3 149 119 171 5.3 1 1 170 120 142 5.3 1 2 140 121 165 5.3 1 0 165 122 221 5.3 1 3 218 123 183 5.3 1 2 181 124 171 5.3 1 1 170 125 152 5.3 1 0 152 126 161 5.3 1 1 160 127 154 5.3 1 1 153 128 166 5.3 1 0 166 129 159 5.3 1 4 155 130 171 5.3 1 0 171 131 132 5.3 1 3 129 132 162 5.3 1 2 160 133 134 5.3 1 4 130 134 147 5.3 1 0 147 135 124 5.3 1 1 123 136 138 5.3 1 0 138 137 148 5.3 1 2 146 138 159 5.3 1 1 158 139 170 5.3 1 1 169 140 167 5.3 1 1 166 141 98 5.3 1 0 98 142 85 5.3 1 0 85 143 57 5.3 1 0 57 144 50 5.3 1 2 48 145 123 5.3 1 0 123 146 72 5.3 1 0 72 147 154 5.3 1 1 153 148 113 5.3 1 2 111 149 57 5.3 1 1 56 150 111 5.3 1 1 110 151 3 5.3 1 0 3 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz ============================================= 88647204 sequences processed in total