SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_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_6_S5_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 2491.23 s (34 us/read; 1.77 M reads/minute). === Summary === Total reads processed: 73,388,785 Reads with adapters: 29,397,922 (40.1%) Reads written (passing filters): 73,388,785 (100.0%) Total basepairs processed: 9,860,957,526 bp Quality-trimmed: 4,346,715 bp (0.0%) Total written (filtered): 9,815,588,776 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 29397922 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 35.2% C: 8.3% G: 16.1% T: 40.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22459608 18347196.2 0 22459608 2 4874628 4586799.1 0 4874628 3 1560261 1146699.8 0 1560261 4 271652 286674.9 0 271652 5 146370 71668.7 0 146370 6 42723 17917.2 0 42723 7 12349 4479.3 0 12349 8 1436 1119.8 0 1436 9 556 280.0 0 59 497 10 1682 70.0 1 16 1666 11 1152 17.5 1 9 1143 12 259 4.4 1 1 258 13 204 4.4 1 0 204 14 237 4.4 1 3 234 15 175 4.4 1 0 175 16 144 4.4 1 1 143 17 157 4.4 1 0 157 18 211 4.4 1 0 211 19 178 4.4 1 0 178 20 209 4.4 1 1 208 21 201 4.4 1 1 200 22 195 4.4 1 2 193 23 290 4.4 1 4 286 24 261 4.4 1 4 257 25 253 4.4 1 3 250 26 238 4.4 1 1 237 27 220 4.4 1 5 215 28 178 4.4 1 1 177 29 243 4.4 1 1 242 30 219 4.4 1 3 216 31 210 4.4 1 1 209 32 197 4.4 1 2 195 33 218 4.4 1 0 218 34 185 4.4 1 0 185 35 225 4.4 1 3 222 36 219 4.4 1 3 216 37 193 4.4 1 1 192 38 243 4.4 1 0 243 39 232 4.4 1 2 230 40 197 4.4 1 0 197 41 199 4.4 1 0 199 42 211 4.4 1 1 210 43 239 4.4 1 4 235 44 215 4.4 1 4 211 45 189 4.4 1 0 189 46 242 4.4 1 0 242 47 205 4.4 1 0 205 48 215 4.4 1 1 214 49 209 4.4 1 0 209 50 185 4.4 1 2 183 51 186 4.4 1 0 186 52 214 4.4 1 7 207 53 212 4.4 1 0 212 54 227 4.4 1 1 226 55 192 4.4 1 2 190 56 186 4.4 1 5 181 57 213 4.4 1 1 212 58 203 4.4 1 0 203 59 233 4.4 1 3 230 60 164 4.4 1 6 158 61 167 4.4 1 3 164 62 202 4.4 1 5 197 63 200 4.4 1 0 200 64 179 4.4 1 1 178 65 191 4.4 1 0 191 66 195 4.4 1 4 191 67 194 4.4 1 2 192 68 204 4.4 1 6 198 69 184 4.4 1 2 182 70 197 4.4 1 2 195 71 208 4.4 1 0 208 72 182 4.4 1 1 181 73 164 4.4 1 0 164 74 215 4.4 1 1 214 75 161 4.4 1 7 154 76 221 4.4 1 1 220 77 203 4.4 1 3 200 78 167 4.4 1 0 167 79 180 4.4 1 1 179 80 178 4.4 1 0 178 81 153 4.4 1 0 153 82 155 4.4 1 0 155 83 163 4.4 1 0 163 84 225 4.4 1 0 225 85 183 4.4 1 0 183 86 153 4.4 1 1 152 87 184 4.4 1 1 183 88 189 4.4 1 0 189 89 189 4.4 1 1 188 90 170 4.4 1 0 170 91 191 4.4 1 5 186 92 219 4.4 1 0 219 93 168 4.4 1 3 165 94 179 4.4 1 3 176 95 201 4.4 1 1 200 96 192 4.4 1 0 192 97 188 4.4 1 2 186 98 167 4.4 1 0 167 99 192 4.4 1 0 192 100 167 4.4 1 2 165 101 180 4.4 1 0 180 102 181 4.4 1 4 177 103 173 4.4 1 0 173 104 159 4.4 1 0 159 105 163 4.4 1 0 163 106 167 4.4 1 1 166 107 226 4.4 1 2 224 108 179 4.4 1 0 179 109 143 4.4 1 0 143 110 182 4.4 1 1 181 111 160 4.4 1 1 159 112 160 4.4 1 0 160 113 190 4.4 1 0 190 114 181 4.4 1 0 181 115 171 4.4 1 5 166 116 146 4.4 1 2 144 117 198 4.4 1 2 196 118 178 4.4 1 0 178 119 186 4.4 1 1 185 120 185 4.4 1 1 184 121 146 4.4 1 0 146 122 178 4.4 1 1 177 123 134 4.4 1 0 134 124 184 4.4 1 0 184 125 170 4.4 1 0 170 126 162 4.4 1 1 161 127 108 4.4 1 2 106 128 198 4.4 1 1 197 129 160 4.4 1 2 158 130 151 4.4 1 1 150 131 195 4.4 1 1 194 132 125 4.4 1 1 124 133 125 4.4 1 0 125 134 147 4.4 1 1 146 135 159 4.4 1 0 159 136 133 4.4 1 1 132 137 144 4.4 1 1 143 138 205 4.4 1 0 205 139 163 4.4 1 0 163 140 152 4.4 1 0 152 141 92 4.4 1 1 91 142 95 4.4 1 0 95 143 77 4.4 1 0 77 144 63 4.4 1 0 63 145 146 4.4 1 0 146 146 117 4.4 1 0 117 147 227 4.4 1 0 227 148 124 4.4 1 0 124 149 70 4.4 1 0 70 150 96 4.4 1 1 95 151 1 4.4 1 0 1 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz ============================================= 73388785 sequences processed in total