SUMMARISING RUN PARAMETERS ========================== Input filename: ERR3932995_2.fastq Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 3.5 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Nextera adapter for trimming (count: 2365). Second best hit was smallRNA (count: 0) Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 100 bp This is cutadapt 3.5 with Python 3.10.12 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ERR3932995_2.fastq Processing reads on 1 core in single-end mode ... Finished in 10.79 s (12 µs/read; 4.95 M reads/minute). === Summary === Total reads processed: 889,123 Reads with adapters: 270,365 (30.4%) Reads written (passing filters): 889,123 (100.0%) Total basepairs processed: 169,693,355 bp Quality-trimmed: 2,733,063 bp (1.6%) Total written (filtered): 166,243,506 bp (98.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 270365 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 43.2% C: 16.5% G: 14.8% T: 25.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 225489 222280.8 0 225489 2 23457 55570.2 0 23457 3 6277 13892.5 0 6277 4 1941 3473.1 0 1941 5 625 868.3 0 625 6 312 217.1 0 312 7 61 54.3 0 61 8 135 13.6 0 135 9 208 3.4 0 185 23 10 261 0.8 1 117 144 11 552 0.2 1 279 273 12 578 0.1 1 232 346 13 414 0.1 1 150 264 14 320 0.1 1 108 212 15 315 0.1 1 77 238 16 292 0.1 1 59 233 17 367 0.1 1 89 278 18 107 0.1 1 21 86 19 145 0.1 1 25 120 20 159 0.1 1 38 121 21 278 0.1 1 71 207 22 246 0.1 1 61 185 23 322 0.1 1 101 221 24 124 0.1 1 29 95 25 217 0.1 1 58 159 26 216 0.1 1 53 163 27 278 0.1 1 105 173 28 254 0.1 1 62 192 29 246 0.1 1 79 167 30 214 0.1 1 66 148 31 211 0.1 1 66 145 32 109 0.1 1 29 80 33 509 0.1 1 132 377 34 489 0.1 1 160 329 35 271 0.1 1 73 198 36 389 0.1 1 121 268 37 258 0.1 1 75 183 38 344 0.1 1 110 234 39 213 0.1 1 66 147 40 294 0.1 1 85 209 41 271 0.1 1 93 178 42 213 0.1 1 50 163 43 184 0.1 1 55 129 44 160 0.1 1 50 110 45 147 0.1 1 40 107 46 148 0.1 1 49 99 47 77 0.1 1 28 49 48 74 0.1 1 21 53 49 68 0.1 1 21 47 50 43 0.1 1 13 30 51 47 0.1 1 14 33 52 41 0.1 1 16 25 53 39 0.1 1 10 29 54 35 0.1 1 9 26 55 31 0.1 1 11 20 56 38 0.1 1 9 29 57 30 0.1 1 13 17 58 24 0.1 1 5 19 59 24 0.1 1 3 21 60 16 0.1 1 5 11 61 22 0.1 1 5 17 62 15 0.1 1 8 7 63 20 0.1 1 3 17 64 14 0.1 1 3 11 65 12 0.1 1 3 9 66 9 0.1 1 3 6 67 11 0.1 1 0 11 68 10 0.1 1 1 9 69 17 0.1 1 5 12 70 13 0.1 1 3 10 71 17 0.1 1 8 9 72 29 0.1 1 5 24 73 43 0.1 1 12 31 74 44 0.1 1 11 33 75 38 0.1 1 13 25 76 49 0.1 1 20 29 77 72 0.1 1 21 51 78 51 0.1 1 17 34 79 67 0.1 1 26 41 80 42 0.1 1 13 29 81 58 0.1 1 17 41 82 21 0.1 1 8 13 83 25 0.1 1 13 12 84 17 0.1 1 9 8 85 14 0.1 1 7 7 86 16 0.1 1 4 12 87 8 0.1 1 2 6 88 8 0.1 1 0 8 89 11 0.1 1 1 10 90 5 0.1 1 2 3 91 7 0.1 1 2 5 92 7 0.1 1 0 7 93 10 0.1 1 4 6 94 2 0.1 1 0 2 95 9 0.1 1 3 6 96 3 0.1 1 1 2 97 10 0.1 1 2 8 98 4 0.1 1 0 4 99 12 0.1 1 5 7 100 8 0.1 1 2 6 101 5 0.1 1 1 4 102 3 0.1 1 1 2 103 4 0.1 1 0 4 104 6 0.1 1 1 5 105 1 0.1 1 1 106 5 0.1 1 1 4 107 4 0.1 1 1 3 108 3 0.1 1 0 3 109 2 0.1 1 0 2 110 5 0.1 1 1 4 111 4 0.1 1 0 4 112 4 0.1 1 1 3 113 5 0.1 1 0 5 114 8 0.1 1 1 7 115 5 0.1 1 0 5 116 4 0.1 1 0 4 117 5 0.1 1 0 5 118 4 0.1 1 1 3 119 4 0.1 1 2 2 120 3 0.1 1 0 3 121 5 0.1 1 0 5 122 4 0.1 1 1 3 123 9 0.1 1 2 7 124 5 0.1 1 0 5 125 3 0.1 1 0 3 126 3 0.1 1 0 3 127 6 0.1 1 1 5 128 3 0.1 1 0 3 129 3 0.1 1 0 3 130 7 0.1 1 2 5 131 4 0.1 1 0 4 132 6 0.1 1 1 5 133 8 0.1 1 2 6 134 1 0.1 1 0 1 135 5 0.1 1 1 4 136 3 0.1 1 1 2 137 5 0.1 1 0 5 138 4 0.1 1 0 4 139 1 0.1 1 0 1 141 2 0.1 1 1 1 142 2 0.1 1 1 1 143 3 0.1 1 0 3 145 4 0.1 1 0 4 146 3 0.1 1 0 3 147 3 0.1 1 1 2 148 1 0.1 1 0 1 149 2 0.1 1 0 2 150 6 0.1 1 0 6 151 3 0.1 1 0 3 152 2 0.1 1 0 2 153 2 0.1 1 1 1 154 4 0.1 1 1 3 155 2 0.1 1 0 2 156 5 0.1 1 0 5 157 1 0.1 1 0 1 158 2 0.1 1 0 2 159 2 0.1 1 1 1 160 2 0.1 1 0 2 163 1 0.1 1 0 1 165 2 0.1 1 0 2 166 2 0.1 1 0 2 167 1 0.1 1 1 168 3 0.1 1 0 3 169 2 0.1 1 0 2 171 2 0.1 1 0 2 172 1 0.1 1 0 1 173 3 0.1 1 0 3 174 1 0.1 1 0 1 175 3 0.1 1 1 2 176 4 0.1 1 0 4 177 1 0.1 1 0 1 178 1 0.1 1 0 1 179 1 0.1 1 0 1 180 2 0.1 1 0 2 181 4 0.1 1 0 4 182 1 0.1 1 0 1 184 2 0.1 1 0 2 185 2 0.1 1 1 1 187 2 0.1 1 0 2 190 2 0.1 1 0 2 193 2 0.1 1 0 2 194 2 0.1 1 0 2 196 1 0.1 1 0 1 197 3 0.1 1 0 3 198 1 0.1 1 0 1 199 1 0.1 1 0 1 200 4 0.1 1 1 3 201 2 0.1 1 0 2 202 2 0.1 1 0 2 203 2 0.1 1 0 2 204 2 0.1 1 0 2 206 1 0.1 1 0 1 207 1 0.1 1 0 1 208 1 0.1 1 0 1 209 1 0.1 1 0 1 213 1 0.1 1 0 1 215 1 0.1 1 0 1 223 2 0.1 1 0 2 226 1 0.1 1 0 1 227 6 0.1 1 0 6 230 1 0.1 1 0 1 237 2 0.1 1 0 2 241 1 0.1 1 0 1 245 2 0.1 1 0 2 246 2 0.1 1 0 2 RUN STATISTICS FOR INPUT FILE: ERR3932995_2.fastq ============================================= 889123 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 889123 Number of sequence pairs removed because at least one read was shorter than the length cutoff (100 bp): 96240 (10.82%)