SUMMARISING RUN PARAMETERS ========================== Input filename: ERR3932950_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: 222). Second best hit was Illumina (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 ERR3932950_2.fastq Processing reads on 1 core in single-end mode ... Finished in 7.95 s (14 µs/read; 4.38 M reads/minute). === Summary === Total reads processed: 580,175 Reads with adapters: 121,004 (20.9%) Reads written (passing filters): 580,175 (100.0%) Total basepairs processed: 133,821,671 bp Quality-trimmed: 1,822,548 bp (1.4%) Total written (filtered): 131,739,881 bp (98.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 121004 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 36.0% C: 18.8% G: 16.0% T: 29.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 98585 145043.8 0 98585 2 14552 36260.9 0 14552 3 3997 9065.2 0 3997 4 1009 2266.3 0 1009 5 266 566.6 0 266 6 91 141.6 0 91 7 25 35.4 0 25 8 23 8.9 0 23 9 51 2.2 0 46 5 10 50 0.6 1 16 34 11 110 0.1 1 41 69 12 88 0.0 1 39 49 13 78 0.0 1 24 54 14 51 0.0 1 11 40 15 62 0.0 1 13 49 16 72 0.0 1 12 60 17 96 0.0 1 22 74 18 50 0.0 1 10 40 19 47 0.0 1 13 34 20 61 0.0 1 16 45 21 65 0.0 1 16 49 22 64 0.0 1 20 44 23 55 0.0 1 16 39 24 36 0.0 1 8 28 25 34 0.0 1 10 24 26 43 0.0 1 14 29 27 42 0.0 1 8 34 28 67 0.0 1 18 49 29 87 0.0 1 27 60 30 32 0.0 1 10 22 31 39 0.0 1 14 25 32 48 0.0 1 14 34 33 45 0.0 1 11 34 34 41 0.0 1 11 30 35 18 0.0 1 8 10 36 36 0.0 1 8 28 37 34 0.0 1 12 22 38 22 0.0 1 7 15 39 29 0.0 1 11 18 40 27 0.0 1 10 17 41 38 0.0 1 12 26 42 26 0.0 1 10 16 43 28 0.0 1 12 16 44 19 0.0 1 6 13 45 24 0.0 1 6 18 46 13 0.0 1 3 10 47 9 0.0 1 2 7 48 7 0.0 1 4 3 49 12 0.0 1 5 7 50 12 0.0 1 1 11 51 10 0.0 1 2 8 52 15 0.0 1 3 12 53 7 0.0 1 1 6 54 12 0.0 1 4 8 55 7 0.0 1 1 6 56 9 0.0 1 0 9 57 8 0.0 1 3 5 58 8 0.0 1 1 7 59 8 0.0 1 3 5 60 4 0.0 1 1 3 61 6 0.0 1 0 6 62 6 0.0 1 1 5 63 7 0.0 1 1 6 64 5 0.0 1 1 4 65 6 0.0 1 1 5 66 9 0.0 1 1 8 67 7 0.0 1 1 6 68 4 0.0 1 1 3 69 6 0.0 1 0 6 70 3 0.0 1 2 1 71 9 0.0 1 2 7 72 4 0.0 1 0 4 73 6 0.0 1 1 5 74 7 0.0 1 1 6 75 10 0.0 1 7 3 76 8 0.0 1 3 5 77 7 0.0 1 0 7 78 2 0.0 1 1 1 79 7 0.0 1 3 4 80 12 0.0 1 4 8 81 6 0.0 1 0 6 82 10 0.0 1 4 6 83 8 0.0 1 2 6 84 2 0.0 1 0 2 85 5 0.0 1 0 5 86 3 0.0 1 1 2 87 7 0.0 1 1 6 88 5 0.0 1 1 4 89 6 0.0 1 0 6 90 6 0.0 1 1 5 91 3 0.0 1 1 2 92 2 0.0 1 1 1 93 5 0.0 1 1 4 94 6 0.0 1 1 5 95 4 0.0 1 0 4 97 3 0.0 1 0 3 98 8 0.0 1 1 7 99 1 0.0 1 0 1 100 6 0.0 1 1 5 101 7 0.0 1 4 3 102 2 0.0 1 0 2 103 5 0.0 1 0 5 104 2 0.0 1 0 2 105 5 0.0 1 1 4 106 2 0.0 1 0 2 107 2 0.0 1 0 2 108 2 0.0 1 0 2 110 2 0.0 1 2 111 5 0.0 1 1 4 112 4 0.0 1 1 3 113 3 0.0 1 0 3 114 3 0.0 1 2 1 115 2 0.0 1 0 2 116 1 0.0 1 0 1 117 2 0.0 1 1 1 118 3 0.0 1 0 3 119 1 0.0 1 0 1 120 3 0.0 1 0 3 121 1 0.0 1 0 1 122 2 0.0 1 0 2 123 1 0.0 1 0 1 124 3 0.0 1 0 3 125 3 0.0 1 2 1 126 1 0.0 1 0 1 127 7 0.0 1 2 5 128 5 0.0 1 1 4 130 3 0.0 1 0 3 131 2 0.0 1 0 2 132 1 0.0 1 0 1 133 1 0.0 1 0 1 136 2 0.0 1 0 2 137 2 0.0 1 0 2 138 2 0.0 1 0 2 139 5 0.0 1 0 5 140 1 0.0 1 0 1 142 2 0.0 1 1 1 143 2 0.0 1 0 2 144 1 0.0 1 1 145 1 0.0 1 0 1 146 3 0.0 1 0 3 147 1 0.0 1 0 1 148 1 0.0 1 1 149 1 0.0 1 0 1 152 1 0.0 1 0 1 153 1 0.0 1 0 1 154 4 0.0 1 1 3 155 1 0.0 1 0 1 156 4 0.0 1 0 4 157 2 0.0 1 0 2 158 4 0.0 1 0 4 159 1 0.0 1 0 1 160 5 0.0 1 0 5 161 1 0.0 1 0 1 163 1 0.0 1 0 1 164 4 0.0 1 0 4 165 2 0.0 1 0 2 166 1 0.0 1 0 1 167 1 0.0 1 0 1 169 1 0.0 1 0 1 170 3 0.0 1 0 3 171 5 0.0 1 1 4 173 2 0.0 1 0 2 175 1 0.0 1 0 1 177 5 0.0 1 0 5 178 4 0.0 1 0 4 179 2 0.0 1 0 2 181 5 0.0 1 0 5 183 1 0.0 1 0 1 184 4 0.0 1 0 4 185 1 0.0 1 0 1 186 1 0.0 1 0 1 187 1 0.0 1 0 1 188 4 0.0 1 0 4 189 2 0.0 1 0 2 191 1 0.0 1 0 1 192 2 0.0 1 0 2 193 4 0.0 1 0 4 194 2 0.0 1 0 2 196 1 0.0 1 0 1 197 2 0.0 1 0 2 198 1 0.0 1 0 1 199 3 0.0 1 0 3 200 1 0.0 1 0 1 201 3 0.0 1 0 3 202 1 0.0 1 0 1 203 2 0.0 1 0 2 205 1 0.0 1 0 1 206 2 0.0 1 0 2 209 4 0.0 1 0 4 210 1 0.0 1 0 1 211 1 0.0 1 0 1 212 1 0.0 1 1 214 1 0.0 1 0 1 215 1 0.0 1 0 1 216 2 0.0 1 0 2 217 1 0.0 1 0 1 218 1 0.0 1 0 1 219 2 0.0 1 0 2 221 1 0.0 1 0 1 222 2 0.0 1 0 2 223 1 0.0 1 0 1 224 2 0.0 1 0 2 225 8 0.0 1 0 8 226 3 0.0 1 0 3 227 1 0.0 1 0 1 228 4 0.0 1 0 4 229 2 0.0 1 0 2 231 1 0.0 1 0 1 234 2 0.0 1 0 2 235 3 0.0 1 0 3 236 2 0.0 1 0 2 238 2 0.0 1 0 2 240 2 0.0 1 0 2 241 2 0.0 1 0 2 242 2 0.0 1 0 2 243 3 0.0 1 0 3 244 2 0.0 1 0 2 248 1 0.0 1 0 1 249 1 0.0 1 0 1 RUN STATISTICS FOR INPUT FILE: ERR3932950_2.fastq ============================================= 580175 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 580175 Number of sequence pairs removed because at least one read was shorter than the length cutoff (100 bp): 23064 (3.98%)