SUMMARISING RUN PARAMETERS ========================== Input filename: ERR3932984_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: 825). 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 ERR3932984_2.fastq Processing reads on 1 core in single-end mode ... Finished in 5.67 s (13 µs/read; 4.75 M reads/minute). === Summary === Total reads processed: 448,631 Reads with adapters: 145,286 (32.4%) Reads written (passing filters): 448,631 (100.0%) Total basepairs processed: 77,326,487 bp Quality-trimmed: 2,151,289 bp (2.8%) Total written (filtered): 74,717,105 bp (96.6%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 145286 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 42.6% C: 17.2% G: 15.3% T: 24.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 120665 112157.8 0 120665 2 12645 28039.4 0 12645 3 3410 7009.9 0 3410 4 837 1752.5 0 837 5 445 438.1 0 445 6 87 109.5 0 87 7 104 27.4 0 104 8 58 6.8 0 58 9 76 1.7 0 68 8 10 104 0.4 1 44 60 11 196 0.1 1 97 99 12 202 0.0 1 79 123 13 188 0.0 1 64 124 14 127 0.0 1 31 96 15 149 0.0 1 37 112 16 152 0.0 1 40 112 17 143 0.0 1 30 113 18 99 0.0 1 19 80 19 104 0.0 1 22 82 20 65 0.0 1 10 55 21 136 0.0 1 19 117 22 151 0.0 1 21 130 23 168 0.0 1 48 120 24 87 0.0 1 21 66 25 104 0.0 1 20 84 26 107 0.0 1 19 88 27 134 0.0 1 39 95 28 150 0.0 1 40 110 29 153 0.0 1 41 112 30 144 0.0 1 33 111 31 213 0.0 1 53 160 32 176 0.0 1 41 135 33 256 0.0 1 69 187 34 172 0.0 1 36 136 35 160 0.0 1 39 121 36 209 0.0 1 56 153 37 75 0.0 1 16 59 38 104 0.0 1 22 82 39 125 0.0 1 34 91 40 102 0.0 1 27 75 41 100 0.0 1 28 72 42 61 0.0 1 15 46 43 107 0.0 1 25 82 44 72 0.0 1 14 58 45 100 0.0 1 16 84 46 168 0.0 1 45 123 47 77 0.0 1 15 62 48 56 0.0 1 10 46 49 78 0.0 1 17 61 50 61 0.0 1 13 48 51 67 0.0 1 15 52 52 80 0.0 1 19 61 53 66 0.0 1 8 58 54 41 0.0 1 6 35 55 46 0.0 1 13 33 56 38 0.0 1 11 27 57 39 0.0 1 10 29 58 44 0.0 1 6 38 59 35 0.0 1 4 31 60 22 0.0 1 7 15 61 29 0.0 1 8 21 62 16 0.0 1 2 14 63 23 0.0 1 3 20 64 21 0.0 1 6 15 65 13 0.0 1 3 10 66 18 0.0 1 2 16 67 15 0.0 1 5 10 68 21 0.0 1 9 12 69 11 0.0 1 5 6 70 16 0.0 1 3 13 71 11 0.0 1 2 9 72 21 0.0 1 3 18 73 19 0.0 1 4 15 74 20 0.0 1 10 10 75 18 0.0 1 7 11 76 30 0.0 1 10 20 77 52 0.0 1 14 38 78 52 0.0 1 17 35 79 54 0.0 1 19 35 80 55 0.0 1 16 39 81 43 0.0 1 20 23 82 29 0.0 1 9 20 83 20 0.0 1 5 15 84 22 0.0 1 4 18 85 7 0.0 1 3 4 86 10 0.0 1 3 7 87 11 0.0 1 1 10 88 14 0.0 1 5 9 89 7 0.0 1 2 5 90 3 0.0 1 1 2 91 7 0.0 1 1 6 92 8 0.0 1 0 8 93 7 0.0 1 2 5 94 8 0.0 1 1 7 95 5 0.0 1 1 4 96 9 0.0 1 2 7 97 5 0.0 1 0 5 98 4 0.0 1 1 3 99 7 0.0 1 2 5 100 7 0.0 1 1 6 101 5 0.0 1 1 4 102 7 0.0 1 2 5 103 6 0.0 1 0 6 104 7 0.0 1 0 7 105 4 0.0 1 1 3 106 5 0.0 1 1 4 107 6 0.0 1 0 6 108 2 0.0 1 1 1 109 3 0.0 1 2 1 110 7 0.0 1 0 7 111 5 0.0 1 1 4 112 5 0.0 1 0 5 113 4 0.0 1 1 3 114 7 0.0 1 1 6 115 5 0.0 1 1 4 116 4 0.0 1 0 4 117 4 0.0 1 0 4 118 5 0.0 1 1 4 119 2 0.0 1 1 1 120 8 0.0 1 1 7 121 5 0.0 1 1 4 122 3 0.0 1 1 2 123 3 0.0 1 0 3 124 3 0.0 1 0 3 125 3 0.0 1 2 1 126 6 0.0 1 1 5 127 9 0.0 1 2 7 128 6 0.0 1 0 6 129 4 0.0 1 0 4 130 4 0.0 1 1 3 131 4 0.0 1 1 3 132 3 0.0 1 2 1 133 3 0.0 1 2 1 134 4 0.0 1 1 3 136 4 0.0 1 0 4 137 4 0.0 1 1 3 138 5 0.0 1 2 3 139 7 0.0 1 3 4 140 4 0.0 1 0 4 141 2 0.0 1 0 2 142 6 0.0 1 1 5 143 5 0.0 1 0 5 144 3 0.0 1 1 2 145 3 0.0 1 0 3 146 4 0.0 1 2 2 147 6 0.0 1 2 4 148 4 0.0 1 0 4 149 4 0.0 1 1 3 150 5 0.0 1 2 3 151 4 0.0 1 1 3 152 3 0.0 1 0 3 153 10 0.0 1 2 8 154 3 0.0 1 1 2 155 2 0.0 1 1 1 156 2 0.0 1 1 1 157 1 0.0 1 1 158 2 0.0 1 0 2 159 2 0.0 1 0 2 160 3 0.0 1 0 3 161 5 0.0 1 1 4 162 1 0.0 1 0 1 163 6 0.0 1 0 6 164 7 0.0 1 2 5 165 6 0.0 1 0 6 166 2 0.0 1 0 2 167 4 0.0 1 1 3 168 4 0.0 1 1 3 169 6 0.0 1 0 6 170 5 0.0 1 0 5 171 3 0.0 1 0 3 172 2 0.0 1 0 2 173 1 0.0 1 0 1 174 2 0.0 1 0 2 175 2 0.0 1 0 2 176 2 0.0 1 0 2 177 4 0.0 1 0 4 178 3 0.0 1 0 3 180 2 0.0 1 0 2 181 2 0.0 1 0 2 182 2 0.0 1 0 2 183 3 0.0 1 0 3 184 3 0.0 1 1 2 185 2 0.0 1 1 1 187 1 0.0 1 0 1 188 2 0.0 1 0 2 189 1 0.0 1 1 190 2 0.0 1 0 2 191 8 0.0 1 0 8 193 3 0.0 1 2 1 194 2 0.0 1 0 2 195 1 0.0 1 0 1 196 4 0.0 1 0 4 197 3 0.0 1 0 3 198 4 0.0 1 1 3 199 3 0.0 1 0 3 201 1 0.0 1 0 1 202 2 0.0 1 1 1 203 2 0.0 1 0 2 204 2 0.0 1 0 2 208 1 0.0 1 0 1 209 2 0.0 1 1 1 210 1 0.0 1 0 1 211 1 0.0 1 0 1 212 1 0.0 1 0 1 213 1 0.0 1 1 214 1 0.0 1 0 1 215 1 0.0 1 0 1 220 1 0.0 1 0 1 221 1 0.0 1 0 1 223 2 0.0 1 0 2 224 1 0.0 1 0 1 231 1 0.0 1 0 1 233 1 0.0 1 0 1 241 1 0.0 1 0 1 243 1 0.0 1 0 1 246 1 0.0 1 0 1 RUN STATISTICS FOR INPUT FILE: ERR3932984_2.fastq ============================================= 448631 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 448631 Number of sequence pairs removed because at least one read was shorter than the length cutoff (100 bp): 101601 (22.65%)