SUMMARISING RUN PARAMETERS ========================== Input filename: ERR3678840_2.fastq Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ERR3678840_2.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 5.76 s (16 us/read; 3.72 M reads/minute). === Summary === Total reads processed: 356,967 Reads with adapters: 105,499 (29.6%) Reads written (passing filters): 356,967 (100.0%) Total basepairs processed: 72,600,278 bp Quality-trimmed: 65 bp (0.0%) Total written (filtered): 72,401,635 bp (99.7%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 105499 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 35.8% C: 18.0% G: 17.3% T: 29.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 85808 89241.8 0 85808 2 12193 22310.4 0 12193 3 2701 5577.6 0 2701 4 1010 1394.4 0 1010 5 534 348.6 0 534 6 236 87.2 0 236 7 153 21.8 0 153 8 177 5.4 0 177 9 260 1.4 0 256 4 10 351 0.3 1 347 4 11 203 0.1 1 196 7 12 374 0.0 1 361 13 13 307 0.0 1 299 8 14 268 0.0 1 265 3 15 207 0.0 1 203 4 16 117 0.0 1 115 2 17 3 0.0 1 0 3 18 10 0.0 1 4 6 19 10 0.0 1 5 5 20 7 0.0 1 0 7 21 2 0.0 1 2 22 12 0.0 1 6 6 23 3 0.0 1 0 3 24 7 0.0 1 2 5 25 5 0.0 1 1 4 26 2 0.0 1 0 2 27 1 0.0 1 1 28 11 0.0 1 4 7 29 7 0.0 1 2 5 30 6 0.0 1 2 4 31 5 0.0 1 4 1 32 3 0.0 1 1 2 33 22 0.0 1 6 16 34 6 0.0 1 2 4 35 7 0.0 1 2 5 36 6 0.0 1 3 3 37 7 0.0 1 4 3 38 8 0.0 1 3 5 39 7 0.0 1 3 4 40 8 0.0 1 5 3 41 12 0.0 1 2 10 42 16 0.0 1 7 9 43 55 0.0 1 23 32 44 26 0.0 1 6 20 45 19 0.0 1 4 15 46 26 0.0 1 4 22 47 9 0.0 1 2 7 48 7 0.0 1 0 7 49 11 0.0 1 5 6 50 4 0.0 1 1 3 51 4 0.0 1 0 4 52 4 0.0 1 1 3 53 1 0.0 1 0 1 54 2 0.0 1 0 2 55 1 0.0 1 0 1 56 3 0.0 1 0 3 57 2 0.0 1 1 1 58 3 0.0 1 0 3 59 4 0.0 1 0 4 61 3 0.0 1 0 3 62 2 0.0 1 0 2 63 1 0.0 1 0 1 64 2 0.0 1 0 2 65 1 0.0 1 1 66 1 0.0 1 0 1 67 1 0.0 1 0 1 68 2 0.0 1 0 2 69 2 0.0 1 0 2 70 2 0.0 1 0 2 71 2 0.0 1 0 2 72 6 0.0 1 0 6 73 1 0.0 1 0 1 74 1 0.0 1 0 1 76 1 0.0 1 0 1 77 3 0.0 1 0 3 78 3 0.0 1 1 2 79 6 0.0 1 1 5 80 8 0.0 1 2 6 81 8 0.0 1 1 7 82 1 0.0 1 0 1 83 4 0.0 1 1 3 84 1 0.0 1 0 1 85 3 0.0 1 0 3 86 3 0.0 1 0 3 87 5 0.0 1 0 5 90 2 0.0 1 0 2 91 1 0.0 1 0 1 92 1 0.0 1 0 1 93 1 0.0 1 0 1 94 1 0.0 1 0 1 95 1 0.0 1 0 1 97 1 0.0 1 0 1 99 3 0.0 1 0 3 101 2 0.0 1 0 2 102 1 0.0 1 0 1 103 3 0.0 1 0 3 105 2 0.0 1 0 2 106 1 0.0 1 0 1 108 1 0.0 1 0 1 109 1 0.0 1 0 1 110 1 0.0 1 0 1 111 3 0.0 1 0 3 112 1 0.0 1 0 1 115 1 0.0 1 0 1 116 1 0.0 1 0 1 118 1 0.0 1 0 1 119 1 0.0 1 0 1 120 3 0.0 1 0 3 122 1 0.0 1 0 1 124 2 0.0 1 0 2 126 1 0.0 1 0 1 127 1 0.0 1 0 1 130 1 0.0 1 0 1 131 3 0.0 1 0 3 133 3 0.0 1 0 3 134 1 0.0 1 0 1 136 2 0.0 1 0 2 137 1 0.0 1 0 1 138 1 0.0 1 0 1 139 2 0.0 1 0 2 140 2 0.0 1 0 2 142 2 0.0 1 0 2 143 1 0.0 1 0 1 144 2 0.0 1 0 2 145 2 0.0 1 0 2 149 2 0.0 1 0 2 150 1 0.0 1 0 1 151 5 0.0 1 0 5 153 3 0.0 1 0 3 155 1 0.0 1 0 1 156 8 0.0 1 0 8 158 1 0.0 1 0 1 159 1 0.0 1 0 1 161 1 0.0 1 0 1 162 1 0.0 1 0 1 164 1 0.0 1 0 1 166 1 0.0 1 0 1 168 3 0.0 1 0 3 171 2 0.0 1 0 2 172 2 0.0 1 0 2 173 1 0.0 1 0 1 175 2 0.0 1 0 2 176 1 0.0 1 0 1 177 2 0.0 1 0 2 178 2 0.0 1 0 2 179 1 0.0 1 0 1 181 1 0.0 1 0 1 183 1 0.0 1 0 1 186 3 0.0 1 0 3 187 2 0.0 1 0 2 188 1 0.0 1 0 1 189 2 0.0 1 0 2 191 1 0.0 1 0 1 192 2 0.0 1 0 2 194 2 0.0 1 0 2 195 1 0.0 1 0 1 197 1 0.0 1 0 1 198 1 0.0 1 0 1 200 3 0.0 1 0 3 201 1 0.0 1 0 1 202 1 0.0 1 0 1 203 1 0.0 1 0 1 209 1 0.0 1 0 1 210 1 0.0 1 0 1 213 1 0.0 1 0 1 214 2 0.0 1 0 2 217 1 0.0 1 0 1 222 4 0.0 1 0 4 223 1 0.0 1 0 1 225 2 0.0 1 0 2 227 1 0.0 1 0 1 228 2 0.0 1 0 2 231 1 0.0 1 0 1 232 1 0.0 1 0 1 233 1 0.0 1 0 1 238 1 0.0 1 0 1 239 1 0.0 1 0 1 241 1 0.0 1 0 1 242 1 0.0 1 0 1 243 1 0.0 1 0 1 247 1 0.0 1 0 1 RUN STATISTICS FOR INPUT FILE: ERR3678840_2.fastq ============================================= 356967 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 356967 Number of sequence pairs removed because at least one read was shorter than the length cutoff (100 bp): 36638 (10.26%)