SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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: 20 bp Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.99 s (27 us/read; 2.20 M reads/minute). === Summary === Total reads processed: 36,456 Reads with adapters: 23,392 (64.2%) Reads written (passing filters): 36,456 (100.0%) Total basepairs processed: 5,477,053 bp Quality-trimmed: 660 bp (0.0%) Total written (filtered): 5,060,825 bp (92.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23392 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.8% C: 31.3% G: 21.4% T: 18.8% none/other: 1.6% Overview of removed sequences length count expect max.err error counts 1 9374 9114.0 0 9374 2 1817 2278.5 0 1817 3 794 569.6 0 794 4 622 142.4 0 622 5 2 35.6 0 2 6 253 8.9 0 253 7 249 2.2 0 249 8 292 0.6 0 292 9 244 0.1 0 243 1 10 228 0.0 1 218 10 11 253 0.0 1 234 19 12 483 0.0 1 457 26 13 7 0.0 1 3 4 14 426 0.0 1 402 24 15 8 0.0 1 2 6 16 499 0.0 1 464 35 17 9 0.0 1 6 3 18 269 0.0 1 252 17 19 848 0.0 1 812 36 20 6 0.0 1 3 3 22 2 0.0 1 2 23 231 0.0 1 221 10 24 600 0.0 1 570 30 25 7 0.0 1 4 3 26 203 0.0 1 191 12 27 194 0.0 1 191 3 28 5 0.0 1 4 1 29 219 0.0 1 212 7 30 216 0.0 1 206 10 31 289 0.0 1 283 6 32 5 0.0 1 3 2 33 325 0.0 1 302 23 34 9 0.0 1 5 4 35 313 0.0 1 303 10 36 3 0.0 1 3 37 169 0.0 1 156 13 38 177 0.0 1 168 9 39 145 0.0 1 138 7 40 125 0.0 1 119 6 41 177 0.0 1 164 13 42 362 0.0 1 338 24 43 60 0.0 1 56 4 44 58 0.0 1 58 45 1 0.0 1 1 46 118 0.0 1 115 3 47 109 0.0 1 101 8 48 116 0.0 1 114 2 49 103 0.0 1 92 11 50 178 0.0 1 170 8 51 101 0.0 1 100 1 52 7 0.0 1 3 4 53 140 0.0 1 128 12 54 218 0.0 1 208 10 55 10 0.0 1 9 1 56 32 0.0 1 27 5 57 225 0.0 1 217 8 58 2 0.0 1 2 59 3 0.0 1 2 1 60 113 0.0 1 110 3 61 2 0.0 1 2 63 51 0.0 1 50 1 64 49 0.0 1 47 2 65 50 0.0 1 46 4 66 64 0.0 1 61 3 67 44 0.0 1 43 1 68 50 0.0 1 49 1 69 8 0.0 1 8 70 11 0.0 1 9 2 71 28 0.0 1 28 72 27 0.0 1 26 1 73 26 0.0 1 24 2 74 17 0.0 1 16 1 75 23 0.0 1 21 2 76 20 0.0 1 19 1 77 19 0.0 1 19 78 26 0.0 1 26 79 18 0.0 1 16 2 80 20 0.0 1 18 2 81 17 0.0 1 17 82 14 0.0 1 13 1 83 9 0.0 1 9 84 14 0.0 1 13 1 85 13 0.0 1 12 1 86 18 0.0 1 17 1 87 13 0.0 1 13 88 11 0.0 1 10 1 89 10 0.0 1 9 1 90 15 0.0 1 15 91 5 0.0 1 5 92 10 0.0 1 10 93 9 0.0 1 9 94 3 0.0 1 2 1 95 7 0.0 1 7 96 5 0.0 1 5 97 5 0.0 1 5 98 3 0.0 1 3 99 6 0.0 1 6 100 8 0.0 1 8 101 1 0.0 1 1 102 6 0.0 1 5 1 103 1 0.0 1 1 104 4 0.0 1 3 1 105 3 0.0 1 3 106 1 0.0 1 1 107 2 0.0 1 2 108 2 0.0 1 2 109 3 0.0 1 2 1 110 1 0.0 1 1 112 2 0.0 1 2 113 1 0.0 1 1 114 2 0.0 1 2 115 2 0.0 1 2 116 2 0.0 1 2 117 4 0.0 1 3 1 118 2 0.0 1 2 120 3 0.0 1 3 121 4 0.0 1 4 122 4 0.0 1 2 2 123 1 0.0 1 1 124 2 0.0 1 2 125 3 0.0 1 2 1 126 4 0.0 1 3 1 127 4 0.0 1 3 1 128 5 0.0 1 5 129 8 0.0 1 7 1 130 5 0.0 1 4 1 131 6 0.0 1 6 132 5 0.0 1 5 133 7 0.0 1 7 134 19 0.0 1 19 135 10 0.0 1 10 136 3 0.0 1 3 137 6 0.0 1 6 138 8 0.0 1 8 139 10 0.0 1 8 2 140 5 0.0 1 5 141 4 0.0 1 4 142 9 0.0 1 8 1 143 5 0.0 1 5 144 1 0.0 1 1 145 3 0.0 1 3 146 9 0.0 1 9 147 3 0.0 1 3 148 8 0.0 1 8 149 4 0.0 1 4 150 3 0.0 1 1 2 151 381 0.0 1 3 378 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz ============================================= 36456 sequences processed in total