SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_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_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1.14 s (27 us/read; 2.19 M reads/minute). === Summary === Total reads processed: 41,460 Reads with adapters: 26,139 (63.0%) Reads written (passing filters): 41,460 (100.0%) Total basepairs processed: 6,228,334 bp Quality-trimmed: 1,175 bp (0.0%) Total written (filtered): 5,826,371 bp (93.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26139 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.4% C: 30.9% G: 21.2% T: 19.5% none/other: 1.0% Overview of removed sequences length count expect max.err error counts 1 11126 10365.0 0 11126 2 2116 2591.2 0 2116 3 918 647.8 0 918 4 706 162.0 0 706 5 5 40.5 0 5 6 298 10.1 0 298 7 258 2.5 0 258 8 279 0.6 0 279 9 264 0.2 0 263 1 10 306 0.0 1 288 18 11 303 0.0 1 269 34 12 492 0.0 1 461 31 13 14 0.0 1 8 6 14 526 0.0 1 491 35 15 9 0.0 1 6 3 16 551 0.0 1 504 47 17 18 0.0 1 12 6 18 333 0.0 1 306 27 19 837 0.0 1 788 49 20 1 0.0 1 1 21 1 0.0 1 0 1 22 3 0.0 1 1 2 23 299 0.0 1 271 28 24 625 0.0 1 580 45 25 11 0.0 1 7 4 26 249 0.0 1 227 22 27 208 0.0 1 197 11 28 6 0.0 1 3 3 29 254 0.0 1 235 19 30 264 0.0 1 245 19 31 292 0.0 1 276 16 32 13 0.0 1 8 5 33 370 0.0 1 345 25 34 6 0.0 1 3 3 35 297 0.0 1 273 24 36 4 0.0 1 2 2 37 166 0.0 1 151 15 38 196 0.0 1 182 14 39 159 0.0 1 153 6 40 131 0.0 1 125 6 41 191 0.0 1 179 12 42 360 0.0 1 333 27 43 61 0.0 1 55 6 44 62 0.0 1 58 4 45 1 0.0 1 0 1 46 170 0.0 1 160 10 47 103 0.0 1 96 7 48 109 0.0 1 99 10 49 123 0.0 1 111 12 50 176 0.0 1 165 11 51 81 0.0 1 77 4 52 5 0.0 1 4 1 53 163 0.0 1 153 10 54 207 0.0 1 194 13 55 18 0.0 1 15 3 56 37 0.0 1 31 6 57 168 0.0 1 161 7 58 3 0.0 1 2 1 59 9 0.0 1 7 2 60 104 0.0 1 102 2 61 1 0.0 1 1 62 5 0.0 1 4 1 63 19 0.0 1 16 3 64 70 0.0 1 68 2 65 49 0.0 1 46 3 66 68 0.0 1 66 2 67 37 0.0 1 35 2 68 29 0.0 1 26 3 69 13 0.0 1 12 1 70 19 0.0 1 18 1 71 20 0.0 1 20 72 20 0.0 1 19 1 73 25 0.0 1 24 1 74 22 0.0 1 21 1 75 17 0.0 1 17 76 17 0.0 1 16 1 77 18 0.0 1 17 1 78 20 0.0 1 19 1 79 20 0.0 1 19 1 80 14 0.0 1 13 1 81 15 0.0 1 14 1 82 15 0.0 1 15 83 12 0.0 1 11 1 84 7 0.0 1 7 85 10 0.0 1 10 86 8 0.0 1 7 1 87 8 0.0 1 8 88 11 0.0 1 10 1 89 14 0.0 1 13 1 90 6 0.0 1 5 1 91 6 0.0 1 5 1 92 5 0.0 1 5 93 1 0.0 1 1 94 5 0.0 1 4 1 95 3 0.0 1 3 96 3 0.0 1 3 97 9 0.0 1 9 98 5 0.0 1 5 99 4 0.0 1 4 100 3 0.0 1 3 101 7 0.0 1 6 1 102 7 0.0 1 7 104 2 0.0 1 2 105 3 0.0 1 3 106 2 0.0 1 2 107 1 0.0 1 1 109 2 0.0 1 2 110 4 0.0 1 3 1 111 1 0.0 1 1 113 2 0.0 1 2 114 2 0.0 1 2 117 1 0.0 1 1 119 1 0.0 1 1 120 2 0.0 1 2 121 1 0.0 1 1 123 2 0.0 1 2 124 2 0.0 1 2 125 1 0.0 1 1 126 2 0.0 1 2 127 2 0.0 1 2 128 3 0.0 1 3 129 6 0.0 1 5 1 130 5 0.0 1 5 131 3 0.0 1 3 132 3 0.0 1 3 133 4 0.0 1 3 1 134 9 0.0 1 9 135 7 0.0 1 6 1 136 8 0.0 1 8 137 5 0.0 1 5 138 6 0.0 1 5 1 139 2 0.0 1 2 140 3 0.0 1 3 141 4 0.0 1 3 1 142 9 0.0 1 9 143 3 0.0 1 3 145 1 0.0 1 1 146 6 0.0 1 6 147 1 0.0 1 1 148 11 0.0 1 11 149 3 0.0 1 3 150 1 0.0 1 1 151 271 0.0 1 5 266 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz ============================================= 41460 sequences processed in total