SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.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_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.98 s (27 us/read; 2.23 M reads/minute). === Summary === Total reads processed: 36,456 Reads with adapters: 23,277 (63.8%) Reads written (passing filters): 36,456 (100.0%) Total basepairs processed: 5,468,053 bp Quality-trimmed: 843 bp (0.0%) Total written (filtered): 5,116,805 bp (93.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23277 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.1% C: 28.0% G: 22.5% T: 20.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9539 9114.0 0 9539 2 1891 2278.5 0 1891 3 931 569.6 0 931 4 660 142.4 0 660 5 9 35.6 0 9 6 246 8.9 0 246 7 265 2.2 0 265 8 305 0.6 0 305 9 225 0.1 0 225 10 229 0.0 1 218 11 11 238 0.0 1 226 12 12 498 0.0 1 473 25 13 2 0.0 1 1 1 14 260 0.0 1 249 11 15 402 0.0 1 380 22 16 3 0.0 1 1 2 17 268 0.0 1 261 7 18 165 0.0 1 158 7 19 294 0.0 1 284 10 20 234 0.0 1 227 7 21 181 0.0 1 175 6 22 212 0.0 1 206 6 23 223 0.0 1 218 5 24 286 0.0 1 278 8 25 204 0.0 1 197 7 26 212 0.0 1 200 12 27 130 0.0 1 121 9 28 329 0.0 1 322 7 29 74 0.0 1 72 2 30 260 0.0 1 253 7 31 91 0.0 1 87 4 32 597 0.0 1 589 8 33 169 0.0 1 159 10 34 46 0.0 1 44 2 35 290 0.0 1 284 6 36 63 0.0 1 59 4 37 125 0.0 1 123 2 38 46 0.0 1 45 1 39 56 0.0 1 56 40 18 0.0 1 17 1 41 130 0.0 1 129 1 42 209 0.0 1 202 7 43 84 0.0 1 78 6 44 100 0.0 1 97 3 45 265 0.0 1 260 5 46 96 0.0 1 91 5 47 61 0.0 1 57 4 48 253 0.0 1 250 3 49 62 0.0 1 61 1 50 14 0.0 1 12 2 51 156 0.0 1 148 8 52 307 0.0 1 302 5 53 95 0.0 1 91 4 54 93 0.0 1 89 4 55 32 0.0 1 32 56 19 0.0 1 19 57 34 0.0 1 32 2 58 41 0.0 1 37 4 59 24 0.0 1 24 60 13 0.0 1 12 1 61 9 0.0 1 8 1 62 11 0.0 1 10 1 63 16 0.0 1 15 1 64 30 0.0 1 30 65 38 0.0 1 33 5 66 31 0.0 1 31 67 45 0.0 1 45 68 39 0.0 1 38 1 69 24 0.0 1 24 70 30 0.0 1 30 71 41 0.0 1 39 2 72 33 0.0 1 33 73 27 0.0 1 26 1 74 16 0.0 1 16 75 22 0.0 1 21 1 76 20 0.0 1 20 77 19 0.0 1 19 78 24 0.0 1 24 79 19 0.0 1 18 1 80 17 0.0 1 17 81 18 0.0 1 18 82 13 0.0 1 13 83 10 0.0 1 9 1 84 12 0.0 1 12 85 13 0.0 1 13 86 17 0.0 1 17 87 14 0.0 1 14 88 12 0.0 1 10 2 89 11 0.0 1 11 90 13 0.0 1 13 91 6 0.0 1 6 92 9 0.0 1 9 93 9 0.0 1 9 94 2 0.0 1 2 95 7 0.0 1 6 1 96 4 0.0 1 4 97 5 0.0 1 5 98 4 0.0 1 4 99 5 0.0 1 5 100 7 0.0 1 7 101 2 0.0 1 2 102 6 0.0 1 6 103 1 0.0 1 1 104 5 0.0 1 4 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 3 110 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 1 1 116 2 0.0 1 2 117 3 0.0 1 2 1 118 2 0.0 1 2 120 3 0.0 1 2 1 121 3 0.0 1 3 122 4 0.0 1 4 123 2 0.0 1 2 124 2 0.0 1 2 125 3 0.0 1 3 126 4 0.0 1 4 127 4 0.0 1 4 128 5 0.0 1 4 1 129 8 0.0 1 8 130 5 0.0 1 5 131 6 0.0 1 6 132 5 0.0 1 4 1 133 7 0.0 1 7 134 19 0.0 1 19 135 10 0.0 1 9 1 136 3 0.0 1 3 137 6 0.0 1 5 1 138 8 0.0 1 7 1 139 9 0.0 1 9 140 5 0.0 1 2 3 141 4 0.0 1 4 142 9 0.0 1 8 1 143 5 0.0 1 3 2 144 1 0.0 1 1 145 3 0.0 1 2 1 146 8 0.0 1 2 6 147 3 0.0 1 2 1 148 8 0.0 1 5 3 149 4 0.0 1 4 150 1 0.0 1 0 1 151 4 0.0 1 3 1 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz ============================================= 36456 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 36456 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 506 (1.39%)