SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_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_L001_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1.12 s (27 us/read; 2.22 M reads/minute). === Summary === Total reads processed: 41,460 Reads with adapters: 26,148 (63.1%) Reads written (passing filters): 41,460 (100.0%) Total basepairs processed: 6,219,292 bp Quality-trimmed: 1,420 bp (0.0%) Total written (filtered): 5,865,672 bp (94.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26148 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.5% C: 27.8% G: 22.1% T: 20.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11262 10365.0 0 11262 2 2324 2591.2 0 2324 3 1069 647.8 0 1069 4 756 162.0 0 756 5 3 40.5 0 3 6 271 10.1 0 271 7 266 2.5 0 266 8 308 0.6 0 308 9 236 0.2 0 235 1 10 314 0.0 1 290 24 11 297 0.0 1 265 32 12 507 0.0 1 474 33 13 3 0.0 1 1 2 14 297 0.0 1 267 30 15 464 0.0 1 435 29 17 309 0.0 1 284 25 18 198 0.0 1 185 13 19 298 0.0 1 275 23 20 242 0.0 1 221 21 21 207 0.0 1 183 24 22 191 0.0 1 177 14 23 267 0.0 1 250 17 24 396 0.0 1 366 30 25 220 0.0 1 200 20 26 175 0.0 1 162 13 27 159 0.0 1 149 10 28 361 0.0 1 334 27 29 83 0.0 1 74 9 30 303 0.0 1 284 19 31 112 0.0 1 102 10 32 492 0.0 1 464 28 33 176 0.0 1 162 14 34 66 0.0 1 56 10 35 265 0.0 1 252 13 36 74 0.0 1 71 3 37 121 0.0 1 114 7 38 83 0.0 1 82 1 39 95 0.0 1 92 3 40 33 0.0 1 30 3 41 123 0.0 1 118 5 42 192 0.0 1 181 11 43 80 0.0 1 73 7 44 123 0.0 1 119 4 45 226 0.0 1 217 9 46 125 0.0 1 118 7 47 75 0.0 1 71 4 48 217 0.0 1 203 14 49 70 0.0 1 68 2 50 21 0.0 1 20 1 51 147 0.0 1 138 9 52 218 0.0 1 204 14 53 86 0.0 1 82 4 54 90 0.0 1 83 7 55 52 0.0 1 50 2 56 20 0.0 1 18 2 57 53 0.0 1 52 1 58 58 0.0 1 58 59 28 0.0 1 21 7 60 16 0.0 1 15 1 61 11 0.0 1 10 1 62 18 0.0 1 15 3 63 21 0.0 1 21 64 27 0.0 1 27 65 30 0.0 1 28 2 66 43 0.0 1 42 1 67 52 0.0 1 51 1 68 45 0.0 1 43 2 69 38 0.0 1 35 3 70 43 0.0 1 42 1 71 24 0.0 1 23 1 72 21 0.0 1 20 1 73 25 0.0 1 23 2 74 23 0.0 1 23 75 17 0.0 1 17 76 17 0.0 1 17 77 19 0.0 1 18 1 78 19 0.0 1 19 79 16 0.0 1 15 1 80 16 0.0 1 15 1 81 16 0.0 1 15 1 82 13 0.0 1 13 83 12 0.0 1 12 84 8 0.0 1 8 85 10 0.0 1 10 86 6 0.0 1 5 1 87 7 0.0 1 7 88 10 0.0 1 10 89 14 0.0 1 14 90 6 0.0 1 6 91 5 0.0 1 5 92 7 0.0 1 7 93 2 0.0 1 2 94 5 0.0 1 5 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 7 102 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 2 118 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 1 1 126 2 0.0 1 2 127 2 0.0 1 2 128 4 0.0 1 4 129 6 0.0 1 6 130 4 0.0 1 4 131 3 0.0 1 3 132 2 0.0 1 2 133 3 0.0 1 2 1 134 10 0.0 1 10 135 7 0.0 1 6 1 136 8 0.0 1 8 137 5 0.0 1 5 138 6 0.0 1 6 139 2 0.0 1 2 140 3 0.0 1 3 141 3 0.0 1 0 3 142 9 0.0 1 7 2 143 3 0.0 1 2 1 145 1 0.0 1 0 1 146 6 0.0 1 2 4 147 1 0.0 1 0 1 148 11 0.0 1 7 4 149 2 0.0 1 1 1 150 2 0.0 1 0 2 151 5 0.0 1 2 3 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz ============================================= 41460 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 41460 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 361 (0.87%)