SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_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/NR012_S1_L001_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 7.21 s (26 us/read; 2.34 M reads/minute). === Summary === Total reads processed: 281,472 Reads with adapters: 120,782 (42.9%) Reads written (passing filters): 281,472 (100.0%) Total basepairs processed: 36,447,504 bp Quality-trimmed: 19,787 bp (0.1%) Total written (filtered): 35,723,779 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 120782 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.5% C: 23.1% G: 16.7% T: 27.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 76746 70368.0 0 76746 2 19123 17592.0 0 19123 3 5743 4398.0 0 5743 4 2596 1099.5 0 2596 5 190 274.9 0 190 6 434 68.7 0 434 7 361 17.2 0 361 8 438 4.3 0 438 9 303 1.1 0 300 3 10 412 0.3 1 367 45 11 385 0.1 1 338 47 12 762 0.0 1 686 76 13 9 0.0 1 4 5 14 484 0.0 1 437 47 15 692 0.0 1 623 69 16 2 0.0 1 1 1 17 452 0.0 1 404 48 18 257 0.0 1 228 29 19 453 0.0 1 405 48 20 332 0.0 1 290 42 21 244 0.0 1 219 25 22 305 0.0 1 278 27 23 372 0.0 1 340 32 24 581 0.0 1 538 43 25 340 0.0 1 304 36 26 316 0.0 1 282 34 27 168 0.0 1 149 19 28 453 0.0 1 408 45 29 108 0.0 1 88 20 30 457 0.0 1 428 29 31 177 0.0 1 150 27 32 759 0.0 1 693 66 33 298 0.0 1 274 24 34 81 0.0 1 70 11 35 413 0.0 1 381 32 36 145 0.0 1 130 15 37 181 0.0 1 163 18 38 105 0.0 1 96 9 39 113 0.0 1 105 8 40 51 0.0 1 44 7 41 173 0.0 1 163 10 42 263 0.0 1 248 15 43 116 0.0 1 100 16 44 154 0.0 1 144 10 45 330 0.0 1 308 22 46 171 0.0 1 156 15 47 112 0.0 1 103 9 48 305 0.0 1 276 29 49 134 0.0 1 123 11 50 41 0.0 1 36 5 51 210 0.0 1 199 11 52 314 0.0 1 297 17 53 117 0.0 1 103 14 54 134 0.0 1 123 11 55 94 0.0 1 86 8 56 42 0.0 1 39 3 57 73 0.0 1 64 9 58 70 0.0 1 65 5 59 42 0.0 1 41 1 60 31 0.0 1 29 2 61 24 0.0 1 19 5 62 27 0.0 1 20 7 63 27 0.0 1 25 2 64 48 0.0 1 44 4 65 55 0.0 1 53 2 66 76 0.0 1 74 2 67 59 0.0 1 59 68 50 0.0 1 48 2 69 54 0.0 1 51 3 70 60 0.0 1 53 7 71 46 0.0 1 44 2 72 48 0.0 1 45 3 73 46 0.0 1 43 3 74 51 0.0 1 47 4 75 48 0.0 1 44 4 76 51 0.0 1 46 5 77 46 0.0 1 42 4 78 42 0.0 1 37 5 79 39 0.0 1 34 5 80 38 0.0 1 32 6 81 41 0.0 1 35 6 82 44 0.0 1 40 4 83 40 0.0 1 33 7 84 33 0.0 1 27 6 85 30 0.0 1 26 4 86 30 0.0 1 25 5 87 32 0.0 1 29 3 88 25 0.0 1 23 2 89 32 0.0 1 28 4 90 33 0.0 1 28 5 91 25 0.0 1 20 5 92 19 0.0 1 17 2 93 22 0.0 1 20 2 94 25 0.0 1 24 1 95 27 0.0 1 23 4 96 23 0.0 1 19 4 97 18 0.0 1 17 1 98 22 0.0 1 18 4 99 26 0.0 1 22 4 100 13 0.0 1 12 1 101 22 0.0 1 16 6 102 19 0.0 1 17 2 103 26 0.0 1 23 3 104 16 0.0 1 15 1 105 15 0.0 1 13 2 106 16 0.0 1 15 1 107 10 0.0 1 7 3 108 11 0.0 1 9 2 109 15 0.0 1 11 4 110 7 0.0 1 7 111 16 0.0 1 15 1 112 11 0.0 1 10 1 113 9 0.0 1 8 1 114 7 0.0 1 7 115 10 0.0 1 9 1 116 11 0.0 1 9 2 117 10 0.0 1 5 5 118 4 0.0 1 1 3 119 9 0.0 1 7 2 120 9 0.0 1 8 1 121 9 0.0 1 8 1 122 3 0.0 1 3 123 6 0.0 1 5 1 124 8 0.0 1 6 2 125 4 0.0 1 4 126 14 0.0 1 11 3 127 6 0.0 1 6 128 8 0.0 1 8 129 4 0.0 1 3 1 130 9 0.0 1 9 131 8 0.0 1 8 132 11 0.0 1 8 3 133 6 0.0 1 6 134 6 0.0 1 6 135 8 0.0 1 7 1 136 5 0.0 1 5 137 9 0.0 1 9 138 5 0.0 1 5 139 7 0.0 1 7 140 2 0.0 1 2 141 4 0.0 1 2 2 142 4 0.0 1 3 1 143 3 0.0 1 3 144 3 0.0 1 2 1 145 5 0.0 1 0 5 146 4 0.0 1 3 1 147 2 0.0 1 0 2 148 9 0.0 1 3 6 151 95 0.0 1 83 12 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz ============================================= 281472 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 281472 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3813 (1.35%)