SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_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/NR021_S8_L002_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 92.95 s (26 us/read; 2.28 M reads/minute). === Summary === Total reads processed: 3,532,417 Reads with adapters: 2,104,235 (59.6%) Reads written (passing filters): 3,532,417 (100.0%) Total basepairs processed: 523,752,676 bp Quality-trimmed: 107,379 bp (0.0%) Total written (filtered): 499,307,219 bp (95.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2104235 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.6% C: 24.2% G: 22.9% T: 22.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 935006 883104.2 0 935006 2 205452 220776.1 0 205452 3 90078 55194.0 0 90078 4 63626 13798.5 0 63626 5 727 3449.6 0 727 6 23747 862.4 0 23747 7 22619 215.6 0 22619 8 26870 53.9 0 26870 9 19116 13.5 0 19027 89 10 23453 3.4 1 22285 1168 11 22380 0.8 1 21062 1318 12 45677 0.2 1 43499 2178 13 267 0.1 1 86 181 14 26102 0.1 1 24555 1547 15 39664 0.1 1 37859 1805 16 155 0.1 1 69 86 17 25075 0.1 1 23887 1188 18 16252 0.1 1 15419 833 19 25135 0.1 1 23806 1329 20 19314 0.1 1 18388 926 21 17365 0.1 1 16477 888 22 18767 0.1 1 17902 865 23 18776 0.1 1 17846 930 24 28530 0.1 1 27083 1447 25 18607 0.1 1 17836 771 26 17570 0.1 1 16733 837 27 10369 0.1 1 9719 650 28 26829 0.1 1 25809 1020 29 5986 0.1 1 5499 487 30 23753 0.1 1 22893 860 31 8001 0.1 1 7469 532 32 44562 0.1 1 43349 1213 33 13829 0.1 1 13159 670 34 4413 0.1 1 4065 348 35 23178 0.1 1 22495 683 36 4811 0.1 1 4512 299 37 9949 0.1 1 9472 477 38 3118 0.1 1 2940 178 39 5489 0.1 1 5229 260 40 1309 0.1 1 1223 86 41 9613 0.1 1 9261 352 42 13101 0.1 1 12699 402 43 4956 0.1 1 4710 246 44 8731 0.1 1 8370 361 45 16619 0.1 1 16155 464 46 6813 0.1 1 6510 303 47 3769 0.1 1 3616 153 48 15026 0.1 1 14589 437 49 3833 0.1 1 3678 155 50 1098 0.1 1 1019 79 51 9289 0.1 1 9011 278 52 15274 0.1 1 14904 370 53 4134 0.1 1 3986 148 54 5251 0.1 1 5085 166 55 2132 0.1 1 2063 69 56 1191 0.1 1 1138 53 57 2299 0.1 1 2215 84 58 2389 0.1 1 2297 92 59 1056 0.1 1 1001 55 60 693 0.1 1 647 46 61 708 0.1 1 657 51 62 635 0.1 1 588 47 63 777 0.1 1 738 39 64 1588 0.1 1 1524 64 65 1955 0.1 1 1868 87 66 2047 0.1 1 1964 83 67 1954 0.1 1 1884 70 68 1866 0.1 1 1781 85 69 1667 0.1 1 1603 64 70 1558 0.1 1 1492 66 71 1433 0.1 1 1377 56 72 1397 0.1 1 1343 54 73 1311 0.1 1 1253 58 74 1112 0.1 1 1053 59 75 1134 0.1 1 1085 49 76 1075 0.1 1 1029 46 77 961 0.1 1 919 42 78 969 0.1 1 932 37 79 908 0.1 1 843 65 80 855 0.1 1 827 28 81 788 0.1 1 751 37 82 752 0.1 1 717 35 83 664 0.1 1 638 26 84 608 0.1 1 580 28 85 572 0.1 1 531 41 86 517 0.1 1 491 26 87 500 0.1 1 472 28 88 502 0.1 1 477 25 89 425 0.1 1 408 17 90 412 0.1 1 384 28 91 406 0.1 1 376 30 92 378 0.1 1 364 14 93 311 0.1 1 288 23 94 349 0.1 1 317 32 95 314 0.1 1 289 25 96 291 0.1 1 270 21 97 264 0.1 1 244 20 98 273 0.1 1 258 15 99 249 0.1 1 231 18 100 247 0.1 1 231 16 101 235 0.1 1 217 18 102 198 0.1 1 182 16 103 191 0.1 1 180 11 104 207 0.1 1 191 16 105 136 0.1 1 123 13 106 155 0.1 1 138 17 107 158 0.1 1 139 19 108 156 0.1 1 138 18 109 149 0.1 1 134 15 110 149 0.1 1 132 17 111 131 0.1 1 121 10 112 93 0.1 1 83 10 113 159 0.1 1 147 12 114 108 0.1 1 96 12 115 101 0.1 1 86 15 116 117 0.1 1 105 12 117 88 0.1 1 80 8 118 113 0.1 1 106 7 119 91 0.1 1 81 10 120 112 0.1 1 105 7 121 89 0.1 1 78 11 122 94 0.1 1 88 6 123 90 0.1 1 78 12 124 87 0.1 1 79 8 125 95 0.1 1 83 12 126 156 0.1 1 149 7 127 127 0.1 1 116 11 128 168 0.1 1 156 12 129 151 0.1 1 127 24 130 134 0.1 1 121 13 131 117 0.1 1 99 18 132 152 0.1 1 143 9 133 115 0.1 1 98 17 134 148 0.1 1 126 22 135 102 0.1 1 93 9 136 125 0.1 1 103 22 137 166 0.1 1 149 17 138 110 0.1 1 99 11 139 119 0.1 1 100 19 140 89 0.1 1 72 17 141 49 0.1 1 42 7 142 108 0.1 1 81 27 143 58 0.1 1 46 12 144 46 0.1 1 30 16 145 49 0.1 1 28 21 146 94 0.1 1 39 55 147 49 0.1 1 34 15 148 167 0.1 1 115 52 149 50 0.1 1 29 21 150 21 0.1 1 11 10 151 338 0.1 1 261 77 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz ============================================= 3532417 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 3532417 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 37926 (1.07%)