SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_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/NR006_S3_L001_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 90.38 s (26 us/read; 2.27 M reads/minute). === Summary === Total reads processed: 3,414,678 Reads with adapters: 2,052,960 (60.1%) Reads written (passing filters): 3,414,678 (100.0%) Total basepairs processed: 511,788,024 bp Quality-trimmed: 118,164 bp (0.0%) Total written (filtered): 489,484,820 bp (95.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2052960 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.3% C: 24.6% G: 20.0% T: 22.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 957570 853669.5 0 957570 2 185662 213417.4 0 185662 3 88214 53354.3 0 88214 4 62857 13338.6 0 62857 5 648 3334.6 0 648 6 22936 833.7 0 22936 7 21575 208.4 0 21575 8 26642 52.1 0 26642 9 18194 13.0 0 18044 150 10 23184 3.3 1 21583 1601 11 22594 0.8 1 20464 2130 12 44904 0.2 1 41486 3418 13 394 0.1 1 140 254 14 26379 0.1 1 23897 2482 15 37633 0.1 1 34681 2952 16 156 0.1 1 67 89 17 24969 0.1 1 23055 1914 18 15222 0.1 1 13957 1265 19 25320 0.1 1 23370 1950 20 18350 0.1 1 16863 1487 21 15725 0.1 1 14432 1293 22 17997 0.1 1 16711 1286 23 18683 0.1 1 17160 1523 24 31064 0.1 1 28646 2418 25 16194 0.1 1 15046 1148 26 15991 0.1 1 14743 1248 27 9854 0.1 1 8749 1105 28 25467 0.1 1 24052 1415 29 5203 0.1 1 4539 664 30 22296 0.1 1 21075 1221 31 7804 0.1 1 7015 789 32 37956 0.1 1 36145 1811 33 13298 0.1 1 12180 1118 34 4051 0.1 1 3571 480 35 18620 0.1 1 17659 961 36 5530 0.1 1 5038 492 37 7956 0.1 1 7339 617 38 4368 0.1 1 4085 283 39 5419 0.1 1 5047 372 40 2384 0.1 1 2228 156 41 8956 0.1 1 8433 523 42 11614 0.1 1 11004 610 43 5102 0.1 1 4746 356 44 7806 0.1 1 7359 447 45 12470 0.1 1 11850 620 46 5755 0.1 1 5352 403 47 4015 0.1 1 3771 244 48 10930 0.1 1 10468 462 49 4516 0.1 1 4246 270 50 1545 0.1 1 1442 103 51 7427 0.1 1 7059 368 52 11021 0.1 1 10573 448 53 4130 0.1 1 3937 193 54 4451 0.1 1 4236 215 55 2750 0.1 1 2622 128 56 1357 0.1 1 1273 84 57 2213 0.1 1 2091 122 58 2275 0.1 1 2152 123 59 1161 0.1 1 1103 58 60 739 0.1 1 682 57 61 628 0.1 1 577 51 62 684 0.1 1 638 46 63 847 0.1 1 799 48 64 1373 0.1 1 1321 52 65 1579 0.1 1 1493 86 66 1616 0.1 1 1543 73 67 1569 0.1 1 1490 79 68 1449 0.1 1 1378 71 69 1380 0.1 1 1323 57 70 1355 0.1 1 1285 70 71 1219 0.1 1 1169 50 72 1120 0.1 1 1065 55 73 989 0.1 1 950 39 74 939 0.1 1 898 41 75 833 0.1 1 798 35 76 880 0.1 1 836 44 77 792 0.1 1 760 32 78 719 0.1 1 680 39 79 660 0.1 1 631 29 80 658 0.1 1 626 32 81 635 0.1 1 608 27 82 550 0.1 1 524 26 83 496 0.1 1 467 29 84 532 0.1 1 505 27 85 454 0.1 1 432 22 86 439 0.1 1 419 20 87 375 0.1 1 359 16 88 384 0.1 1 363 21 89 367 0.1 1 356 11 90 357 0.1 1 347 10 91 323 0.1 1 308 15 92 278 0.1 1 267 11 93 275 0.1 1 263 12 94 227 0.1 1 214 13 95 234 0.1 1 224 10 96 199 0.1 1 183 16 97 214 0.1 1 194 20 98 342 0.1 1 285 57 99 253 0.1 1 223 30 100 225 0.1 1 211 14 101 211 0.1 1 182 29 102 180 0.1 1 168 12 103 137 0.1 1 126 11 104 155 0.1 1 143 12 105 124 0.1 1 122 2 106 113 0.1 1 104 9 107 296 0.1 1 288 8 108 113 0.1 1 107 6 109 111 0.1 1 107 4 110 108 0.1 1 102 6 111 110 0.1 1 104 6 112 105 0.1 1 101 4 113 106 0.1 1 97 9 114 81 0.1 1 76 5 115 114 0.1 1 109 5 116 105 0.1 1 94 11 117 96 0.1 1 87 9 118 97 0.1 1 88 9 119 92 0.1 1 87 5 120 93 0.1 1 89 4 121 83 0.1 1 77 6 122 91 0.1 1 88 3 123 99 0.1 1 91 8 124 107 0.1 1 92 15 125 112 0.1 1 104 8 126 95 0.1 1 89 6 127 115 0.1 1 104 11 128 105 0.1 1 101 4 129 79 0.1 1 76 3 130 138 0.1 1 127 11 131 122 0.1 1 113 9 132 107 0.1 1 97 10 133 87 0.1 1 80 7 134 123 0.1 1 109 14 135 102 0.1 1 93 9 136 106 0.1 1 92 14 137 93 0.1 1 78 15 138 89 0.1 1 76 13 139 92 0.1 1 77 15 140 45 0.1 1 35 10 141 57 0.1 1 43 14 142 78 0.1 1 61 17 143 29 0.1 1 15 14 144 27 0.1 1 13 14 145 13 0.1 1 7 6 146 19 0.1 1 9 10 147 21 0.1 1 9 12 148 50 0.1 1 29 21 149 16 0.1 1 8 8 150 19 0.1 1 10 9 151 150 0.1 1 26 124 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz ============================================= 3414678 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 3414678 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 99013 (2.90%)