Question: Hello, I am attempting to use PAMLX v1.3.1 to calculate dN/dS statistics for the SLC22A12 gene. I got the program to run, but it printed empty files when using the YN00 functionality.

The (verbose) output is below. Can anyone help me understand what the problem is, or if not, what the next troubleshooting steps might be?

```
/Volumes/pamlX1.3.1+paml4.8a-osx-x86_64/pamlX.app/Contents/paml4.8/bin/yn00 running...
YN00 in paml version 4.8a, August 2014
Reading options from yn00.ctl.tmp..
5 icode | icode 0.00
6 weighting | weighting 0.00
7 commonkappa | commonkappa 1.00
8 commonf3x4 | commonf3x4 0.00
9 ndata | ndata 1.00

processing fasta file
reading seq# 1 gi|399498484|dbj|AB738914.1| 3234 sites
reading seq# 2 gi|399498482|dbj|AB738913.1| 3234 sites
reading seq# 3 gi|426369028|ref|XM_004051452.1| 3234 sites
reading seq# 4 gi|694945115|ref|XM_003951921.2| 3234 sites
reading seq# 5 gi|37181473|gb|AY358183.1| 3234 sites
ns = 5 ls = 3234
Reading sequences, sequential format..
Reading seq # 1: gi|399498484|dbj|AB738914.1|
Reading seq # 2: gi|399498482|dbj|AB738913.1|
Reading seq # 3: gi|426369028|ref|XM_004051452.
Reading seq # 4: gi|694945115|ref|XM_003951921.
Reading seq # 5: gi|37181473|gb|AY358183.1|
Sites with gaps or missing data are removed.

777 ambiguity characters in seq. 1
1572 ambiguity characters in seq. 2
3 ambiguity characters in seq. 3
329 ambiguity characters in seq. 4
820 ambiguity characters in seq. 5
633 sites are removed. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078
Sequences read..
Counting site patterns.. 0:00

119 patterns at 445 / 445 sites (100.0%), 0:00

stop codon TAA in seq # 1: gi|399498484|dbj|AB738914.1|

codons in other sequences are
seq # 1 gi|399498484|dbj|AB738914.1| TAA
seq # 2 gi|399498482|dbj|AB738913.1| TAA
seq # 3 gi|426369028|ref|XM_004051452. TAA
seq # 4 gi|694945115|ref|XM_003951921. TAA
seq # 5 gi|37181473|gb|AY358183.1| TAA
/Volumes/pamlX1.3.1+paml4.8a-osx-x86_64/pamlX.app/Contents/paml4.8/bin/yn00 finished
```

Answer: PAML halts execution when it identifies a stop codon in the sequences, as indicated above:

stop codon TAA in seq # 1: gi|399498484|dbj|AB738914.1|

Make sure you remove any terminal (or internal - potentially a problem!) stop codons prior to execution.