How come I'm not getting a dN/dS in my output file

[JAM]

I'm trying to get the average dN/dS for the entire tree, I'm running mode = 0. Yet, my output file does not have a dN/dS printed out. I attached my control file and screenshot of my output file. Any ideas of what I could be doing wrong. Thanks in advance for any help offered.

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Codon position x base (3x4) table, overall

position  1:    T:0.21108    C:0.25373    A:0.32882    G:0.20636

position  2:    T:0.40644    C:0.28178    A:0.19059    G:0.12118

position  3:    T:0.21908    C:0.27579    A:0.45483    G:0.05031

Average         T:0.27887    C:0.27043    A:0.32475    G:0.12595

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):

  0.01958765  0.02465826  0.04066624  0.00449795

  0.01357970  0.01709504  0.02819304  0.00311834

  0.00918531  0.01156309  0.00000000  0.00000000

  0.00584023  0.00735208  0.01212500  0.00134111

  0.02354484  0.02963984  0.04888184  0.00540665

  0.01632314  0.02054867  0.03388873  0.00374832

  0.01104098  0.01389913  0.02292235  0.00253536

  0.00702010  0.00883738  0.01457455  0.00161204

  0.03051345  0.03841239  0.06334947  0.00700687

  0.02115432  0.02663049  0.04391883  0.00485771

  0.01430879  0.01801287  0.02970671  0.00328576

  0.00909785  0.01145299  0.00000000  0.00000000

  0.01914978  0.02410704  0.03975718  0.00439741

  0.01327614  0.01671290  0.02756280  0.00304863

  0.00897998  0.01130461  0.01864349  0.00206209

  0.00570968  0.00718773  0.01185395  0.00131113

TREE #  1:  (1, 2, (((((((3, 4, 5), 6, (73, 74, 75)), (76, (77, 78))), (((62, 69), (67, 68)), (70, 71))), 10, (12, 16, 19, 20), (21, (29, 30))), (((((((((7, 8, 83), ((9, 56, 57), 61)), ((58, 59), 60)), 41), ((11, 81), (28, (35, ((36, 37), 38))))), (((((22, 31), 23, 25, 26), 24), (47, 49)), ((55, 72), (63, (64, 65), 66)))), ((27, 32, 33, 34), (45, (48, 54))), 46, (50, 51), 52), 53), 39, 44, (79, 80, 82)), (13, (14, 15, 17, 18))), (40, (42, 43))));   MP score: 4469

lnL(ntime:140  np:142): -34946.486437      +0.000000

  84..1    84..2    84..85   85..86   86..87   87..88   88..89   89..90   90..91   91..3    91..4    91..5    90..6    90..92   92..73   92..74   92..75   89..93   93..76   93..94   94..77   94..78   88..95   95..96   96..97   97..62   97..69   96..98   98..67   98..68   95..99   99..70   99..71   87..10   87..100 100..12  100..16  100..19  100..20   87..101 101..21  101..102 102..29  102..30   86..103 103..104 104..105 105..106 106..107 107..108 108..109 109..110 110..111 111..7   111..8   111..83  110..112 112..113 113..9   113..56  113..57  112..61  109..114 114..115 115..58  115..59  114..60  108..41  107..116 116..117 117..11  117..81  116..118 118..28  118..119 119..35  119..120 120..121 121..36  121..37  120..38  106..122 122..123 123..124 124..125 125..126 126..22  126..31  125..23  125..25  125..26  124..24  123..127 127..47  127..49  122..128 128..129 129..55  129..72  128..130 130..63  130..131 131..64  131..65  130..66  105..132 132..133 133..27  133..32  133..33  133..34  132..134 134..45  134..135 135..48  135..54  105..46  105..136 136..50  136..51  105..52  104..53  103..39  103..44  103..137 137..79  137..80  137..82   86..138 138..13  138..139 139..14  139..15  139..17  139..18   85..140 140..40  140..141 141..42  141..43 

 0.000274 0.000004 0.003245 0.000542 0.000274 0.000274 0.000273 0.000274 0.000274 0.000004 0.000004 0.000004 0.000004 0.000274 0.000274 0.000004 0.000541 0.000004 0.000274 0.000274 0.000004 0.000004 0.001350 0.000543 0.001080 0.000274 0.000004 0.000273 0.000004 0.000004 0.000541 0.000274 0.000004 0.001620 0.003241 0.000004 0.000541 0.000273 0.000540 0.001890 0.000274 0.000541 0.000004 0.000004 0.000812 0.001083 0.001560 0.538161 0.163144 0.114172 0.062298 0.013112 0.003566 0.001904 0.001088 0.001359 0.003261 0.000276 0.001089 0.002724 0.003541 0.002177 0.011926 0.000319 0.001897 0.001306 0.002734 0.063359 0.175188 0.001123 0.000817 0.000817 0.000788 0.000276 0.000276 0.000546 0.001362 0.000276 0.000004 0.000276 0.000277 0.171425 0.124601 0.047403 0.000967 0.001621 0.001079 0.001347 0.001886 0.004324 0.003238 0.001460 0.041916 0.004174 0.006671 0.172053 0.002254 0.000275 0.000004 0.002383 0.001089 0.001089 0.000004 0.000004 0.001634 0.004008 0.005989 0.000541 0.001890 0.002701 0.001889 0.009571 0.002156 0.001284 0.003868 0.004134 0.003575 0.002163 0.001023 0.000329 0.003303 0.003524 0.003241 0.004055 0.006512 0.000004 0.000004 0.000004 0.000809 0.001353 0.001892 0.000004 0.000004 0.000274 0.000004 0.002436 0.000539 0.001083 0.000004 0.000541 7.876402 0.041451

[JAM]

I have uploaded the complete output file 

[astronautmike02]

Hi

Your output file seems to be incomplete, which means the run did not finish for some reason. Maybe you computer turned off or hibernated while running. Try running again and make sure it finishes. Once you do that, your file should contain the estimated dn/ds coefficient right below the tree.

[Ziheng]

yes, there should be more output in the file, with some annotations of the parameter estimates.

the last two numbers 

7.876402 0.041451

are for kappa and w (dN/dS), so the estimate for w is 0.0414.

this is very low (<<1) and seems to be typical of mt genes.

ziheng

[Pouya M. Noparvar]

Hi every body,

I have the similar problem but my output is finished. my sequence is aa i checked phy, tree and clt files multiple times but i cant find any reason or solution for incomplete output.

can anybody help me with this chalenge?

Pouya

[Janet Young]

hi Pouya,

dN/dS is a metric you can only obtain from nucleotide alignments, so you won't get it in amino acid mode. The output file will look very different for amino acid  alignments than it does for nucleotide alignments.

I think your analysis is complete - I think the "Time used: 1:39" line at the end of the outputs (the log file and the out_M0.txt file) means it finished fine.

all the best,

Janet