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I think I already posted a thread with the same issue in the auto section, but it looks like it's gone. Anyways, when I run 

 HHEd -A -D -T 1 -H hmm12/macros -H hmm12/hmmdefs -M hmm13 tree.hed triphones1

 

I eventually get the error message:

"

AU ./interim_files/fulllist

 Creating HMMset using trees to add unseen triphones

  ERROR [+2662]  AssignStructure: cannot find tree for b state 2

 FATAL ERROR - Terminating program C:\cygwin\HTK\htk-3.3-windows-binary\htk\HHEd

.exe

"

 

And the hmm13 files aren't created. There's a whole bunch of "warnings earlier", for example...

 

"

TB 350.00 ST__4_ {}

 Tree based clustering

 WARNING [-2631]  TreeBuildCommand: No items to cluster for ST__4_

 in C:\cygwin\HTK\htk-3.3-windows-binary\htk\HHEd.exe

 

TB 350.00 ST_si_4_ {}

 Tree based clustering

 WARNING [-2631]  TreeBuildCommand: No items to cluster for ST_si_4_

 in C:\cygwin\HTK\htk-3.3-windows-binary\htk\HHEd.exe

"

 

 

I don't know if that would elucidate the issue. I'll try to post the entire program output in a followup, if I can get the entire program output.