I am trying to run an analysis on a fixed species tree with three species. When I try and run the control file I get an error message that says "Error:raise NS in source file." I have compared this control fine with another that seems to work fine, but cannot find any difference. Any help with this would be great!
Chris
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Anonymous
Anonymous
-
2013-06-27
I noticed that if I decrease the number of sequences per species in the control file the error disappears. I have gone over the number of sequences etc. many times and everything appears accurate. I tried creating a reduced data set and I do not receive this error. Perhaps I have too many sequences (~570) in the sequence file?
When I run the reduced data set I receive a different error stating "Error: sequences must be tagged by population ID." However, every sequence in the alignment file does in fact have an individual ID that is mapped to a species in the Imap file. Perhaps it is something simple that I am not seeing....
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Anonymous
Anonymous
-
2013-10-13
The source file bpp.c has a line near the beginning which looks like this
define NS 500
Check the value there. If this is smaller than the maximum number of sequences in one alignment at any locus, the program won't run. You can increase the value and recompile.
I am not sure about the second error message. Each seq must end with a tag, like
Seq1^specimen123
Does saving the file again help?
Perhaps you can prepare a smaller data set with say 5 seqs from each species and see whether it runs.
Ziheng
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I am trying to run an analysis on a fixed species tree with three species. When I try and run the control file I get an error message that says "Error:raise NS in source file." I have compared this control fine with another that seems to work fine, but cannot find any difference. Any help with this would be great!
Chris
I noticed that if I decrease the number of sequences per species in the control file the error disappears. I have gone over the number of sequences etc. many times and everything appears accurate. I tried creating a reduced data set and I do not receive this error. Perhaps I have too many sequences (~570) in the sequence file?
When I run the reduced data set I receive a different error stating "Error: sequences must be tagged by population ID." However, every sequence in the alignment file does in fact have an individual ID that is mapped to a species in the Imap file. Perhaps it is something simple that I am not seeing....
The source file bpp.c has a line near the beginning which looks like this
define NS 500
Check the value there. If this is smaller than the maximum number of sequences in one alignment at any locus, the program won't run. You can increase the value and recompile.
I am not sure about the second error message. Each seq must end with a tag, like
Seq1^specimen123
Does saving the file again help?
Perhaps you can prepare a smaller data set with say 5 seqs from each species and see whether it runs.
Ziheng