Hello!
I'm trying to implement BPP2 using 21 species in my guide tree, and the program keeps giving me the following error: "Error: raise NSPECIES". The number is definitely 21. I wonder whether there's a maximum number of species the program can deal with... any clue? Thanks!
Ivan Prates, City College of New York
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Has there been any response on this issue? I wish to analyze a dataset that probably hosts more that 30 species. Is this doable with the current version of the software. I have seen that there is a limit of 20 species in the bpp.c file, can we change this?
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Hi, Ari,
I had written to the paml forum long time ago on this issue, and I had received the reply that there is indeed a 20 species limit. So, what I did was breaking my species down into two groups. I was using version 2.1.
Hope this helps. Cheers!
Last edit: MargaritaM 2013-01-25
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The current version is 2.2. the following line in bpp.c sets the maximum # of species in the guide tree. Currently it is set to 50.
define NSPECIES 50 / max # of species /
I found the following item in the bppHistory file, which suggests that the change occurred between 2.1 and 2.2.
(*) The internal species tree representation has changed, allowing a greater number
of species/populations on the guide tree.
best,
ziheng
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Anonymous
Anonymous
-
2014-04-22
Hi Ziheng,
May I ask a question about estimating theta and tau with fixed tree? I have a pretty large dataset (86 taxa and 300 loci, totally ~450,000bp sequences). It runs on version 2.2 with changing Nspecies setup, but it seems slow. So I am not sure whether it could really work with this large dataset. Or is it possible to run with multicores?
Thank you so much,
Xin
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Anonymous
Anonymous
-
2014-10-16
If the tree is fixed, the program should run o.k.
If you are de limiting species, the data set will be too big.
We have not got a plan to parallelize the code yet. We are still trying to improve the serial version.
Ziheng
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Anonymous
Anonymous
-
2014-10-11
Hi,
I'm trying to run the joint species delimitation and species tree estimation model in BPP3. The example datasets work fine but now I've begun exploring with my own, still greatly reduced, dataset (7 loci from 20 samples which fall into anywhere between 4 and 6 species). The program seems to work fine when I define 4 or 6 species but I get an "Error: raise NS in source file." error message when I define 20 species (one per sample). The bpp.c file suggests that up to 47 species should be allowed. I tried raising this number (50, 100, 200) and recompiling, but still get the same message. This happens on both the Mac and PC version. Any idea of what is going on?
Thanks so much for any help!
Dietrich
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The limits are <= 47 populations and <= 200 sequences at each locus.
I just tested the program using 47 populations, and it runs fine.
Most likely there are some other errors in your data files.
if you can't resolve this, you can email me a copy of your data files (3 of them) so that i can have a look.
best,
ziheng
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Anonymous
Anonymous
-
2014-10-16
It was discovered that there were errors in the control file bpp.ctl, and the problem was not due to those limits in the program.
This closes this post,
Ziheng.
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Anonymous
Anonymous
-
2015-06-01
If I can't speak English, how can I use this software...
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Anonymous
Anonymous
-
2017-06-12
Post awaiting moderation.
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Hello!
I'm trying to implement BPP2 using 21 species in my guide tree, and the program keeps giving me the following error: "Error: raise NSPECIES". The number is definitely 21. I wonder whether there's a maximum number of species the program can deal with... any clue? Thanks!
Ivan Prates, City College of New York
Has there been any response on this issue? I wish to analyze a dataset that probably hosts more that 30 species. Is this doable with the current version of the software. I have seen that there is a limit of 20 species in the bpp.c file, can we change this?
Hi, Ari,
I had written to the paml forum long time ago on this issue, and I had received the reply that there is indeed a 20 species limit. So, what I did was breaking my species down into two groups. I was using version 2.1.
Hope this helps. Cheers!
Last edit: MargaritaM 2013-01-25
The current version is 2.2. the following line in bpp.c sets the maximum # of species in the guide tree. Currently it is set to 50.
define NSPECIES 50 / max # of species /
I found the following item in the bppHistory file, which suggests that the change occurred between 2.1 and 2.2.
(*) The internal species tree representation has changed, allowing a greater number
of species/populations on the guide tree.
best,
ziheng
Hi Ziheng,
May I ask a question about estimating theta and tau with fixed tree? I have a pretty large dataset (86 taxa and 300 loci, totally ~450,000bp sequences). It runs on version 2.2 with changing Nspecies setup, but it seems slow. So I am not sure whether it could really work with this large dataset. Or is it possible to run with multicores?
Thank you so much,
Xin
If the tree is fixed, the program should run o.k.
If you are de limiting species, the data set will be too big.
We have not got a plan to parallelize the code yet. We are still trying to improve the serial version.
Ziheng
Hi,
I'm trying to run the joint species delimitation and species tree estimation model in BPP3. The example datasets work fine but now I've begun exploring with my own, still greatly reduced, dataset (7 loci from 20 samples which fall into anywhere between 4 and 6 species). The program seems to work fine when I define 4 or 6 species but I get an "Error: raise NS in source file." error message when I define 20 species (one per sample). The bpp.c file suggests that up to 47 species should be allowed. I tried raising this number (50, 100, 200) and recompiling, but still get the same message. This happens on both the Mac and PC version. Any idea of what is going on?
Thanks so much for any help!
Dietrich
the code has right now
define NSPECIES 47 / max # of species /
define NS 200 / max # of sequences /
The limits are <= 47 populations and <= 200 sequences at each locus.
I just tested the program using 47 populations, and it runs fine.
Most likely there are some other errors in your data files.
if you can't resolve this, you can email me a copy of your data files (3 of them) so that i can have a look.
best,
ziheng
It was discovered that there were errors in the control file bpp.ctl, and the problem was not due to those limits in the program.
This closes this post,
Ziheng.
If I can't speak English, how can I use this software...