Running species delimitation, my first gene (mt) loads in fine, then my second gene (of five), no matter which one it is - ends up with an "error" that I've pasted below. I'm sure it's something silly I'm missing either in my data or the control file. I'm using the latest version of BPP (with the GUI BPPX). Any help or suggestions would be much appreciated!
Thanks,
Alex
ns = 116 ls = 209
Reading sequences, sequential format..
Reading seq # 1: 65381a^1
Reading seq # 2: 65381b^1
Reading seq # 3: 65392a^2
Reading seq # 4: 65392b^2
Reading seq # 5: 65496a^3
Reading seq # 6: 65496b^3
Reading seq # 7: 68719a^4 Reading seq ETC ETC ETC* <-- Cutting out the long part of the list
Reading seq #116: MHP8482_Rb^59
Sequences read..
Counting site patterns.. 0:00
11 patterns at 209 / 209 sites (100.0%), 0:00
Counting site patterns again, for JC69.
new no. site patterns: 7
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Anonymous
Anonymous
-
2013-10-07
I think I may have figured it out but it's one of a few things. The thing that sticks out, though, is that in the GUI, when you try to change the sequences per population, there is a bug where you can't enter over 99. Three digits is out. If you change the actual control file you can then load the file back into the GUI and it works like normal.
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thanks for noting this. i'll ask xu bo to change bppX.
ziheng
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Anonymous
Anonymous
-
2015-06-05
Hi, you still can't enter more than 99 in nloci.
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Anonymous
Anonymous
-
2014-04-14
Hi there,
I'm using bppX to try to delimit some cryptic species I am working on. When I ran bppX with the example files it ran well and completed the analysis quickly. Unfortunately when I tried to run my own data (several times) I received a "killed" message that is hard to decipher, perhaps someone could assist please?
My data set has 13 putative "species" and two genes with several hundred sequences for each of the two genes. Below is the error message that I receive from bppX:
It appears from the control file (attached) that the bpp programme reads everything in the control file okay until it gets to the newick tree and then it seems to be "killed" when it hits the name of the first individual sequence in the tree (called 33Lukosi)... and then the programme quits for some unknown reason.
Also, do the sequence names in the phylip file have to be fewer than 10 characters for the programme to run correctly?
Any help or suggestions are greatly appreciated, thanks in advance!
something seems to be wrong with the sequence data file.
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Anonymous
Anonymous
-
2014-04-22
I've solved one problem, but now getting a different error message. In the first instance, I'd had the wrong newick tree in my file, because I'd used the full species tree rather than the simplified version with just the species names that were delimited as input.
Unfortunately, I have tried to run it again, both using bppX and bpp.exe (Windows) and am now getting the following cryptic error message:
"Error: too many daughter nodes, raise MAXNSONS."
Any idea what "MAXNSONS" is and how I can fix it please? Suggestions greatly appreciated!
Thanks,
Jen
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Anonymous
Anonymous
-
2014-05-29
I had the same problem "Error: too many daughter nodes, raise MAXNSONS". How can it be solved? My tree is fully resolved but I had that same problem. How can I raise the MAXNSONS?
Thanks,
Claydson
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HI,
Running species delimitation, my first gene (mt) loads in fine, then my second gene (of five), no matter which one it is - ends up with an "error" that I've pasted below. I'm sure it's something silly I'm missing either in my data or the control file. I'm using the latest version of BPP (with the GUI BPPX). Any help or suggestions would be much appreciated!
Thanks,
Alex
ns = 116 ls = 209
Reading sequences, sequential format..
Reading seq # 1: 65381a^1
Reading seq # 2: 65381b^1
Reading seq # 3: 65392a^2
Reading seq # 4: 65392b^2
Reading seq # 5: 65496a^3
Reading seq # 6: 65496b^3
Reading seq # 7: 68719a^4
Reading seq ETC ETC ETC* <-- Cutting out the long part of the list
Reading seq #116: MHP8482_Rb^59
Sequences read..
Counting site patterns.. 0:00
Counting site patterns again, for JC69.
new no. site patterns: 7
E:\Documents\Alex\Lab\Programs\BPP\bpp2.2\bpp.exe -- killed
I think I may have figured it out but it's one of a few things. The thing that sticks out, though, is that in the GUI, when you try to change the sequences per population, there is a bug where you can't enter over 99. Three digits is out. If you change the actual control file you can then load the file back into the GUI and it works like normal.
thanks for noting this. i'll ask xu bo to change bppX.
ziheng
Hi, you still can't enter more than 99 in nloci.
Hi there,
I'm using bppX to try to delimit some cryptic species I am working on. When I ran bppX with the example files it ran well and completed the analysis quickly. Unfortunately when I tried to run my own data (several times) I received a "killed" message that is hard to decipher, perhaps someone could assist please?
My data set has 13 putative "species" and two genes with several hundred sequences for each of the two genes. Below is the error message that I receive from bppX:
C:\Users\Jen\Desktop\bpp\bppX\bpp.exe running...
bp&p Version 2.2, December 2012
Reading options from bpp.ctl.tmp..
13 species: 1 (4) 2 (8) 3 (11) 4 (94) 5 (2) 6 (9) 7 (4) 8 (54) 9 (4) 10 (98) 11 (42) 12 (55) 13 (7)
Species 33Lukosi?
C:\Users\Jen\Desktop\bpp\bppX\bpp.exe -- killed
It appears from the control file (attached) that the bpp programme reads everything in the control file okay until it gets to the newick tree and then it seems to be "killed" when it hits the name of the first individual sequence in the tree (called 33Lukosi)... and then the programme quits for some unknown reason.
Also, do the sequence names in the phylip file have to be fewer than 10 characters for the programme to run correctly?
Any help or suggestions are greatly appreciated, thanks in advance!
Jen
there is a cryptic error message
"Species 33Lukosi?"
something seems to be wrong with the sequence data file.
I've solved one problem, but now getting a different error message. In the first instance, I'd had the wrong newick tree in my file, because I'd used the full species tree rather than the simplified version with just the species names that were delimited as input.
Unfortunately, I have tried to run it again, both using bppX and bpp.exe (Windows) and am now getting the following cryptic error message:
"Error: too many daughter nodes, raise MAXNSONS."
Any idea what "MAXNSONS" is and how I can fix it please? Suggestions greatly appreciated!
Thanks,
Jen
the guide tree has to be fully resolved.
I had the same problem "Error: too many daughter nodes, raise MAXNSONS". How can it be solved? My tree is fully resolved but I had that same problem. How can I raise the MAXNSONS?
Thanks,
Claydson
the tree has to be a fully resolved tree and has to be rooted. for example ((A, B), C); is fine, but (A, B, C) is not.
pls check.