Hi, when I try to run codonphyml with the following command line (the input file is "codon" from the examples):
codonphyml -i codon -m GY -f m -n 1 -b 0 -a e -c 4 -v e -o tlr -q --fmodel CF3X4
I get an error:
. 88 patterns found (out of a total of 100 sites).
. Calculation of pairwise distances completed in 2 sec.
. Building BioNJ tree...
. This analysis requires at least 32 Mo of memory space.
. site = 0
. invar = 0.000000
. scale_left = 0 scale_rght = 0
. Lk = 0 LOG(Lk) = -inf < -1.79769E+308
. Err in file lk.c at line 685
If I set these settings in the interactive mode, it runs fine.
For an input file of 4 sequences the same thing happens (demands 14 Mo of memory space).
Am I doing something wrong? Is there something that could solve this?
Thanks!
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Hi Sorry for the late reply again! So you try to run the exact command line above with the sample codon file, correct? Please, let me know so I can try to reproduce the bug. Best.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Sorry for the late reply again! So you try to run the exact command line above with the sample codon file, correct? Please, let me know so I can try to reproduce the bug. Best.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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Hi, when I try to run codonphyml with the following command line (the input file is "codon" from the examples):
codonphyml -i codon -m GY -f m -n 1 -b 0 -a e -c 4 -v e -o tlr -q --fmodel CF3X4
I get an error:
. 88 patterns found (out of a total of 100 sites).
. 38 sites without polymorphism (38.00%).
. Computing pairwise distances...100.00% concluded.
. Calculation of pairwise distances completed in 2 sec.
. Building BioNJ tree...
. This analysis requires at least 32 Mo of memory space.
. site = 0
. invar = 0.000000
. scale_left = 0 scale_rght = 0
. Lk = 0 LOG(Lk) = -inf < -1.79769E+308
. Err in file lk.c at line 685
If I set these settings in the interactive mode, it runs fine.
For an input file of 4 sequences the same thing happens (demands 14 Mo of memory space).
Am I doing something wrong? Is there something that could solve this?
Thanks!
Hi Sorry for the late reply again! So you try to run the exact command line above with the sample codon file, correct? Please, let me know so I can try to reproduce the bug. Best.
Hi sorry for the late reply. Last semester was a busy one. Can you please attach the data set so i can test and look for the same error.
Best wishes for 2016!
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Hi, I'm getting the same error. Was there a solution?
Cheers
Hi Sorry for the late reply again! So you try to run the exact command line above with the sample codon file, correct? Please, let me know so I can try to reproduce the bug. Best.