Dear all,
I'm having problems with phyloch's raxml command (I'm running R version
3.0.2). For instance, if I run:
>data(woodmouse)
>MLtree <- raxml(woodmouse, runs = c(2, 5))
...
RAxML was called as follows:
./raxmlHPC -f d -m GTRCAT -s fromR -# 2 -n fromR.tre
Partition: 0 with name: No Name Provided
Base frequencies: 0.307 0.261 0.126 0.306
Error: you need to specify a random number seed with "-p" for the
randomized stepwise addition
parsimony algorithm or random tree building algorithm such that runs can be
reproduced and debugged ... exiting
done.
Non-parametric bootstrapping ...
Error, in bipartition and IC computation mode you must specify a file
containing multiple trees with the "-z" option
done.
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
cannot open file 'RAxML_result.fromR.tre.RUN.': No such file or directory
Any help will be greatly appreciated.
Jonathan
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