Thank you very much for this useful software. I have encountered some problems when using this software and hope to get your help.
Firstly, the software is installed according to the guidance provided by you. The data used in the running process is the example data provided by you (gen.txt, pheno.txt and tree.txt in example/example_data), and the command is as follows:
Several files are generated after the run, but also generated the following error message:
Calculating kinship matrix.
Get kinship matrix
Sh: / Users/local/Documents/software/Rworks/bugwas-master/gemma/gemma.0.93 b: always execute a binary file
Kinship matrix calculated successfully.
Rescaled variants.
Single value decomposition complete.
Principle component analysis complete.
Sh: / Users/local/Documents/software/Rworks/bugwas-master/gemma/gemma.0.93 b: always execute a binary file
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
cannot open file '/Users/local/Documents/software/Rworks/bugwas-master/bugwas/R/output//Users/local/Documents/software/Rworks/bugwas-master/example/example_data/prefix_biallelic_lmmout_patterns.log.txt': No such file or directory.
Therefore, I ask for your help to see what the problem is, thank you.
Wish you a happy life.
Thank you very much for this useful software. I have encountered some problems when using this software and hope to get your help. Firstly, the software is installed according to the guidance provided by you. The data used in the running process is the example data provided by you (gen.txt, pheno.txt and tree.txt in example/example_data), and the command is as follows:
data <- lin_loc(gen = "/Users/local/Documents/software/Rworks/bugwas-master/example/example_data/gen.txt", pheno = "/Users/local/Documents/software/Rworks/bugwas-master/example/example_data/pheno.txt", phylo = "/Users/local/Documents/software/Rworks/bugwas-master/example/example_data/tree.txt", prefix = "/Users/local/Documents/software/Rworks/bugwas-master/example/example_data/prefix", gem.path = "/Users/local/Documents/software/Rworks/bugwas-master/gemma/gemma.0.93b")
Several files are generated after the run, but also generated the following error message: Calculating kinship matrix. Get kinship matrix Sh: / Users/local/Documents/software/Rworks/bugwas-master/gemma/gemma.0.93 b: always execute a binary file Kinship matrix calculated successfully. Rescaled variants. Single value decomposition complete. Principle component analysis complete. Sh: / Users/local/Documents/software/Rworks/bugwas-master/gemma/gemma.0.93 b: always execute a binary file Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file '/Users/local/Documents/software/Rworks/bugwas-master/bugwas/R/output//Users/local/Documents/software/Rworks/bugwas-master/example/example_data/prefix_biallelic_lmmout_patterns.log.txt': No such file or directory.
Therefore, I ask for your help to see what the problem is, thank you. Wish you a happy life.