prophyle : Unfinished, an error occurred (error code 1) during "make test"

[albertw1706]

[karel-brinda]

Unfortunately, just from a screenshot like this nothing meaningful can be said. The relevant error message and command might be above the screenshot; the OS, type of computer, .... are not provided, etc. Might be related to something like a non-standard shell, but this would require a proper description and full log info.

[albertw1706]

Sorry for not being clear last time, it was about the zlib.h that cannot be found. I am currently using Ubuntu 20.04.

[karel-brinda]

ProPhyle uses two C/C++ tools distributed in its directory, which use kseq to read FASTA files. For them to be compiled correctly, they require zlib as a dependency. The solution is to install the missing package through the Ubuntu package manager sudo apt-get install libz-dev.

[albertw1706]

Seems like zlib have already be downloaded in my machine. I think this might be a similar issue with the "Cannot find zlib.h." thread. Do you have any guide to fix this as I have tried the solution from Arnie, but it does not seem to work?

[karel-brinda]

I would suggest to manually cd to the directory with prophyle_index and running make manually. It might be an issue with the default compiler, and in such a case it might help to change it by make CC=my_correct_gcc_executable.

[karel-brinda]

This is the directory in your case:

Btw. prophex (prophyle_index) is based on bwa so all these issues are related to compilation of bwa.

[karel-brinda]

One additional suggestion. Go to the directory as described above, run make clean and then make.