Hello -  I am working with the .bgen files from the UK Biobank imputed data and trying to use qctool to help convert these files.

 

I am having problems building the tool and after trying to troubleshoot for a couple days, am still stuck.

I have downloaded the latest version of the qctool V2 available. The configure step ran successively but then I run into problems.

 

When I run the ./waf-1.5.18 configure, this is my output:

 

$ ./waf-1.5.18 configure

Setting blddir to                        : /mnt/speed/glymourlab/Teresa/gavinband-qctool-621f8d24625b/build 

('Using prefix\t\t\t\t :', '/usr/local')

Checking for program g++ or c++          : /usr/bin/g++ 

Checking for program cpp                 : /usr/bin/cpp 

Checking for program ar                  : /usr/bin/ar 

Checking for program ranlib              : /usr/bin/ranlib 

Checking for g++                         : ok  

Checking for program gcc or cc           : /usr/bin/gcc 

Checking for gcc                         : ok  

Checking for compiler flags -std=c++11   : no 

Checking for library blas                : yes 

Checking for library lapack              : yes 

Checking for header sys/time.h           : yes 

Checking for static library z            : yes 

Checking for library dl                  : yes 

Checking for library rt                  : yes 

Checking for library m                   : yes 

Checking for library pthread             : yes 

Checking for library readline            : yes 

'configure' finished successfully (3.162s)

 

I then try ./waf-1.5.18 and this error:

 

Build failed:  -> task failed (err #1): 

                {task: cxx PloidyConvertingSNPDataSource.cpp -> PloidyConvertingSNPDataSource_1.o}

 

 

Do you have any thoughts on what could be happening? Thank you very much for any help, I am pretty new to linux, fyi.

 

Teresa