Problem on running HAWK 0.9.8 beta: on the EIG6.0.1-Hawk/bin/smartpca step
leoisl opened this issue · comments
Hello,
I am trying to run HAWK 0.9.8 beta (downloaded from http://atifrahman.github.io/HAWK/) on bacterial strains where I do not have a reference genome. I managed to run HAWK 0.8.3 Beta on these strains, but I can't do it for the new HAWK version associated with the publication https://elifesciences.org/articles/32920. I am blocked when running EIG6.0.1-Hawk/bin/smartpca -V -p <hawk_dir>/parfile.txt
. The main problem is that smartpca
takes 3 input files:
genotypename: gwas_eigenstratX.geno
snpname: gwas_eigenstratX.snp
indivname: gwas_eigenstratX.ind
but the previous steps (k-mer counting with script supplements/countKmers
and the lines before invoking smartpca
in script supplements/runHawk
) did not produce gwas_eigenstratX.geno
and gwas_eigenstratX.snp
, but only gwas_eigenstratX.ind
. Since these files do not exist, smartpca
fails, and since these 3 input files are required, I do not manage to run them. I also did not find any documentation on this regard.
Could you point me any direction on how to solve this?
Thank you in advance.
Did you update hawkDir correctly to run the latest version of hawk (0.9.8)? The new version should generate gwas_eigenstratX.geno and gwas_eigenstratX.snp. Lines 621 to 642 here
https://github.com/atifrahman/HAWK/blob/master/hawk.cpp
Hello,
Thanks for the fast and detailed answer. Hawk is running ok, the problem was on my end, I had a mistake in my runHawk shell script. Sorry about this, thank you again for the answer.