Thanks so much for sharing this great pipeline. I just ran into an issue with gmap in the refine pipeline. The gmap_build.py and gmap.py scripts in the dependencies folder both call gmap_build and gmap with an argument that specifies both the database output directory and the database prefix in one file path. The gmap version that installed with my eukmetasanity installation threw an error with this, saying that that the database name and the database path have to be separate arguments. I was able to fix this by editing the arguments in the run function.
Thanks so much for sharing this great pipeline. I just ran into an issue with gmap in the refine pipeline. The
gmap_build.pyandgmap.pyscripts in the dependencies folder both callgmap_buildandgmapwith an argument that specifies both the database output directory and the database prefix in one file path. The gmap version that installed with my eukmetasanity installation threw an error with this, saying that that the database name and the database path have to be separate arguments. I was able to fix this by editing the arguments in the run function.