Open VibrantStarling opened 3 years ago
I had the same issue and I think I've figured it out. Assuming you've installed the appropriate conda packages for CONCOCT, blas, mkl, and llvm-openmp, the issue is that libmkl_intel_thread.so can't find libiomp5.so in the environment's lib
. This is because installing CONCOCT 1.1.0 downgraded llvm-openmp (12.0.1 to 8.?) which for some reason got rid of it. The hack is to symlink libiomp5.so to lib
until there is a more permanent fix, like so:
ln -s ../anaconda3/pkgs/intel-openmp-2019.4-243/lib/libiomp5.so ../anaconda3/envs/binning/lib/libiomp5.so
Update: After I added the symlink, CONCOCT works great on command line, but it still fails in metaWRAP. I've tried updating llvm-openmp
and intel-openmp
but still, same issue and I have no idea how to fix it.
I have this problem too
Hi I'm having an issue with running concoct. It fails to run and produces the following warning. I've also tried running it in the metaWRAP environment step by step according to concocts' instructions and it fails in the same way at the "concoct" stage with the symbol lookup error. Initially ran it with metabat and maxbin at the same time and got the same error.
Unsure how to address this as it seems like it might be an issue in the program itself but i don't really know. Any ideas?
I'm running metawrap 1.2.1 in debian on a remote server.