I passed the installation but got an error related with loading the shared library libffindex.so.0.1. >>
Preparing HHblits files for local
CMD: /home/yjx/Programs/JAMg/3rd_party/hhsuite/bin/ffindex_from_fasta -s /data/YJX/PacBio/Pilon/S288c_pilon.fasta.masked.exons.aa.trim.db /data/YJX/PacBio/Pilon/S288c_pilon.fasta.masked.exons.aa.trim.db.idx /data/YJX/PacBio/Pilon/S288c_pilon.fasta.masked.exons.aa.trim
/home/yjx/Programs/JAMg/3rd_party/hhsuite/bin/ffindex_from_fasta: error while loading shared libraries: libffindex.so.0.1: cannot open shared object file: No such file or directory
Error, cmd died with ret 32512
For your reference, I did find a copy of "libffindex.so.0.1" under "~/Programs/JAMg/3rd_party/hhsuite/lib64" but somehow the binaries compiled with JAMg still complains about this. I got around this problem by using a standalone version of hhsuite to replace the version compiled with JAMg.