Hey everyone, I encountered this issue but was able to fix it myself. I'll leave it here, in case anyone encounters the same problem.
I created a custom database starting with MSA files, based on the tutorial. When I tried to open the nohup log, it was asking me if I really wanted to open it, since it could be a binary and the names of my files where butchered, like
AAA32308.1__J02451_CDS.faa.mafft<AA>p<A0>^C 58656246 1045 126 0
but I thought nothing of it.
Later I ran hhblits against this database and kept getting segmentation faults along the way. I traced it back to the part of the database creation, where you add a consensus sequence (that prints the previous table). Apparently, the file names can't be longer than 32 symbols, otherwise it will cause trouble. Once I cut the file names to the allowed size, all went smoothly.
Edit: I just saw, this is also the case for ffindex_build -s ../<db>_msa.ff{data,index} . already
Hey everyone, I encountered this issue but was able to fix it myself. I'll leave it here, in case anyone encounters the same problem.
I created a custom database starting with MSA files, based on the tutorial. When I tried to open the nohup log, it was asking me if I really wanted to open it, since it could be a binary and the names of my files where butchered, like
AAA32308.1__J02451_CDS.faa.mafft<AA>p<A0>^C 58656246 1045 126 0but I thought nothing of it. Later I ran hhblits against this database and kept getting segmentation faults along the way. I traced it back to the part of the database creation, where you add a consensus sequence (that prints the previous table). Apparently, the file names can't be longer than 32 symbols, otherwise it will cause trouble. Once I cut the file names to the allowed size, all went smoothly.Edit: I just saw, this is also the case for
ffindex_build -s ../<db>_msa.ff{data,index} .already