Segmentation Fault with HHblits

[TejaNimmKU]

Context

I am working on building a customized database of HHblits compatible MSAs.

Steps to Reproduce

I started with a .fasta file for the sequences to include in the database and ran the first command in the documentation: ffindex_from_fasta -s _fas.ff{data,index} <db.fas>

With my inputs the first command was: ffindex_from_fasta -s fim_usher_fas.ff{data,index} fim_usher.fasta

This successfully gave me:
data file: fim_usher_fas.ffdata
index file: fim_usher_fas.ffindex
fasta file: fim_usher.fasta

The issue occurred on the second step to build an MSA with HHblits. This is the command that was given:
mpirun -np <number_threads>
hhblits_mpi -i _fas -d <path_to/uniclust30> -oa3m _a3m_wo_ss -n 2 -cpu 1 -v 0

These are some of the commands I ran:
hhblits -i fim_usher.fasta -d uniclust30_2017_10/ -oa3m fim_usher_a3m_wo_ss -n 2 -cpu 1 -v 0
hhblits -i fim_usher_fas -d uniclust30_2017_10/ -oa3m fim_usher_a3m_wo_ss -n 2 -cpu 1 -v 5

Expected Behavior

MSAs should be written to the ffindex _a3m_wo_ss.ff{data,index} or fim_usher_a3m_wo_ss.ff{data,index} in this case.

Current Behavior

For "-v 0":
Segmentation fault

For "-v 5":

• 12:39:59.486 DEBUG1: 12 5
• 12:39:59.486 INFO: Search results will be written to fim_usher_fas.hhr
  Segmentation fault