BLAST version in fragmentation tools for ab initio

[NooraAz]

There is a version incompatibility between the nr library and the BLAST version that causes the following error when running make_fragments.pl:

[fastacmd] ERROR: ERROR: Cannot initialize readdb for nr database

That's because the default nr library is upgraded to V5, but fastacmd can only read V4. There are two options here:

1. Downgrading nr library
2. Upgrading BLAST

The new BLAST is faster, but it needs more work and rewriting of code. Downgrading nr is an easier fix.

I want to know your opinion, before working on it, should we downgrade nr or upgrade BLAST? And of course, I would appreciate any help in fixing this.