I was having difficulty running run_lips.pl despite instituting the suggested changes to run_lips.pl. The result was the truncated file error from alignblast.pl that everyone mentions. The suggested changes are documented in the thread below.
Both the original script and the edited run_lips.pl returned the same empty file from blastpgp. After directly entering the command generated by run_lips.pl, the result was a missing database file, nr.pin. Unfortunately, all the database files were present according to this post.
The reason appeared to be an old version of blastpgp contained within older versions of Rosetta. We downloaded the newest version of BLAST+, 2.2.27 from this link. Blastpgp was not located within this download. Either NCBI isn't supporting anymore (or forgot), or we may have grabbed the wrong one.
We went back to 2.2.26 and blastpgp was present. I then tried to run run_lips.pl, but I again received a truncated file. I entered the generated command into the command line and recieved absolutely nothing. I looked for instructions to the use of blastpgp and found the document below. This document and the options returned by entering blastpgp - suggested that the -d switch only specifies the type of database, not the location.
I then placed all the database files,the blast suite, and the fasta and span files into one directory with run_lips.pl. With the changes to run_lips.pl listed in the first link and passing the string 'nr' for the database path, I was able to get a positive response from all with no errors.
There may have been some directory issues as I didn't have permission to write in the nr database directory or the blastpgp directories. I copied everything to a directory in which I had all the available permissions. I hope this helps someone in the future.