I know that there have been a number of posts about this problems but none of them post solution to this so hopefully someone can help.
I am attempting to run_lips.pl with the following command
/home/eliza/rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl eliza.FASTA eliza.span /home/eliza/ncbi/blastpgp /home/eliza/ncbi/nr /home/eliza/rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl
But I get the error....
Error in alignblast.pl: blast output file eliza.FASTA truncated:
readline() on closed filehandle MSA at /home/eliza/rosetta/rosetta_
source/src/apps/public/membrane_abinitio/run_lips.pl line 91.
This is, I believe, because blastpgp is returning and empty file.
I downloaded the nr database from
and unpacked it to /home/eliza/ncbi/ this gives a single large file called 'nr'.
when I run blastpgp directly i do not get an error message but this generates an empty file as well. Clearly there is something wrong with my blastpgp setup and/or nr database.
I installed blast2 (which includes blastpgp from Ubuntu aptget) and I have also downloaded the executables from the blast legacy files from the ncbi website in case the ubuntu provided version was corrupt in some way but i get the same result with both so i don't think its that.
I would be grateful for any help you could give.