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    Your problem is actually not related to membrane ab initio protocol. You need to follow the documentation carefully – it says that you should specify “path to nr database” – /home/albert/install/rosetta-3.2/blast-db in your command line is not a correct path – correct path should look like “/scratch/shared/genomes/nr” (see documentation) – with “nr” at the end – not “blast-db”. Blast nr database contains many files, but they all begin with “nr”. Always pay attention to error and/or warning messages that you are getting – you could have figured out the source of the problem if you’ve tested blastpgp program by itself and if you’ve read the warning in your log: [blastpgp] WARNING: Unable to open