I'm trying to run Rosetta to do a fold and dock of the C-terminal of SARS-CoV-2 spike protein.
When I run make_fragments.pl for the first time, it downloads a bunch of nr*.gz files, and then fails with the following error:
[fastacmd] ERROR: ERROR: Cannot initialize readdb for nr database
This is a new Rosetta install of the latest version.
Digging into this a bit, make_fragments.pl runs install_dependencies.pl which runs fastacmd -D 1, like this:
my $cmd = "$Bin/blast/bin/fastacmd -D 1 > $datdir/nr";
In my case the data is in /mnt/data/rosetta/tools/fragment_tools/databases so I tried changing to that directory and running /mnt/data/rosetta/tools/fragment_tools/blast/bin/fastacmd -D 1 directly; same error.
The databases directory is rather large, 217GB. It contains nr.00.phd nr.00.phi nr.00.phr nr.00.pin nr.00.pog nr.00.ppd nr.00.ppi nr.00.psq nr.00.tar.gz.md5 and so on, for nr.00 through nr.38; also nr.pal nr.pdb nr.pos nr.pot nr.ptf nr.pto. It doesn't seem like there were any issues with downloading and unpacking the nr database.
I'm not sure why fastacmd produces an error or how to fix it. What is it looking for? Why is the thing it's looking for not there?
Environment: Rosetta 2020.08.61146 (rosetta_bin_linux_3.12_bundle.tgz), Ubuntu 18.04 on AWS instance