I have recently been trying to install the dependencies for make_fragments.pl (/tools/fragment_tools/make_fragments.pl) with the provided install_dependencies.pl in the same directory. The installation goes fine until attempting to download the NR database. The directory hard-coded into the script (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.9.0+-src.tar.gz) no longer exists. I have tried pointing the script to both the new version of the database (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.10.0+-src.tar.gz) and to the new location of the old version in the script (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-src.tar.gz). In either case, the package is downloaded, update_blastdb.pl is moved and ran, and the 39 tarballs of the NR database are successfully downloaded and extracted.
What I am having trouble with is in the subsequent fastacmd step. When this runs in the script, I get the following error:
Generating nr fasta. Be very patient ......
[The directory to]/rosetta_bin_linux_2019.35.60890_bundle/tools/fragment_tools/blast/bin/fastacmd -D 1 > /[The directory to]/rosetta_bin_linux_2019.35.60890_bundle/tools/fragment_tools/databases/nr[fastacmd] ERROR: ERROR: Cannot initialize readdb for nr database
ERROR! [The directory to]/rosetta_bin_linux_2019.35.60890_bundle/tools/fragment_tools/blast/bin/fastacmd -D 1 > [The directory to]/rosetta_bin_linux_2019.35.60890_bundle/tools/fragment_tools/databases/nr failed.
I have tried this in the latest numbered release (rosetta_bin_linux_2019.35.60890_bundle) and the latest release (rosetta_bin_linux_2020.03.61102_bundle) running on Ubuntu version 18.04. I have also tried downloading the “nr” fasta directly to avoid fastacmd but that led to other complications. If it would be of help, I have attached the entire log of “./install_dependencies.pl overwrite”. (with modified path to version 2.9.0 as described above).
Any help on how to successfully patch this script would be greatly appreciated. Thank you.