I just installed
a new BLAST database, but it doesn't show up in the
birchadmin menus for Update, Add or Delete. What
happened?
When you launch any BioLegato application such as birchadmin,
the information for the menus are read at run time. That means
that to refresh the +/- listings of which databases are
installed, you need to quit birchadmin and restart it to see
those changes take effect.
What can cause a
download to stall?
There are many reasons
why a download may stall. A simple one is that your internet
connection temporarily was lost, you ran out of disk space, or
the load at the FTP site (eg. NCBI, EBI, DDBJ) was high. One
other reason might be that NCBI is in the process of updating
the FTP site with new files, which happens with each new
GenBank release. If blastdbkit.py tries to download a file as
that file is being updated on the FTP site, this will cause
blastdbkit to hang.
How do I recover
from a stalled download?
Blastdbkit.py is
designed to look for newly updated files each time it runs, so
you can always restart the download and blastdbkit.py will
resume the download. However, if the download stalled because
NCBI was updating the FTP site, you need to wait until the FTP
site is updated. You can tell if an update is in progress by
running birchadmin --> UpdateAddInstall --> BLASTDB
- Report on local or remote BLAST Databases. Click on Report:
FTP Database to bring up a report on the current state
of the FTP site. If you see divisions of the database that
have the current date and time, then an update of the FTP site
is probably in progress. A complete update of the FTP site may
take several days, so keep checking periodically until you see
no new files appearing on the site. Then it should be okay to
resume your downloads.
