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Known issues
The following are not ITEP issues but issues that can arise when using ITEP with underlying dependencies. This page is intended to provide quick diagnostics for common problems.
Certain versions of SQLite are known to have issues that affect ITEP. This includes versions prior to 3.7.15.2 (you may get "database or disk is full" errors because of the large database size, even if your disk is not full) and 3.8 (which has some stability problems leading to incomplete loading of data into the database). Versions 3.7.15.2 and 3.11.0 are known to work. When in doubt, download and install the latest version from SQLite's website.
If you get errors parsing Genbank files, try upgrading your distribution of Biopython. They have fixed (and are constantly fixing) many issues related to Genbank files. We require Biopython version 1.61 or better. Later versions are less likely to have problems with recently-downloaded Genbank files.
RPSBLAST requires a large amount of memory - in particular, it requires more than can be allocated on a 32 bit machine. Unfortunately this means that you must use the 64-bit version, and not all hosts support this.
NCBI relatively recently changed the syntax of RPSBLAST and the format of its CDD database on the FTP site. Unfortunately this means that you must upgrade in order to use this program. They did not change the name of the RPSBLAST program while changing the syntax. To check if you have a recent enough version, check the format of the help text which should have the 'new style':
$ rpsblast -h
USAGE
rpsblast [-h] [-help] [-import_search_strategy filename]
...
DESCRIPTION
Reverse Position Specific BLAST 2.2.28+
2.2.28+ is known to work. If you get syntax errors trying to run RPSBLAST (setup_step4.sh), first upgrade your BLAST+ to the latest version. Then if you have an old version of the CDD in the cd_db/ directory you will also need to delete it because the new RPSBLAST is not compatible with the old CDD. Finally delete any old files in the rpsblast_res/ directory so you aren't mixing results from two different databases. After doing these things, rerun setup_step4.sh and it should work.
If you get a "database or disk is full" error and your disk is not full, try upgrading your version of SQLite - we encountered this with versions earlier than 3.7.15.2. So We require SQLite3 version 3.7.15.2 or better
If you're curious this occurs due to this bug that was fixed in that version:
https://www.sqlite.org/src/info/e24ba5bee4
If you get a "SQLite header and source version mismatch" when installing the new version make sure you run ldconfig afterwards. See here:
http://stackoverflow.com/questions/6696861/how-do-i-upgrade-my-sqlite3-package-on-debian-lenny
If you have a later version of sqlite3 than 3.7.15.2 and get a "database or disk is full" error when ITEP attempts to VACUUM the database, it could be be due to running out of space in the partition in which /tmp/ is found. See here for details:
You'll need to configure sqlite3 to use a different partition or make your /tmp/ partition bigger or just don't worry about it as long as all the data is loaded. If ITEP fails when VACUUM is run it will just mean your database will take up more hard drive space than it would otherwise, as all VACUUM does is try to clean up memory from deleted tables.