PhyloPythiaS software FAQ!
1. Question: I get the following
uninitialized constant SQLite3::Driver::Native::Driver::API (NameError)
Latest check for this fix was on Nov. 9 2011, Ubuntu 11.10 (32 bit).
- Install packages (might need root permissions).
apt-get install rubygems libsqlite3-dev
- Install the sqlite3-ruby gem (might need root permissions).
gem install sqlite3-ruby
- Delete the shipped sqlite3-ruby from "svm_struct_phylo_distr" directory.
rm -fr scripts/lib/rubygems/sqlite3-ruby-1.2.5/
- Please let us know if this doesn't fix the problem: phylopythias AT uni-duesseldorf.de
2. Question: How to find if the predictions are affected by a bug (version 1.2, 1.2.1 and 1.3)
- Find the PhyloPythiaS output file: its the file with extension ".out" and NOT ".PP.out".
- Run the command on this file: cat file.out | cut -f5 | sort | uniq | sort -nr
- If you see any negative numbers in the output of this command except "-1" then you need a software update.
- Download and install the latest version, you can rerun predictions with the models created with version 1.2.1
- If the problem persists, please let us know: phylopythias AT uni-duesseldorf.de
3. Question: Can I use models created by one version to make predictions using another version?
- Models created with versions 1.2 and 1.2.1 can be used with version 1.3 and it is recommended.
- Models created with version 1.1 should not be used with later verions.
- Models created with newer versions should not be used with older versions.
- Incompatibilty can be evident by the problem described in Question #2.