cleanup temp_blast_folder

During the process of data loading, some temporary files are created that can later be deleted. Sometimes, it makes sense to reuse them to save time on lengthy operations. For example, when finding gene ortholog pairs, the protein sequences are generated from the records in the database and saved in FASTA files in the sub-folder of the main temporary folder. These protein files can be reused for multiple ortholog finding procedures. If this folder (_blast subfolder of the temporary directory) takes too much space, you can run this cleanup command. 

cleanup blast_folder

With the older versions of PersephoneShell, the process of deleting a map set or an annotation track was leaving the corresponding BLAST files behind. To save the disk space and avoid confusion, when the BLAST index files are no longer needed and cannot be reused, run the command cleanup blast_folder [-t]. 

Note

The latest version of PersephoneShell automatically deletes the BLAST files if they are no longer associated with the existing map sets or tracks. This is included in the action of the commands delete mapset and delete tracktreenode.

cleanup sequence_storage

Remove the "orphan" files from the storage that do not have corresponding records in the database. This situation might be a result of upgrading from an older version of PersephoneShell.