Database issue after cisTEM crash

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Database issue after cisTEM crash


I had cisTEM open and running for particle picking. Unfortunately, while it was saving the particle coordinates the GUI crashed. This crash has led to me being unable to even load the project, where, after opening the cisTEM GUI and then selecting the project name, the GUI crashes and it prints this error to the terminal: 

Oops. Could not find array position of asset with ID 1130282
Segmentation fault (core dumped)

How do we recover the database from this type of issue?



Hi Mike,

Hi Mike,

I apologise, this is a very serious error and really shouldn't be able to happen.  I will look into this to make sure it doesn't happen again in future versions.

For your current project, if your project doesn't open you will have to edit the database file to fix the problem.  You can do this using sqlite3 and sql commands - you probably already have sqlite3 installed, but if not you will need to install it.

It looks to me that the problem has something to do with particle position asset groups. The simplest fix may be to simply delete all particle position asset groups from the database.

First please backup your database file by copying it somewhere (it will be in your project directory and ends in .db). After you have backed up then please open the database file by running :-

sqlite3 my_database.db

Type the following command :-

select * from particle_position_group_list;

This should print a list of all your groups (hopefully there are not a lot of them).  The important number here is the group_id (the first column).  For each group that you have, you have to run the following sql command, replacing the $group_id with the current group id:-

drop table particle_position_group_$group_id;

When you have run that command for each of the group_ids, run the following command :-

delete from particle_position_group_list;

After this, I hope you will be able to open your project again.  Please let me know how it goes.





Thanks Tim - that worked! 

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