Flexibility, GC content and stability of BPs not showing in private DB

[cacereslab]

Flexibility, GC content and stability of BPs not showing in private DB have 0 values for multiple inversions (10, 11, 12), but not for public DB.

[RuthGG]

The public database has the correct numbers in the breakpoints table, but the private has almost all these columns set to 0. I made a test copy of the public columns in the private database with the query:

UPDATE  `INVFEST-DB`.breakpoints dev  INNER JOIN  `INVFEST-DB-PUBLIC`.breakpoints  pub
ON dev.id =  pub.id 
 SET dev.Flexibility = pub.Flexibility,dev.GC = pub.GC ,dev.Stability = pub.Stability, dev.Mech = pub.Mech;

When the data is changed to zeros again we'll and try to identify the process that is failing within the time fork from this update until we notice the change. Most probably is a failure in the BreakSeq process.

[RuthGG]

A possible source of error in the BreakSeq process was found in the file tool_predicitons.php. In line 422:

Before:

exec("nohup ./run_breakseq.sh > /dev/null 2>&1 &");

After:

exec("nohup ./php/run_breakseq.sh > /dev/null 2>&1 &");

I don't know exactly if this error in the code was related to the issue, but it is clear that it prevented the correct execution of BreakSeq after adding predictions to the database.

The changes are pushed in the commit Reference to BreakSeq corrected.

[RuthGG]

For the record: The tests with the BreakSeq process yesterday in the development version have changed the values for the public version that were copied 3 days ago, but not the public version nor the freeze version. This connection between both databases has to be solved.