Matrix files won't load correctly in MySQL table

[Rachel-Duffie]

I have been stuck because I cannot successfully generate the MySQL table - each time I run diagnose_mysql_table.pl it reports that the table load status fails. I have repeated the load_table.sh script on all sorted sam files and get the same result (with the same number of missing lines (223,137)) each time. Is there a problem with my sam files, mySQL database, or should I continue trying to run load_table.sh?

[rosbashlab]

Running diagnose_mysql_table.pl is optional as it does not make changes to the MySQL table. It counts the number of entries in the MySQL table and then compares it with the total number of lines in all the matrix files (provided as arguments to the script). You can run this script (diagnose_mysql_table.pl) at any point, provided that you accounted for all matrix files that were uploaded to the MySQL table. Otherwise, if you have data from other experimental runs in the same MySQL table, that may be in an issue. You can also log into MySQL and see if the tables are getting populated with the matrix files you provided. If you open the MySQL tables, you should see the same information as the matrix file. Finally, if you don't see any obvious problem, you can proceed with the rest of the analysis.