Entering edit mode
3.7 years ago
mthm
▴
50
I have tried to run CreateGFF3sForClassifFeatures.py in REPET pipeline once before. then,for some reason I removed the whole directory and tried to re-run the script, but because I ran it before, the data files have already been created in mysql and apparently are not re-writable! problem is that I have already deleted the previous outputs and now due to this error I don't get any output at all.
2021-03-01 12:48:00 - CreateGFF3sForClassifFeatures - INFO - START CreateGFF3sForClassifFeatures (2021-03-01 12:48:00)
2021-03-01 12:48:00 - CreateGFF3sForClassifFeatures - INFO - Creating consensus table...
2021-03-01 12:48:00 - DbMySql - ERROR - FAILED to execute query 'CREATE TABLE monCan3F9_ConsensusLib_seq (accession varchar(255),sequence longtext,description varchar(255),length int unsigned) ENGINE = MyISAM': Table 'monCan3F9_ConsensusLib_seq' already exists. 2 retries left.
2021-03-01 12:48:05 - DbMySql - ERROR - FAILED to execute query 'CREATE TABLE monCan3F9_ConsensusLib_seq (accession varchar(255),sequence longtext,description varchar(255),length int unsigned) ENGINE = MyISAM': Table 'monCan3F9_ConsensusLib_seq' already exists. 1 retries left.
2021-03-01 12:48:10 - DbMySql - ERROR - FAILED to execute query 'CREATE TABLE monCan3F9_ConsensusLib_seq (accession varchar(255),sequence longtext,description varchar(255),length int unsigned) ENGINE = MyISAM': Table 'monCan3F9_ConsensusLib_seq' already exists. 0 retries left.
2021-03-01 12:48:15 - DbMySql - ERROR - ERROR: can't execute 'CREATE TABLE monCan3F9_ConsensusLib_seq (accession varchar(255),sequence longtext,description varchar(255),length int unsigned) ENGINE = MyISAM' after several tries
Traceback (most recent call last):
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_mysql_exceptions.DatabaseError: ERROR: can't execute 'CREATE TABLE monCan3F9_ConsensusLib_seq (accession varchar(255),sequence longtext,description varchar(255),length int unsigned) ENGINE = MyISAM' after several tries
Is it safe to delete the tables in mysql manually? is it even possible?
I would first create a backup of the table and then proceed with delete! But yes, you can manually delete a MySQL table!