I'm setting up a local database for gene annotation following the instructions on this page. They provide an .sql file to create some MySQL table structures (step 4) and several data files to populate the tables (steps 5-7). I've completed the setup process through step 5, but I am getting errors at step 6. What's unnerving is that the error I'm getting is different based on which directory I execute the mysqlimport
command from.
standage@farnsworth:~$ mysqlimport -u wendel2go -p --fields-terminated-by='\t' b2g Desktop/gene2accession
Enter password:
mysqlimport: Error: 13, Can't get stat of '/var/lib/mysql/Desktop/gene2accession' (Errcode: 2), when using table: gene2accession
standage@farnsworth:~$ cd Desktop/
standage@farnsworth:~/Desktop$ mysqlimport -u wendel2go -p --fields-terminated-by='\t' b2g gene2accession
Enter password:
mysqlimport: Error: 29, File '/var/lib/mysql/b2g/gene2accession' not found (Errcode: 2), when using table: gene2accession
I'm not getting very informative results when I'm googling this error. Any ideas?
Update: I still get an error when I use the full path of the file, but the file not found is different now.
standage@farnsworth:~$ mysqlimport -u root -p --fields-terminated-by='\t' b2g /home/standage/Desktop/gene2accession
Enter password:
mysqlimport: Error: 29, File '/home/standage/Desktop/gene2accession' not found (Errcode: 13), when using table: gene2accession
standage@farnsworth:~$ list /home/standage/Desktop/gene2accession
-rw-r--r-- 1 standage standage 1.6G 2010-12-01 14:31 /home/standage/Desktop/gene2accession
The file exists, and it's not a permissions issue.
Best Answer
Try the full path to the file:
Replace "username" with your user name.