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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?

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1 Answer 1

up vote 7 down vote accepted

Turns out that the --local option was needed. The command worked when I issued it as thus.

mysqlimport -u root -p --fields-terminated-by='\t' --local b2g /home/standage/Desktop/gene2accession
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