Help needed for local Blast2GO Database Installation on Mac system

Question

[zhuhong]

Hello and good day everyone,

I'd like to install local Blast2GO database into my desktop. It is mac os x operating system. I already followed the 'Step-by-Step Description' provided on the blast2go website.

Actually, this is what I did:

1. Download this zip file "local_b2g_db" and unzip it
2. Install a MySQL Database Server
3. Download and unzip the following 4 files:
   • go_201405-assocdb-data
   • gene_info
   • gene2accession
   • idmapping.tb

After these three steps were finished, I moved all these files into my working directory at /Users/redspider/b2g. Then I used a script as follows as outlined here to import the data:

#!/bin/sh
godbname=go_201405-assocdb-data
dbname=b2gdb         
dbuser=root                          
dbpass=test123                 
dbhost=localhost                       
dbport=3306                            
path=/Users/redspider/b2g

echo 1. Create the DB Tables and user
mysql -h$dbhost -P$dbport -u$dbuser -p$dbpass < b2gdb.sql

echo 2. Import $godbname
mysql -h$dbhost -P$dbport -u$dbuser -p$dbpass $dbname < $godbname

echo 3. Import gene2accession
mysql -h$dbhost -P$dbport -u$dbuser -p$dbpass $dbname -e"LOAD DATA LOCAL INFILE '$path"/gene2accession"' INTO TABLE gene2accession FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';"

echo 4. Import gene_info
mysql -h$dbhost -P$dbport -u$dbuser -p$dbpass $dbname -e"LOAD DATA LOCAL INFILE '$path"/gene_info"' INTO TABLE gene_info FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';"

echo 5. Import idmapping.tb
java -cp .:mysql-connector-java-5.0.8-bin.jar: ImportIdMapping $path/idmapping.tb $dbhost:$dbport $dbname blast2go blast4it
echo All data imported.

Unfortunately, I've been getting stuck at 'echo 2'. The problem was that mysql seemed to quit automatically just after ~30 min once the script started (the following information showed the database/table status when the process halted).

zhuhong:redspider root# mysql -u root -p
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 18
Server version: 5.6.17 MySQL Community Server (GPL)

Copyright (c) 2000, 2014, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> show databases;
+--------------------+
| Database |
+--------------------+
| information_schema |
| b2gdb |
| mysql |
| performance_schema |
| test |
+--------------------+
5 rows in set (0.06 sec)

mysql> use b2gdb;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------+
| Tables_in_b2gdb |
+-----------------+
| assoc_rel |
| association |
| gene2accession |
| gene_info |
| gi2uniprot |
+-----------------+
5 rows in set (0.00 sec)

When I checked my Error log file, I noticed suspicious warning messages like

2014-05-22 15:37:02 232 [Warning] Warning: Enabling keys got errno 0 on b2gdb.association, retrying

I've tried several times but always got these warnings and the data import never accomplished : ( So, I'm really hoping for suggestion to solve this problem. Thank you.

Best,
Hong

SCBG, CAS

[hpmcwill]

You might be better off asking the Blast2GO folks about his (see Blast2GO Support) or adding it to the discussion on the Blast2GO Google Group.