Question: Help needed for local Blast2GO Database Installation on Mac system
0
gravatar for zhuhong
5.1 years ago by
zhuhong0
China
zhuhong0 wrote:

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 (http://www.blast2go.com/b2gsupport/resources/35-localb2gdb).

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 (referred to http://blog.shenwei.me/) 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

blast • 2.9k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 5.1 years ago by zhuhong0

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.

ADD REPLYlink written 5.1 years ago by hpmcwill1.1k
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