Closed mhjiang97 closed 3 years ago
Hi. Did you download the 2.3 version: http://projects.insilico.us.com/SpliceSeq_2.3/SpliceSeq.zip?
Also, could you look in the SpliceSeq directory to see if any file with a .log extension has an error message.
Michael Ryan, PhD
In Silico Solutions
From: Minghao Jiang @.*** Sent: Tuesday, April 13, 2021 3:44 AM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Subscribed Subject: [MD-Anderson-Bioinformatics/SpliceSeq] spliceseq can't connect to mysql (#9)
Hi,
I’d like to use SpliceSeq to quantify splicing events in my RNA-seq data. But SpliceSeq can’t connect to MySQL after configuring it.
Settings are:
DBURL jdbc:mysql://localhost
SGDatabase splicegraph
DBUser mjiang
DBPassword mjiang
I'm sure that I can log in mysql through mysql -u mjiang -p -h localhost and there's a database named splicegraph
$mysql -u mjiang -p -h localhost
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 88
Server version: 8.0.23 MySQL Community Server - GPL
Copyright (c) 2000, 2021, Oracle and/or its affiliates.
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> use splicegraph;
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_splicegraph |
+--------------------------+
| attribute |
| exon |
| graph |
| graph_ncbi_annotation |
| graph_uniprot_annotation |
| graph_uniprot_map |
| isoform |
| isoform_ex_seq |
| protein_feature_ref |
| splice |
| uniprot_exon_align |
| uniprot_feature_ref |
| uniprot_prot_seq |
| version |
+--------------------------+
14 rows in set (0.00 sec)
mysql>
Could you give me some advice about configuring SpliceSeq or mysql? Thanks in advance.
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Hi,
I ran SpliceSeq version 2.3
then configured it, and the log file read:
2021-04-14 10:13:42,068 [AWT-EventQueue-0] INFO - Application name set to SpliceSeq in configuration
2021-04-14 10:13:42,069 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:13:42,069 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:13:42,071 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:13:42,071 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:13:42,072 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:13:42,072 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:13:42,072 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:13:42,072 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:13:42,075 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:13:42,075 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:14:12,902 [AWT-EventQueue-0] ERROR - java.sql.SQLException: The url does not correspond with any known host: please check Ratway url.
2021-04-14 10:14:12,915 [AWT-EventQueue-0] ERROR - java.sql.SQLException: The url does not correspond with any known host: please check Ratway url.
2021-04-14 10:14:12,917 [AWT-EventQueue-0] ERROR - java.sql.SQLException: The url does not correspond with any known host: please check Ratway url.
2021-04-14 10:14:12,938 [AWT-EventQueue-0] ERROR - java.sql.SQLException: The url does not correspond with any known host: please check Ratway url.
2021-04-14 10:15:02,956 [AWT-EventQueue-0] ERROR - Error loading samples: java.sql.SQLException: The url does not correspond with any known host: please check Ratway url.
2021-04-14 10:15:16,105 [AWT-EventQueue-0] ERROR - java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct.
2021-04-14 10:15:19,884 [AWT-EventQueue-0] ERROR - Error loading samples: java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct.
2021-04-14 10:15:27,650 [AWT-EventQueue-0] ERROR - java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct.
2021-04-14 10:17:03,659 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:03,659 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:03,660 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:03,660 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:03,661 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:03,661 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:03,662 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:03,662 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:03,662 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:03,662 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:04,295 [AWT-EventQueue-0] ERROR - java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct.
2021-04-14 10:17:04,956 [AWT-EventQueue-0] ERROR - java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct.
2021-04-14 10:17:05,110 [AWT-EventQueue-0] ERROR - Failed to create DB Connection
2021-04-14 10:17:05,110 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
2021-04-14 10:17:09,357 [AWT-EventQueue-0] ERROR - Error loading samples: java.lang.NullPointerException
2021-04-14 10:17:09,370 [AWT-EventQueue-0] ERROR - Failed to create DB Connection
2021-04-14 10:17:09,371 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
2021-04-14 10:17:22,716 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:22,716 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:22,717 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:22,717 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:22,718 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:22,718 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:22,718 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:22,719 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:22,719 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:22,719 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:22,721 [AWT-EventQueue-0] ERROR - Failed to create DB Connection
2021-04-14 10:17:22,721 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
2021-04-14 10:17:22,723 [AWT-EventQueue-0] ERROR - Failed to create DB Connection
2021-04-14 10:17:22,723 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
2021-04-14 10:17:24,571 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:24,571 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:24,572 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:24,572 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:24,573 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:24,573 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:24,574 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:24,574 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:24,574 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME
2021-04-14 10:17:24,575 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path
2021-04-14 10:17:24,576 [AWT-EventQueue-0] ERROR - Failed to create DB Connection
2021-04-14 10:17:24,576 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
2021-04-14 10:17:24,578 [AWT-EventQueue-0] ERROR - Failed to create DB Connection
2021-04-14 10:17:24,578 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
How are you starting the SpliceSeq viewer? When DB connection fails, there should be a program stack trace in the window where you started spliceseq. Can you get a screen shot of the stack trace? For example if running on windows in a command prompt window by typing java –jar spliceseq.jar, then see what messages are printed in the window. On a mac it is a terminal window I think.
Like this:
Mike
From: Minghao Jiang @.*** Sent: Tuesday, April 13, 2021 10:21 PM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Michael Ryan; Comment Subject: Re: [MD-Anderson-Bioinformatics/SpliceSeq] spliceseq can't connect to mysql (#9)
Hi, I ran SpliceSeq version 2.3 then configured it, and the log file read:
2021-04-14 10:13:42,068 [AWT-EventQueue-0] INFO - Application name set to SpliceSeq in configuration 2021-04-14 10:13:42,069 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:13:42,069 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:13:42,071 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:13:42,071 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:13:42,072 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:13:42,072 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:13:42,072 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:13:42,072 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:13:42,075 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:13:42,075 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:14:12,902 [AWT-EventQueue-0] ERROR - java.sql.SQLException: The url does not correspond with any known host: please check Ratway url. 2021-04-14 10:14:12,915 [AWT-EventQueue-0] ERROR - java.sql.SQLException: The url does not correspond with any known host: please check Ratway url. 2021-04-14 10:14:12,917 [AWT-EventQueue-0] ERROR - java.sql.SQLException: The url does not correspond with any known host: please check Ratway url. 2021-04-14 10:14:12,938 [AWT-EventQueue-0] ERROR - java.sql.SQLException: The url does not correspond with any known host: please check Ratway url. 2021-04-14 10:15:02,956 [AWT-EventQueue-0] ERROR - Error loading samples: java.sql.SQLException: The url does not correspond with any known host: please check Ratway url. 2021-04-14 10:15:16,105 [AWT-EventQueue-0] ERROR - java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct. 2021-04-14 10:15:19,884 [AWT-EventQueue-0] ERROR - Error loading samples: java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct. 2021-04-14 10:15:27,650 [AWT-EventQueue-0] ERROR - java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct. 2021-04-14 10:17:03,659 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:03,659 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:03,660 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:03,660 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:03,661 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:03,661 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:03,662 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:03,662 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:03,662 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:03,662 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:04,295 [AWT-EventQueue-0] ERROR - java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct. 2021-04-14 10:17:04,956 [AWT-EventQueue-0] ERROR - java.sql.SQLException: Cannot communicate with the Ratway webapp: please check if the url is correct. 2021-04-14 10:17:05,110 [AWT-EventQueue-0] ERROR - Failed to create DB Connection 2021-04-14 10:17:05,110 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException 2021-04-14 10:17:09,357 [AWT-EventQueue-0] ERROR - Error loading samples: java.lang.NullPointerException 2021-04-14 10:17:09,370 [AWT-EventQueue-0] ERROR - Failed to create DB Connection 2021-04-14 10:17:09,371 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException 2021-04-14 10:17:22,716 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:22,716 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:22,717 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:22,717 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:22,718 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:22,718 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:22,718 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:22,719 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:22,719 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:22,719 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:22,721 [AWT-EventQueue-0] ERROR - Failed to create DB Connection 2021-04-14 10:17:22,721 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException 2021-04-14 10:17:22,723 [AWT-EventQueue-0] ERROR - Failed to create DB Connection 2021-04-14 10:17:22,723 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException 2021-04-14 10:17:24,571 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:24,571 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:24,572 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:24,572 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:24,573 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:24,573 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:24,574 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:24,574 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:24,574 [AWT-EventQueue-0] INFO - Retrieving application path from environment variable SPLICESEQ_HOME 2021-04-14 10:17:24,575 [AWT-EventQueue-0] WARN - SPLICESEQ_HOME was not read from the environment, assuming relative path 2021-04-14 10:17:24,576 [AWT-EventQueue-0] ERROR - Failed to create DB Connection 2021-04-14 10:17:24,576 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException 2021-04-14 10:17:24,578 [AWT-EventQueue-0] ERROR - Failed to create DB Connection 2021-04-14 10:17:24,578 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
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I typed java -jar SpliceSeq.jar
on my Mac, and configured it.
I'm sorry that i don't know how to attach pictures in the github, and the screenshot of the stack trace was:
** BEGIN NESTED EXCEPTION **
java.io.EOFException
STACKTRACE:
java.io.EOFException
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
at com.mysql.jdbc.MysqlIO.readPacket(MysqlIO.java:483)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:992)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:2572)
at com.mysql.jdbc.Connection.<init>(Connection.java:1485)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:266)
at java.sql.DriverManager.getConnection(DriverManager.java:571)
at java.sql.DriverManager.getConnection(DriverManager.java:233)
at splicetool.common.util.DB.getConnection(DB.java:4104)
at splicetool.common.util.DB.connectionValid(DB.java:49)
at splicetool.viewer.Application.run(Application.java:254)
at splicetool.viewer.Main.createAndShowGUI(Main.java:124)
at splicetool.viewer.Main.access$000(Main.java:27)
at splicetool.viewer.Main$1.run(Main.java:158)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:745)
at java.awt.EventQueue.access$300(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:706)
at java.awt.EventQueue$3.run(EventQueue.java:704)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:715)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
** END NESTED EXCEPTION **
Last packet sent to the server was 1 ms ago.
at com.mysql.jdbc.MysqlIO.readPacket(MysqlIO.java:554)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:992)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:2572)
at com.mysql.jdbc.Connection.<init>(Connection.java:1485)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:266)
at java.sql.DriverManager.getConnection(DriverManager.java:571)
at java.sql.DriverManager.getConnection(DriverManager.java:233)
at splicetool.common.util.DB.getConnection(DB.java:4104)
at splicetool.common.util.DB.connectionValid(DB.java:49)
at splicetool.viewer.Application.changeViewType(Application.java:468)
at splicetool.viewer.Application.run(Application.java:286)
at splicetool.viewer.Main.createAndShowGUI(Main.java:124)
at splicetool.viewer.Main.access$000(Main.java:27)
at splicetool.viewer.Main$1.run(Main.java:158)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:745)
at java.awt.EventQueue.access$300(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:706)
at java.awt.EventQueue$3.run(EventQueue.java:704)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:715)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
2021-04-15 10:47:28,061 [AWT-EventQueue-0] ERROR - Failed to create DB Connection
2021-04-15 10:47:28,061 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
I have not seen this problem before. It is not a user id or password problem. I did find a similar issue with a solution reported in the link below. Could you try that please and let me know if it works.
https://forums.mysql.com/read.php?39,52805,273371
Mike
From: Minghao Jiang @.*** Sent: Wednesday, April 14, 2021 10:51 PM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Michael Ryan; Comment Subject: Re: [MD-Anderson-Bioinformatics/SpliceSeq] spliceseq can't connect to mysql (#9)
I typed java -jar SpliceSeq.jar on my Mac, and configured it.
I'm sorry that i don't know how to attach pictures in the github, and the screenshot of the stack trace was:
BEGIN NESTED EXCEPTION
java.io.EOFException
STACKTRACE:
java.io.EOFException
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
at com.mysql.jdbc.MysqlIO.readPacket(MysqlIO.java:483)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:992)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:2572)
at com.mysql.jdbc.Connection.
END NESTED EXCEPTION
Last packet sent to the server was 1 ms ago.
at com.mysql.jdbc.MysqlIO.readPacket(MysqlIO.java:554)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:992)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:2572)
at com.mysql.jdbc.Connection.
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Hi, I'm here again.
I added mysqld : ALL : ALLOW
into /etc/hosts
Now, the error from SpliceSeq is:
java.sql.SQLException: Unknown initial character set index '255' received from server. Initial client character set can be forced via the 'characterEncoding' property.
at com.mysql.jdbc.Connection.configureClientCharacterSet(Connection.java:2268)
at com.mysql.jdbc.Connection.initializePropsFromServer(Connection.java:3748)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:2585)
at com.mysql.jdbc.Connection.<init>(Connection.java:1485)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:266)
at java.sql.DriverManager.getConnection(DriverManager.java:571)
at java.sql.DriverManager.getConnection(DriverManager.java:233)
at splicetool.common.util.DB.getConnection(DB.java:4104)
at splicetool.common.util.DB.connectionValid(DB.java:49)
at splicetool.viewer.Application.run(Application.java:254)
at splicetool.viewer.Main.createAndShowGUI(Main.java:124)
at splicetool.viewer.Main.access$000(Main.java:27)
at splicetool.viewer.Main$1.run(Main.java:158)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:745)
at java.awt.EventQueue.access$300(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:706)
at java.awt.EventQueue$3.run(EventQueue.java:704)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:715)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
2021-04-20 15:13:22,005 [AWT-EventQueue-0] ERROR - Failed to create DB Connection
2021-04-20 15:13:22,005 [AWT-EventQueue-0] ERROR - java.lang.NullPointerException
Thank you for your patience!
Hi,
I’d like to use SpliceSeq to quantify splicing events in my RNA-seq data. But SpliceSeq can’t connect to MySQL after configuring it.
Settings are:
I'm sure that I can log in mysql through
mysql -u mjiang -p -h localhost
and there's a database namedsplicegraph
Could you give me some advice about configuring SpliceSeq or mysql? Thanks in advance.