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rockt / SETH

SNP Extraction Tool for Human Variations
rockt.github.com/SETH
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Database '/path/to/derby/database/dbSNP137' not found. #28

Closed YaoXinZhi closed 3 years ago

YaoXinZhi commented 3 years ago

I encountered this problem when I ran the script. Please tell me what should I do?

[xzyao@localhost SETH-1.3.1]$ java -cp seth-1.3-Snapshot-jar-with-dependencies.jar de.hu.berlin.wbi.process.Normalize resources/property.xml resources/snpExample.txt Normalising mutations from 'resources/snpExample.txt' and properties from 'resources/property.xml' Exception in thread "main" java.lang.IllegalStateException: java.sql.SQLException: Database '/path/to/derby/database/dbSNP137' not found. at de.hu.berlin.wbi.objects.DatabaseConnection.connect(DatabaseConnection.java:128) at de.hu.berlin.wbi.process.Normalize.main(Normalize.java:65) Caused by: java.sql.SQLException: Database '/path/to/derby/database/dbSNP137' not found. at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source) at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source) at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source) at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source) at org.apache.derby.impl.jdbc.EmbedConnection.newSQLException(Unknown Source) at org.apache.derby.impl.jdbc.EmbedConnection.handleDBNotFound(Unknown Source) at org.apache.derby.impl.jdbc.EmbedConnection.(Unknown Source) at org.apache.derby.jdbc.InternalDriver$1.run(Unknown Source) at org.apache.derby.jdbc.InternalDriver$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at org.apache.derby.jdbc.InternalDriver.getNewEmbedConnection(Unknown Source) at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source) at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source) at org.apache.derby.jdbc.AutoloadedDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:247) at de.hu.berlin.wbi.objects.DatabaseConnection.connect(DatabaseConnection.java:126) ... 1 more Caused by: ERROR XJ004: Database '/path/to/derby/database/dbSNP137' not found. at org.apache.derby.iapi.error.StandardException.newException(Unknown Source) at org.apache.derby.impl.jdbc.SQLExceptionFactory.wrapArgsForTransportAcrossDRDA(Unknown Source) ... 18 more

Erechtheus commented 3 years ago

This error tells you that SETH could not find the local dbSNP database at the location '/path/to/derby/database/dbSNP137'. The question is, do you need the normalization of mutations?

If yes, follow the instructions under Section "NEN" described here: https://rockt.github.io/SETH/

YaoXinZhi commented 3 years ago

Yes, I need to carry out the NEN task, thank you for your answer, I have solved this problem