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rockt / SETH

SNP Extraction Tool for Human Variations
rockt.github.com/SETH
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Unable to run NEN example #39

Closed yuanhao96 closed 2 years ago

yuanhao96 commented 2 years ago

SETH installed following https://rockt.github.io/SETH/: git clone https://github.com/rockt/SETH.git cd SETH mvn clean compile assembly:single mv ./target/seth-1.3.2-Snapshot-jar-with-dependencies.jar seth.jar

Works well running NER example: java -cp seth.jar seth.ner.wrapper.SETHNERAppMut "G-banding and spectral karyotyping showed 46,XX,t(9;11)(p22;p15)."

Error when running NEN example: java -cp seth.jar de.hu.berlin.wbi.process.Normalize resources/seth_properties.xml resources/snpExample.txt

Normalising mutations from 'resources/snpExample.txt' and properties from 'resources/seth_properties.xml' Exception in thread "main" java.lang.IllegalStateException: org.postgresql.util.PSQLException: Connection to 127.0.0.1:5432 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections. at de.hu.berlin.wbi.objects.DatabaseConnection.connect(DatabaseConnection.java:111) at de.hu.berlin.wbi.process.Normalize.main(Normalize.java:48) Caused by: org.postgresql.util.PSQLException: Connection to 127.0.0.1:5432 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections. at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:319) at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:49) at org.postgresql.jdbc.PgConnection.(PgConnection.java:223) at org.postgresql.Driver.makeConnection(Driver.java:400) at org.postgresql.Driver.connect(Driver.java:259) at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:677) at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:228) at de.hu.berlin.wbi.objects.DatabaseConnection.connect(DatabaseConnection.java:109) ... 1 more Caused by: java.net.ConnectException: Connection refused (Connection refused) at java.base/java.net.PlainSocketImpl.socketConnect(Native Method) at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399) at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242) at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224) at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:403) at java.base/java.net.Socket.connect(Socket.java:609) at org.postgresql.core.PGStream.createSocket(PGStream.java:241) at org.postgresql.core.PGStream.(PGStream.java:98) at org.postgresql.core.v3.ConnectionFactoryImpl.tryConnect(ConnectionFactoryImpl.java:109) at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:235)

Erechtheus commented 2 years ago

Hi! You need to set-up a local dbSNP database before you can normalize mutations. You can either download old dumps of dbSNP or buid a dbSNP database by yourself. See (Rebuilding the database for SNP normalization) This page should help you (https://github.com/rockt/SETH/blob/gh-pages/index.md).

Erechtheus commented 2 years ago

Please re-open this issue if necessary