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seqcode / chexmix

ChExMix: the ChIP-exo mixture model
MIT License
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database server connection issue retrieving sequences #4

Open ml31k opened 3 years ago

ml31k commented 3 years ago

Hello, Running into some issues where the program seems to be accessing a web resource/database (?) for retrieving sequences. I'm running on my cluster where the job nodes do not have external network access, but I also don't see any indication as to why it requires web access.

Thanks! M

Command used to run (all args point to local files): module load java/11; module load meme/4.12.0; java -Xmx36G -jar ~/mdwilson/external/ChExMix/v0.5.1/chexmix_v0.51.jar --out CEBPA --threads 16 --geninfo mmus.geninfo --seq /home/mliang/mdwilson/genomes/mmus/Mus_musculus.GRCm38.68.dna.chromosomes.fa --memepath /hpf/tools/centos6/meme/4.12.0/bin/meme --back mmus.back --design CEBPA.design --round 5 --minfold 2 --exclude mmus.exclude

Error log below:

Excluding 165 regions from mmus.exclude
Processing HitLoaders for:  CEBPA   1
Processing HitLoaders for:  CEBPA   2
Processing HitLoaders for:  CEBPA   3
Processing HitLoaders for:  CEBPA   DEFAULT
Processing HitLoaders for:  CEBPA   DEFAULT
Loading data from CEBPA:1:signal    Loaded.
Loading data from CEBPA:2:signal    Loaded.
Loading data from CEBPA:3:signal    Loaded.
Loading data from CEBPA:DEFAULT:control Loaded.
Loading data from CEBPA:DEFAULT:control Loaded.
Calculating scaling factors for condition:  CEBPA   Complete.
Loaded all experiments:
 Condition CEBPA:   #Replicates:    3
    Replicate:  CEBPA:1
        Signal: 20198686.0  Control:    9786137.0   ScalingFactor:  1.642
    Replicate:  CEBPA:2
        Signal: 19633038.0  Control:    9786137.0   ScalingFactor:  1.717
    Replicate:  CEBPA:3
        Signal: 18055053.0  Control:    9786137.0   ScalingFactor:  1.465
    Pooled replicates for condition:    CEBPA
        Signal: 57886777.0  Control:9786137.0   ScalingFactor:4.764
Finding potential binding regions.
PotentialRegionFilter: condition genomic threshold for CEBPA with bin width 50.0 = 10.0
PotentialRegionFilter: replicate genomic threshold for CEBPA:1 with bin width 50.0 = 6.0
PotentialRegionFilter: replicate genomic threshold for CEBPA:2 with bin width 50.0 = 6.0
PotentialRegionFilter: replicate genomic threshold for CEBPA:3 with bin width 50.0 = 6.0
112355 potential regions found. Total length: 1.7005575E7
Initializing mixture model
Caching sequences
Jul 23, 2021 2:17:46 PM org.apache.tomcat.jdbc.pool.ConnectionPool init
SEVERE: Unable to create initial connections of pool.
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:404)
    at com.mysql.jdbc.Util.getInstance(Util.java:387)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:917)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:896)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:885)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:860)
    at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2163)
    at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2088)
    at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:806)
    at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:404)
    at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:410)
    at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:328)
    at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:307)
    at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:200)
    at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:699)
    at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:633)
    at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:484)
    at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:142)
    at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:115)
    at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:102)
    at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:126)
    at org.seqcode.data.connections.DatabaseConnectionManager.getConnection(DatabaseConnectionManager.java:75)
    at org.seqcode.genome.sequence.SequenceGenerator.cache(SequenceGenerator.java:129)
    at org.seqcode.genome.sequence.SequenceGenerator.execute(SequenceGenerator.java:164)
    at org.seqcode.genome.sequence.SequenceGenerator.setupRegionCache(SequenceGenerator.java:283)
    at org.seqcode.projects.chexmix.motifs.MotifPlatform.<init>(MotifPlatform.java:81)
    at org.seqcode.projects.chexmix.mixturemodel.BindingMixture.<init>(BindingMixture.java:98)
    at org.seqcode.projects.chexmix.ChExMix.runMixtureModel(ChExMix.java:199)
    at org.seqcode.projects.chexmix.ChExMix.main(ChExMix.java:352)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:404)
    at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:988)
    at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
    at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2251)
    at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2104)
    ... 27 more
Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
    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:591)
    at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:211)
    at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:300)
    ... 29 more

com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:404)
    at com.mysql.jdbc.Util.getInstance(Util.java:387)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:917)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:896)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:885)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:860)
    at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2163)
    at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2088)
    at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:806)
    at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:404)
    at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:410)
    at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:328)
    at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:307)
    at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:200)
    at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:699)
    at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:633)
    at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:484)
    at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:142)
    at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:115)
    at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:102)
    at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:126)
    at org.seqcode.data.connections.DatabaseConnectionManager.getConnection(DatabaseConnectionManager.java:75)
    at org.seqcode.genome.sequence.SequenceGenerator.cache(SequenceGenerator.java:129)
    at org.seqcode.genome.sequence.SequenceGenerator.execute(SequenceGenerator.java:164)
    at org.seqcode.genome.sequence.SequenceGenerator.setupRegionCache(SequenceGenerator.java:283)
    at org.seqcode.projects.chexmix.motifs.MotifPlatform.<init>(MotifPlatform.java:81)
    at org.seqcode.projects.chexmix.mixturemodel.BindingMixture.<init>(BindingMixture.java:98)
    at org.seqcode.projects.chexmix.ChExMix.runMixtureModel(ChExMix.java:199)
    at org.seqcode.projects.chexmix.ChExMix.main(ChExMix.java:352)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:404)
    at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:988)
    at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
    at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2251)
    at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2104)
    ... 27 more
Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
    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:591)
    at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:211)
    at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:300)
    ... 29 more
Exception in thread "main" org.seqcode.data.connections.DatabaseException: Couldn't get any sequence for chr1:3010271-3010430
    at org.seqcode.genome.sequence.SequenceGenerator.execute(SequenceGenerator.java:207)
    at org.seqcode.genome.sequence.SequenceGenerator.setupRegionCache(SequenceGenerator.java:283)
    at org.seqcode.projects.chexmix.motifs.MotifPlatform.<init>(MotifPlatform.java:81)
    at org.seqcode.projects.chexmix.mixturemodel.BindingMixture.<init>(BindingMixture.java:98)
    at org.seqcode.projects.chexmix.ChExMix.runMixtureModel(ChExMix.java:199)
    at org.seqcode.projects.chexmix.ChExMix.main(ChExMix.java:352)
nbartonicek commented 1 year ago

I'm experiencing the same issue. Does the tool need any external information, or is this just a memory problem?

cmatKhan commented 1 month ago

Bump -- same issue