Hi
I am using Biomart 0.8 rc5. I have sorted out the problem with the server but
am unable to get any data. I am getting the following error in the log file:
java.net.ConnectException: Connection timed out
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
at java.net.Socket.connect(Socket.java:519)
at java.net.Socket.connect(Socket.java:469)
at sun.net.NetworkClient.doConnect(NetworkClient.java:163)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)
at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)
at sun.net.www.http.HttpClient.New(HttpClient.java:306)
at sun.net.www.http.HttpClient.New(HttpClient.java:323)
at
sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:852)
at
sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:793)
at
sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:718)
at
sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:896)
at
org.biomart.queryEngine.SubQuery.executeMartServiceQuery(SubQuery.java:773)
at org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:698)
at
org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerThread.java:173)
at
org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:75)
at
org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:36)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)
2011-05-06 15:47:28,880 WARN [1763281041@qtp-1697022030-7:Slf4jLog.java:76]:
/martservice/results: java.io.IOException: Closed
I am having a similar problem with our COSMIC mart. It seems to work fine using
rc4 but I don't get any data using rc5.
Do you have any idea what might be wrong?
Thanks
Rebecca
On 5 May 2011, at 15:32, Brett Whitty wrote:
> Hi Rebecca,
>
> That does seem unusual. Can you please tell me what version of BioMart
> you're running?
> Also, what are the specs if the server you're running on? You should have
> a look at the memory usage of the biomart java process as it's starting up
> to see if there's a problem with memory usage and available memory on the
> server.
>
> Also, it might be worth checking the log files under 'dist/logs' for any
> informative messages on startup; maybe post anything unusual you might
> find to the list. You can also try increasing the logging level to 'DEBUG'
> by adding 'log.level = DEBUG' in your biomart.properties file and see if
> that reveals anything more.
>
> Regards,
>
> Brett
>
> On 5/5/11 10:05 AM, "Rebecca Shepherd" <[email protected]> wrote:
>
>> I have our version of the ICGC mart up and running. However, it is taking
>> over 40 minutes for the server to start. Is there anything I can do to
>> speed it up?
>
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