exomiser error occurs when submits multiple jobs

[Jihoon-Yoon]

Hi Veronique,
Thanks for your great contribution!

Recently, I found an error related to the annotation with exomiser.
As I am dealing with more than thousands of samples, I annotate them in parallel using our HPC.
What I found is that connecting to exomiser is sometimes fail may be due to the occupied port numbers by other jobs.

The below is the error msg I got:

``
org.apache.catalina.LifecycleException: Protocol handler start failed
at org.apache.catalina.connector.Connector.startInternal(Connector.java:1008)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardService.addConnector(StandardService.java:226)
at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.addPreviouslyRemovedConnectors(TomcatWebServer.java:259)
at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.start(TomcatWebServer.java:197)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.startWebServer(ServletWebServerApplicationContext.java:311)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.finishRefresh(ServletWebServerApplicationContext.java:164)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:552)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:142)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:775)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:316)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1260)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1248)
at org.monarchinitiative.exomiser.rest.prioritiser.ExomiserPrioritiserServer.main(ExomiserPrioritiserServer.java:35)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:87)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51)
Caused by: java.net.BindException: Address already in use
at sun.nio.ch.Net.bind0(Native Method)
at sun.nio.ch.Net.bind(Net.java:461)
at sun.nio.ch.Net.bind(Net.java:453)
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:222)
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:85)
at org.apache.tomcat.util.net.NioEndpoint.initServerSocket(NioEndpoint.java:236)
at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
at org.apache.tomcat.util.net.AbstractEndpoint.bindWithCleanup(AbstractEndpoint.java:1085)
at org.apache.tomcat.util.net.AbstractEndpoint.start(AbstractEndpoint.java:1171)
at org.apache.coyote.AbstractProtocol.start(AbstractProtocol.java:568)
at org.apache.catalina.connector.Connector.startInternal(Connector.java:1005)
... 22 common frames omitted

2021-12-07 10:28:51.513 INFO 111985 --- [ main] o.apache.catalina.core.StandardService : Stopping service [Tomcat]
2021-12-07 10:28:51.515 WARN 111985 --- [ main] o.a.c.loader.WebappClassLoaderBase : The web application [exomiser#api#prioritise] appears to have started a thread named [exomiser-phenotype-2007 housekeeper] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
sun.misc.Unsafe.park(Native Method)
java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
java.lang.Thread.run(Thread.java:748)
2021-12-07 10:28:51.520 INFO 111985 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.
2021-12-07 10:28:51.521 ERROR 111985 --- [ main] o.s.b.d.LoggingFailureAnalysisReporter :

---

APPLICATION FAILED TO START

---

Description:

The Tomcat connector configured to listen on port 50000 failed to start. The port may already be in use or the connector may be misconfigured.

Action:

Verify the connector's configuration, identify and stop any process that's listening on port 50000, or configure this application to listen on another port.

2021-12-07 10:28:51.524 INFO 111985 --- [ main] o.s.s.concurrent.ThreadPoolTaskExecutor : Shutting down ExecutorService 'applicationTaskExecutor'
2021-12-07 10:28:51.526 INFO 111985 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-2007 - Shutdown initiated...
2021-12-07 10:28:51.528 INFO 111985 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-2007 - Shutdown completed.
``

Can you make AnnotSV to use Exomiser in parallel so that I can annotate multiple jobs simultaneously?
Thank you so much!

[lgmgeo]

Hi Jihoon-Yoon,

Thank you for your interesting feedback. Indeed, this is a really interesting and useful feature to add, I keep that in mind.

Unfortunately, it could take a long time. First, the analyzes for my lab. And then, in my free time, the development of AnnotSV.
In 2022, I would finally like to carry out the Python refactoring of the AnnotSV code.
But I wrote your feature on my to-do list.

Best regards,

Véronique