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Fail to run interproscan test commanline for "pthread_create failed" #277

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ClownJay opened this issue Jul 8, 2022 · 0 comments
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@ClownJay
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ClownJay commented Jul 8, 2022

I wonder whether anyone can help me with the error I'm getting with InterProScan when I ran the test command as follows.

$ ./interproscan.sh -i test_all_appl.fasta -f tsv
08/07/2022 17:44:27:058 Welcome to InterProScan-5.56-89.0
08/07/2022 17:44:27:059 Running InterProScan v5 in STANDALONE mode... on Linux
[1.393s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 4k, detached.
[1.423s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 4k, detached.
[1.432s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 4k, detached.
[1.472s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[1.473s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[1.473s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[......]
[6.388s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.388s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.391s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.398s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.439s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.444s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.444s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.467s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.467s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.467s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.468s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.468s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.468s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.468s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.492s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.524s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
[6.616s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.apache.activemq.xbean.XBeanBrokerService#0' defined in class path resource [spring/jms/master/standalone-master-context.xml]: Invocation of init method failed; nested exception is java.lang.OutOfMemoryError: unable to create native thread: possibly out of memory or process/resource limits reached
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1799)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:594)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:516)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:324)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:897)
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:879)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:551)
        at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:144)
        at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:95)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:233)
Caused by: java.lang.OutOfMemoryError: unable to create native thread: possibly out of memory or process/resource limits reached
        at java.base/java.lang.Thread.start0(Native Method)
        at java.base/java.lang.Thread.start(Thread.java:803)
        at java.base/java.util.Timer.<init>(Timer.java:177)
        at org.apache.activemq.thread.Scheduler.doStart(Scheduler.java:72)
        at org.apache.activemq.util.ServiceSupport.start(ServiceSupport.java:55)
        at org.apache.activemq.broker.BrokerService.getScheduler(BrokerService.java:2862)
        at org.apache.activemq.broker.BrokerService.createRegionBroker(BrokerService.java:2406)
        at org.apache.activemq.broker.BrokerService.createRegionBroker(BrokerService.java:2391)
        at org.apache.activemq.broker.BrokerService.createBroker(BrokerService.java:2348)
        at org.apache.activemq.broker.BrokerService.getBroker(BrokerService.java:1045)
        at org.apache.activemq.broker.BrokerService.getAdminConnectionContext(BrokerService.java:2619)
        at org.apache.activemq.broker.BrokerService.startVirtualConsumerDestinations(BrokerService.java:2780)
        at org.apache.activemq.broker.BrokerService.startDestinations(BrokerService.java:2610)
        at org.apache.activemq.broker.BrokerService.doStartBroker(BrokerService.java:739)
        at org.apache.activemq.broker.BrokerService.startBroker(BrokerService.java:733)
        at org.apache.activemq.broker.BrokerService.start(BrokerService.java:636)
        at org.apache.activemq.xbean.XBeanBrokerService.afterPropertiesSet(XBeanBrokerService.java:73)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1925)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1867)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1795)
        ... 12 more
[6.645s][warning][os,thread] Failed to start thread - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 0k, detached.

And the ulimit information is as follows.

$ ulimit -a
-t: cpu time (seconds)              unlimited
-f: file size (blocks)              unlimited
-d: data seg size (kbytes)          unlimited
-s: stack size (kbytes)             8192
-c: core file size (blocks)         0
-m: resident set size (kbytes)      unlimited
-u: processes                       36
-n: file descriptors                4096
-l: locked-in-memory size (kbytes)  64
-v: address space (kbytes)          unlimited
-x: file locks                      unlimited
-i: pending signals                 4124768
-q: bytes in POSIX msg queues       819200
-e: max nice                        0
-r: max rt priority                 0
-N 15:                              unlimited

The version of interproscan is

$ ./interproscan.sh -version
InterProScan version 5.56-89.0
InterProScan 64-Bit build  (requires Java 11)
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