Local Interproscan Problems

Question

[jflowers002]

I am trying to run Interproscan locally on 64 bit linux with Java 1.8 and I keep getting a memory error with each attempt no matter how much I increase Xmx. I am only testing this on one sequence so memory should not be an issue. Here is the very long error message. Any help understanding would be greatly appreciated.

Matches for any sequences that are not represented in the lookup service will be calculated locally.
2017-02-22 01:18:02,192 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.java.lang.IllegalStateException: IOException thrown when attempting to run binary
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:140)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
        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.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
        at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
        at com.sun.proxy.$Proxy100.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Cannot run program "python": error=12, Cannot allocate memory
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
        at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:146)
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:138)
        ... 24 more
Caused by: java.io.IOException: error=12, Cannot allocate memory
        at java.lang.UNIXProcess.forkAndExec(Native Method)
        at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
        at java.lang.ProcessImpl.start(ProcessImpl.java:134)
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
        ... 26 more
2017-02-22 01:18:02,225 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepMobiDBRunBinary
2017-02-22 01:18:02,193 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.java.lang.IllegalStateException: IOException thrown when attempting to run binary
        ...
2017-02-22 01:18:13,215 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepSFLDRunHmmer3
2017-02-22 01:18:13,230 [responseMonitorJmsContainer-1] [org.hibernate.engine.jdbc.spi.SqlExceptionHelper:127] WARN - SQL Error: 42102, SQLState: 42S02
2017-02-22 01:18:13,232 [responseMonitorJmsContainer-1] [org.hibernate.engine.jdbc.spi.SqlExceptionHelper:129] ERROR - Table "STEP_EXECUTION" not found; SQL statement:
select stepexecut0_.id as id1_90_0_, stepexecut0_.time_completed as time_com2_90_0_, stepexecut0_.time_created as time_cre3_90_0_, stepexecut0_.exception_first_chunk as exceptio4_90_0_, stepexecut0_.proportion_completed as proporti5_90_0_, stepexecut0_.time_started_running as time_sta6_90_0_, stepexecut0_.state as state7_90_0_, stepexecut0_.step_instance_id as step_ins9_90_0_, stepexecut0_.time_submitted as time_sub8_90_0_, exceptionc1_.step_execution_id as step_exe1_12_1_, exceptionc1_.exception_chunks as exceptio2_12_1_, exceptionc1_.chunk_index as chunk_in3_1_, stepinstan2_.id as id1_91_2_, stepinstan2_.bottom_model as bottom_m2_91_2_, stepinstan2_.bottom_protein as bottom_p3_91_2_, stepinstan2_.step_id as step_id4_91_2_, stepinstan2_.time_created as time_cre5_91_2_, stepinstan2_.top_model as top_mode6_91_2_, stepinstan2_.top_protein as top_prot7_91_2_, dependsupo3_.step_instance_id as step_ins1_93_3_, stepinstan4_.id as depends_2_93_3_, stepinstan4_.id as id1_91_4_, stepinstan4_.bottom_model as bottom_m2_91_4_, stepinstan4_.bottom_protein as bottom_p3_91_4_, stepinstan4_.step_id as step_id4_91_4_, stepinstan4_.time_created as time_cre5_91_4_, stepinstan4_.top_model as top_mode6_91_4_, stepinstan4_.top_protein as top_prot7_91_4_, parameters5_.step_instance_id as step_ins1_92_5_, parameters5_.parameters as paramete2_92_5_, parameters5_.parameters_key as paramete3_5_ from public.step_execution stepexecut0_ left outer join public.exception_chunk exceptionc1_ on stepexecut0_.id=exceptionc1_.step_execution_id inner join public.step_instance stepinstan2_ on stepexecut0_.step_instance_id=stepinstan2_.id left outer join public.step_instance_step_instance dependsupo3_ on stepinstan2_.id=dependsupo3_.step_instance_id left outer join public.step_instance stepinstan4_ on dependsupo3_.depends_upon_id=stepinstan4_.id left outer join public.step_instance_parameters parameters5_ on stepinstan4_.id=parameters5_.step_instance_id where stepexecut0_.id=? [42102-189]
2017-02-22 01:18:13,717 [main] [uk.ac.ebi.interpro.scan.jms.master.AbstractMaster:249] WARN - Unable to delete temporary directory /mnt/c/Users/jflowers/bin/interproscan-5.22-61.0/temp/SEA-JFLOWERS10_20170222_011732337_kpdc
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

[jflowers002]

BTW, I tested java out with another program and it works fine.

[GenoMax]

How are you running Interproscan? Can you post the command you are using? Have you installed all dependencies? Does this computer have direct/proxy internet access?

[jflowers002]

I downloaded the entire interproscan database to run locally. All dependencies are installed and work fine. Here is my command line entry: sudo ./interproscan.sh -i test_proteins.fasta -f tsv

Thanks for any insight.

Answer 1

[jflowers002]

Update: So, I am running this on Bash on Windows, and it turned out that I needed to change the page filing in windows to make it work in bash. See helpful response from someone having a similar issues on an un-related program.

"I had a similar problem, and in my case I needed to update the size of the pagefile. Changing this parameter is a pain. Here's how I found it: Control Panel > System and Security > System > Advanced System Settings > Advanced > Performance Settings ... > Advanced > Virtual Memory Change...

Then uncheck automatic paging file box and enter a custom min and starting size. In my case I increased those sizes to 2500 and it solved my issue."