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ebi-pf-team / interproscan

Genome-scale protein function classification
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Error when running TMHMM with Interproscan-5.60-92.0 #311

Open krostifangers opened 1 year ago

krostifangers commented 1 year ago

Hello I am working on fungi and I wanted to use interproscan in order to predict secretome using SignalP4.1, Phobius and TMHMM2.0.c I get the binaries, install them in the proper folders. Interproscan works well with SignalP4.1 and Phobius. However, using TMHMM I have the following message :

[TMHMM-2.0c] Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally. 02/03/2023 14:59:49:578 Uploaded 12163 unique sequences for analysis 02/03/2023 15:00:31:332 87% completed 2023-03-02 15:00:37,835 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 139 Command: bin/tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/krostif/recherche/interproscan-5.60-92.0/tempotmhmm/golum_20230302_145932713_1ga0//jobTMHMM/000000000001_000000012163.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032 Error output from binary: decodeanhmm 1.1g and many other java error messages.

Here I give you a copy of my properties file :

TMHMM 2.0

Note: TMHMM binary not distributed with InterProScan 5, please install separately e.g. in ${bin.directory}/tmhmm/2.0c/decodeanhmm

tmhmm.signature.library.release=2.0c binary.tmhmm.path=${bin.directory}/tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64 tmhmm.model.path=data/tmhmm/2.0c/TMHMM2.0.model

Do you know where the problem is? Thank you in advance All the best Christophe

Carolinacanettieri commented 2 months ago

Hi, I am having a similar problem but using InterProScan v5.69-101.0. Here is the error output message:

2024-09-19 00:47:58,750 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:216] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 139 Command: /users-d2/carolina.kurotusch/programs/tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64 /users-d2/carolina.kurotusch/programs/tmhmm-2.0c/lib/TMHMM2.0.model /users-d2/carolina.kurotusch/path/to/temp/hercules12_20240919_004730409_dw02//jobTMHMM/000000000001_000000000226.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032 Error output from binary: decodeanhmm 1.1g Copyright (C) 1998 by Anders Krogh

`at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.69-101.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor98.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:564) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at java.lang.Thread.run(Thread.java:832) [?:?]`

2024-09-19 00:47:58,759 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2024-09-19 00:47:58,761 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepTMHMMRunBinary 2024-09-19 00:47:58,895 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 79 is being re-run following a failure.

matthiasblum commented 2 months ago

Hi @Carolinacanettieri,

Would you mind sharing your input sequences so I can try to reproduce the error?