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ebi-pf-team / interproscan

Genome-scale protein function classification
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Interproscan failing: Exception thrown by StandaloneBlackBoxMaster. #189

Closed aberaslop closed 3 years ago

aberaslop commented 3 years ago

Hi,

I am trying to run Interproscan, but I am finding some errors that I do not know how to solve. Any help would be appreciated.

I am running InterProScan-5.48-83.0 in a Linux Debian system. When I run ./interproscan.sh, I think everything is installed:

[...] Available analyses: TIGRFAM (15.0) : TIGRFAMs are protein families based on hidden Markov models (HMMs). SFLD (4) : SFLD is a database of protein families based on hidden Markov models (HMMs). Phobius (1.01) : A combined transmembrane topology and signal peptide predictor. SignalP_GRAM_NEGATIVE (4.1) : SignalP (gram-negative) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for gram-negative prokaryotes. SUPERFAMILY (1.75) : SUPERFAMILY is a database of structural and functional annotations for all proteins and genomes. PANTHER (15.0) : The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Gene3D (4.2.0) : Structural assignment for whole genes and genomes using the CATH domain structure database. Hamap (2020_05) : High-quality Automated and Manual Annotation of Microbial Proteomes. ProSiteProfiles (2019_11) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. Coils (2.2.1) : Prediction of coiled coil regions in proteins. SMART (7.1) : SMART allows the identification and analysis of domain architectures based on hidden Markov models (HMMs). CDD (3.18) : CDD predicts protein domains and families based on a collection of well-annotated multiple sequence alignment models. PRINTS (42.0) : A compendium of protein fingerprints - a fingerprint is a group of conserved motifs used to characterise a protein family. ProSitePatterns (2019_11) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. SignalP_EUK (4.1) : SignalP (eukaryotes) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for eukaryotes. Pfam (33.1) : A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). MobiDBLite (2.0) : Prediction of intrinsically disordered regions in proteins. SignalP_GRAM_POSITIVE (4.1) : SignalP (gram-positive) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for gram-positive prokaryotes. PIRSF (3.10) : The PIRSF concept is used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. TMHMM (2.0c) : Prediction of transmembrane helices in proteins.

However, when I run the test dataset: ./interproscan.sh -i test_all_appl.fasta -f tsv -dp I get a bunch of errors. It ends up advising me to check the log files, but none have been created. I have pasted the errors below. Thank you!

26/02/2021 02:10:01:999 Welcome to InterProScan-5.48-83.0 26/02/2021 02:10:02:008 Running InterProScan v5 in STANDALONE mode... on Linux 26/02/2021 02:11:10:913 Loading file /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/test_all_appl.fasta 26/02/2021 02:11:10:917 Running the following analyses: [CDD-3.18,Coils-2.2.1,Gene3D-4.2.0,Hamap-2020_05,MobiDBLite-2.0,PANTHER-15.0,Pfam-33.1,Phobius-1.01,PIRSF-3.10,PRINTS-42.0,ProSitePatterns-2019_11,ProSiteProfiles-2019_11,SFLD-4,SignalP_EUK-4.1,SignalP_GRAM_NEGATIVE-4.1,SignalP_GRAM_POSITIVE-4.1,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0,TMHMM-2.0c] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 2021-02-26 02:11:26,576 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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

2021-02-26 02:11:26,594 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] 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: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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-5.48-83.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at java.lang.Thread.run(Thread.java:834) [?:?]

2021-02-26 02:11:26,625 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source)
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.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
at java.base/java.lang.Thread.run(Thread.java:834)

2021-02-26 02:11:26,631 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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

2021-02-26 02:11:26,632 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepTMHMMRunBinary 2021-02-26 02:11:26,692 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:166] WARN - StepInstance 32 is being re-run following a failure. 26/02/2021 02:11:27:789 25% completed 26/02/2021 02:11:49:455 50% completed 2021-02-26 02:12:28,689 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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

2021-02-26 02:12:28,690 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] 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: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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-5.48-83.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at java.lang.Thread.run(Thread.java:834) [?:?]

2021-02-26 02:12:28,692 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source)
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.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
at java.base/java.lang.Thread.run(Thread.java:834)

2021-02-26 02:12:28,696 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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

2021-02-26 02:12:28,697 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepTMHMMRunBinary 2021-02-26 02:12:28,784 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:166] WARN - StepInstance 32 is being re-run following a failure. 2021-02-26 02:12:33,891 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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

2021-02-26 02:12:33,892 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] 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: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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-5.48-83.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
at java.lang.Thread.run(Thread.java:834) [?:?]

2021-02-26 02:12:33,893 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source)
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.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
at java.base/java.lang.Thread.run(Thread.java:834)

2021-02-26 02:12:33,895 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model /home/aberas2/funannotate-conda/external_software/interproscan-5.48-83.0/temp/loma_20210226_021017280_cybo//jobTMHMM/000000000001_000000000005.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

2021-02-26 02:12:33,895 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepTMHMMRunBinary 2021-02-26 02:12:33,989 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 32 : Run TMHMM binary for selected protein sequences for proteins 1 to 5 has failed irretrievably. Available StackTraces follow. 2021-02-26 02:12:33,990 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2021-02-26 02:12:33,990 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:332] ERROR - Exception thrown by StandaloneBlackBoxMaster: java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information. at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:43) ~[interproscan-5.jar:?] at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:157) [interproscan-5.jar:?] at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:475) [interproscan-5.jar:?] java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information. at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:43) at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:157) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:475) InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

gsn7 commented 3 years ago

There seems to be a problem with TMHMM. First, check if you can run InterProScan with TMHMM excluded: ./interproscan.sh -i test_all_appl.fasta -f tsv -dp -exclappl tmhmm

Furthermore, I would like to see what files you have for TMHMM. Can you let me know the output of the command: ls -l data/tmhmm/2.0c/

aberaslop commented 3 years ago

Hi, @gsn7, thanks for your answer!

Running Interproscan with TMHMM excluded worked.

the output of ls -l data/tmhmm/2.0c/ is: total 24 -rw-r--r-- 1 aberas2 users 22262 Feb 19 07:16 TMHMM2.0.model

gsn7 commented 3 years ago

what do you get when you issue the command: bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 data/tmhmm/2.0c/TMHMM2.0.model test_all_appl.fasta -N 1 -PrintNumbers

aberaslop commented 3 years ago

That would output:

decodeanhmm 1.1g Copyright (C) 1998 by Anders Krogh Segmentation fault

Something tells me this is not good...

aberaslop commented 3 years ago

Dear @gsn7, I have been reading more of the posts, and it seems, based on issue #170, that not running tmhmm is not critical if we run Phobius instead. Is this correct?

Thanks!

gsn7 commented 3 years ago

yes, if you have Phobius you don't need to run TMHMMM. Phobius gives better predictions and it will also give you all the predictions that you would get from TMHMM. Removing the data/tmhmm/2.0c folder will automatically disable TMHMM, so you don't have to add the exclude parameter

aberaslop commented 3 years ago

Great, I will do that then. Thank you for your help!