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ebi-pf-team / interproscan

Genome-scale protein function classification
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Error with pfsearchV3 after installing pcre2 and pftools3 #353

Closed asupandy closed 3 months ago

asupandy commented 8 months ago

Hi all,

I've just downloaded interproscan and tried running the 2 two test case commands:

./interproscan.sh -i test_all_appl.fasta -f tsv -dp
./interproscan.sh -i test_all_appl.fasta -f tsv

The ./interproscan.sh -i test_all_appl.fasta -f tsv ran perfectly.

But the ./interproscan.sh -i test_all_appl.fasta -f tsv -dp gave the following error:

Error output from binary:
bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3)
Error running prosite binary bin/prosite/pfsearchV3

According to #288, I installed and compiled both pftools3 and pcre2. I updated the interproscan.properties accordingly as well. When I re-ran ./interproscan.sh -i test_all_appl.fasta -f tsv -dp, I got the following error codes, which if I understand correctly, points to pfsearchV3 as the problem.

Is there anything that I should be trying or steps that I'm missing?

12/03/2024 15:11:33:566 Running the following analyses:
[AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2023_05,MobiDBLite-2.0,NCBIfam-13.0,PANTHER-18.0,Pfam-36.0,PIRSF-3.10,PIRSR-2023_05,PRINTS-42.0,ProSitePatterns-2023_05,ProSiteProfiles-2023_05,SFLD-4,SMART-9.0,SUPERFAMILY-1.75]
Pre-calculated match lookup service DISABLED.  Please wait for match calculations to complete...
2024-03-12 15:11:44,896 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

2024-03-12 15:11:44,905 [amqEmbeddedWorkerJmsContainer-8] [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: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.66-98.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor87.invoke(Unknown Source) ~[?:?]
        at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
        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 jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833) [?:?]
2024-03-12 15:11:44,917 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

        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.GeneratedMethodAccessor87.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
        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:367)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
        at jdk.proxy2/jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
        at java.base/java.lang.Thread.run(Thread.java:833)
2024-03-12 15:11:44,917 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2024-03-12 15:11:44,953 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 30 is being re-run following a failure.
12/03/2024 15:11:48:113 26% completed
2024-03-12 15:12:01,486 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

2024-03-12 15:12:01,488 [amqEmbeddedWorkerJmsContainer-6] [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: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.66-98.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor87.invoke(Unknown Source) ~[?:?]
        at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
        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 jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833) [?:?]
2024-03-12 15:12:01,490 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

        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.GeneratedMethodAccessor87.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
        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:367)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
        at jdk.proxy2/jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
        at java.base/java.lang.Thread.run(Thread.java:833)
2024-03-12 15:12:01,492 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2024-03-12 15:12:01,506 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 30 is being re-run following a failure.
2024-03-12 15:12:12,583 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

2024-03-12 15:12:12,584 [amqEmbeddedWorkerJmsContainer-6] [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: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.66-98.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor87.invoke(Unknown Source) ~[?:?]
        at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
        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 jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833) [?:?]
2024-03-12 15:12:12,586 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.fasta /data/Adeline/interproscan/interproscan-5.66-98.0/temp/id-division.dom.pitt.edu_20240312_151122132_5p80//jobPrositeProfiles/000000000001_000000000006.raw.out "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3" -f -o 7 -t 4
Error output from binary:
Error running prosite binary "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

        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.GeneratedMethodAccessor87.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
        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:367)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
        at jdk.proxy2/jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
        at java.base/java.lang.Thread.run(Thread.java:833)
2024-03-12 15:12:12,587 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2024-03-12 15:12:12,633 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 30 : Run ps_scan.pl and pfscan Binary for selected proteins for proteins 1 to 6 has failed irretrievably.  Available StackTraces follow.
2024-03-12 15:12:12,633 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
2024-03-12 15:12:12,634 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:363] 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:169) [interproscan-5.jar:?]
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413) [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:169)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
laisecf commented 8 months ago

Hello and sorry for the late answer! Can you send us the binary, so we can try to reproduce your issue? Alternatively you can use our Docker image (https://hub.docker.com/r/interpro/interproscan).

asupandy commented 8 months ago

Sorry, I'm very new to coding. Can you please explain how I can find the binary?

laisecf commented 8 months ago

No problem! The binary is on the path "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

asupandy commented 8 months ago

I've attached the pfsearchV3 binary in this email! Please let me know if there's anything else needed.

From: Laise Florentino @.> Sent: Wednesday, March 27, 2024 6:20 AM To: ebi-pf-team/interproscan @.> Cc: Supandy, Adeline @.>; Author @.> Subject: Re: [ebi-pf-team/interproscan] Error with pfsearchV3 after installing pcre2 and pftools3 (Issue #353)

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No problem! The binary is on the path "/data/Adeline/interproscan/interproscan-5.66-98.0/pftools3/build/src/C/pfsearchV3"

— Reply to this email directly, view it on GitHubhttps://github.com/ebi-pf-team/interproscan/issues/353#issuecomment-2022399163, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BG5BP4H5ATLUYBVN7LOLWM3Y2KFMNAVCNFSM6AAAAABES3RLC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRSGM4TSMJWGM. You are receiving this because you authored the thread.Message ID: @.***>

laisecf commented 7 months ago

Hi! I didn't receive the binary in the attachment. Can you try sending again, please? :)

PS: Did you try the Docker image (https://hub.docker.com/r/interpro/interproscan)