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ebi-pf-team / interproscan

Genome-scale protein function classification
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Error while running InterProscan using the test E. coli protein fasta. #379

Closed Vijithkumar2020 closed 1 month ago

Vijithkumar2020 commented 1 month ago

I was running InterProscan (v.5.69-101.0), using the test e-coli file. But the run was terminated prematurely, rending the following run report. I am not able to understand this. Can you help me resolve this issue?

sudo docker run --rm \
    -v $PWD/interproscan-5.69-101.0/data:/opt/interproscan/data \
    -v $PWD/input:/input \
    -v $PWD/temp:/temp \
    -v $PWD/output:/output \
    interpro/interproscan:5.69-101.0 \
    --input /input/e-coli.fa \
    --output-dir /output \
    --tempdir /temp \
    --cpu 8
[sudo] password for palmyra: 
Unable to find image 'interpro/interproscan:5.69-101.0' locally
5.69-101.0: Pulling from interpro/interproscan
Digest: sha256:f20ada500a162e967366cbe42eb10773946ea7b5b71d9c04610d10905f0054a9
Status: Downloaded newer image for interpro/interproscan:5.69-101.0
25/09/2024 06:33:01:152 Welcome to InterProScan-5.69-101.0
25/09/2024 06:33:01:153 Running InterProScan v5 in STANDALONE mode... on Linux
25/09/2024 06:33:10:106 RunID: 2fc1c09e9843_20240925_063309521_2csm
25/09/2024 06:33:28:178 Loading file /input/e-coli.fa
25/09/2024 06:33:28:181 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-15.0,Pfam-37.0,PIRSF-3.10,PIRSR-2023_05,PRINTS-42.0,ProSitePatterns-2023_05,ProSiteProfiles-2023_05,SFLD-4,SMART-9.0,SUPERFAMILY-1.75]
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.
25/09/2024 06:35:17:300 87% completed
2024-09-25 06:35:22,789 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

2024-09-25 06:35:22,803 [amqEmbeddedWorkerJmsContainer-1] [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: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
    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: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:829) [?:?]
2024-09-25 06:35:22,814 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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 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.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 com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:829)
2024-09-25 06:35:22,816 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPIRSRRunHmmer3
2024-09-25 06:35:22,900 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 13 is being re-run following a failure.
2024-09-25 06:35:23,946 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

2024-09-25 06:35:23,946 [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: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
    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: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:829) [?:?]
2024-09-25 06:35:23,947 [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: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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 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.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 com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:829)
2024-09-25 06:35:23,949 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPIRSRRunHmmer3
2024-09-25 06:35:24,000 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 18 is being re-run following a failure.
2024-09-25 06:35:27,913 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

2024-09-25 06:35:27,914 [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: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
    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: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:829) [?:?]
2024-09-25 06:35:27,915 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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 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.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 com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:829)
2024-09-25 06:35:27,916 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPIRSRRunHmmer3
2024-09-25 06:35:27,969 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 13 is being re-run following a failure.
2024-09-25 06:35:29,013 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

2024-09-25 06:35:29,013 [amqEmbeddedWorkerJmsContainer-5] [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: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
    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: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:829) [?:?]
2024-09-25 06:35:29,015 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000000001_000000004000.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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 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.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 com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:829)
2024-09-25 06:35:29,016 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPIRSRRunHmmer3
2024-09-25 06:35:29,069 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 18 is being re-run following a failure.
2024-09-25 06:35:32,984 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

2024-09-25 06:35:32,985 [amqEmbeddedWorkerJmsContainer-3] [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: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
    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: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:829) [?:?]
2024-09-25 06:35:32,986 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -E 0.01 --acc --cpu 1 -o /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.out --domtblout /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.domtblout.out -A /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.raw.align.out data/pirsr/2023_05/sr_hmm_all /temp/2fc1c09e9843_20240925_063309521_2csm//jobPIRSR/000000004001_000000004360.fasta 
Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2023_05/sr_hmm_all.
HMM file data/pirsr/2023_05/sr_hmm_all not found (nor an .h3m binary of it)

    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 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.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 com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:829)
2024-09-25 06:35:32,987 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPIRSRRunHmmer3
2024-09-25 06:35:33,030 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 13 : Run hmmer3 Binary for selected proteins for proteins 4001 to 4360 has failed irretrievably.  Available StackTraces follow.
2024-09-25 06:35:33,030 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
2024-09-25 06:35:33,031 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:363] ERROR - Exception thrown by StandaloneBlackBoxMaster:
matthiasblum commented 1 month ago

Hi @Vijithkumar2020,

Sorry for the slow reply. From the directory where you ran Docker, can you check whether the $PWD/interproscan-5.69-101.0/data/pirsr/2023_05 does exist?

Vijithkumar2020 commented 1 month ago

Thank you for your response. Yes, $PWD/interproscan-5.69-101.0/data/pirsr/2023_05 does exist. However, the process runs painfully slower. The machine is a local server with 256GB memory, and 8 core cpu. Here is the hitherto run report. Looking forward to a response. https://docs.google.com/document/d/1RH8SHBXB1UJ-b6zu6ePkLnFDcf4DcUsTRYVZQKsXBvU/edit?usp=sharing

On Tue, Oct 1, 2024 at 3:30 PM Matthias Blum @.***> wrote:

Hi @Vijithkumar2020 https://github.com/Vijithkumar2020,

Sorry for the slow reply. From the directory where you ran Docker, can you check whether the $PWD/interproscan-5.69-101.0/data/pirsr/2023_05 does exist?

— Reply to this email directly, view it on GitHub https://github.com/ebi-pf-team/interproscan/issues/379#issuecomment-2385353769, or unsubscribe https://github.com/notifications/unsubscribe-auth/APVJDNZDUBDVP3CC3QVZ34LZZJXE3AVCNFSM6AAAAABO6MWPAWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBVGM2TGNZWHE . You are receiving this because you were mentioned.Message ID: @.***>

matthiasblum commented 1 month ago

The logs you added to Google Docs do not contain the same error (missing file). The error seems to be related to the match lookup service. You can turn off the match lookup with the -dp option.

I also noted the following line:

27/09/2024 09:12:04:929 Uploaded 505641 unique sequences for analysis

This is a large number of sequences. InterProScan5 isn't very efficient with large input files. I'd suggest splitting in 10-15 smaller files.

Vijithkumar2020 commented 1 month ago

Thank you for your valuable suggestion. I have started re-running, with the match lookup turned off. Here is the updated docker command. Kindly let me know if this is good to go. The smaller files contain 50k sequences. Looking forward to a response from you.

sudo docker run --rm \ -v $PWD/interproscan-5.69-101.0/data:/opt/interproscan/data \ -v $PWD/input:/input \ -v $PWD/temp:/temp \ -v $PWD/output:/output \ interpro/interproscan:5.69-101.0 \ --input /input/out_1.fasta \ --output-dir /output \ --tempdir /temp \ --cpu 8 \ --formats tsv,xml \ -dp

Regards

On Tue, Oct 1, 2024 at 4:41 PM Matthias Blum @.***> wrote:

The logs you added to Google Docs do not contain the same error (missing file). The error seems to be related to the match lookup service. You can turn off the match lookup with the -dp option.

I also noted the following line:

27/09/2024 09:12:04:929 Uploaded 505641 unique sequences for analysis

This is a large number of sequences. InterProScan5 isn't very efficient with large input files. I'd suggest splitting in 10-15 smaller files.

— Reply to this email directly, view it on GitHub https://github.com/ebi-pf-team/interproscan/issues/379#issuecomment-2385494838, or unsubscribe https://github.com/notifications/unsubscribe-auth/APVJDN33VOVDX4PYGHSRJ5LZZJ7NPAVCNFSM6AAAAABO6MWPAWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBVGQ4TIOBTHA . You are receiving this because you were mentioned.Message ID: @.***>

matthiasblum commented 1 month ago

This looks OK. Have you had troubles running the command you posted?