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Interproscan error #83

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amardeepranu opened this issue Dec 21, 2023 · 3 comments
Open

Interproscan error #83

amardeepranu opened this issue Dec 21, 2023 · 3 comments
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@mberacochea
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@amardeepranu
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Seeing the following error pretty randomly:

ERROR ~ Error executing process > 'GAP:ANNOTATE:IPS (4)'

Caused by:
  Process `GAP:ANNOTATE:IPS (4)` terminated with an error exit status (231)

Command executed:

  interproscan.sh     -cpu 8     -dp     --goterms     -pa     -f TSV     --input protein_catalogue-90.4.faa     -o protein_catalogue-90.4.IPS.tsv

Command exit status:
  231

Command output:
  2023-12-21 04:36:10,501 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 7 is being re-run following a failure.
  2023-12-21 04:36:34,277 [amqEmbeddedWorkerJmsContainer-6] [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 -Z 17929 --cut_ga --cpu 1 -o temp/defdc38590ee_20231221_041344507_5lx8//jobPfam/000000005001_000000010000.raw.out data/pfam/35.0/pfam_a.hmm temp/defdc38590ee_20231221_041344507_5lx8//jobPfam/000000005001_000000010000.fasta 
  Error output from binary:
  
  Error: File existence/permissions problem in trying to open HMM file data/pfam/35.0/pfam_a.hmm.
  HMM file data/pfam/35.0/pfam_a.hmm not found (nor an .h3m binary of it)
  
  
  2023-12-21 04:36:34,277 [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: bin/hmmer/hmmer3/3.3/hmmsearch -Z 17929 --cut_ga --cpu 1 -o temp/defdc38590ee_20231221_041344507_5lx8//jobPfam/000000005001_000000010000.raw.out data/pfam/35.0/pfam_a.hmm temp/defdc38590ee_20231221_041344507_5lx8//jobPfam/000000005001_000000010000.fasta 
  Error output from binary:
  
  Error: File existence/permissions problem in trying to open HMM file data/pfam/35.0/pfam_a.hmm.
  HMM file data/pfam/35.0/pfam_a.hmm not found (nor an .h3m binary of it)
  
  
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.62-94.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor101.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: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) [?:?]
  2023-12-21 04:36:34,278 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
  2023-12-21 04:36:34,278 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPfamRunHmmer3
  2023-12-21 04:36:34,322 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 360 : Run HMMER 3 Binary for selected proteins for proteins 5001 to 10000 has failed irretrievably.  Available StackTraces follow.
  2023-12-21 04:36:34,323 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
  2023-12-21 04:36:34,323 [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:?]

Command error:
        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)
  2023-12-21 04:36:34,277 [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: bin/hmmer/hmmer3/3.3/hmmsearch -Z 17929 --cut_ga --cpu 1 -o temp/defdc38590ee_20231221_041344507_5lx8//jobPfam/000000005001_000000010000.raw.out data/pfam/35.0/pfam_a.hmm temp/defdc38590ee_20231221_041344507_5lx8//jobPfam/000000005001_000000010000.fasta 
  Error output from binary:
  
  Error: File existence/permissions problem in trying to open HMM file data/pfam/35.0/pfam_a.hmm.
  HMM file data/pfam/35.0/pfam_a.hmm not found (nor an .h3m binary of it)
  
  
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.62-94.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor101.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: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) [?:?]
  2023-12-21 04:36:34,278 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
  2023-12-21 04:36:34,278 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPfamRunHmmer3
  2023-12-21 04:36:34,322 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 360 : Run HMMER 3 Binary for selected proteins for proteins 5001 to 10000 has failed irretrievably.  Available StackTraces follow.
  2023-12-21 04:36:34,323 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
  2023-12-21 04:36:34,323 [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
@amardeepranu
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This was fixed by downloading the latest interproscan dbs here: http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.65-97.0/interproscan-5.65-97.0-64-bit.tar.gz

However I'm running into another consistent error - any help would be appreciated:

ERROR ~ Error executing process > 'GAP:ANNOTATE:IPS (9)'

Caused by:
  Process `GAP:ANNOTATE:IPS (9)` terminated with an error exit status (231)

Command executed:

  interproscan.sh     -cpu 32     -dp     --goterms     -pa     -f TSV     --input protein_catalogue-90.9.faa     -o protein_catalogue-90.9.IPS.tsv

Command exit status:
  231

Command output:
  java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information.
  /mnt/eat 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:?]
  p: wheat uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413) [interproscan-5.jar:?]
  11:49:24.034 [responseMonitorJmsContainer-1] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "STEP_EXECUTION" not found; SQL statement:
  select stepexecut0_.id as id1_110_0_, stepexecut0_.time_completed as time_com2_110_0_, stepexecut0_.time_created as time_cre3_110_0_, stepexecut0_.exception_first_chunk as exceptio4_110_0_, stepexecut0_.proportion_completed as proporti5_110_0_, stepexecut0_.time_started_running as time_sta6_110_0_, stepexecut0_.state as state7_110_0_, stepexecut0_.step_instance_id as step_ins9_110_0_, stepexecut0_.time_submitted as time_sub8_110_0_, exceptionc1_.step_execution_id as step_exe1_15_1_, exceptionc1_.exception_chunks as exceptio2_15_1_, exceptionc1_.chunk_index as chunk_in3_1_, stepinstan2_.id as id1_111_2_, stepinstan2_.bottom_model as bottom_m2_111_2_, stepinstan2_.bottom_protein as bottom_p3_111_2_, stepinstan2_.step_id as step_id4_111_2_, stepinstan2_.time_created as time_cre5_111_2_, stepinstan2_.top_model as top_mode6_111_2_, stepinstan2_.top_protein as top_prot7_111_2_, dependsupo3_.step_instance_id as step_ins1_113_3_, stepinstan4_.id as depends_2_113_3_, stepinstan4_.id as id1_111_4_, stepinstan4_.bottom_model as bottom_m2_111_4_, stepinstan4_.bottom_protein as bottom_p3_111_4_, stepinstan4_.step_id as step_id4_111_4_, stepinstan4_.time_created as time_cre5_111_4_, stepinstan4_.top_model as top_mode6_111_4_, stepinstan4_.top_protein as top_prot7_111_4_, parameters5_.step_instance_id as step_ins1_112_5_, parameters5_.parameters as paramete2_112_5_, parameters5_.parameters_key as paramete3_5_ from public.step_execution stepexecut0_ left outer join public.exception_chunk exceptionc1_ on stepexecut0_.id=exceptionc1_.step_execution_id inner join public.step_instance stepinstan2_ on stepexecut0_.step_instance_id=stepinstan2_.id left outer join public.step_instance_step_instance dependsupo3_ on stepinstan2_.id=dependsupo3_.step_instance_id left outer join public.step_instance stepinstan4_ on dependsupo3_.depends_upon_id=stepinstan4_.id left outer join public.step_instance_parameters parameters5_ on stepinstan4_.id=parameters5_.step_instance_id where stepexecut0_.id=? [42102-199]
  2023-12-21 11:49:24,980 [amqEmbeddedWorkerJmsContainer-13] [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/2022_05/prosite_profiles temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.fasta temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4 
  Error output from binary:
  Error occured while accessing file temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.fasta
  The error reads : No such file or directory
  Error found.
  Error running prosite binary bin/prosite/pfsearchV3
  
  2023-12-21 11:49:24,980 [amqEmbeddedWorkerJmsContainer-13] [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/2022_05/prosite_profiles temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.fasta temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4 
  Error output from binary:
  Error occured while accessing file temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.fasta
  The error reads : No such file or directory
  Error found.
  Error running prosite binary bin/prosite/pfsearchV3
  
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.62-94.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor91.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: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) [?:?]
  2023-12-21 11:49:24,981 [amqEmbeddedWorkerJmsContainer-13] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
  2023-12-21 11:49:24,981 [amqEmbeddedWorkerJmsContainer-13] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
  11:49:24.984 [responseMonitorJmsContainer-1] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "STEP_EXECUTION" not found; SQL statement:
  select stepexecut0_.id as id1_110_0_, stepexecut0_.time_completed as time_com2_110_0_, stepexecut0_.time_created as time_cre3_110_0_, stepexecut0_.exception_first_chunk as exceptio4_110_0_, stepexecut0_.proportion_completed as proporti5_110_0_, stepexecut0_.time_started_running as time_sta6_110_0_, stepexecut0_.state as state7_110_0_, stepexecut0_.step_instance_id as step_ins9_110_0_, stepexecut0_.time_submitted as time_sub8_110_0_, exceptionc1_.step_execution_id as step_exe1_15_1_, exceptionc1_.exception_chunks as exceptio2_15_1_, exceptionc1_.chunk_index as chunk_in3_1_, stepinstan2_.id as id1_111_2_, stepinstan2_.bottom_model as bottom_m2_111_2_, stepinstan2_.bottom_protein as bottom_p3_111_2_, stepinstan2_.step_id as step_id4_111_2_, stepinstan2_.time_created as time_cre5_111_2_, stepinstan2_.top_model as top_mode6_111_2_, stepinstan2_.top_protein as top_prot7_111_2_, dependsupo3_.step_instance_id as step_ins1_113_3_, stepinstan4_.id as depends_2_113_3_, stepinstan4_.id as id1_111_4_, stepinstan4_.bottom_model as bottom_m2_111_4_, stepinstan4_.bottom_protein as bottom_p3_111_4_, stepinstan4_.step_id as step_id4_111_4_, stepinstan4_.time_created as time_cre5_111_4_, stepinstan4_.top_model as top_mode6_111_4_, stepinstan4_.top_protein as top_prot7_111_4_, parameters5_.step_instance_id as step_ins1_112_5_, parameters5_.parameters as paramete2_112_5_, parameters5_.parameters_key as paramete3_5_ from public.step_execution stepexecut0_ left outer join public.exception_chunk exceptionc1_ on stepexecut0_.id=exceptionc1_.step_execution_id inner join public.step_instance stepinstan2_ on stepexecut0_.step_instance_id=stepinstan2_.id left outer join public.step_instance_step_instance dependsupo3_ on stepinstan2_.id=dependsupo3_.step_instance_id left outer join public.step_instance stepinstan4_ on dependsupo3_.depends_upon_id=stepinstan4_.id left outer join public.step_instance_parameters parameters5_ on stepinstan4_.id=parameters5_.step_instance_id where stepexecut0_.id=? [42102-199]

Command error:
        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) [?:?]
  2023-12-21 11:49:24,981 [amqEmbeddedWorkerJmsContainer-13] [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/2022_05/prosite_profiles temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.fasta temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4 
  Error output from binary:
  Error occured while accessing file temp/50704931c152_20231221_114327559_8nnx//jobPrositeProfiles/000000004001_000000006000.fasta
  The error reads : No such file or directory
  Error found.
  Error running prosite binary bin/prosite/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.GeneratedMethodAccessor91.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: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)
  2023-12-21 11:49:24,981 [amqEmbeddedWorkerJmsContainer-13] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
  11:49:24.984 [responseMonitorJmsContainer-1] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "STEP_EXECUTION" not found; SQL statement:
  select stepexecut0_.id as id1_110_0_, stepexecut0_.time_completed as time_com2_110_0_, stepexecut0_.time_created as time_cre3_110_0_, stepexecut0_.exception_first_chunk as exceptio4_110_0_, stepexecut0_.proportion_completed as proporti5_110_0_, stepexecut0_.time_started_running as time_sta6_110_0_, stepexecut0_.state as state7_110_0_, stepexecut0_.step_instance_id as step_ins9_110_0_, stepexecut0_.time_submitted as time_sub8_110_0_, exceptionc1_.step_execution_id as step_exe1_15_1_, exceptionc1_.exception_chunks as exceptio2_15_1_, exceptionc1_.chunk_index as chunk_in3_1_, stepinstan2_.id as id1_111_2_, stepinstan2_.bottom_model as bottom_m2_111_2_, stepinstan2_.bottom_protein as bottom_p3_111_2_, stepinstan2_.step_id as step_id4_111_2_, stepinstan2_.time_created as time_cre5_111_2_, stepinstan2_.top_model as top_mode6_111_2_, stepinstan2_.top_protein as top_prot7_111_2_, dependsupo3_.step_instance_id as step_ins1_113_3_, stepinstan4_.id as depends_2_113_3_, stepinstan4_.id as id1_111_4_, stepinstan4_.bottom_model as bottom_m2_111_4_, stepinstan4_.bottom_protein as bottom_p3_111_4_, stepinstan4_.step_id as step_id4_111_4_, stepinstan4_.time_created as time_cre5_111_4_, stepinstan4_.top_model as top_mode6_111_4_, stepinstan4_.top_protein as top_prot7_111_4_, parameters5_.step_instance_id as step_ins1_112_5_, parameters5_.parameters as paramete2_112_5_, parameters5_.parameters_key as paramete3_5_ from public.step_execution stepexecut0_ left outer join public.exception_chunk exceptionc1_ on stepexecut0_.id=exceptionc1_.step_execution_id inner join public.step_instance stepinstan2_ on stepexecut0_.step_instance_id=stepinstan2_.id left outer join public.step_instance_step_instance dependsupo3_ on stepinstan2_.id=dependsupo3_.step_instance_id left outer join public.step_instance stepinstan4_ on dependsupo3_.depends_upon_id=stepinstan4_.id left outer join public.step_instance_parameters parameters5_ on stepinstan4_.id=parameters5_.step_instance_id where stepexecut0_.id=? [42102-199]
  InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

@amardeepranu
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Getting these errors even when running on the test dataset:

ERROR ~ Error executing process > 'GAP:ANNOTATE:IPS (2)'

Caused by:
  Process `GAP:ANNOTATE:IPS (2)` terminated with an error exit status (231)

Command executed:

  interproscan.sh     -cpu 8     -dp     --goterms     -pa     -f TSV     --input protein_catalogue-90.2.faa     -o protein_catalogue-90.2.IPS.tsv

Command exit status:
  231

Command output:
  Caused by: org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "PROSITE_PAT_RAW_MATCH" not found; SQL statement:
  select prositepat0_.id as id1_87_, prositepat0_.loc_fragment_dcs_tatus as loc_frag2_87_, prositepat0_.location_end as location3_87_, prositepat0_.location_start as location4_87_, prositepat0_.model_id as model_id5_87_, prositepat0_.numeric_sequence_id as numeric_6_87_, prositepat0_.sequence_id as sequence7_87_, prositepat0_.signature_library as signatur8_87_, prositepat0_.sig_lib_release as sig_lib_9_87_, prositepat0_.cigar_alignment as cigar_al1_68_, prositepat0_.pattern_level as pattern_1_82_ from public.prosite_pat_raw_match prositepat0_ where prositepat0_.numeric_sequence_id>=? and prositepat0_.numeric_sequence_id<=? and prositepat0_.sig_lib_release=? [42102-199]

@mberacochea
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Hi @amardeepranu

Thank you for reporting the issue. It's pretty odd, I haven't seen that one.

How are you running the pipeline? Locally in your laptop using docker, or with a different setup?.

I'll try to reproduce this on my side.

Cheers

@mberacochea mberacochea self-assigned this Jan 8, 2024
@mberacochea mberacochea added the bug Something isn't working label Jan 8, 2024
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