amardeepranu
commented
8 months ago 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
mberacochea
Seeing the following error pretty randomly: