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ebi-pf-team / interproscan

Genome-scale protein function classification
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IPScan gene3d_main.hmm Error #300

Closed kalonji08 closed 2 years ago

kalonji08 commented 2 years ago

Hello I'm using interproscan-5.59-91.0

Everything worked fined for the first few runs then i started getting the following error:

    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
    at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:19:55,280 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_081922022_kov0//jobGene3d/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_081922022_kov0//jobGene3d/000000000001_000000000006.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_081922022_kov0//jobGene3d/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. HMM file data/gene3d/4.3.0/gene3d_main.hmm 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 jdk.internal.reflect.GeneratedMethodAccessor93.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)

2022-11-22 08:19:55,281 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCathGene3dRunHmmer3 2022-11-22 08:19:55,406 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 55 : Run HMMER3 for proteins 1 to 6 has failed irretrievably. Available StackTraces follow. 2022-11-22 08:19:55,406 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2022-11-22 08:19:55,406 [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

kalonji08 commented 2 years ago

here is the full Log

22/11/2022 08:27:09:233 Welcome to InterProScan-5.59-91.0 22/11/2022 08:27:09:234 Running InterProScan v5 in STANDALONE mode... on Linux 22/11/2022 08:27:16:811 RunID: kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b 22/11/2022 08:27:27:877 Loading file /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/test_all_appl.fasta 22/11/2022 08:27:27:879 Running the following analyses: [AntiFam-7.0,CDD-3.18,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2021_04,MobiDBLite-2.0,Pfam-35.0,PIRSF-3.10,PIRSR-2021_05,PRINTS-42.0,ProSitePatterns-2022_01,ProSiteProfiles-2022_01,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 2022-11-22 08:27:33,760 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer2/2.3.2/hmmpfam --acc -A 0 --cpu 1 -E 0.01 -Z 350000 data/smart/7.1/smart.HMMs.bin /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSMART/000000000001_000000000006.fasta Error output from binary:

FATAL: Failed to open HMM database data/smart/7.1/smart.HMMs.bin Usage: hmmpfam [-options] Available options are: -h : help; print brief help on version and usage -n : nucleic acid models/sequence (default protein) -A : sets alignment output limit to best domain alignments -E : sets E value cutoff (globE) to ; default 10 -T : sets T bit threshold (globT) to ; no threshold by default -Z : sets Z (# models) for E-value calculation

2022-11-22 08:27:33,766 [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/hmmer2/2.3.2/hmmpfam --acc -A 0 --cpu 1 -E 0.01 -Z 350000 data/smart/7.1/smart.HMMs.bin /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSMART/000000000001_000000000006.fasta Error output from binary:

FATAL: Failed to open HMM database data/smart/7.1/smart.HMMs.bin Usage: hmmpfam [-options] Available options are: -h : help; print brief help on version and usage -n : nucleic acid models/sequence (default protein) -A : sets alignment output limit to best domain alignments -E : sets E value cutoff (globE) to ; default 10 -T : sets T bit threshold (globT) to ; no threshold by default -Z : sets Z (# models) for E-value calculation

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:33,780 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:33,781 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepSMARTRunBinary 2022-11-22 08:27:33,838 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 71 is being re-run following a failure. 2022-11-22 08:27:33,933 [amqEmbeddedWorkerJmsContainer-7] [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 378 --acc --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.domtblout.out -A /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.align.out data/sfld/4/sfld.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/sfld/4/sfld.hmm. HMM file data/sfld/4/sfld.hmm not found (nor an .h3m binary of it)

2022-11-22 08:27:33,935 [amqEmbeddedWorkerJmsContainer-7] [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 378 --acc --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.domtblout.out -A /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.align.out data/sfld/4/sfld.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/sfld/4/sfld.hmm. HMM file data/sfld/4/sfld.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:33,936 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:33,937 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepSFLDRunHmmer3 2022-11-22 08:27:33,964 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 88 is being re-run following a failure. 2022-11-22 08:27:34,055 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 2 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_01/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_01/evaluator.dat -r -s -o ipro /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: Cannot open data/prosite/2022_01/prosite_patterns.dat : No such file or directory at bin/prosite/ps_scan.pl line 2077.

2022-11-22 08:27:34,055 [amqEmbeddedWorkerJmsContainer-4] [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: 2 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_01/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_01/evaluator.dat -r -s -o ipro /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: Cannot open data/prosite/2022_01/prosite_patterns.dat : No such file or directory at bin/prosite/ps_scan.pl line 2077.

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:34,056 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:34,056 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary 2022-11-22 08:27:34,088 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 60 is being re-run following a failure. 2022-11-22 08:27:34,172 [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 --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobAntiFam/000000000001_000000000006.raw.out data/antifam/7.0/AntiFam.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobAntiFam/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/antifam/7.0/AntiFam.hmm. HMM file data/antifam/7.0/AntiFam.hmm not found (nor an .h3m binary of it)

2022-11-22 08:27:34,173 [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 --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobAntiFam/000000000001_000000000006.raw.out data/antifam/7.0/AntiFam.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobAntiFam/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/antifam/7.0/AntiFam.hmm. HMM file data/antifam/7.0/AntiFam.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:34,174 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:34,175 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepAntiFamRunHmmer3 2022-11-22 08:27:34,213 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 55 is being re-run following a failure. 2022-11-22 08:27:34,339 [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 -Z 4488 --cut_tc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobTIGRFAM/000000000001_000000000006.raw.out data/tigrfam/15.0/TIGRFAMs_HMM.LIB /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobTIGRFAM/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/tigrfam/15.0/TIGRFAMs_HMM.LIB. HMM file data/tigrfam/15.0/TIGRFAMs_HMM.LIB not found (nor an .h3m binary of it)

2022-11-22 08:27:34,347 [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 -Z 4488 --cut_tc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobTIGRFAM/000000000001_000000000006.raw.out data/tigrfam/15.0/TIGRFAMs_HMM.LIB /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobTIGRFAM/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/tigrfam/15.0/TIGRFAMs_HMM.LIB. HMM file data/tigrfam/15.0/TIGRFAMs_HMM.LIB not found (nor an .h3m binary of it)

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:34,348 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:34,348 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepTIGRFAMRunHmmer3 2022-11-22 08:27:34,471 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 51 is being re-run following a failure. 2022-11-22 08:27:34,513 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/prints/fingerPRINTScan data/prints/42.0/prints.pval /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPRINTS-42.0/000000000001_000000000006.fasta -e 0.0001 -d 10 -E 257043 84355444 -fj -o 15 Error output from binary: cannot open input file data/prints/42.0/prints.pval

2022-11-22 08:27:34,514 [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/prints/fingerPRINTScan data/prints/42.0/prints.pval /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPRINTS-42.0/000000000001_000000000006.fasta -e 0.0001 -d 10 -E 257043 84355444 -fj -o 15 Error output from binary: cannot open input file data/prints/42.0/prints.pval

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:34,515 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:34,516 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrintsRunFingerPrintScan 2022-11-22 08:27:34,598 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 48 is being re-run following a failure. 2022-11-22 08:27:34,842 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.1b1/hmmsearch -E 0.01 --acc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.domtblout.out -A /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.align.out data/pirsr/2021_05/sr_hmm_all /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2021_05/sr_hmm_all. HMM file data/pirsr/2021_05/sr_hmm_all not found (nor an .h3m binary of it)

2022-11-22 08:27:34,843 [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/hmmer3/3.1b1/hmmsearch -E 0.01 --acc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.domtblout.out -A /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.align.out data/pirsr/2021_05/sr_hmm_all /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2021_05/sr_hmm_all. HMM file data/pirsr/2021_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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:34,844 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:34,845 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPIRSRRunHmmer3 2022-11-22 08:27:34,956 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 42 is being re-run following a failure. 2022-11-22 08:27:38,949 [amqEmbeddedWorkerJmsContainer-7] [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 /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPfam/000000000001_000000000006.raw.out data/pfam/35.0/pfam_a.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPfam/000000000001_000000000006.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)

2022-11-22 08:27:38,951 [amqEmbeddedWorkerJmsContainer-7] [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 /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPfam/000000000001_000000000006.raw.out data/pfam/35.0/pfam_a.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPfam/000000000001_000000000006.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:38,952 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:38,953 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPfamRunHmmer3 2022-11-22 08:27:38,980 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 40 is being re-run following a failure. 2022-11-22 08:27:39,066 [amqEmbeddedWorkerJmsContainer-4] [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 100 --domE 100 --incE 100 --incdomE 100 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.raw.out --tblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.raw.tblout.out data/hamap/2021_04/hamap.hmm.lib /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/hamap/2021_04/hamap.hmm.lib. HMM file data/hamap/2021_04/hamap.hmm.lib not found (nor an .h3m binary of it)

2022-11-22 08:27:39,067 [amqEmbeddedWorkerJmsContainer-4] [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 100 --domE 100 --incE 100 --incdomE 100 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.raw.out --tblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.raw.tblout.out data/hamap/2021_04/hamap.hmm.lib /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/hamap/2021_04/hamap.hmm.lib. HMM file data/hamap/2021_04/hamap.hmm.lib not found (nor an .h3m binary of it)

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:39,067 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:39,068 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepHamapHMMRunHmmer3 2022-11-22 08:27:39,101 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 32 is being re-run following a failure. 2022-11-22 08:27:39,185 [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 -Z 65245 -E 0.001 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. HMM file data/gene3d/4.3.0/gene3d_main.hmm not found (nor an .h3m binary of it)

2022-11-22 08:27:39,185 [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 -Z 65245 -E 0.001 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. HMM file data/gene3d/4.3.0/gene3d_main.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:39,186 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:39,187 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCathGene3dRunHmmer3 2022-11-22 08:27:39,229 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 30 is being re-run following a failure. 2022-11-22 08:27:39,370 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 3 Command: bin/blast/ncbi-blast-2.10.1+/rpsblast -query /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.18/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 11 Error output from binary: BLAST engine error: Cannot retrieve path to RPS database

2022-11-22 08:27:39,370 [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: 3 Command: bin/blast/ncbi-blast-2.10.1+/rpsblast -query /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.18/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 11 Error output from binary: BLAST engine error: Cannot retrieve path to RPS database

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:39,371 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:39,372 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCDDRunBinaryRPSblast 2022-11-22 08:27:39,473 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 25 is being re-run following a failure. 2022-11-22 08:27:39,525 [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/hmmscan -E 0.01 --acc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSF/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSF/000000000001_000000000006.raw.domtblout.out data/pirsf/3.10/sf_hmm_all /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSF/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsf/3.10/sf_hmm_all. HMM file data/pirsf/3.10/sf_hmm_all not found (nor an .h3m binary of it); also looked in PFAMDB

2022-11-22 08:27:39,525 [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/hmmscan -E 0.01 --acc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSF/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSF/000000000001_000000000006.raw.domtblout.out data/pirsf/3.10/sf_hmm_all /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSF/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsf/3.10/sf_hmm_all. HMM file data/pirsf/3.10/sf_hmm_all not found (nor an .h3m binary of it); also looked in PFAMDB

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:39,526 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:39,526 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPIRSFRunHmmer3 2022-11-22 08:27:39,597 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 21 is being re-run following a failure. 2022-11-22 08:27:39,854 [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/hmmscan -E 10 -Z 15438 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSuperFamily-1.75/000000000001_000000000006.raw.out data/superfamily/1.75/hmmlib_1.75 /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSuperFamily-1.75/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/superfamily/1.75/hmmlib_1.75. HMM file data/superfamily/1.75/hmmlib_1.75 not found (nor an .h3m binary of it); also looked in PFAMDB

2022-11-22 08:27:39,854 [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/hmmscan -E 10 -Z 15438 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSuperFamily-1.75/000000000001_000000000006.raw.out data/superfamily/1.75/hmmlib_1.75 /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSuperFamily-1.75/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/superfamily/1.75/hmmlib_1.75. HMM file data/superfamily/1.75/hmmlib_1.75 not found (nor an .h3m binary of it); also looked in PFAMDB

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:39,855 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:39,856 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepSuperFamilyRunHmmer3-1.75 2022-11-22 08:27:39,953 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 13 is being re-run following a failure. 2022-11-22 08:27:43,818 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer2/2.3.2/hmmpfam --acc -A 0 --cpu 1 -E 0.01 -Z 350000 data/smart/7.1/smart.HMMs.bin /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSMART/000000000001_000000000006.fasta Error output from binary:

FATAL: Failed to open HMM database data/smart/7.1/smart.HMMs.bin Usage: hmmpfam [-options] Available options are: -h : help; print brief help on version and usage -n : nucleic acid models/sequence (default protein) -A : sets alignment output limit to best domain alignments -E : sets E value cutoff (globE) to ; default 10 -T : sets T bit threshold (globT) to ; no threshold by default -Z : sets Z (# models) for E-value calculation

2022-11-22 08:27:43,819 [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/hmmer2/2.3.2/hmmpfam --acc -A 0 --cpu 1 -E 0.01 -Z 350000 data/smart/7.1/smart.HMMs.bin /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSMART/000000000001_000000000006.fasta Error output from binary:

FATAL: Failed to open HMM database data/smart/7.1/smart.HMMs.bin Usage: hmmpfam [-options] Available options are: -h : help; print brief help on version and usage -n : nucleic acid models/sequence (default protein) -A : sets alignment output limit to best domain alignments -E : sets E value cutoff (globE) to ; default 10 -T : sets T bit threshold (globT) to ; no threshold by default -Z : sets Z (# models) for E-value calculation

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:43,820 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:43,821 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepSMARTRunBinary 2022-11-22 08:27:43,864 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 71 is being re-run following a failure. 2022-11-22 08:27:43,965 [amqEmbeddedWorkerJmsContainer-7] [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 65245 -E 0.001 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobFunFam/000000000001_000000000006.raw.out data/gene3d/4.3.0/gene3d_main.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobFunFam/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. HMM file data/gene3d/4.3.0/gene3d_main.hmm not found (nor an .h3m binary of it)

2022-11-22 08:27:43,965 [amqEmbeddedWorkerJmsContainer-7] [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 65245 -E 0.001 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobFunFam/000000000001_000000000006.raw.out data/gene3d/4.3.0/gene3d_main.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobFunFam/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. HMM file data/gene3d/4.3.0/gene3d_main.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:43,966 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:43,966 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCathFunFamRunHmmer3 2022-11-22 08:27:43,988 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 9 is being re-run following a failure. 2022-11-22 08:27:44,077 [amqEmbeddedWorkerJmsContainer-4] [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 378 --acc --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.domtblout.out -A /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.align.out data/sfld/4/sfld.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/sfld/4/sfld.hmm. HMM file data/sfld/4/sfld.hmm not found (nor an .h3m binary of it)

2022-11-22 08:27:44,078 [amqEmbeddedWorkerJmsContainer-4] [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 378 --acc --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.domtblout.out -A /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.raw.align.out data/sfld/4/sfld.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSFLD/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/sfld/4/sfld.hmm. HMM file data/sfld/4/sfld.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:44,079 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:44,079 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepSFLDRunHmmer3 2022-11-22 08:27:44,115 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 88 is being re-run following a failure. 2022-11-22 08:27:44,245 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 2 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_01/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_01/evaluator.dat -r -s -o ipro /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: Cannot open data/prosite/2022_01/prosite_patterns.dat : No such file or directory at bin/prosite/ps_scan.pl line 2077.

2022-11-22 08:27:44,246 [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: 2 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_01/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_01/evaluator.dat -r -s -o ipro /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: Cannot open data/prosite/2022_01/prosite_patterns.dat : No such file or directory at bin/prosite/ps_scan.pl line 2077.

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:44,246 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:44,246 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary 2022-11-22 08:27:44,372 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 60 is being re-run following a failure. 2022-11-22 08:27:44,380 [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 --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobAntiFam/000000000001_000000000006.raw.out data/antifam/7.0/AntiFam.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobAntiFam/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/antifam/7.0/AntiFam.hmm. HMM file data/antifam/7.0/AntiFam.hmm not found (nor an .h3m binary of it)

2022-11-22 08:27:44,381 [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 --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobAntiFam/000000000001_000000000006.raw.out data/antifam/7.0/AntiFam.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobAntiFam/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/antifam/7.0/AntiFam.hmm. HMM file data/antifam/7.0/AntiFam.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:44,382 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:44,383 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepAntiFamRunHmmer3 2022-11-22 08:27:44,501 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 55 is being re-run following a failure. 2022-11-22 08:27:44,536 [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 -Z 4488 --cut_tc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobTIGRFAM/000000000001_000000000006.raw.out data/tigrfam/15.0/TIGRFAMs_HMM.LIB /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobTIGRFAM/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/tigrfam/15.0/TIGRFAMs_HMM.LIB. HMM file data/tigrfam/15.0/TIGRFAMs_HMM.LIB not found (nor an .h3m binary of it)

2022-11-22 08:27:44,536 [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 -Z 4488 --cut_tc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobTIGRFAM/000000000001_000000000006.raw.out data/tigrfam/15.0/TIGRFAMs_HMM.LIB /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobTIGRFAM/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/tigrfam/15.0/TIGRFAMs_HMM.LIB. HMM file data/tigrfam/15.0/TIGRFAMs_HMM.LIB not found (nor an .h3m binary of it)

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:44,537 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:44,537 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepTIGRFAMRunHmmer3 2022-11-22 08:27:44,629 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 51 is being re-run following a failure. 2022-11-22 08:27:44,865 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.1b1/hmmsearch -E 0.01 --acc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.domtblout.out -A /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.align.out data/pirsr/2021_05/sr_hmm_all /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2021_05/sr_hmm_all. HMM file data/pirsr/2021_05/sr_hmm_all not found (nor an .h3m binary of it)

2022-11-22 08:27:44,866 [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/hmmer3/3.1b1/hmmsearch -E 0.01 --acc --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.domtblout.out -A /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.raw.align.out data/pirsr/2021_05/sr_hmm_all /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPIRSR/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/pirsr/2021_05/sr_hmm_all. HMM file data/pirsr/2021_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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:44,867 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:44,868 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPIRSRRunHmmer3 2022-11-22 08:27:44,888 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 42 is being re-run following a failure. 22/11/2022 08:27:45:025 25% completed 2022-11-22 08:27:48,751 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/prints/fingerPRINTScan data/prints/42.0/prints.pval /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPRINTS-42.0/000000000001_000000000006.fasta -e 0.0001 -d 10 -E 257043 84355444 -fj -o 15 Error output from binary: cannot open input file data/prints/42.0/prints.pval

2022-11-22 08:27:48,751 [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/prints/fingerPRINTScan data/prints/42.0/prints.pval /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPRINTS-42.0/000000000001_000000000006.fasta -e 0.0001 -d 10 -E 257043 84355444 -fj -o 15 Error output from binary: cannot open input file data/prints/42.0/prints.pval

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:48,752 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:48,753 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrintsRunFingerPrintScan 2022-11-22 08:27:48,881 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 48 is being re-run following a failure. 2022-11-22 08:27:49,091 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer2/2.3.2/hmmpfam --acc -A 0 --cpu 1 -E 0.01 -Z 350000 data/smart/7.1/smart.HMMs.bin /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSMART/000000000001_000000000006.fasta Error output from binary:

FATAL: Failed to open HMM database data/smart/7.1/smart.HMMs.bin Usage: hmmpfam [-options] Available options are: -h : help; print brief help on version and usage -n : nucleic acid models/sequence (default protein) -A : sets alignment output limit to best domain alignments -E : sets E value cutoff (globE) to ; default 10 -T : sets T bit threshold (globT) to ; no threshold by default -Z : sets Z (# models) for E-value calculation

2022-11-22 08:27:49,092 [amqEmbeddedWorkerJmsContainer-4] [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/hmmer2/2.3.2/hmmpfam --acc -A 0 --cpu 1 -E 0.01 -Z 350000 data/smart/7.1/smart.HMMs.bin /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobSMART/000000000001_000000000006.fasta Error output from binary:

FATAL: Failed to open HMM database data/smart/7.1/smart.HMMs.bin Usage: hmmpfam [-options] Available options are: -h : help; print brief help on version and usage -n : nucleic acid models/sequence (default protein) -A : sets alignment output limit to best domain alignments -E : sets E value cutoff (globE) to ; default 10 -T : sets T bit threshold (globT) to ; no threshold by default -Z : sets Z (# models) for E-value calculation

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:49,092 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:49,093 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepSMARTRunBinary 2022-11-22 08:27:49,125 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 71 : Run HMM on selected proteins for proteins 1 to 6 has failed irretrievably. Available StackTraces follow. 2022-11-22 08:27:49,126 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2022-11-22 08:27:49,126 [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:?] 2022-11-22 08:27:49,255 [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 -Z 17929 --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPfam/000000000001_000000000006.raw.out data/pfam/35.0/pfam_a.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPfam/000000000001_000000000006.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)

2022-11-22 08:27:49,255 [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 -Z 17929 --cut_ga --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPfam/000000000001_000000000006.raw.out data/pfam/35.0/pfam_a.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobPfam/000000000001_000000000006.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:49,256 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:49,256 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPfamRunHmmer3 2022-11-22 08:27:49,391 [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 100 --domE 100 --incE 100 --incdomE 100 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.raw.out --tblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.raw.tblout.out data/hamap/2021_04/hamap.hmm.lib /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/hamap/2021_04/hamap.hmm.lib. HMM file data/hamap/2021_04/hamap.hmm.lib not found (nor an .h3m binary of it)

2022-11-22 08:27:49,391 [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 100 --domE 100 --incE 100 --incdomE 100 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.raw.out --tblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.raw.tblout.out data/hamap/2021_04/hamap.hmm.lib /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobHAMAP/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/hamap/2021_04/hamap.hmm.lib. HMM file data/hamap/2021_04/hamap.hmm.lib not found (nor an .h3m binary of it)

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:49,400 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:49,400 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepHamapHMMRunHmmer3 08:27:49.407 [responseMonitorJmsContainer-1] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "STEPEXECUTION" not found; SQL statement: select stepexecut0.id as id1_1090, stepexecut0_.time_completed as time_com2_1090, stepexecut0_.time_created as time_cre3_1090, stepexecut0_.exception_first_chunk as exceptio4_1090, stepexecut0_.proportion_completed as proporti5_1090, stepexecut0_.time_started_running as time_sta6_1090, stepexecut0_.state as state7_1090, stepexecut0_.step_instance_id as step_ins9_1090, stepexecut0_.time_submitted as time_sub8_1090, exceptionc1_.step_execution_id as step_exe1_151, exceptionc1_.exception_chunks as exceptio2_151, exceptionc1_.chunk_index as chunk_in31, stepinstan2_.id as id1_1102, stepinstan2_.bottom_model as bottom_m2_1102, stepinstan2_.bottom_protein as bottom_p3_1102, stepinstan2_.step_id as step_id4_1102, stepinstan2_.time_created as time_cre5_1102, stepinstan2_.top_model as top_mode6_1102, stepinstan2_.top_protein as top_prot7_1102, dependsupo3_.step_instance_id as step_ins1_1123, stepinstan4_.id as depends_2_1123, stepinstan4_.id as id1_1104, stepinstan4_.bottom_model as bottom_m2_1104, stepinstan4_.bottom_protein as bottom_p3_1104, stepinstan4_.step_id as step_id4_1104, stepinstan4_.time_created as time_cre5_1104, stepinstan4_.top_model as top_mode6_1104, stepinstan4_.top_protein as top_prot7_1104, parameters5_.step_instance_id as step_ins1_1115, parameters5_.parameters as paramete2_1115, parameters5_.parameters_key as paramete35 from public.stepexecution stepexecut0 left outer join public.exceptionchunk exceptionc1 on stepexecut0.id=exceptionc1.step_execution_id inner join public.stepinstance stepinstan2 on stepexecut0_.step_instanceid=stepinstan2.id left outer join public.step_instance_stepinstance dependsupo3 on stepinstan2.id=dependsupo3.step_instance_id left outer join public.stepinstance stepinstan4 on dependsupo3_.depends_uponid=stepinstan4.id left outer join public.step_instanceparameters parameters5 on stepinstan4.id=parameters5.step_instanceid where stepexecut0.id=? [42102-199] 2022-11-22 08:27:49,546 [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 -Z 65245 -E 0.001 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. HMM file data/gene3d/4.3.0/gene3d_main.hmm not found (nor an .h3m binary of it)

2022-11-22 08:27:49,547 [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 -Z 65245 -E 0.001 --cpu 1 -o /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.raw.out --domtblout /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/kalonjilab2/my_interproscan/interproscan-5.59-91.0/temp/kalonjilab2-PowerEdge-T430_20221122_082714899_hq9b//jobGene3d/000000000001_000000000006.fasta Error output from binary:

Error: File existence/permissions problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. HMM file data/gene3d/4.3.0/gene3d_main.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-5.59-91.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor94.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-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:829) [?:?]

2022-11-22 08:27:49,548 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2022-11-22 08:27:49,548 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCathGene3dRunHmmer3 08:27:49.553 [responseMonitorJmsContainer-1] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "STEPEXECUTION" not found; SQL statement: select stepexecut0.id as id1_1090, stepexecut0_.time_completed as time_com2_1090, stepexecut0_.time_created as time_cre3_1090, stepexecut0_.exception_first_chunk as exceptio4_1090, stepexecut0_.proportion_completed as proporti5_1090, stepexecut0_.time_started_running as time_sta6_1090, stepexecut0_.state as state7_1090, stepexecut0_.step_instance_id as step_ins9_1090, stepexecut0_.time_submitted as time_sub8_1090, exceptionc1_.step_execution_id as step_exe1_151, exceptionc1_.exception_chunks as exceptio2_151, exceptionc1_.chunk_index as chunk_in31, stepinstan2_.id as id1_1102, stepinstan2_.bottom_model as bottom_m2_1102, stepinstan2_.bottom_protein as bottom_p3_1102, stepinstan2_.step_id as step_id4_1102, stepinstan2_.time_created as time_cre5_1102, stepinstan2_.top_model as top_mode6_1102, stepinstan2_.top_protein as top_prot7_1102, dependsupo3_.step_instance_id as step_ins1_1123, stepinstan4_.id as depends_2_1123, stepinstan4_.id as id1_1104, stepinstan4_.bottom_model as bottom_m2_1104, stepinstan4_.bottom_protein as bottom_p3_1104, stepinstan4_.step_id as step_id4_1104, stepinstan4_.time_created as time_cre5_1104, stepinstan4_.top_model as top_mode6_1104, stepinstan4_.top_protein as top_prot7_1104, parameters5_.step_instance_id as step_ins1_1115, parameters5_.parameters as paramete2_1115, parameters5_.parameters_key as paramete35 from public.stepexecution stepexecut0 left outer join public.exceptionchunk exceptionc1 on stepexecut0.id=exceptionc1.step_execution_id inner join public.stepinstance stepinstan2 on stepexecut0_.step_instanceid=stepinstan2.id left outer join public.step_instance_stepinstance dependsupo3 on stepinstan2.id=dependsupo3.step_instance_id left outer join public.stepinstance stepinstan4 on dependsupo3_.depends_uponid=stepinstan4.id left outer join public.step_instanceparameters parameters5 on stepinstan4.id=parameters5.step_instanceid where stepexecut0.id=? [42102-199]

kalonji08 commented 2 years ago

Nevermind, i accidentally deleted the data directory everything is good now