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ebi-pf-team / interproscan

Genome-scale protein function classification
Apache License 2.0
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Error exit codes:1 and 25 #314

Closed GiuseppePin closed 11 months ago

GiuseppePin commented 1 year ago

Hello, I get the following errors when I try to run the first test: ./interproscan.sh -i test_all_appl.fasta -f tsv -dp. Can you help me to figure out how to solve it? 10/03/2023 09:58:24:535 Welcome to InterProScan-5.61-93.0 10/03/2023 09:58:24:536 Running InterProScan v5 in STANDALONE mode... on Linux 10/03/2023 09:58:29:527 RunID: Hybrid_20230310_095828958_43mt 10/03/2023 09:58:39:368 Loading file /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/test_all_appl.fasta 10/03/2023 09:58:39:369 Running the following analyses: [AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2021_04,MobiDBLite-2.0,PANTHER-17.0,Pfam-35.0,PIRSF-3.10,PIRSR-2021_05,PRINTS-42.0,ProSitePatterns-2022_05,ProSiteProfiles-2022_05,SFLD-4,SMART-9.0,SUPERFAMILY-1.75,TIGRFAM-15.0] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 2023-03-10 09:58:45,322 [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 10 -Z 15438 --cpu 1 -o /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobSuperFamily/000000000001_000000000006.raw.out data/superfamily/1.75/hmmlib_1.75 /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobSuperFamily/000000000001_000000000006.fasta Error output from binary:

Error: File format problem, trying to open HMM file data/superfamily/1.75/hmmlib_1.75. Opened data/superfamily/1.75/hmmlib_1.75.h3m, a pressed HMM file; but format of its .h3i file unrecognized

2023-03-10 09:58:45,327 [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 10 -Z 15438 --cpu 1 -o /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobSuperFamily/000000000001_000000000006.raw.out data/superfamily/1.75/hmmlib_1.75 /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobSuperFamily/000000000001_000000000006.fasta Error output from binary:

Error: File format problem, trying to open HMM file data/superfamily/1.75/hmmlib_1.75. Opened data/superfamily/1.75/hmmlib_1.75.h3m, a pressed HMM file; but format of its .h3i file unrecognized

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.61-93.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor93.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) [?:?]

2023-03-10 09:58:45,337 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmscan -E 10 -Z 15438 --cpu 1 -o /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobSuperFamily/000000000001_000000000006.raw.out data/superfamily/1.75/hmmlib_1.75 /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobSuperFamily/000000000001_000000000006.fasta Error output from binary:

Error: File format problem, trying to open HMM file data/superfamily/1.75/hmmlib_1.75. Opened data/superfamily/1.75/hmmlib_1.75.h3m, a pressed HMM file; but format of its .h3i file unrecognized

    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)

2023-03-10 09:58:45,338 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepSuperFamilyRunHmmer3 2023-03-10 09:58:45,411 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 78 is being re-run following a failure. 2023-03-10 09:58:45,913 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: python3 bin/prosite/runprosite.py data/prosite/2022_05/prosite_profiles /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositeProfiles/000000000001_000000000006.fasta /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4 Error output from binary: bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3) Error running prosite binary bin/prosite/pfsearchV3

2023-03-10 09:58:45,914 [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: python3 bin/prosite/runprosite.py data/prosite/2022_05/prosite_profiles /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositeProfiles/000000000001_000000000006.fasta /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4 Error output from binary: bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3) Error running prosite binary bin/prosite/pfsearchV3

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.61-93.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor93.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) [?:?]

2023-03-10 09:58:45,915 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/prosite/runprosite.py data/prosite/2022_05/prosite_profiles /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositeProfiles/000000000001_000000000006.fasta /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4 Error output from binary: bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3) Error running prosite binary bin/prosite/pfsearchV3

    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)

2023-03-10 09:58:45,915 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary 2023-03-10 09:58:45,999 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 58 is being re-run following a failure. 10/03/2023 09:58:50:732 25% completed 2023-03-10 09:58:51,306 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps490117-1.tmp /tmp/ps490117-3.tmp > /tmp/ps490117-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

2023-03-10 09:58:51,306 [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: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps490117-1.tmp /tmp/ps490117-3.tmp > /tmp/ps490117-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.61-93.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor93.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) [?:?]

2023-03-10 09:58:51,307 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps490117-1.tmp /tmp/ps490117-3.tmp > /tmp/ps490117-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    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)

2023-03-10 09:58:51,307 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary 2023-03-10 09:58:51,397 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 18 is being re-run following a failure. 2023-03-10 09:59:01,829 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps144816-1.tmp /tmp/ps144816-3.tmp > /tmp/ps144816-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

2023-03-10 09:59:01,829 [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: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps144816-1.tmp /tmp/ps144816-3.tmp > /tmp/ps144816-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.61-93.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor93.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) [?:?]

2023-03-10 09:59:01,830 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps144816-1.tmp /tmp/ps144816-3.tmp > /tmp/ps144816-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    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)

2023-03-10 09:59:01,830 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary 2023-03-10 09:59:01,915 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 18 is being re-run following a failure. 2023-03-10 09:59:07,351 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps983356-1.tmp /tmp/ps983356-3.tmp > /tmp/ps983356-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

2023-03-10 09:59:07,351 [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: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps983356-1.tmp /tmp/ps983356-3.tmp > /tmp/ps983356-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.61-93.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor93.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) [?:?]

2023-03-10 09:59:07,352 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 25 Command: bin/prosite/ps_scan.pl -d data/prosite/2022_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2022_05/evaluator.dat -r -s -o ipro /home/giuseppe/programs/my_interproscan/interproscan-5.61-93.0/temp/Hybrid_20230310_095828958_43mt//jobPrositePatterns/000000000001_000000000006.fasta Error output from binary: bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3) Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps983356-1.tmp /tmp/ps983356-3.tmp > /tmp/ps983356-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    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)

2023-03-10 09:59:07,352 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary 2023-03-10 09:59:07,366 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 18 : Run ps_scan.pl and pfscan Binary for selected proteins for proteins 1 to 6 has failed irretrievably. Available StackTraces follow. 2023-03-10 09:59:07,366 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2023-03-10 09:59:07,366 [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

sjfleck commented 1 year ago

I'm getting this same error. I think this is the only issue that mentions "GLIBC_2.27". I'll let you know if I'm able to solve the issue

Unfortunately, it seems like we may be out of luck. When I run "ldd --version" on my cluster, I get this: ldd (GNU libc) 2.17 Copyright (C) 2012 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Written by Roland McGrath and Ulrich Drepper.

I don't have root access where I'm trying to run interproscan, so I don't think there's anything I can do about it. I just can't use the newest version. I'm still looking into the issue, but I may be out of luck

sjfleck commented 1 year ago

it turns out that my university had an option to use a newer set of modules that they were going to force us to start using this summer. I now have access to glibc 2.35. Unfortunately, the "`GLIBC_2.27' not found (required by bin/prosite/pfscanV3)" error is still being thrown. I went from glibc 2.17 to glibc 2.35, neither of which work for pfscanV3. I wish there was a way around this somehow. I really wanted to use the newest version

tgrego commented 1 year ago

Hi, you will likely have to compile the pfscanV3/pfsearchV3 binaries from source.

The source code is available at https://github.com/sib-swiss/pftools3/ you can find the compiling instructions in https://github.com/sib-swiss/pftools3/blob/master/INSTALL

You can then replace the provided binaries with your compiled version and that will make sure the GLIBC is compatible. If you get affinity issues with the standard binary, you should compile using the 'cmake -DUSE_AFFINITY=OFF ..' build option.