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ebi-pf-team / interproscan

Genome-scale protein function classification
Apache License 2.0
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error while loading shared libraries: libpcre2-8.so.0: cannot open shared object file: No such file or directory #331

Closed alexvasilikop closed 1 year ago

alexvasilikop commented 1 year ago

Hello,

I get the following error when trying to run interproscan. I tried to install the libraries suggested in the documentation but the problem persists

sudo apt-get install -y libgomp1
./interproscan.sh -i $infile -d $outdir -iprlookup -goterms
12/07/2023 13:49:17:926 Welcome to InterProScan-5.63-95.0
12/07/2023 13:49:17:928 Running InterProScan v5 in STANDALONE mode... on Linux
12/07/2023 13:49:26:890 RunID: urbe-2_20230712_134926514_3dwi
12/07/2023 13:49:47:787 Loading file /mnt/sda1/Alex/15.FUNCTIONAL_ANNOTATION/Adineta_ricciae/Adineta_ricciae.proteins.renamed_chromosomes.renamed_headers.fasta
12/07/2023 13:49:47:790 Running the following analyses:
[AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2023_01,MobiDBLite-2.0,NCBIfam-12.0,PANTHER-17.0,Pfam-35.0,Phobius-1.01,PIRSF-3.10,PIRSR-2021_05,PRINTS-42.0,ProSitePatterns-2022_05,ProSiteProfiles-2022_05,SFLD-4,SignalP_EUK-4.1,SignalP_GRAM_NEGATIVE-4.1,SignalP_GRAM_POSITIVE-4.1,SMART-9.0,SUPERFAMILY-1.75,TMHMM-2.0c]
Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally.
12/07/2023 13:49:59:438 Uploaded 34240 unique sequences for analysis
12/07/2023 13:52:03:004 87% completed
2023-07-12 13:52:58,729 [amqEmbeddedWorkerJmsContainer-5] [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 /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPrositePatterns/000000033001_000000034240.fasta 
Error output from binary:
bin/prosite/pfscanV3: error while loading shared libraries: libpcre2-8.so.0: cannot open shared object file: No such file or directory
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps870530-1.tmp /tmp/ps870530-3.tmp  > /tmp/ps870530-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

2023-07-12 13:52:58,736 [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: 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 /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPrositePatterns/000000033001_000000034240.fasta 
Error output from binary:
bin/prosite/pfscanV3: error while loading shared libraries: libpcre2-8.so.0: cannot open shared object file: No such file or directory
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps870530-1.tmp /tmp/ps870530-3.tmp  > /tmp/ps870530-2.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-5.63-95.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor103.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at java.lang.Thread.run(Thread.java:829) [?:?]
2023-07-12 13:52:58,744 [amqEmbeddedWorkerJmsContainer-5] [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 /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPrositePatterns/000000033001_000000034240.fasta 
Error output from binary:
bin/prosite/pfscanV3: error while loading shared libraries: libpcre2-8.so.0: cannot open shared object file: No such file or directory
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /tmp/ps870530-1.tmp /tmp/ps870530-3.tmp  > /tmp/ps870530-2.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.GeneratedMethodAccessor103.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)
2023-07-12 13:52:58,746 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary
2023-07-12 13:52:59,139 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 1478 is being re-run following a failure.
^C2023-07-12 13:54:05,735 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 130
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 17929 --cut_ga --cpu 1 -o /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPfam/000000000001_000000005500.raw.out data/pfam/35.0/pfam_a.hmm /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPfam/000000000001_000000005500.fasta 
Error output from binary:

2023-07-12 13:54:05,736 [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: 130
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 17929 --cut_ga --cpu 1 -o /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPfam/000000000001_000000005500.raw.out data/pfam/35.0/pfam_a.hmm /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPfam/000000000001_000000005500.fasta 
Error output from binary:

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.63-95.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor103.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at java.lang.Thread.run(Thread.java:829) [?:?]
2023-07-12 13:54:05,737 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 130
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 17929 --cut_ga --cpu 1 -o /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPfam/000000000001_000000005500.raw.out data/pfam/35.0/pfam_a.hmm /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPfam/000000000001_000000005500.fasta 
Error output from binary:

    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.GeneratedMethodAccessor103.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)
2023-07-12 13:54:05,738 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPfamRunHmmer3
13:54:05.738 [main] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Database is already closed (to disable automatic closing at VM shutdown, add ";DB_CLOSE_ON_EXIT=FALSE" to the db URL) [90121-199]
2023-07-12 13:54:05,740 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 130
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --notextw --cpu 1 -o /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPanther/000000000551_000000001100.raw.out --domtblout /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPanther/000000000551_000000001100.raw.domtblout.out data/panther/17.0/famhmm/binHmm /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPanther/000000000551_000000001100.fasta 
Error output from binary:

2023-07-12 13:54:05,740 [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: 130
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --notextw --cpu 1 -o /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPanther/000000000551_000000001100.raw.out --domtblout /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPanther/000000000551_000000001100.raw.domtblout.out data/panther/17.0/famhmm/binHmm /mnt/sda1/Alex/software/my_interproscan/interproscan-5.63-95.0/temp/urbe-2_20230712_134926514_3dwi//jobPanther/000000000551_000000001100.fasta 
Error output from binary:

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.63-95.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor103.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at java.lang.Thread.run(Thread.java:829) [?:?]
2023-07-12 13:54:05,741 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :

Any help would be appreciated Thanks Alex

tgrego commented 1 year ago

Hi Alex, it looks like a system library required by the prosite binaries is missing. You can install it with sudo apt-get install -y libpcre2-dev

alexvasilikop commented 1 year ago

many thanks