Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

java.lang.NullPointerException: Alignment must not be null #236

Open
lecorguille opened this issue Nov 8, 2021 · 6 comments
Open

java.lang.NullPointerException: Alignment must not be null #236

lecorguille opened this issue Nov 8, 2021 · 6 comments

Comments

@lecorguille
Copy link

With @jadeleconte, we went though those issue:

Our current versions:

$ interproscan.sh --version
InterProScan version 5.52-86.0
InterProScan 64-Bit build  (requires Java 11)

$ /opt/interproscan/bin/prosite/pfscan --version
pfscan 2.3 revision 5.d
$ /opt/interproscan/bin/prosite/pfscanV3
 Version 3.2.11 built on Nov  8 2021 at 09:53:10.

Our current error:

08/11/2021 12:36:17:742 Welcome to InterProScan-5.52-86.0
08/11/2021 12:36:17:745 Running InterProScan v5 in STANDALONE mode... on Linux
08/11/2021 12:36:22:737 RunID: n75_20211108_123622495_flb7
08/11/2021 12:36:29:460 Loading file /projet/sbr/cyanorak/current/common/genomics/functional_annotation/interproscan/3-pfam_go_interpro_prosites_TIGRfam_2021-08-24/./input_interproscan/Pro_AS9601_NO_STAR.fasta
08/11/2021 12:36:29:462 Running the following analyses:
[Pfam-33.1,ProSitePatterns-2021_01,ProSiteProfiles-2021_01,SignalP_GRAM_NEGATIVE-4.1,TIGRFAM-15.0]
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.
08/11/2021 12:36:49:976 85% completed
2021-11-08 12:37:03,673 [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.NullPointerException: Alignment must not be null
        at uk.ac.ebi.interpro.scan.model.raw.alignment.CigarAlignmentEncoder.encode(CigarAlignmentEncoder.java:51) ~[interproscan-model-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.prosite.PrositePfsearchMatchParser.createMatch(PrositePfsearchMatchParser.java:75) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.prosite.PrositePfsearchMatchParser.createMatch(PrositePfsearchMatchParser.java:26) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.AbstractLineMatchParser.parse(AbstractLineMatchParser.java:66) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:101) ~[interproscan-management-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor105.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at java.lang.Thread.run(Thread.java:834) [?:?]
2021-11-08 12:37:03,679 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
2021-11-08 12:37:03,679 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesParseRawOutput
2021-11-08 12:37:03,790 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 31 is being re-run following a failure.
2021-11-08 12:37:21,632 [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.NullPointerException: Alignment must not be null
        at uk.ac.ebi.interpro.scan.model.raw.alignment.CigarAlignmentEncoder.encode(CigarAlignmentEncoder.java:51) ~[interproscan-model-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.prosite.PrositePfsearchMatchParser.createMatch(PrositePfsearchMatchParser.java:75) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.prosite.PrositePfsearchMatchParser.createMatch(PrositePfsearchMatchParser.java:26) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.AbstractLineMatchParser.parse(AbstractLineMatchParser.java:66) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:101) ~[interproscan-management-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor105.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at java.lang.Thread.run(Thread.java:834) [?:?]
2021-11-08 12:37:21,633 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
2021-11-08 12:37:21,634 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesParseRawOutput
2021-11-08 12:37:21,685 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 31 is being re-run following a failure.
2021-11-08 12:37:26,688 [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.NullPointerException: Alignment must not be null
        at uk.ac.ebi.interpro.scan.model.raw.alignment.CigarAlignmentEncoder.encode(CigarAlignmentEncoder.java:51) ~[interproscan-model-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.prosite.PrositePfsearchMatchParser.createMatch(PrositePfsearchMatchParser.java:75) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.prosite.PrositePfsearchMatchParser.createMatch(PrositePfsearchMatchParser.java:26) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.io.match.AbstractLineMatchParser.parse(AbstractLineMatchParser.java:66) ~[interproscan-io-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:101) ~[interproscan-management-5.52-86.0.jar:?]
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
        at jdk.internal.reflect.GeneratedMethodAccessor105.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
        at java.lang.Thread.run(Thread.java:834) [?:?]
2021-11-08 12:37:26,688 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
2021-11-08 12:37:26,689 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesParseRawOutput
2021-11-08 12:37:26,693 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 31 : Parse the output from the Prosite binary for proteins 1 to 1925 has failed irretrievably.  Available StackTraces follow.
2021-11-08 12:37:26,693 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
2021-11-08 12:37:26,693 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:349] 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:167) [interproscan-5.jar:?]
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:495) [interproscan-5.jar:?]
@abretaud
Copy link
Contributor

I'm having the same problem with 5.54-87.0, any clue from anyone?

@abretaud
Copy link
Contributor

Ok problem solved for me: I still had the --no-affinity option set in pfsearchv3.binary.switches.prositeprofiles, while using pftools 3.2.11 which doesn't have this option anymore. The jobPrositeProfiles output files were full of pftools usage info.
I just removed the --no-affinity option and now it works

@courtneystairs
Copy link

Hi Anthony! I'm getting the same error however I built pftools with the no-affinity option.

Can you point me to where I can find the pfsearchv3.binary.switches.prositeprofiles file and where I could make the edits? I am struggling to find it in the interproscan directories.

Thanks :)

@abretaud
Copy link
Contributor

Hi @courtneystairs,
pfsearchv3.binary.switches.prositeprofiles is in the interproscan.properties file

@Lsz-20
Copy link

Lsz-20 commented Feb 26, 2022

@abretaud i have the same question,but my 'pfsearchv3.binary.switches.prositeprofiles=-f -o 7;' has no --no-affinity
the version is 5.54
Thanks!

@aagatam
Copy link

aagatam commented Apr 22, 2022

Hi! Did anyone solve it? I'm running into the same problem in version 5.55.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
5 participants
@abretaud @lecorguille @aagatam @courtneystairs @Lsz-20