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ebi-pf-team / interproscan

Genome-scale protein function classification
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ERROR - Command line failed with exit code: 25 #159

Closed mictadlo closed 3 years ago

mictadlo commented 4 years ago

Hi, InterProScan-5.46-81.0 caused ERROR - Command line failed with exit code: 25

21/08/2020 00:51:34:759 Welcome to InterProScan-5.46-81.0
21/08/2020 00:51:34:763 Running InterProScan v5 in STANDALONE mode... on Linux
21/08/2020 00:52:05:571 Loading file /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/./QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54
21/08/2020 00:52:05:577 Running the following analyses:
[CDD-3.17,Coils-2.2.1,Gene3D-4.2.0,Hamap-2020_01,MobiDBLite-2.0,Pfam-33.1,PIRSF-3.10,PRINTS-42.0,ProSitePatterns-2019_11,ProSiteProfiles-2019_11,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0]
Pre-calculated match lookup service DISABLED.  Please wait for match calculations to complete...
21/08/2020 01:38:28:312 25% completed
2020-08-21 01:54:23,630 [amqEmbeddedWorkerJmsContainer-1] [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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1: 13876 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps630173-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps630173-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 01:54:23,640 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] 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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1: 13876 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps630173-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps630173-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.46-81.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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) [?:?]
2020-08-21 01:54:23,669 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1: 13876 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps630173-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps630173-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)
2020-08-21 01:54:23,670 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1: 13876 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps630173-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps630173-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 01:54:23,670 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2020-08-21 01:54:23,787 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:165] WARN - StepInstance 10 is being re-run following a failure.
2020-08-21 01:58:48,171 [amqEmbeddedWorkerJmsContainer-2] [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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta 
Error output from binary:
sh: line 1: 47552 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps125910-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps125910-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 01:58:48,171 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] 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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta 
Error output from binary:
sh: line 1: 47552 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps125910-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps125910-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.46-81.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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) [?:?]
2020-08-21 01:58:48,172 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta 
Error output from binary:
sh: line 1: 47552 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps125910-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps125910-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)
2020-08-21 01:58:48,173 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta 
Error output from binary:
sh: line 1: 47552 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps125910-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps125910-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 01:58:48,173 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2020-08-21 01:58:48,271 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:165] WARN - StepInstance 19 is being re-run following a failure.
2020-08-21 02:03:24,389 [amqEmbeddedWorkerJmsContainer-2] [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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1:  3439 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps601568-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps601568-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 02:03:24,390 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] 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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1:  3439 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps601568-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps601568-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.46-81.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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) [?:?]
2020-08-21 02:03:24,390 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1:  3439 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps601568-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps601568-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)
2020-08-21 02:03:24,391 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1:  3439 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps601568-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps601568-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 02:03:24,391 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2020-08-21 02:03:24,457 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:165] WARN - StepInstance 10 is being re-run following a failure.
2020-08-21 02:03:30,822 [amqEmbeddedWorkerJmsContainer-2] [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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta 
Error output from binary:
sh: line 1:  4122 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps177337-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps177337-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 02:03:30,823 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] 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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta 
Error output from binary:
sh: line 1:  4122 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps177337-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps177337-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.46-81.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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) [?:?]
2020-08-21 02:03:30,823 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta 
Error output from binary:
sh: line 1:  4122 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps177337-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps177337-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)
2020-08-21 02:03:30,824 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta 
Error output from binary:
sh: line 1:  4122 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps177337-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000001001_000000001209.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000001001_000000001209//ps177337-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 02:03:30,824 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2020-08-21 02:03:30,886 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:165] WARN - StepInstance 19 is being re-run following a failure.
21/08/2020 02:03:36:141 50% completed
2020-08-21 02:04:24,006 [amqEmbeddedWorkerJmsContainer-2] [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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1:  8052 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps44076-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps44076-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 02:04:24,007 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:213] 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/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1:  8052 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps44076-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps44076-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.46-81.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source) ~[?:?]
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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) [?:?]
2020-08-21 02:04:24,007 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:215] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1:  8052 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps44076-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps44076-1.tmp at bin/prosite/ps_scan.pl line 1960.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
    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:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:197)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:834)
2020-08-21 02:04:24,009 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2019_11/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2019_11/prosite_models /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta 
Error output from binary:
sh: line 1:  8052 Segmentation fault      (core dumped) bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps44076-1.tmp
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2019_11/prosite_models/PS01031.prf /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles/000000000001_000000001000.fasta C=6.5 > /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp/cl4n054_20200821_005148356_8stu//jobPrositeProfiles//cl4n054/tmpdir_000000000001_000000001000//ps44076-1.tmp at bin/prosite/ps_scan.pl line 1960.

2020-08-21 02:04:24,009 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:219] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2020-08-21 02:04:24,025 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 10 : Run ps_scan.pl and pfscan Binary for selected proteins for proteins 1 to 1000 has failed irretrievably.  Available StackTraces follow.
2020-08-21 02:04:24,026 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
2020-08-21 02:04:24,026 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:331] 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:156) [interproscan-5.jar:?]
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:475) [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:156)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:475)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

-----
PBS Job 7397666.pbs
CPU time  : 01:41:08
Wall time : 01:13:23
Mem usage : 4149420kb

What did I miss?

Thank you in advance,

Michal

gsn7 commented 4 years ago

what is the linux distribution (and version) you are running? and were you able to successfully execute the test command: ./interproscan.sh -i test_all_appl.fasta -f tsv -dp

If the test command works, then it is likely the problem is with your temporary directory path (--tempdir option). /scratch/waterhouse_team/QLD/sparse-orginal-77/bionano/juicer/juicebox2fasta/annotation/hisat2-scallop/noFixMate/all-merged-clean/hybridv2/interpro/unchar/QLDall-merged-clean.bam.fasta.transdecoder.genome-VS-QLDv0.81.augustus.all.clean-swissprot-and-NR.no_TE.unchar_hypo.AA.fasta.54-tmp. It is too long and one of the old binaries in InterProScan has problems if the file path is say more than 255 characters
InterProScan will create a unique temp directory for each run, and clean it up afterwards, so your --tempdir value doesn't need to match the input sequence path and be that long