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ebi-pf-team / interproscan

Genome-scale protein function classification
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Test run failed on interproscan-5.42-78.0 #144

Closed zhangchiqian closed 4 years ago

zhangchiqian commented 4 years ago

I have installed the newest version of interproscan-5.42-78.0 on my Ubuntu 18.04 64 bit (a VirtualBox based guest OS on Windows 10). On Ubuntu, I first created a fresh condo environment and then installed interproscan-5.42-78.0. I checked and made sure that my java, perl, and python3 meets the pre-requirement. I then installed interproscan-5.42-78.0. After installation, I first run ./interproscan.sh, which seems all right and did not give me any errors. I then run ./interproscan.sh -i ~/Documents/Interproscan_5/interproscan-5.42-78.0/test_proteins.fasta -f tsv -d ~/Documents/Inter5_Rst and got the following error message. I searched on-line but could not clove the issues. Can anyone help me for that? Thanks!

03/04/2020 17:58:51:209 Welcome to InterProScan-5.42-78.0 03/04/2020 17:58:51:211 Running InterProScan v5 in STANDALONE mode... on Linux 03/04/2020 17:59:44:920 Loading file /home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/test_proteins.fasta 03/04/2020 17:59:44:960 Running the following analyses: [CDD-3.17,Coils-2.2.1,Gene3D-4.2.0,Hamap-2020_01,MobiDBLite-2.0,Pfam-32.0,PIRSF-3.02,PRINTS-42.0,ProSitePatterns-2019_11,ProSiteProfiles-2019_11,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,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. 03/04/2020 18:00:46:493 25% completed ERROR: uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep - Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:200)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at jdk.internal.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy142.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:193)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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)

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:200)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at jdk.internal.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy142.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:193)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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)

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - StepExecution with errors - stepName: stepMobiDBRunBinary WARN : uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster - StepInstance 13 is being re-run following a failure. ERROR: uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep - Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:200)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at jdk.internal.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy142.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:193)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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)

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:200)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at jdk.internal.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy142.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:193)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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)

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - StepExecution with errors - stepName: stepMobiDBRunBinary WARN : uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster - StepInstance 13 is being re-run following a failure. ERROR: uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep - Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:200)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at jdk.internal.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy142.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:193)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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)

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:200)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at jdk.internal.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: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.$Proxy142.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:193)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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)

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - 2. The exception is :java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python3 bin/mobidb/2.0/mobidb_lite.py /home/zhangchiqian/temp/zhangchiqian-VirtualBox_20200403_175911547_7c80//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last): File "bin/mobidb/2.0/mobidb_lite.py", line 197, in logger.set_logger(ARGS.log, ARGS.logLevel) File "/home/zhangchiqian/Documents/Interproscan_5/interproscan-5.42-78.0/bin/mobidb/2.0/mdblib/logger.py", line 17, in set_logger logging.basicConfig(level=level, File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 1987, in basicConfig fmt = Formatter(fs, dfs, style) File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 576, in init self._style.validate() File "/home/zhangchiqian/miniconda3/envs/Inter5/lib/python3.8/logging/init.py", line 428, in validate if not self.validation_pattern.search(self._fmt): TypeError: expected string or bytes-like object

ERROR: uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener - StepExecution with errors - stepName: stepMobiDBRunBinary FATAL: uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError - Analysis step 13 : Run mobi-db Binary for selected proteins for proteins 1 to 6 has failed irretrievably. Available StackTraces follow. FATAL: uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError - The JVM will now exit with a non-zero exit status. ERROR: uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster - 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:42) at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:147) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:460) 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:42) at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:147) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:460) 18:02:32.942 [amqEmbeddedWorkerJmsContainer-6] WARN org.hibernate.engine.jdbc.spi.SqlExceptionHelper - SQL Error: 42102, SQLState: 42S02 18:02:37.562 [amqEmbeddedWorkerJmsContainer-6] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "TIGRFAM_HMMER3_RAW_MATCH" not found; SQL statement: insert into public.tigrfam_hmmer3_raw_match (loc_fragment_dcs_tatus, location_end, location_start, model_id, numeric_sequence_id, sequence_id, signature_library, sig_lib_release, evalue, hmm_bounds, hmm_end, hmm_start, location_score, score, domain_bias, domain_ce_value, domain_ie_value, envelope_end, envelope_start, expected_accuracy, full_sequence_bias, split_group, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) [42102-199] InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

gsn7 commented 4 years ago

we have tested interproscan-5.42-78.0 on Ubuntu 18.04 with Python 3.6.x up to 3.7.6 and it works fine. You are using python 3.8 which seems to have introduced changes that break interproscan, so I would suggest you use any of Python 3.6.x up to 3.7.6

zhangchiqian commented 4 years ago

Thanks a lot for the reply. I will follow your guidance and install the pipeline with Python 3.6 or 3.7. Then, I will report the results here. However, Python 3.8 is installed on my Ubuntu system-wide, and I do not want to downgrade it. Do you think that it is possible I create a condo environment with Python 3.6/3.7 and then install the pipeline? Many thanks!

gsn7 commented 4 years ago

conda environment with Python 3.6/3.7 should work

gsn7 commented 4 years ago

interproscan now works on python 3.8