ebi-pf-team / interproscan Goto Github PK

Genome-scale protein function classification

License: Apache License 2.0

Java 51.45% Shell 0.63% Perl 2.91% Python 14.22% CSS 0.46% JavaScript 0.11% C++ 2.27% Makefile 0.23% FreeMarker 1.27% C 26.27% M4 0.03% TeX 0.01% Roff 0.14% Dockerfile 0.01%

interproscan's Introduction

interproscan

What is InterProScan?

InterPro is a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains.

Users who have novel nucleotide or protein sequences that they wish to functionally characterise can use the software package InterProScan to run the scanning algorithms from the InterPro database in an integrated way. Sequences are submitted in FASTA format. Matches are then calculated against all of the required member database's signatures and the results are then output in a variety of formats.

Documentation

For more information on downloading, installing and running InterProScan please see the InterProScan readthedocs.

Contact us

For further assistance please contact us.

interproscan's People

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interproscan's Issues

Connection errors while using Interproscan

Hi,

I get the following error of not being able to access www.ebi.ac.uk:80 while running Interproscan. While I do get valid results (all of the values in the columns of the output file), I still see the following error message. Is this indicative of a deeper issue or is this message just informational?

Thank you,
Lili


2016-06-07 13:51:07,036 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:260] WARN - org.apache.http.conn.HttpHostConnectException: Connect to www.ebi.ac.uk:80 [www.ebi.ac.uk/193.62.193.80] failed: Connection refused
2016-06-07 13:51:07,036 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:262] WARN -

The following problem was encountered by the pre-calculated match lookup service:
Connect to www.ebi.ac.uk:80 [www.ebi.ac.uk/193.62.193.80] failed: Connection refused
Pre-calculated match lookup service failed - analysis proceeding to run locally
============================================================

The pre-calculated match lookup service has been configured in the interproscan.properties file.
  precalculated match lookup service url : http://www.ebi.ac.uk/interpro/match-lookup
  precalculated match lookup service proxy host :   proxy port : 3128

Unfortunately the web service has failed. Check the configuration of this service
in the interproscan.properties file and, if necessary, set the following property to look like this:

precalculated.match.lookup.service.url=

If the problem persists, check if this is a firewall or proxy issue. If it is a proxy issue, then setting
the following property in the interproscan.properties file should work:

precalculated.match.lookup.service.proxy.host=
precalculated.match.lookup.service.proxy.port=

If this still does not work please inform the InterPro team of this error
by sending an email to:

[email protected]

In the meantime, the analysis will continue to run locally.

Interproscan get stuck in "90% completed"

Hi,

Whenever I use interproscan on about 10000 protein sequences, it will get stuck in "90% completed". I provided 16 cores for this job and used the default interproscan.properties file.

22/04/2017 16:16:51:838 Running the following analyses:
[CDD-3.14,Coils-2.2.1,Gene3D-4.1.0,Hamap-201701.18,MobiDBLite-1.0,Pfam-30.0,PIRSF-3.01,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-2
0.132,ProSiteProfiles-20.132,SFLD-2,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.
22/04/2017 16:47:05:527 25% completed
22/04/2017 17:03:46:760 51% completed
22/04/2017 17:11:33:174 75% completed
22/04/2017 17:22:40:969 90% completed

Could you please help me out about this?

Many thanks,

Regards,

Tom

I'm on ubuntu 16.04 and when I run InterproScan5 I get an error about libgnutls.so.28.

I have searched online for solutions but there is nothing for me,please help me!!!
Firstly,this is my java version
tyyl@tyyl-MS-7623:~$ java -version java version "1.8.0_151" Java(TM) SE Runtime Environment (build 1.8.0_151-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.151-b12, mixed mode)

this is where my java is:
/usr/lib/jvm/java-8-oracle/jre/bin/java

and JAVA_HOME point to the path:
JAVA_HOME=/usr/lib/jvm/java-8-oracle/ export PATH=$JAVA_HOME/bin:$PATH
did i do this correctly?If there is something wrong, please tell me....

Secondly, this is my python version:
tyyl@tyyl-MS-7623:~$ python --version Python 2.7.12

Thirdly, this is my perl version:
tyyl@tyyl-MS-7623:~$perl -version This is perl 5, version 22, subversion 1 (v5.22.1) built for x86_64-linux-gnu-thread-multi (with 58 registered patches, see perl -V for more detail) Copyright 1987-2015, Larry Wall Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit. Complete documentation for Perl, including FAQ lists, should be found on this system using "man perl" or "perldoc perl". If you have access to the Internet, point your browser at http://www.perl.org/, the Perl Home Page.

everything seems ready to run, but when i start i can't figure out what happened.please help me, I have nothing to do but write here to search for help!!!!

`tyyl@tyyl-MS-7623:~/my_interproscan/interproscan-5.26-65.0$ ./interproscan.sh -i test_proteins.fasta
25/10/2017 21:37:29:269 Welcome to InterProScan-5.26-65.0
25/10/2017 21:37:46:118 Running InterProScan v5 in STANDALONE mode... on Linux
25/10/2017 21:38:07:234 Loading file /home/tyyl/my_interproscan/interproscan-5.26-65.0/test_proteins.fasta
25/10/2017 21:38:07:256 Running the following analyses:
[CDD-3.16,Coils-2.2.1,Gene3D-4.1.0,Hamap-201701.18,MobiDBLite-1.0,Pfam-31.0,PIRSF-3.02,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-20.132,ProSiteProfiles-20.132,SFLD-3,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.
2017-10-25 21:38:17,468 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

2017-10-25 21:38:17,518 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:748)

2017-10-25 21:38:17,524 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepCDDRunBinaryRPSblast
2017-10-25 21:38:17,569 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1
Command: python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /home/tyyl/my_interproscan/interproscan-5.26-65.0/bin/mobidb/binx /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobMobiDBLite/000000000001_000000000006.fasta
Error output from binary:
Traceback (most recent call last):
File "bin/mobidb/mobidb-lite.py", line 455, in
out = run_mobidb(binDirectory, args.threads, args.longOutput, acc, seq, args.architecture, verbose = args.verbose)
File "bin/mobidb/mobidb-lite.py", line 169, in run_mobidb
disbinFile, flatFile = generate_files(acc, seq)
File "bin/mobidb/mobidb-lite.py", line 149, in generate_files
f_disbin.write("1\n{0}\n{1}".format(len(seq),seq))
File "/usr/lib/python3.5/tempfile.py", line 622, in func_wrapper
return func(*args, **kwargs)
TypeError: a bytes-like object is required, not 'str'

2017-10-25 21:38:17,572 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /home/tyyl/my_interproscan/interproscan-5.26-65.0/bin/mobidb/binx /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobMobiDBLite/000000000001_000000000006.fasta
Error output from binary:
Traceback (most recent call last):
File "bin/mobidb/mobidb-lite.py", line 455, in
out = run_mobidb(binDirectory, args.threads, args.longOutput, acc, seq, args.architecture, verbose = args.verbose)
File "bin/mobidb/mobidb-lite.py", line 169, in run_mobidb
disbinFile, flatFile = generate_files(acc, seq)
File "bin/mobidb/mobidb-lite.py", line 149, in generate_files
f_disbin.write("1\n{0}\n{1}".format(len(seq),seq))
File "/usr/lib/python3.5/tempfile.py", line 622, in func_wrapper
return func(*args, **kwargs)
TypeError: a bytes-like object is required, not 'str'

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:748)

2017-10-25 21:38:17,579 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepMobiDBRunBinary
2017-10-25 21:38:17,704 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 18 is being re-run following a failure.
2017-10-25 21:38:17,798 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 5 is being re-run following a failure.
25/10/2017 21:38:17:866 29% completed
2017-10-25 21:38:23,608 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

2017-10-25 21:38:23,609 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:748)

2017-10-25 21:38:23,610 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepCDDRunBinaryRPSblast
2017-10-25 21:38:23,775 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 5 is being re-run following a failure.
2017-10-25 21:38:24,084 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1
Command: python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /home/tyyl/my_interproscan/interproscan-5.26-65.0/bin/mobidb/binx /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobMobiDBLite/000000000001_000000000006.fasta
Error output from binary:
Traceback (most recent call last):
File "bin/mobidb/mobidb-lite.py", line 455, in
out = run_mobidb(binDirectory, args.threads, args.longOutput, acc, seq, args.architecture, verbose = args.verbose)
File "bin/mobidb/mobidb-lite.py", line 169, in run_mobidb
disbinFile, flatFile = generate_files(acc, seq)
File "bin/mobidb/mobidb-lite.py", line 149, in generate_files
f_disbin.write("1\n{0}\n{1}".format(len(seq),seq))
File "/usr/lib/python3.5/tempfile.py", line 622, in func_wrapper
return func(*args, **kwargs)
TypeError: a bytes-like object is required, not 'str'

2017-10-25 21:38:24,088 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /home/tyyl/my_interproscan/interproscan-5.26-65.0/bin/mobidb/binx /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobMobiDBLite/000000000001_000000000006.fasta
Error output from binary:
Traceback (most recent call last):
File "bin/mobidb/mobidb-lite.py", line 455, in
out = run_mobidb(binDirectory, args.threads, args.longOutput, acc, seq, args.architecture, verbose = args.verbose)
File "bin/mobidb/mobidb-lite.py", line 169, in run_mobidb
disbinFile, flatFile = generate_files(acc, seq)
File "bin/mobidb/mobidb-lite.py", line 149, in generate_files
f_disbin.write("1\n{0}\n{1}".format(len(seq),seq))
File "/usr/lib/python3.5/tempfile.py", line 622, in func_wrapper
return func(*args, **kwargs)
TypeError: a bytes-like object is required, not 'str'

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:748)

2017-10-25 21:38:24,094 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepMobiDBRunBinary
2017-10-25 21:38:24,206 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 18 is being re-run following a failure.
2017-10-25 21:38:28,915 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

2017-10-25 21:38:28,916 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /home/tyyl/my_interproscan/interproscan-5.26-65.0/temp/tyyl-MS-7623_20171025_213746100_k67z//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:748)

2017-10-25 21:38:28,917 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepCDDRunBinaryRPSblast
2017-10-25 21:38:28,998 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 5 : Run CDD Binary for selected proteins for proteins 1 to 6 has failed irretrievably. Available StackTraces follow.
2017-10-25 21:38:28,999 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2017-10-25 21:38:28,999 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:241] 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:42)
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:128)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:377)
2017-10-25 21:38:29,459 [responseMonitorJmsContainer-1] [org.hibernate.engine.jdbc.spi.SqlExceptionHelper:127] WARN - SQL Error: 42102, SQLState: 42S02
2017-10-25 21:38:29,461 [responseMonitorJmsContainer-1] [org.hibernate.engine.jdbc.spi.SqlExceptionHelper:129] ERROR - Table "STEP_EXECUTION" not found; SQL statement:
select stepexecut0_.id as id1_90_0_, stepexecut0_.time_completed as time_com2_90_0_, stepexecut0_.time_created as time_cre3_90_0_, stepexecut0_.exception_first_chunk as exceptio4_90_0_, stepexecut0_.proportion_completed as proporti5_90_0_, stepexecut0_.time_started_running as time_sta6_90_0_, stepexecut0_.state as state7_90_0_, stepexecut0_.step_instance_id as step_ins9_90_0_, stepexecut0_.time_submitted as time_sub8_90_0_, exceptionc1_.step_execution_id as step_exe1_12_1_, exceptionc1_.exception_chunks as exceptio2_12_1_, exceptionc1_.chunk_index as chunk_in3_1_, stepinstan2_.id as id1_91_2_, stepinstan2_.bottom_model as bottom_m2_91_2_, stepinstan2_.bottom_protein as bottom_p3_91_2_, stepinstan2_.step_id as step_id4_91_2_, stepinstan2_.time_created as time_cre5_91_2_, stepinstan2_.top_model as top_mode6_91_2_, stepinstan2_.top_protein as top_prot7_91_2_, dependsupo3_.step_instance_id as step_ins1_93_3_, stepinstan4_.id as depends_2_93_3_, stepinstan4_.id as id1_91_4_, stepinstan4_.bottom_model as bottom_m2_91_4_, stepinstan4_.bottom_protein as bottom_p3_91_4_, stepinstan4_.step_id as step_id4_91_4_, stepinstan4_.time_created as time_cre5_91_4_, stepinstan4_.top_model as top_mode6_91_4_, stepinstan4_.top_protein as top_prot7_91_4_, parameters5_.step_instance_id as step_ins1_92_5_, parameters5_.parameters as paramete2_92_5_, parameters5_.parameters_key as paramete3_5_ from public.step_execution stepexecut0_ left outer join public.exception_chunk exceptionc1_ on stepexecut0_.id=exceptionc1_.step_execution_id inner join public.step_instance stepinstan2_ on stepexecut0_.step_instance_id=stepinstan2_.id left outer join public.step_instance_step_instance dependsupo3_ on stepinstan2_.id=dependsupo3_.step_instance_id left outer join public.step_instance stepinstan4_ on dependsupo3_.depends_upon_id=stepinstan4_.id left outer join public.step_instance_parameters parameters5_ on stepinstan4_.id=parameters5_.step_instance_id where stepexecut0_.id=? [42102-189]
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details`

README.md update - could you perhaps add some information about the programming language(s) used and required?

Hello ebi-team for InterProScan!

A suggestion:

README.md update - could you perhaps add some information about the programming language(s) used and required?

The reason why I ask is that you mention that linux is the primary target platform, but the readme is a bit sparses. For example, I am wondering which programming language(s) are used. I ask that in particular because I am used to the C/C++ family, also python (ncbi-blast+, relion, viennarna etc...) but not so used to Java. So I'd like to know, if possible, beforehand downloading the source. Please do feel free to close this issue at any moment in time - thank you!

ERROR when running PANTHER analysis

Hello, I am new to interproscan and want to perform PANTHER analysis. At first, I got the error message that PANTHER didn't exist or deactivated. I then edited the properties file and PANTHER seemed to be able to run. However, after several minutes the program failed.
The PANTHER database I used was 11.0, which was just released on July 15th
Frankly, I don't really understand the error messages. I attached the output log here for your inspection. Many thanks
nohup.txt

mobidb.py failed, the error message could have been better

I'm running InterPro scan for the next release of Wormbase ParaSite.
The pipeline choked on our input:

python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /nfs/software/ensembl/RHEL7-JUL2017-core2/linuxbrew/Cellar/interproscan/5.27-66.0/bin/mobidb/binx in.fasta
Error output from binary:
Traceback (most recent call last):
  File "bin/mobidb/mobidb-lite.py", line 455, in <module>
    out = run_mobidb(binDirectory, args.threads, args.longOutput, acc, seq, args.architecture, verbose = args.verbose)
  File "bin/mobidb/mobidb-lite.py", line 198, in run_mobidb
    if ele.get():
  File "/usr/lib64/python2.7/multiprocessing/pool.py", line 554, in get
    raise self._value
OSError: [Errno 7] Argument list too long

The input file contained a bad protein - it had about 3000 X's at the end, and then an M. I've uploaded it here: https://gist.github.com/wbazant/fdd29d04c6d205b8f7b59bc462e8c8ee

The error message didn't help me, and I discovered what the problem is essentially by luck - and removing the X's made it all good again. If you endavour to support finding features in proteins with thousands of X's you could improve the error message that happens.

Using interproscan on a HPC Cluster

on HPC cluster, databases often have to be separated from the installation directory of a software. Is it possible to store the data directory of interproscan in a different location outside the installation directory ?

Interproscan data graphical visualization

Are there any tools to visualise the data other than BlAst2Go. I came across IPRStats but it doesn't work on Interproscan5 files.

Thanks

Installing 5.26-65.0 on an old Centos6 HPC

Hi,

as the title suggests, I'm trying to install interproscan on an old (-ish) centos 6 based cluster.

I've recompiled a number of the included binaries to work with our older version of GLIBC as expected. I wasn't successful in compiling 'cath-resolve-hits' from source, but the centos6 pre-compiled binary seems to work just fine. I also applied the fix for that mentioned in issue #25.

However that fix appears not to have worked. The stacktrace from Java is kind of overwhelming, but I think this is the relevant part:

$ interproscan.sh -i /path/to/some/.faa/file -f tsv
2017-11-08 16:23:57,741 [amqEmbeddedWorkerJmsContainer-8] uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.IllegalStateException: IOException thrown when attempting to parse /ibers/ernie/home/maf54/temp/bert_20171108_162240951_ak7l//jobGene3d/000000000001_000000000011_one.raw.out
    at uk.ac.ebi.interpro.scan.management.model.implementations.gene3d.Gene3DParseAndPersistOutputStep.execute(Gene3DParseAndPersistOutputStep.java:117)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    at sun.reflect.GeneratedMethodAccessor94.invoke(Unknown Source)
.
.
.
.

I'm somewhat out of ideas. I've attached the full output if it is of interest.
interproscan_out.txt

Error in running Interpro using test files

Hi,

I've installed Interpro on my Mac OS X and have attempted to execute a test run from my terminal as follows:

$ ./interproscan.sh -f TSV -i ~/Documents/interproscan-5.18-57.0/test_proteins_new.fasta -b ~/Documents/interproscan-5.18-57.0/output_test.tsv

Unfortunately I encounter 'fatal' errors when executing the line above. I've attached the full output log file to this message.

log.txt

Can someone kindly assist me in rectifying this issue?

Thank you,
Lili

Build custom iprmatch db

Is it possible to build a custom interpro match database for local service to provide annotations already run (but not in the IPR master database). I have the generated XML locally for new proteomes not in uniprot but need to re-search these after improvements to the genome annotation and gene models and would prefer to not have the expense of re-running all.

rpsblast not working, libgnutls.so.28: cannot open shared object file: No such file or directory

Hi everyone :).

I just downloaded the latest version of Interproscan, 5.26-65.0 , and it seems that the ncbi-blast-2.6.0+/rpsblast is not working.
The system throws the following error during execution:

2017-10-05 12:40:49,595 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /exports/mm-hpc/bacteriologie/bastian/data/metronidazol_resistance_new/HKF5JBBXX_103099-001-025_assembly/ray_run141/opera/ray.gapfiller/annotationHKF5JBBXX_103099-001-025//temp/weaselshark_20171005_115510659_fx2d//jobCDD/000000002001_000000003000.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5 
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

2017-10-05 12:40:49,598 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /exports/mm-hpc/bacteriologie/bastian/data/metronidazol_resistance_new/HKF5JBBXX_103099-001-025_assembly/ray_run141/opera/ray.gapfiller/annotationHKF5JBBXX_103099-001-025//temp/weaselshark_20171005_115510659_fx2d//jobCDD/000000002001_000000003000.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5 
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

	at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
	at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
	at sun.reflect.GeneratedMethodAccessor96.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
	at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
	at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
	at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
	at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
	at java.lang.Thread.run(Thread.java:748)
2017-10-05 12:40:49,600 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepCDDRunBinaryRPSblast
2017-10-05 12:40:49,692 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 101 is being re-run following a failure.

No clue what's happening here.
I think I already had the same problem with the previous version, where I just replaced the binary with a working version, but thought I should report it back.

This happens on Ubuntu 14.04.5 LTS, the whole thing is executed on a HPC cluster.

Unrelated to the bug report: Thanks guys for the good work, my daily work would be harder without this tool :).

Updated EBI pages to point to github

http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan5_soap

still points to google code

What's the problem about running the interproscan?

Hello, I want to use this popular programme, but there are something wrong (see below), may be the problem from java. I would like to thank any advice and guidance.

[xxxxxxx@localhost interproscan-5.26-65.0]$ ./interproscan.sh
Java HotSpot(TM) 64-Bit Server VM warning: Ignoring option UseFastAccessorMethods; support was removed in 9.0
22/10/2017 21:51:54:313 Welcome to InterProScan-5.26-65.0
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by javassist.util.proxy.SecurityActions (file:/home/wushengdan/software/my_interproscan/interproscan-5.26-65.0/lib/javassist-3.18.1-GA.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of javassist.util.proxy.SecurityActions
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2017-10-22 21:52:08,329 [main] [org.springframework.context.support.AbstractApplicationContext:544] WARN - Exception encountered during context initialization - cancelling refresh attempt
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'berkeleyMarshaller' defined in class path resource [spring/berkeley-oxm-context.xml]: Invocation of init method failed; nested exception is org.springframework.oxm.UncategorizedMappingException: Unknown JAXB exception; nested exception is javax.xml.bind.JAXBException

with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1578)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:545)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:305)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:301)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:196)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:772)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:835)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:537)
at org.springframework.context.support.ClassPathXmlApplicationContext.(ClassPathXmlApplicationContext.java:139)
at org.springframework.context.support.ClassPathXmlApplicationContext.(ClassPathXmlApplicationContext.java:93)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:217)
Caused by: org.springframework.oxm.UncategorizedMappingException: Unknown JAXB exception; nested exception is javax.xml.bind.JAXBException
with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
at org.springframework.oxm.jaxb.Jaxb2Marshaller.convertJaxbException(Jaxb2Marshaller.java:915)
at org.springframework.oxm.jaxb.Jaxb2Marshaller.getJaxbContext(Jaxb2Marshaller.java:485)
at org.springframework.oxm.jaxb.Jaxb2Marshaller.afterPropertiesSet(Jaxb2Marshaller.java:457)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1637)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1574)
... 12 more
Caused by: javax.xml.bind.JAXBException
with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:241)
at javax.xml.bind.ContextFinder.find(ContextFinder.java:477)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:656)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:599)
at org.springframework.oxm.jaxb.Jaxb2Marshaller.createJaxbContextFromClasses(Jaxb2Marshaller.java:525)
at org.springframework.oxm.jaxb.Jaxb2Marshaller.getJaxbContext(Jaxb2Marshaller.java:478)
... 15 more
Caused by: java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:496)
at javax.xml.bind.ContextFinder.safeLoadClass(ContextFinder.java:594)
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:239)
... 20 more
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'berkeleyMarshaller' defined in class path resource [spring/berkeley-oxm-context.xml]: Invocation of init method failed; nested exception is org.springframework.oxm.UncategorizedMappingException: Unknown JAXB exception; nested exception is javax.xml.bind.JAXBException
with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1578)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:545)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:305)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:301)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:196)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:772)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:835)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:537)
at org.springframework.context.support.ClassPathXmlApplicationContext.(ClassPathXmlApplicationContext.java:139)
at org.springframework.context.support.ClassPathXmlApplicationContext.(ClassPathXmlApplicationContext.java:93)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:217)
Caused by: org.springframework.oxm.UncategorizedMappingException: Unknown JAXB exception; nested exception is javax.xml.bind.JAXBException
with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
at org.springframework.oxm.jaxb.Jaxb2Marshaller.convertJaxbException(Jaxb2Marshaller.java:915)
at org.springframework.oxm.jaxb.Jaxb2Marshaller.getJaxbContext(Jaxb2Marshaller.java:485)
at org.springframework.oxm.jaxb.Jaxb2Marshaller.afterPropertiesSet(Jaxb2Marshaller.java:457)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1637)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1574)
... 12 more
Caused by: javax.xml.bind.JAXBException
with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:241)
at javax.xml.bind.ContextFinder.find(ContextFinder.java:477)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:656)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:599)
at org.springframework.oxm.jaxb.Jaxb2Marshaller.createJaxbContextFromClasses(Jaxb2Marshaller.java:525)
at org.springframework.oxm.jaxb.Jaxb2Marshaller.getJaxbContext(Jaxb2Marshaller.java:478)
... 15 more
Caused by: java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:496)
at javax.xml.bind.ContextFinder.safeLoadClass(ContextFinder.java:594)
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:239)
... 20 more

Need help installing interproscan on a server with multiple users

Hello,

I would like to install interproscan on a server that is used by multiple users.
Do you have any advice for doing this (i.e. modifying the properties file to point to the path where specific files and libraries are stored)?

I tried to run the interproscan test but received this error message:

For the (-u) option you specified a location which is not writable:
/usr/local/interproscan/interproscan-5.26-65.0/test_proteins.fasta

Thanks!

erro while after # the lookup function

Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

Refuses to run if home directory not accessible

We're trying to set up interproscan to run as a web service, under the www user, which has no home directory. Unfortunately the program throws and exception and exits immediately when it is not able to create the hidden .interproscan-5 directory...even though only an empty file is put into it in our usage. So my question: is this directory really so essential that the program has to have a hard block on it?

FATAL - Analysis step 73 : Parse output from HMMER3 and CathResolveHits has failed

Hi,

I can run InterProScan (v5.25-64.0) on the test file test_proteins.fasta but I get an error when I try to use my own data.

Any suggestions on what went wrong?

I used the command:

interproscan.sh -i rhiMar2.2.all.maker.proteins.head100.fasta -f xml -goterms -iprlookup -T $TMPDIR > rhiMar2.2.all.maker.proteins.head100.interpro.out

My input file looks like this:

[z3101118@kdm subset.2017-08-03]$ head rhiMar2.2.all.maker.proteins.head100.fasta
>maker-ctg29523_RHIMB__RM170330.29523-snap-gene-0.0-mRNA-1 protein AED:0.08 eAED:0.31 QI:100|0|0|1|0|0|2|0|194
MHSTTCVSQDQGMNSATAGMMWPDWGYCPKEGQERVDRQGLSLSSRVTLAVKGNCIPTQF
TKSRCQTLILTVTNSQLTDIDLYVLGRYTPQGSQMPIFQLYWKSFENKSKPFEATPSPDD
INLLLPSQYDLIARAPYTMQKTLAVETGFSDHNLWLEWASYIASQMNRTGCITCAPAQPH
LGTMYKYICQSDGQ
>snap_masked-ctg3453_RHIMB__RM170330.3453-processed-gene-0.3-mRNA-1 protein AED:0.04 eAED:0.04 QI:740|1|0.88|1|0.37|0.66|9|0|127
MRPQQQDIERPFLPQQRPQLHWKENTAENEENEAIHKTFNYFLEFVPTNDIERFVRELGL
TNNEINWAKHDNIGTYNQHYSMLLKLQQDRKFDVNIWLNKLYDIKMGEVAQKITEKLTRD
GLCETST
>maker-ctg3453_RHIMB__RM170330.3453-snap-gene-0.12-mRNA-1 protein AED:0.06 eAED:0.07 QI:0|0|0|1|0.33|0|4|0|431

And got this error:

[z3101118@kdm subset.2017-08-03]$ cat rhiMar2.2.all.maker.proteins.head100.interpro.out
03/08/2017 13:02:45:106 Welcome to InterProScan-5.25-64.0
03/08/2017 13:02:51:575 Running InterProScan v5 in STANDALONE mode... on Linux
03/08/2017 13:03:04:858 Loading file /srv/scratch/z3101118/WhiteP.CaneToad-Jan16/analysis/2017-08-03.interproscan/subset.2017-08-03/rhiMar2.2.all.maker.proteins.head100.fasta
03/08/2017 13:03:04:861 Running the following analyses:
[CDD-3.16,Coils-2.2.1,Gene3D-4.1.0,Hamap-201701.18,MobiDBLite-1.0,PANTHER-11.1,Pfam-31.0,Phobius-1.01,PIRSF-3.02,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-20.132,ProSiteProfiles-20.132,SFLD-2,SignalP_EUK-4.1,SignalP_GRAM_NEGATIVE-4.1,SignalP_GRAM_POSITIVE-4.1,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0,TMHMM-2.0c]
Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally.
03/08/2017 13:03:22:929 26% completed
2017-08-03 13:03:47,209 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.NumberFormatException: For input string: "by"
	at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
	at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
	at java.lang.Double.parseDouble(Double.java:538)
	at uk.ac.ebi.interpro.scan.io.gene3d.CathResolverRecord.valueOf(CathResolverRecord.java:106)
	at uk.ac.ebi.interpro.scan.io.gene3d.CathResolveHitsOutputParser.parse(CathResolveHitsOutputParser.java:40)
	at uk.ac.ebi.interpro.scan.management.model.implementations.gene3d.Gene3DParseAndPersistOutputStep.execute(Gene3DParseAndPersistOutputStep.java:115)
	at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
	at sun.reflect.GeneratedMethodAccessor98.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
	at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
	at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
	at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
	at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
	at java.lang.Thread.run(Thread.java:745)
2017-08-03 13:03:47,212 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepGene3dParseOutputs
2017-08-03 13:03:47,226 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 73 is being re-run following a failure.
2017-08-03 13:03:47,230 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.NumberFormatException: For input string: "by"
	at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
	at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
	at java.lang.Double.parseDouble(Double.java:538)
	at uk.ac.ebi.interpro.scan.io.gene3d.CathResolverRecord.valueOf(CathResolverRecord.java:106)
	at uk.ac.ebi.interpro.scan.io.gene3d.CathResolveHitsOutputParser.parse(CathResolveHitsOutputParser.java:40)
	at uk.ac.ebi.interpro.scan.management.model.implementations.gene3d.Gene3DParseAndPersistOutputStep.execute(Gene3DParseAndPersistOutputStep.java:115)
	at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
	at sun.reflect.GeneratedMethodAccessor98.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
	at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
	at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
	at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
	at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
	at java.lang.Thread.run(Thread.java:745)
2017-08-03 13:03:47,231 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepGene3dParseOutputs
2017-08-03 13:03:47,359 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 73 is being re-run following a failure.
2017-08-03 13:03:47,362 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.NumberFormatException: For input string: "by"
	at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
	at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
	at java.lang.Double.parseDouble(Double.java:538)
	at uk.ac.ebi.interpro.scan.io.gene3d.CathResolverRecord.valueOf(CathResolverRecord.java:106)
	at uk.ac.ebi.interpro.scan.io.gene3d.CathResolveHitsOutputParser.parse(CathResolveHitsOutputParser.java:40)
	at uk.ac.ebi.interpro.scan.management.model.implementations.gene3d.Gene3DParseAndPersistOutputStep.execute(Gene3DParseAndPersistOutputStep.java:115)
	at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
	at sun.reflect.GeneratedMethodAccessor98.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
	at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
	at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
	at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
	at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
	at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
	at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
	at java.lang.Thread.run(Thread.java:745)
2017-08-03 13:03:47,362 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepGene3dParseOutputs
2017-08-03 13:03:47,481 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 73 : Parse output from HMMER3 and CathResolveHits for proteins 1 to 12 has failed irretrievably.  Available StackTraces follow.
2017-08-03 13:03:47,481 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2017-08-03 13:03:47,481 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:241] 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:42)
	at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:128)
	at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:375)

Thanks,

Tim

Idea: Stop codons in amino acid sequence

Would it be a "wise" idea to mark stop codons (*) as X? such that protein sequences with a predicted but not necessary a stop codon can still be analyzed? Or do not all applications like this character?

allow symlinking interproscan.sh

Posting as a ticket as I'm not sure PRs on this repo are easily mergeable for you.

It would be useful if interproscan.sh could be symlinked into the path. However, it currently finds its location with cd $(dirname "$0"), which does not traverse symlinks. Replacing the line with the below code fixes this (tediously avoiding GNU readlink's -f option not available everywhere).

INSTALL_DIR="${BASH_SOURCE[0]}"
while [ -h "$INSTALL_DIR" ]; do
  cd "$(dirname "$INSTALL_DIR")"
  INSTALL_DIR="$(readlink "$(basename "$INSTALL_DIR")")"
done
cd "$(dirname "$INSTALL_DIR")"
INSTALL_DIR="$(pwd)/"

Individual interproscan.properties files

The way our system is setup does not allow users to make changes to software installed on the system. They simply use the tools that we set up for them. Therefore they are unable to edit the interproscan.properties file for their individualized run, and multiple copies of interproscan need to be installed for each users's needs. To work around this we introduced a simple change that allowed them to set an environmental variable which would point towards their file.

In interproscan-5.jar, there is a file spring/spring-properties-context.xml. In the block

<property name="locations">
  <list>
    <value>file:interproscan.properties</value>
    <value>file:${user.home}/.interproscan-5/interproscan.properties</value>
    <value>file:${system.interproscan.properties}</value>
  </list>
</property>

we added

<value>file:${INTER_CONFIG_DIR}/interproscan.properties</value>

so that if you set

export INTER_CONFIG_DIR=/absolute/path/to/directory/with/interproscan.properties

it would run off of an editable version of interproscan.properties. If possible, it would be nice if this feature could be included in the official version of interproscan.

ERROR:Is there something wrong with my JVM?

Hello, I wanted to perform SUPERFAMILY prediction via interproscan but I got some error messages. It never happened before. Can you tell me what should I do? Many thanks. (I also attached some of my sequences)
test.txt

08/09/2016 16:37:21:639 Welcome to InterProScan-5.19-58.0
08/09/2016 16:37:27:326 Running InterProScan v5 in STANDALONE mode... on Linux
08/09/2016 16:37:39:003 Loading file /Users/dragon/lipase-commercial-aa/
08/09/2016 16:37:39:007 Running the following analyses:
[SUPERFAMILY-1.75]
Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete...
2016-09-08 16:37:39,021 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Could not read the fastaFileInputStream.
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:136)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy93.loadSequences(Unknown Source)
at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:245)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Is a directory
at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
at sun.nio.ch.FileDispatcherImpl.read(FileDispatcherImpl.java:46)
at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
at sun.nio.ch.IOUtil.read(IOUtil.java:197)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:159)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at java.io.BufferedReader.fill(BufferedReader.java:161)
at java.io.BufferedReader.readLine(BufferedReader.java:324)
at java.io.BufferedReader.readLine(BufferedReader.java:389)
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:62)
... 38 more
2016-09-08 16:37:39,025 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepLoadFromFasta
2016-09-08 16:37:39,112 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:76] WARN - StepInstance 1 is being re-run following a failure.
08/09/2016 16:37:39:127 Loading file /Users/dragon/lipase-commercial-aa/
08/09/2016 16:37:39:128 Running the following analyses:
[SUPERFAMILY-1.75]
Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete...
2016-09-08 16:37:39,129 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Could not read the fastaFileInputStream.
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:136)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy93.loadSequences(Unknown Source)
at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:245)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Is a directory
at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
at sun.nio.ch.FileDispatcherImpl.read(FileDispatcherImpl.java:46)
at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
at sun.nio.ch.IOUtil.read(IOUtil.java:197)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:159)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at java.io.BufferedReader.fill(BufferedReader.java:161)
at java.io.BufferedReader.readLine(BufferedReader.java:324)
at java.io.BufferedReader.readLine(BufferedReader.java:389)
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:62)
... 38 more
2016-09-08 16:37:39,131 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepLoadFromFasta
2016-09-08 16:37:39,245 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 1 : Load proteins from a fasta file and create required JobInstance objects for proteins null to null has failed irretrievably. Available StackTraces follow.
2016-09-08 16:37:39,246 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2016-09-08 16:37:39,246 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:149] 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:42)
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:67)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:327)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

error while loading shared libraries: libgnutls.so.28: ca nnot open shared object file: No such file or directory

Hi,

I have just installed interproscan on a cluster running linux:
version
InterProScan version 5.26-65.0
InterProScan 64-Bit build (requires Java 1.8)

System:
linux 2.6.32-696.10.3.el6.x86_64 #1 SMP Tue Sep 26 18:14:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
perl, v5.10.1 (*) built for x86_64-linux-thread-multi
Python 2.7.10
'java version "1.8.0_66"
Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)

I am getting the following error outputs when running the test command (with or without the -dp option)
./interproscan.sh -i test_proteins.fasta -f tsv &>out_test1

out_test1:
14/11/2017 09:27:40:445 Welcome to InterProScan-5.26-65.0
14/11/2017 09:27:48:973 Running InterProScan v5 in STANDALONE mode... on Linux
14/11/2017 09:27:58:978 Loading file /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/test_proteins.fasta
14/11/2017 09:27:58:981 Running the following analyses:
[CDD-3.16,Coils-2.2.1,Gene3D-4.1.0,Hamap-201701.18,MobiDBLite-1.0,PANTHER-12.0,Pfam-31.0,PIRSF-3.02,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-20.132,ProSiteProfiles-20.132,SFLD-3,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.
2017-11-14 09:28:08,156 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

2017-11-14 09:28:08,159 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2017-11-14 09:28:08,160 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepCDDRunBinaryRPSblast
2017-11-14 09:28:08,183 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 4 is being re-run following a failure.
14/11/2017 09:28:09:699 29% completed
2017-11-14 09:28:13,199 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

2017-11-14 09:28:13,200 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 127
Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobCDD/000000000001_000000000006.fasta -db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5
Error output from binary:
bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2017-11-14 09:28:13,200 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepCDDRunBinaryRPSblast
2017-11-14 09:28:13,232 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 4 is being re-run following a failure.
2017-11-14 09:28:14,955 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1
Command: bin/sfld/sfld_postprocess -s data/sfld/3/sfld_sites.annot -a /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobSFLD/000000000001_000000000006.raw.align.out -O /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobSFLD/000000000001_000000000006.raw.out -d /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobSFLD/000000000001_000000000006.raw.domtblout.out -o /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobSFLD/000000000001_000000000006_one.raw.out
Error output from binary:
bin/sfld/sfld_postprocess: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by bin/sfld/sfld_postprocess)

2017-11-14 09:28:14,955 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: bin/sfld/sfld_postprocess -s data/sfld/3/sfld_sites.annot -a /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobSFLD/000000000001_000000000006.raw.align.out -O /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobSFLD/000000000001_000000000006.raw.out -d /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobSFLD/000000000001_000000000006.raw.domtblout.out -o /data/dpearton/working/my_interproscan/interproscan-5.26-65.0/temp/hippo1_20171114_092748970_dtwd//jobSFLD/000000000001_000000000006_one.raw.out
Error output from binary:
bin/sfld/sfld_postprocess: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by bin/sfld/sfld_postprocess)

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2017-11-14 09:28:14,956 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepSFLDPostProcessorBinaryRun
2017-11-14 09:28:15,068 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 15 : Run sfld postprocessing binary for selected proteins for proteins 1 to 6 has failed irretrievably. Available StackTraces follow.
2017-11-14 09:28:15,069 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2017-11-14 09:28:15,069 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:241] 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:42)
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:128)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:377)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

Interproscan with TORQUE?

I want to use InterProScan 5.21-60.0 on our cluster which is running TORQUE. I have seen these instructions:

https://freelancingscience.com/2008/07/10/configuring-torque-and-interproscan/
ftp://ftp.hgc.jp/pub/mirror/ebi/software/iprscan/4/FAQs.html

But they do not seem applicable to the version I have. Can I set up InterProScan 5.21-60.0 with TORQUE?

Thanks!
Matt

problems_ERROR - Command line failed with exit code: 139

Hi,
I'm having this problem with some files:

30/05/2017 09:40:11:480 Welcome to InterProScan-5.24-63.0
30/05/2017 09:40:20:600 Running InterProScan v5 in STANDALONE mode... on Linux
30/05/2017 09:40:32:183 Loading file Dnoxia.faa.00105.fa
30/05/2017 09:40:32:189 Running the following analyses:
[CDD-3.14,Coils-2.2.1,Gene3D-4.1.0,Hamap-201701.18,MobiDBLite-1.0,Pfam-31.0,PIRSF-3.02,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-20.132,ProSiteProfiles-20.132,SFLD-2,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.
30/05/2017 09:41:00:421 26% completed
30/05/2017 09:41:18:407 50% completed
30/05/2017 09:41:42:448 75% completed
2017-05-30 09:42:01,533 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 139
Command: bin/sfld/sfld_postprocess -s data/sfld/2/sfld_sites.annot -a /home//tmp/titan_20170530_094020591_evo//jobSFLD/000000000002_000000000091.raw.align.out -O /home//tmp/titan_20170530_094020591_evo//jobSFLD/000000000002_000000000091.raw.out -d /home//tmp/titan_20170530_094020591_evo//jobSFLD/000000000002_000000000091.raw.domtblout.out -o /home//tmp/titan_20170530_094020591_evo//jobSFLD/000000000002_000000000091_one.raw.out
Error output from binary:

2017-05-30 09:42:01,535 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 139
Command: bin/sfld/sfld_postprocess -s data/sfld/2/sfld_sites.annot -a /home/tmp/titan_20170530_094020591_evo//jobSFLD/000000000002_000000000091.raw.align.out -O /home/tmp/titan_20170530_094020591_evo//jobSFLD/000000000002_000000000091.raw.out -d /home/tmp/titan_20170530_094020591_evo//jobSFLD/000000000002_000000000091.raw.domtblout.out -o /home/tmp/titan_20170530_094020591_evo//jobSFLD/000000000002_000000000091_one.raw.out
Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:748)

2017-05-30 09:42:01,536 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepSFLDPostProcessorBinaryRun
2017-05-30 09:42:01,631 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 92 : Run sfld postprocessing binary for selected proteins for proteins 2 to 91 has failed irretrievably. Available StackTraces follow.
2017-05-30 09:42:01,632 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2017-05-30 09:42:01,632 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:227] 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:42)
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:115)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:375)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

cluster mode question

Hello,

The instructions show this application working on LSF and SGE. We are using Slurm as our workload manager will this work in cluster mode using slurm.

thank you

Testing the service with server ip address

thanks for your great contributiuon to makw such a big software for us.
I want to ask if I want to test the lookup service with a sever ip address, can you give us an example

Interproscan on Bash on Windows

I have been trying to run Interproscan 5.22-61 in the bash terminal for a Bash on Windows installation, and I keep getting the following error:

Command: bin/gene3d/DomainFinder3 -l 5900 -e 0.001 -i /mnt/c/Users/jflowers/bin/interproscan-5.22-61.0/temp/SEA-JFLOWERS10_20170308_010158429_jixk//jobGene3d/000000000001_000000000002.input.ssf -o /mnt/c/Users/jflowers/bin/interproscan-5.22-61.0/temp/SEA-JFLOWERS10_20170308_010158429_jixk//jobGene3d/000000000001_000000000002.output.ssf
Error output from binary:
bin/gene3d/DomainFinder3: 1: bin/gene3d/DomainFinder3: Syntax error: "(" unexpected

I am not sure where this syntax error is coming from.

Thanks,

Jason

pantherScore.pl error

Hi there, I'm getting the error messages below when trying to run a multifasta protein file of ~3000 sequences. The test file runs without error. I notice that the perl command has the parameter -I before the script name pantherScore.pl, not sure if this has something to do with it. I am using interproscan-5.18-57.0.

Thanks,

Dion

07/06/2016 11:02:00:499 Running the following analyses:
[SignalP_EUK-4.1,PIRSF-3.01,Pfam-29.0,SignalP_GRAM_POSITIVE-4.1,TMHMM-2.0c,PRINTS-42.0,ProSiteProfiles-20.119,PANTHER-10.0,Coils-2.2.1,Hamap-201511.02,ProSitePatterns-20.119,SUPERFAMILY-1.75,ProDom-2006.1,SMART-7.1,SignalP_GRAM_NEGATIVE-4.1,Gene3D-3.5.0,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.
2016-06-07 11:19:08,457 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:156] ERROR - Command line failed with exit code: 255
Command: perl -I bin/panther/pantherScore/1.04/lib bin/panther/pantherScore/1.04/pantherScore.pl -l /media/4tb1/Users/leppd/Shared/Panther -D I -E 1e-3 -n -c 1 -B bin/blast/2.2.24/bin/blastall -H bin/hmmer/hmmer2/2.3.2/hmmsearch -i /media/Scratch/Users/dlepp/TZ2_MycotoxGenome/MiSeq_run2/temp/Onguel669835_20160607_110149684_kanw//jobPanther/000000000501_000000000921.fasta -T /media/4tb1/tmp/panther_tmp_files
Error output from binary:

2016-06-07 11:19:08,462 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 255
Command: perl -I bin/panther/pantherScore/1.04/lib bin/panther/pantherScore/1.04/pantherScore.pl -l /media/4tb1/Users/leppd/Shared/Panther -D I -E 1e-3 -n -c 1 -B bin/blast/2.2.24/bin/blastall -H bin/hmmer/hmmer2/2.3.2/hmmsearch -i /media/Scratch/Users/dlepp/TZ2_MycotoxGenome/MiSeq_run2/temp/Onguel669835_20160607_110149684_kanw//jobPanther/000000000501_000000000921.fasta -T /media/4tb1/tmp/panther_tmp_files
Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:158)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2016-06-07 11:19:08,465 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:203] ERROR - StepExecution with errors - stepName: stepPantherRunBinary
2016-06-07 11:19:08,644 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:72] WARN - StepInstance 54 is being re-run following a failure.
07/06/2016 11:22:36:871 25% completed
2016-06-07 11:23:32,036 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:156] ERROR - Command line failed with exit code: 255
Command: perl -I bin/panther/pantherScore/1.04/lib bin/panther/pantherScore/1.04/pantherScore.pl -l /media/4tb1/Users/leppd/Shared/Panther -D I -E 1e-3 -n -c 1 -B bin/blast/2.2.24/bin/blastall -H bin/hmmer/hmmer2/2.3.2/hmmsearch -i /media/Scratch/Users/dlepp/TZ2_MycotoxGenome/MiSeq_run2/temp/Onguel669835_20160607_110149684_kanw//jobPanther/000000000501_000000000921.fasta -T /media/4tb1/tmp/panther_tmp_files
Error output from binary:

2016-06-07 11:23:32,037 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 255
Command: perl -I bin/panther/pantherScore/1.04/lib bin/panther/pantherScore/1.04/pantherScore.pl -l /media/4tb1/Users/leppd/Shared/Panther -D I -E 1e-3 -n -c 1 -B bin/blast/2.2.24/bin/blastall -H bin/hmmer/hmmer2/2.3.2/hmmsearch -i /media/Scratch/Users/dlepp/TZ2_MycotoxGenome/MiSeq_run2/temp/Onguel669835_20160607_110149684_kanw//jobPanther/000000000501_000000000921.fasta -T /media/4tb1/tmp/panther_tmp_files
Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:158)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2016-06-07 11:23:32,038 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:203] ERROR - StepExecution with errors - stepName: stepPantherRunBinary
2016-06-07 11:23:32,117 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:72] WARN - StepInstance 54 is being re-run following a failure.
2016-06-07 11:24:59,216 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:156] ERROR - Command line failed with exit code: 255
Command: perl -I bin/panther/pantherScore/1.04/lib bin/panther/pantherScore/1.04/pantherScore.pl -l /media/4tb1/Users/leppd/Shared/Panther -D I -E 1e-3 -n -c 1 -B bin/blast/2.2.24/bin/blastall -H bin/hmmer/hmmer2/2.3.2/hmmsearch -i /media/Scratch/Users/dlepp/TZ2_MycotoxGenome/MiSeq_run2/temp/Onguel669835_20160607_110149684_kanw//jobPanther/000000000501_000000000921.fasta -T /media/4tb1/tmp/panther_tmp_files
Error output from binary:

2016-06-07 11:24:59,216 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 255
Command: perl -I bin/panther/pantherScore/1.04/lib bin/panther/pantherScore/1.04/pantherScore.pl -l /media/4tb1/Users/leppd/Shared/Panther -D I -E 1e-3 -n -c 1 -B bin/blast/2.2.24/bin/blastall -H bin/hmmer/hmmer2/2.3.2/hmmsearch -i /media/Scratch/Users/dlepp/TZ2_MycotoxGenome/MiSeq_run2/temp/Onguel669835_20160607_110149684_kanw//jobPanther/000000000501_000000000921.fasta -T /media/4tb1/tmp/panther_tmp_files
Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:158)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.GeneratedMethodAccessor93.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2016-06-07 11:24:59,217 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:203] ERROR - StepExecution with errors - stepName: stepPantherRunBinary
2016-06-07 11:24:59,264 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 54 : Run PANTHER binary for selected proteins for proteins 501 to 921 has failed irretrievably. Available StackTraces follow.
2016-06-07 11:24:59,267 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2016-06-07 11:24:59,267 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:145] 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:42)
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:63)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:326)
2016-06-07 11:24:59,312 [main] [uk.ac.ebi.interpro.scan.jms.master.AbstractMaster:249] WARN - Unable to delete temporary directory /media/Scratch/Users/dlepp/TZ2_MycotoxGenome/MiSeq_run2/temp/Onguel669835_20160607_110149684_kanw
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

Interpreting E-values on Interpro

Hi,

I was reading the manual on Github about e-values:

"9.Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)"

In the process of determining a threshold cutoff for e-values, I presume that the each of the source member databases have their own cutoff scores? Is that information provided on Interpro, or must I search through each source database to find such threshold cutoffs?

thanks,
Lili

Error: Unable to find original database file: work/template/interpro.zip

I'm getting the below error regarding the original database file - what does this mean?

Thanks!
-Roxanne-

./interproscan.sh -i test_proteins.fasta -f tsv
04/11/2016 12:03:36:304 Welcome to InterProScan-5.21-60.0
04/11/2016 12:03:41:932 Running InterProScan v5 in STANDALONE mode... on Mac OS X
2016-11-04 12:03:41,933 [Thread-7] [uk.ac.ebi.interpro.scan.jms.activemq.CleanRunDatabase:100] FATAL - Unable to find original database file: work/template/interpro.zip
Exception in thread "Thread-7" java.lang.IllegalStateException: Unable to find original database file
at uk.ac.ebi.interpro.scan.jms.activemq.CleanRunDatabase.cleanInstalledDatabase(CleanRunDatabase.java:101)
at uk.ac.ebi.interpro.scan.jms.activemq.CleanRunDatabase.run(CleanRunDatabase.java:76)
at java.lang.Thread.run(Thread.java:745)

Support Slurm as a cluster option in interproscan.properties

I plan to use interproscan on a Slurm cluster and I'll be editing the interproscan.properties to work on it. I can submit a pull request with the interproscan.properties edited to include those changes so others won't have to do that step if they plan on using Slurm.

Problem with setting up port number for local lookup service

Hi,

I am trying to set up the port number to run the local lookup service. But it stated that some apps are missing. Are they essential? If the answer is yes, I need to find out whether I could install them on the HPC units.

cd /path-to-lookup_service_5.25-64.0
java -Xmx2000m -jar server-5.25-64.0-jetty-console.war --headless --port 9123
321 [main] INFO org.simplericity.jettyconsole.DefaultJettyManager - Added web application on path / from war /scratch/gpfs/maglau/lookup_service_5.25-64.0/server-5.25-64.0-jetty-console.war
321 [main] INFO org.simplericity.jettyconsole.DefaultJettyManager - Starting web application on port 9123
323 [main] INFO org.eclipse.jetty.server.Server - jetty-8.1.12.v20130726
1296 [main] INFO org.eclipse.jetty.plus.webapp.PlusConfiguration - No Transaction manager found - if your webapp requires one, please configure one.
3577 [main] INFO org.eclipse.jetty.webapp.StandardDescriptorProcessor - NO JSP Support for /, did not find org.apache.jasper.servlet.JspServlet
3601 [main] INFO / - No Spring WebApplicationInitializer types detected on classpath
3906 [main] INFO / - Initializing Spring root WebApplicationContext
Initializing BerkeleyDB Match Database (creating indexes): Please wait...

Thanks,
Maggie

Java 9.0

The message is pretty clear that InterProScan cannot run on 1.9 but do you know when it will?

Java version 1.8 is required to run InterProScan.
Detected version 9.0
Please install the correct version.

make major versions interoperable

It would be really nice if there was a way to keep interoperability on the major version numbers for local installs that use the lookup service, especially given how often there are new releases.

We have analyses where we run Interproscan on thousands of sequences, so of course we setup our own local installation.

However, with every new release of interpro (currently every couple of months), our local install cannot make use of the lookup service. So we have to install and test the new versions (not a trivial process), or have really slow local lookups. However, setting up our own lookup server looks to be way more work than re-installing Interproscan itself.

In my mind, any release of software marked the same by major version (e.g. v5.x.y) should all work together. When the major release changes, it is expected that they will no longer work. However, this is not the case for Interproscan.

I realize that this is partly due to how the software and databases are tied together, however it seems there should be some kind of possible solution where the regular expressions and hidden markov models in each database get a set of version tags, so that older versions of local installations could still use the online lookup service?

Potential hangup on cluster ?

Hi,

I am using Interproscan - which is very nice by the way - to analyze ~30,000 arabidopsis proteins.

This is an LSF cluster. Jobs were submitted to LSF and appeared to complete fine, calculations appear to come back to the master node, but this has then been running for a long time. Eg. over 5 days, using 4 cores on a fast 3.3. ghz server.

Is this normal ? Am I just being impatient ? Are there any other logs other than those created by default under the directory iprscan/logs (eg. in /tmp/ ?).

Thanks

Readout:

/mnt/NAS10/bioinformatics/programs/interproscan/interproscan-5.19-58.0/interproscan.sh -mode cluster -clusterrunid KWS_cluster_jobid_big_12123 -i /mnt/scratch/colin/interproscan/Araport11_genes.201606_cln.pep2.fasta -b /mnt/scratch/colin/interproscan/Araport11_genes.201606_cln.pep2.fasta -f xml --disable-precalc -goterms
12/10/2016 15:03:36:520 Welcome to InterProScan-5.19-58.0
The Project/Cluster Run ID for this run is: KWS_cluster_jobid_big_12123
12/10/2016 15:03:42:942 Running InterProScan v5 in CLUSTER mode... on Linux
12/10/2016 15:03:42:942 Interproscan 5 Master process running on: tcp://serv01:62325
12/10/2016 15:03:57:058 Loading file /mnt/scratch/colin/interproscan/Araport11_genes.201606_cln.pep2.fasta
12/10/2016 15:03:57:064 Running the following analyses:
[CDD-3.14,PIRSF-3.01,Pfam-29.0,PRINTS-42.0,ProSiteProfiles-20.119,PANTHER-10.0,Coils-2.2.1,Hamap-201605.11,ProSitePatterns-20.119,SUPERFAMILY-1.75,ProDom-2006.1,SMART-7.1,Gene3D-3.5.0,TIGRFAM-15.0]
Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete...
12/10/2016 15:05:19:566 Uploaded/Stored 40784 sequences for analysis
12/10/2016 15:34:58:829 25% completed
12/10/2016 16:48:18:319 50% completed
12/10/2016 19:58:40:990 75% completed
13/10/2016 09:33:56:757 90% completed
2016-10-13 15:09:00,917 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-13 20:42:40,410 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-14 05:46:48,708 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised

2016-10-15 05:23:13,702 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-15 08:57:11,902 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-16 08:20:58,474 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-16 22:44:58,742 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-17 03:01:07,909 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-17 06:11:15,664 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-18 11:30:43,957 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised
2016-10-18 13:51:07,182 [pool-1-thread-1] [uk.ac.ebi.interpro.scan.jms.stats.StatsUtil:532] WARN - JobRequestQueue: not initialised

How to control cpu and memory usage?

I'm running interproscan in standalone mode.

On the wiki, there is this information for setting the number of embedded.workers:
https://github.com/ebi-pf-team/interproscan/wiki/ImprovingPerformance#case-1-running-interproscan-in-standalone-mode-default

There is also this flag that you can use with interproscan.sh:
-cpu,--cpu <CPU> Optional, number of cores for inteproscan.
How do these options interact?

Similarly, is there a way to give a memory limit? I see there are options in the properties file if you are running in cluster mode, but are there similar options in standalone? I saw this issue, where it was recommended to set the memory limit in the -Xmx parameter in the call to interproscan-5.jar in interproscan.sh. But, if I do that, I keep running out of memory even though I'm setting it to lower than what is available. I'm not very familiar with memory allocation in Java.

Thanks

Encountering Exception

Hello,

I am running the following command:

nohup /opt/rit/app/interproscan/5.15-54.0/interproscan.sh -i plantfdb_674.fas -b plantfdb_674_interproscan > plantfdb_674_interproscan.output 2> plantfdb_674_interproscan.error

I am getting the following error:

Exception in thread "main" org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'htmlWriter' defined in class path resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Cannot resolve reference to bean 'freeMarkerConfigHtmlWriter' while setting bean property 'freeMarkerConfig'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'freeMarkerConfigHtmlWriter' defined in class path resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Cannot resolve reference to bean 'templateLoaderHtmlWriter' while setting bean property 'templateLoader'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'templateLoaderHtmlWriter' defined in class path resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [freemarker.cache.FileTemplateLoader]: Constructor threw exception; nested exception is java.io.FileNotFoundException: data/freemarker/WEB-INF/freemarker does not exist.
	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
	at org.springframework.context.support.ClassPathXmlApplicationContext.(ClassPathXmlApplicationContext.java:139)
	at org.springframework.context.support.ClassPathXmlApplicationContext.(ClassPathXmlApplicationContext.java:93)
	at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:171)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'freeMarkerConfigHtmlWriter' defined in class path resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Cannot resolve reference to bean 'templateLoaderHtmlWriter' while setting bean property 'templateLoader'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'templateLoaderHtmlWriter' defined in class path resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [freemarker.cache.FileTemplateLoader]: Constructor threw exception; nested exception is java.io.FileNotFoundException: data/freemarker/WEB-INF/freemarker does not exist.
	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
	... 15 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'templateLoaderHtmlWriter' defined in class path resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [freemarker.cache.FileTemplateLoader]: Constructor threw exception; nested exception is java.io.FileNotFoundException: data/freemarker/WEB-INF/freemarker does not exist.
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
	... 25 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [freemarker.cache.FileTemplateLoader]: Constructor threw exception; nested exception is java.io.FileNotFoundException: data/freemarker/WEB-INF/freemarker does not exist.
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
	... 34 more
Caused by: java.io.FileNotFoundException: data/freemarker/WEB-INF/freemarker does not exist.
	at freemarker.cache.FileTemplateLoader$1.run(FileTemplateLoader.java:125)
	at java.security.AccessController.doPrivileged(Native Method)
	at freemarker.cache.FileTemplateLoader.(FileTemplateLoader.java:122)
	at freemarker.cache.FileTemplateLoader.(FileTemplateLoader.java:108)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
	... 36 more

The command runs fine when executed with -appl ProDom,Pfam but fails when all other application runs are requested.

Please help.

Thank you.

issue with the latest version 5.20

Hello,

while 5.19 works fine, 5.20 throws the following error on 2 different 64bit Linux systems:

bin/sfld/sfld_postprocess: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by bin/sfld/sfld_postprocess)

At the same time, libc6 is updated to the latest on both of the 2 machines.

Thanks

Interproscan license

Hi,

I was wondering under what licence agreement is interproscan published and as well if users where able to deactivate parts of the software where getting a license would be difficult?

Issues with glibc?

Hi, I am getting following error when running 5-24.63 Tried with previous versions, and it seems to occur from 5-20-59 version.

03/08/2017 11:32:19:066 50% completed
2017-08-03 11:32:24,005 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1
Command: bin/gene3d/4.1.0/cath-resolve-hits --input-format=hmmer_domtmblout --output-file /tmp/c442-904.stampede.tacc.utexas.edu_20170803_112325528_bdp0//jobGene3d/000000000001_000000000359_one.raw.out /tmp/c442-904.stampede.tacc.utexas.edu_20170803_112325528_bdp0//jobGene3d/000000000001_000000000359.raw.domtblout.out 
Error output from binary:
bin/gene3d/4.1.0/cath-resolve-hits: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by bin/gene3d/4.1.0/cath-resolve-hits)

oracle driver missing

When compiling interpro from source I get a error that oracle.jdbc is missing.

[ERROR] Failed to execute goal on project interproscan-persistence: Could not resolve dependencies for project uk.ac.ebi.interpro.scan:interproscan-persistence:jar:5.15-54.0: Could not find artifact com.oracle.jdbc:com.springsource.oracle.jdbc:jar:10.2.0.2 in apache-maven-snapshots (http://svn.apache.org/maven-snapshot-repository/) -> [Help 1]

Interproscan looking for file that is not present in temp directory

Hi,

I am testing a new installation of interproscan (v 6.23-62.0). I am using the provided test_protein.fasta file and using the following command:

$ ./interproscan.sh -dp -i test_proteins.fasta -f tsv -T /dev/shm/

The program runs till 75% completion and then dies throwing an IOException.
I've attached the output in the interproscan.log
interproscan.log.txt

The error indicates that it couldn't find the file /dev/shm/uga-a24852b.scm_20170322_171029961_l0md//jobGene3d/000000000001_000000000006_one.raw.out in the /dev/shm (my temp area).
I don't see any temp file created with the name 000000000001_000000000006_one.raw.out instead I see files created with the name 000000000001_000000000006.raw.out.

Is this a buy or am I doing something wrong?

Thanks,
Raj

Exceptions and warining at run completion

I have been analyzing a big set of protein sequences with interproscan for the last 45 CPU days / 19 real-time days and on the very last step interproscan crashed with a number of warnings and exceptions. It is particularly frustrating because it deleted all of the data in the temp folder while seemingly not creating any output. Right at the moment I have the process in a moribund state still there (see also my settings here):

$ ps aux | grep [j]ava
user   27414  235  6.5 16828564 8627544 ?    Sl   Jul07 65790:11 /usr/bin/java -XX:+UseParallelGC -XX:ParallelGCThreads=4 -XX:+AggressiveOpts -XX:+UseFastAccessorMethods -Xms256M -Xmx8192M -jar interproscan-5.jar -f GFF3 -f TSV -f HTML -iprlookup --pathways --disable-precalc -b mydir/myoutput -i myfasta.fa -u /my/path

The temp folder contains only one empty subfolder, the final output folder is empty:

$ ls -l temp/mynode_20160707_094129330_ea9k/jobWriteOutput/
total 0
$ ls -l mydir
total 0

Here is how it looked like sometime before the crash:

$ ls -l /my/backup/temp/mynode_20160707_094129330_ea9k/
total 604
drwxrwxr-x  2 user user   4096 Jul 13 05:33 jobCDD
drwxrwxr-x  2 user user   4096 Jul 13 01:05 jobCoils
drwxrwxr-x  2 user user  32768 Jul 16 02:01 jobGene3d
drwxrwxr-x 35 user user  12288 Jul 13 01:48 jobHAMAP
drwxrwxr-x  2 user user   4096 Jul  7 09:41 jobLoadFromFasta
drwxrwxr-x  2 user user   4096 Jul 13 07:21 jobPfam
drwxrwxr-x  2 user user  24576 Jul 12 23:20 jobPIRSF-3.01
drwxrwxr-x  2 user user  40960 Jul 13 00:17 jobPRINTS-42.0
drwxrwxr-x  2 user user  12288 Jul 12 22:57 jobProDom-2006.1
drwxrwxr-x  2 user user  12288 Jul 12 20:31 jobPrositePatterns
drwxrwxr-x  2 user user 266240 Jul 12 23:58 jobPrositeProfiles
drwxrwxr-x  2 user user  81920 Jul 13 00:09 jobSMART
drwxrwxr-x  2 user user  90112 Jul 13 00:36 jobSuperFamily-1.75
drwxrwxr-x  2 user user  12288 Jul 12 22:21 jobTIGRFAM-15.0

And here is the log:

07/07/2016 09:41:23:150 Welcome to InterProScan-5.19-58.0
07/07/2016 09:41:29:331 Running InterProScan v5 in STANDALONE mode... on Linux
07/07/2016 09:41:45:776 Loading file myfasta.fa
07/07/2016 09:41:45:779 Running the following analyses:
[CDD-3.14,PIRSF-3.01,Pfam-29.0,PRINTS-42.0,ProSiteProfiles-20.119,Coils-2.2.1,Hamap-201605.11,ProSitePatterns-20.119,SUPERFAMILY-1.75,ProDom-2006.1,SMART-7.1,Gene3D-3.5.0,TIGRFAM-15.0]
Pre-calculated match lookup service DISABLED.  Please wait for match calculations to complete...
07/07/2016 11:32:02:802 Uploaded/Stored 329021 sequences for analysis
10/07/2016 06:58:17:688 25% completed
13/07/2016 00:34:00:987 50% completed
14/07/2016 19:43:23:438 75% completed
22/07/2016 00:06:45:536 90% completed
2016-07-26 17:27:26,394 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.LoadContexts:98] WARN - HHH000100: Fail-safe cleanup (collections) : org.hibernate.engine.loading.internal.CollectionLoadContext@470621c<rs=rs913259387: null>
2016-07-26 17:27:27,254 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.CollectionLoadContext:377] WARN - HHH000160: On CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [597714] entries
2016-07-26 17:36:48,018 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.LoadContexts:98] WARN - HHH000100: Fail-safe cleanup (collections) : org.hibernate.engine.loading.internal.CollectionLoadContext@2a9d0111<rs=rs914012782: null>
2016-07-26 17:36:48,019 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.CollectionLoadContext:377] WARN - HHH000160: On CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [600810] entries
2016-07-26 17:44:00,890 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.LoadContexts:98] WARN - HHH000100: Fail-safe cleanup (collections) : org.hibernate.engine.loading.internal.CollectionLoadContext@10d52e80<rs=rs914755499: null>
2016-07-26 17:44:00,891 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.CollectionLoadContext:377] WARN - HHH000160: On CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [603392] entries
2016-07-26 17:52:34,462 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.LoadContexts:98] WARN - HHH000100: Fail-safe cleanup (collections) : org.hibernate.engine.loading.internal.CollectionLoadContext@59fc52d5<rs=rs915538909: null>
2016-07-26 17:52:34,462 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.CollectionLoadContext:377] WARN - HHH000160: On CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [595814] entries
2016-07-26 18:00:12,711 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.LoadContexts:98] WARN - HHH000100: Fail-safe cleanup (collections) : org.hibernate.engine.loading.internal.CollectionLoadContext@7433e830<rs=rs916271449: null>
2016-07-26 18:00:12,711 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.CollectionLoadContext:377] WARN - HHH000160: On CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [603392] entries
2016-07-26 18:14:11,880 [main] [org.hibernate.engine.loading.internal.LoadContexts:98] WARN - HHH000100: Fail-safe cleanup (collections) : org.hibernate.engine.loading.internal.CollectionLoadContext@462fadef<rs=rs917437921: null>
2016-07-26 18:14:11,882 [main] [org.hibernate.engine.loading.internal.CollectionLoadContext:377] WARN - HHH000160: On CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [1] entries
2016-07-26 18:14:12,280 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.LoadContexts:98] WARN - HHH000100: Fail-safe cleanup (collections) : org.hibernate.engine.loading.internal.CollectionLoadContext@6259d3c4<rs=rs917012334: null>
2016-07-26 18:14:12,281 [amqEmbeddedWorkerJmsContainer-14] [org.hibernate.engine.loading.internal.CollectionLoadContext:377] WARN - HHH000160: On CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [600222] entries
2016-07-26 18:14:33,565 [main] [uk.ac.ebi.interpro.scan.jms.main.Run:1239] WARN - At run completion, unable to delete temporary directory /my/path/temp/mynode_20160707_094129330_ea9k
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "ActiveMQ Broker[localhost] Scheduler" java.lang.OutOfMemoryError: GC overhead limit exceeded
2016-07-26 18:25:23,811 [ActiveMQ VMTransport: vm://localhost#1-10453] [org.apache.activemq.broker.region.RegionBroker:814] WARN - Caught an exception sending to DLQ: Message ID:mynode-52747-1467877289129-3:1:18:1:2321 dropped=false acked=false locked=true
java.lang.IllegalStateException: Timer already cancelled.
    at java.util.Timer.sched(Timer.java:397)
    at java.util.Timer.schedule(Timer.java:248)
    at org.apache.activemq.thread.Scheduler.executePeriodically(Scheduler.java:41)
    at org.apache.activemq.broker.region.Queue.start(Queue.java:949)
    at org.apache.activemq.broker.region.AbstractRegion.addDestination(AbstractRegion.java:161)
    at org.apache.activemq.broker.region.RegionBroker.addDestination(RegionBroker.java:348)
    at org.apache.activemq.broker.region.RegionBroker.sendToDeadLetterQueue(RegionBroker.java:804)
    at org.apache.activemq.broker.BrokerFilter.sendToDeadLetterQueue(BrokerFilter.java:318)
    at org.apache.activemq.advisory.AdvisoryBroker.sendToDeadLetterQueue(AdvisoryBroker.java:505)
    at org.apache.activemq.broker.BrokerFilter.sendToDeadLetterQueue(BrokerFilter.java:318)
    at org.apache.activemq.broker.BrokerFilter.sendToDeadLetterQueue(BrokerFilter.java:318)
    at org.apache.activemq.broker.MutableBrokerFilter.sendToDeadLetterQueue(MutableBrokerFilter.java:330)
    at org.apache.activemq.broker.region.PrefetchSubscription.sendToDLQ(PrefetchSubscription.java:540)
    at org.apache.activemq.broker.region.PrefetchSubscription.acknowledge(PrefetchSubscription.java:397)
    at org.apache.activemq.broker.region.AbstractRegion.acknowledge(AbstractRegion.java:526)
    at org.apache.activemq.broker.region.RegionBroker.acknowledge(RegionBroker.java:484)
    at org.apache.activemq.broker.BrokerFilter.acknowledge(BrokerFilter.java:87)
    at org.apache.activemq.broker.BrokerFilter.acknowledge(BrokerFilter.java:87)
    at org.apache.activemq.broker.TransactionBroker.acknowledge(TransactionBroker.java:276)
    at org.apache.activemq.broker.MutableBrokerFilter.acknowledge(MutableBrokerFilter.java:97)
    at org.apache.activemq.broker.TransportConnection.processMessageAck(TransportConnection.java:555)
    at org.apache.activemq.command.MessageAck.visit(MessageAck.java:245)
    at org.apache.activemq.broker.TransportConnection.service(TransportConnection.java:338)
    at org.apache.activemq.broker.TransportConnection$1.onCommand(TransportConnection.java:188)
    at org.apache.activemq.transport.ResponseCorrelator.onCommand(ResponseCorrelator.java:116)
    at org.apache.activemq.transport.MutexTransport.onCommand(MutexTransport.java:50)
    at org.apache.activemq.transport.vm.VMTransport.iterate(VMTransport.java:270)
    at org.apache.activemq.thread.PooledTaskRunner.runTask(PooledTaskRunner.java:133)
    at org.apache.activemq.thread.PooledTaskRunner$1.run(PooledTaskRunner.java:48)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

I realize that any further experimenting would cost me days, so the question is what causes this problem and how to avoid it. I also guess it is not the behavior one would expect from such a long-running process: to delete temporary files before making sure the outputs were written successfully.

Error using packaged binaries - rpsbproc

Hi Interproscan,

I'm trying to run the Interproscan pipeline, but am having trouble with some of the packaged compiled binaries, specifically rpsbproc:

 ./rpsbproc  -h
./rpsbproc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by ./rpsbproc)

This is on RHEL 6.7 x86_64, with the 64bit binaries.

It looks like this is an issue with the upstream NCBI binary - I downloaded both the compiled binary and the src from the ncbi ftp server but the compiled version gives the same GLIBC error, and the src have a bunch of ncbi specific paths & includes and no ./configure file. I'm not sure I want to shave the yak all the way down to compiling it.

The rpsblast binary does run successfully, and the standard blast I have on my system only contains rpsblast, not rpsbproc.

I understand this isn't a problem with interproscan per se, but do you have any guidance for me? I checked the wiki compiling binaries FAQ and list of specific binary instructions but rpsbproc isn't in there.

Can you tell me the 'nix version you test on to see if I may just break down and VM / docker image of what I need? Thanks in advance for any suggestions,
Erik

SignalP fails to run because default batch size 16000 greater than default max sequences 10000 in SignalP script

Discovered a weird problem today:

By default, the SignalP perl script that one downloads from http://www.cbs.dtu.dk/services/SignalP/ has max sequences set to 10,000:

# max number of sequences per run (any number can be handled)
my $MAX_ALLOWED_ENTRIES=10000;

However, the default batch size for SignalP in interproscan.properties is 16,000:

analysis.max.sequence.count.SIGNALP=16000

As a result, when I submit a file with, say 20,000 sequences, then it gets split into two batches (1-16000, and 16001-20000) but only the second one finishes as the first one has too many sequences for SignalP to process.

Fixing either my $MAX_ALLOWED_ENTRIES=10000000; or analysis.max.sequence.count.SIGNALP=10000 solves the problem.

May I request that future editions of interproscan.properties have analysis.max.sequence.count.SIGNALP=10000 and a warning to check that this is <= the limit in the SignalP script?

gene3d hangs for particular sequence groups

We run the latest interproscan-5.23-62.0 on sequence chunk from a de novo assembly. For many of the chunks, interproscan gets stuck in the java process, after all calculations have finished. The process does not finish after 16 hours (we did not wait longer).
We can reproduce the error when only requesting gene3d:
interproscan-5.23-62.0/interproscan.sh -dp --goterms -i test.fasta2.reform.fasta -appl gene3d -f tsv
whereas all other methods without gene3d run fine without problems:
interproscan-5.23-62.0/interproscan.sh -dp --goterms -i test.fasta2.reform.fasta -appl cdd,coils,gene3d,hamap,mobidblite,panther,pfam,phobius,pirsf,prints,prodom,prositepatterns,prositeprofiles,sfld,signalp_euk,signalp_gram_negative,signalp_gram_positive,smart,superfamily,tigrfam,tmhmm -f tsv

We did not change any gene3d related parameter in interproscan.properties. The temporary directory is in a local path under /tmp, excluding NFS delays as a reason.

Very strange: if we further split the input file test.fasta2.reform.fasta, all smaller parts of it run fine. The problem is therefore not the result of a single sequence...

Thanks for your help!!
Best,
Thomas

test.fasta2.reform.fasta.zip

interproscan-5.26-65.0 fails in mobidb-lite.py

Hello:
I'm trying to run Interproscan-5.26-65.0 using a nucleotide fasta, but it fails at mobidb-lite step even with the test file.

The command that causes this issue is: ./interproscan.sh -t n -i test_nt_seqs.fasta

Full error is:

2017-11-09 18:26:37,137 [amqEmbeddedWorkerJmsContainer-10] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1
Command: python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /media/gabo/ba45dce6-59ea-4965-834d-639da4d43d71/my_interproscan/interproscan-5.26-65.0/bin/mobidb/binx /media/gabo/ba45dce6-59ea-4965-834d-639da4d43d71/my_interproscan/interproscan-5.26-65.0/temp/precision_20171109_182423769_2hyh//jobMobiDBLite/000000000001_000000000073.fasta
Error output from binary:
Traceback (most recent call last):
File "bin/mobidb/mobidb-lite.py", line 455, in
out = run_mobidb(binDirectory, args.threads, args.longOutput, acc, seq, args.architecture, verbose = args.verbose)
File "bin/mobidb/mobidb-lite.py", line 198, in run_mobidb
if ele.get():
File "/usr/lib/python2.7/multiprocessing/pool.py", line 567, in get
raise self._value
IndexError: list index out of range

I spoke to the guys developing mobidb and they told me that mobidb only accepts aminoacid sequences, so I guess something weird is going on in the translation step

Has someone else found the same issue? currently I'm trying Interproscan with mobidb analysis disabled

Cheers,

Gabriel

SFLD crashes for some sequences

A recent run of interproscan against a proteome resulted in failure of approximately 5% of the sequences, although nothing was apparently wrong with them. One example is attached. A java exception is thrown pointing to SFLD. The error occurs with a freshly downloaded interproscan-5.22-61.0, using Oracle java 1.8.0_121.

commandline to reproduce:
/tmp/interproscan-5.22-61.0/interproscan.sh -i failing_sequence.fa --output-file failing_sequence.fa.xml --formats XML -dp -appl sfld

failing_sequence.fa.zip
interproscan_out.txt

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Whenever I use interproscan on about 10000 protein sequences, it will get stuck in "90% completed". I provided 16 cores for this job and used the default interproscan.properties file.

Matches for any sequences that are not represented in the lookup service will be calculated locally. 22/04/2017 16:47:05:527 25% completed 22/04/2017 17:03:46:760 51% completed 22/04/2017 17:11:33:174 75% completed 22/04/2017 17:22:40:969 90% completed

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Matches for any sequences that are not represented in the lookup service will be calculated locally.
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22/04/2017 17:22:40:969 90% completed