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[interhelp #28703] installation problems in ubuntu 14.04 LTS #53

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Download and install interProScan-5.7-48.0 and panther-data-9.0
2. Custom java installation to match version requirements (1.7.0_40 Oracle JRE)
3. Run ./interproscan.sh

What is the expected output? What do you see instead?
Running interproscan.sh should output usage instructions. Instead, it outputs 
various java errors (see below).
A similar error occurs when a query is made.

What version of the product are you using? On what operating system?
interProScan-5.7-48.0
panther-data-9.0
Ubuntu 14.04.1 LTS 64bits
Java(TM) SE Runtime Environment (build 1.7.0_40-b43) 64bits
Perl v5.18.2

Please provide any additional information below.
The same problem occurs with newer and older java versions:
1.8.0_20 oracle
1.6.0_32 openjdk
1.7.0_65 openjdk
1.7.0_67 oracle

Output of ./interproscan.sh:

08/10/2014 15:54:32:873 Welcome to InterProScan-5.7-48.0
Exception in thread "main" 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'stepPirsfOverlapPostProcessing-2.84' defined in class path resource 
[spring/jobs/jobPIRSF-2.84-context.xml]: Cannot create inner bean 
'uk.ac.ebi.interpro.scan.business.postprocessing.pirsf.hmmer2.OverlapPostProcess
or#49d71441' of type 
[uk.ac.ebi.interpro.scan.business.postprocessing.pirsf.hmmer2.OverlapPostProcess
or] while setting bean property 'postProcessor'; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 
'uk.ac.ebi.interpro.scan.business.postprocessing.pirsf.hmmer2.OverlapPostProcess
or#49d71441' defined in class path resource 
[spring/jobs/jobPIRSF-2.84-context.xml]: Cannot resolve reference to bean 
'pirsfDatFileInfoHolder-2.84' while setting bean property 
'pirsfDatFileInfoHolder'; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'pirsfDatFileInfoHolder-2.84' defined in class path resource 
[spring/jobs/jobPIRSF-2.84-context.xml]: Instantiation of bean failed; nested 
exception is org.springframework.beans.BeanInstantiationException: Could not 
instantiate bean class 
[uk.ac.ebi.interpro.scan.io.pirsf.hmmer2.PirsfDatFileInfoHolder]: Constructor 
threw exception; nested exception is java.lang.IllegalStateException: pirsf.dat 
does not exist
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveInnerBean(BeanDefinitionValueResolver.java:281)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:120)
    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.<init>(ClassPathXmlApplicationContext.java:139)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:128)
Caused by: org.springframework.beans.factory.BeanCreationException: Error 
creating bean with name 
'uk.ac.ebi.interpro.scan.business.postprocessing.pirsf.hmmer2.OverlapPostProcess
or#49d71441' defined in class path resource 
[spring/jobs/jobPIRSF-2.84-context.xml]: Cannot resolve reference to bean 
'pirsfDatFileInfoHolder-2.84' while setting bean property 
'pirsfDatFileInfoHolder'; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'pirsfDatFileInfoHolder-2.84' defined in class path resource 
[spring/jobs/jobPIRSF-2.84-context.xml]: Instantiation of bean failed; nested 
exception is org.springframework.beans.BeanInstantiationException: Could not 
instantiate bean class 
[uk.ac.ebi.interpro.scan.io.pirsf.hmmer2.PirsfDatFileInfoHolder]: Constructor 
threw exception; nested exception is java.lang.IllegalStateException: pirsf.dat 
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.BeanDefinitionValueResolver.resolveInnerBean(BeanDefinitionValueResolver.java:270)
    ... 15 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error 
creating bean with name 'pirsfDatFileInfoHolder-2.84' defined in class path 
resource [spring/jobs/jobPIRSF-2.84-context.xml]: Instantiation of bean failed; 
nested exception is org.springframework.beans.BeanInstantiationException: Could 
not instantiate bean class 
[uk.ac.ebi.interpro.scan.io.pirsf.hmmer2.PirsfDatFileInfoHolder]: Constructor 
threw exception; nested exception is java.lang.IllegalStateException: pirsf.dat 
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)
    ... 21 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not 
instantiate bean class 
[uk.ac.ebi.interpro.scan.io.pirsf.hmmer2.PirsfDatFileInfoHolder]: Constructor 
threw exception; nested exception is java.lang.IllegalStateException: pirsf.dat 
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)
    ... 30 more
Caused by: java.lang.IllegalStateException: pirsf.dat does not exist
    at uk.ac.ebi.interpro.scan.io.pirsf.hmmer2.PirsfDatFileParser.parse(PirsfDatFileParser.java:60)
    at uk.ac.ebi.interpro.scan.io.pirsf.hmmer2.PirsfDatFileInfoHolder.<init>(PirsfDatFileInfoHolder.java:17)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
    at java.lang.reflect.Constructor.newInstance(Unknown Source)
    at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
    ... 32 more

Original issue reported on code.google.com by conxorxa...@gmail.com on 8 Oct 2014 at 2:20

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 9 Oct 2014 at 2:20

GoogleCodeExporter commented 9 years ago 
Hi,

Thank you for the message.

It could sound like a Java version problem, InterProScan 5 won't work with Java 
1.8, but if you tested it with 1.7.0_40 then that should have been OK...
https://code.google.com/p/interproscan/wiki/InstallationRequirements

So that's interesting! I have a couple of questions...

#1. Did you make any changes to your configuration, for the 
"pirsf.dat.path.2.84" property in your interproscan.properties configuration 
file? I assume the pirsf.dat it references does exist in that location and the 
file permissions are OK? And did you do the md5sum check on the download, so it 
looks like the download wasn't corrupted? The pirsf.dat file should look like 
this...

https://code.google.com/p/interproscan/source/browse/trunk/core/jms-implementati
on/support-mini-x86-32/data/pirsf/2.84/pirsf.dat

#2. Is pirsf.dat the only file causing a problem, if you turn off the PIRSF 
analysis using the -appl flag does everything else work OK?

https://code.google.com/p/interproscan/wiki/HowToRun

We didn't manage to recreate the same problem here yet, but we'll see if we can 
think of anything!

Thanks,

Matt

Original comment by Mr.Matth...@gmail.com on 9 Oct 2014 at 2:52

GoogleCodeExporter commented 9 years ago 
Hi Matt,

Thanks for your answer. I did the md5sum and everything was OK for both panther 
and interpro. However, for some unknwon reasons, there were problems with the 
data/pirsf/2.84/pirsf.dat permissions (and other configuration files). 
Re-extracting the package solved the issue, so, it must have been my fault 
(i.e., the out-of-the-box file permissions are OK).

Thanks again for your help.

Best,

XGB

Original comment by conxorxa...@gmail.com on 10 Oct 2014 at 9:39

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 14 Nov 2014 at 12:01