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ebi-pf-team / interproscan

Genome-scale protein function classification
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Interproscan with TORQUE? #19

Closed mcsimenc closed 7 years ago

mcsimenc commented 7 years ago

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

gsn7 commented 7 years ago

You can setup Interproscan5 with TORQUE, other users have previously mentioned this. We have not tested it though as we don't have a TORQUE cluster to test on. Have you tried to create a simple job script like the following and run it?

!/bin/bash

PBS -l nodes=1:ppn=8

PBS -M example@example.com

PBS -m abe

PBS -N interproscan5Job

PBS -o /-path/to/output-file-name

PBS -j oe

/path/to/interproscan.sh -i /path/to/test_all_appl.fasta -b /path/to/test_all_appl.result

tcfhcdg commented 7 years ago

Hello interproscan tem I would like to run interproscan on cluster through PBS /torque. I tried wtih the test script and could not succeed because of the GLIBC_2.14. The reason is the entire software stack of CentOS 6.8 which our cluster is running was built on top of glibc 2.12 which at the moment can't be upgraded to glibc 2.14.

Could you please guide me how to resolve the issue? The script I use and the out put is as follows: ##################

!/bin/bash

PBS -l nodes=1:ppn=4

PBS -M tajammul.hussain@bci.tu-dortmund.de

PBS -m abe

PBS -N interproscan5Job

PBS -o /home/tb44227/nobackup/my_interproscan/interproscan-5.22-61.0/test_ipr_cluste_torque

PBS -j oe

PBS -q short

PBS -l walltime=01:00:00

 /home/tb44227/nobackup/my_interproscan/interproscan-5.22-61.0/interproscan.sh -i   /home/tb44227/nobackup/my_interproscan/interproscan-5.22-61.0/test_all_appl.fasta -b   /home/tb44227/nobackup/my_interproscan/interproscan-5.22-61.0/test_all_appl.result

######################

08/03/2017 17:04:08:903 Welcome to InterProScan-5.22-61.0
08/03/2017 17:04:16:447 Running InterProScan v5 in STANDALONE mode... on Linux
08/03/2017 17:04:35:348 Loading file /home/tb44227/nobackup/my_interproscan/interproscan-5.22-61.0/test_all_appl.fasta
08/03/2017 17:04:35:351 Running the following analyses:
[CDD-3.14,Coils-2.2.1,Gene3D-3.5.0,Hamap-201605.11,MobiDBLite-1.0,PANTHER-11.1,Pfam-30.0,PIRSF-3.01,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-20.119,ProSiteProfiles-20.119,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.
08/03/2017 17:04:41:878 29% completed
2017-03-08 17:04:57,518 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:156] ERROR - Command line failed with exit code: 1
Command: bin/sfld/sfld_postprocess -s data/sfld/2/sfld_sites.annot -a /home/tb44227/temp/lido-bl23041_20170308_170416446_6lyw//jobSFLD/000000000001_000000000003.raw.align.out -O /home/tb44227/temp/lido-bl23041_20170308_170416446_6lyw//jobSFLD/000000000001_000000000003.raw.out -d /home/tb44227/temp/lido-bl23041_20170308_170416446_6lyw//jobSFLD/000000000001_000000000003.raw.domtblout.out -o /home/tb44227/temp/lido-bl23041_20170308_170416446_6lyw//jobSFLD/000000000001_000000000003_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)**

2017-03-08 17:04:57,523 [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: 1
Command: bin/sfld/sfld_postprocess -s data/sfld/2/sfld_sites.annot -a /home/tb44227/temp/lido-bl23041_20170308_170416446_6lyw//jobSFLD/000000000001_000000000003.raw.align.out -O /home/tb44227/temp/lido-bl23041_20170308_170416446_6lyw//jobSFLD/000000000001_000000000003.raw.out -d /home/tb44227/temp/lido-bl23041_20170308_170416446_6lyw//jobSFLD/000000000001_000000000003.raw.domtblout.out -o /home/tb44227/temp/lido-bl23041_20170308_170416446_6lyw//jobSFLD/000000000001_000000000003_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:158)
        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$1.proceedWithInvocation(TransactionInterceptor.java:99)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
        at com.sun.proxy.$Proxy100.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)
2017-03-08 17:04:57,524 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepSFLDPostProcessorBinaryRun
2017-03-08 17:04:57,644 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 3 : Run sfld postprocessing binary for selected proteins for proteins 1 to 3 has failed irretrievably.  Available StackTraces follow.
2017-03-08 17:04:57,646 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2017-03-08 17:04:57,646 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:166] 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:73)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:336)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
mifraser commented 7 years ago

Hi,

This is a general error that is not specific to PBS/Torque.

The binaries that we distribute with InterProScan should work on most linux systems. However, in some cases they may not work on a particular system. If this happens you need to compile the binary on your own system in order for it to work.

In this case you'll need the instructions for recompiling sfld_preprocess/sfld_postprocess binaries documented at the bottom of https://github.com/ebi-pf-team/interproscan/wiki/CompilingBinaries

Hope that helps?

Matt