Question: How to run Interproscan with old GLIBC 2.12 on centos cluster?
0
gravatar for tcf.hcdg
11 weeks ago by
tcf.hcdg40
European Union
tcf.hcdg40 wrote:

Hello

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.

My question is is there a way to do interproscan with glibc 2.12 or there is some way to fix this issue (other then upgrading glibc 2.12 to glibc 2.14 )

I am sure there must be some way. Any idea?

The script I use and the out put is as follows:

<h6>#</h6>
#!/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

# start of similation interproscan on torque
# test input file iin the interproscan directory
 /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
<h6>#</h6>
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
interproscan cluster • 199 views
ADD COMMENTlink modified 5 weeks ago by Michael Dondrup41k • written 11 weeks ago by tcf.hcdg40

Take a look at this thread. Depending on your comfort level with system tasks you may be able to follow suggestions there.

ADD REPLYlink written 11 weeks ago by genomax28k
0
gravatar for pbigbig
5 weeks ago by
pbigbig170
United States
pbigbig170 wrote:

Hi,

I suggest that you download the binary files of sfld from here: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/bin/ then replace all files in ${INTERPROSCAN5HOME}/bin/sfld/ with them, it worked for me.

ADD COMMENTlink written 5 weeks ago by pbigbig170

I guess you meant ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/bin/sfld_binary.zip

ADD REPLYlink written 5 weeks ago by Michael Dondrup41k
0
gravatar for Michael Dondrup
5 weeks ago by
Bergen, Norway
Michael Dondrup41k wrote:

We had the same problem and solved it by re-compiling the few binary that are causing problems:

Follow the instructions at https://github.com/ebi-pf-team/interproscan/wiki/CompilingBinaries

sfld_preprocess/sfld_postprocess Instructions for compiling the "sfld_preprocess" and "sfld_postprocess" binaries can be found in the src/sfld/1/README file in your extracted InterProScan 5 distribution (release 5.22-61.0 onwards).

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Michael Dondrup41k
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