[InterProScan5] Binary problem? Problem running interproscan-5.14-53.0 for protein sequences
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Entering edit mode
3.8 years ago
1206005324 • 0

Dear all,

I have a trouble in using InterProScan.

I downloaded InterProScan5 and checked with md5sum and it worked fine.

However, when I tried with the test file, I had a problem from the first line.

Here is my command:

./interproscan.sh -i input1.txt.fa -iprlookup -goterms -format html -b ./result1.html

Here is my version:

Python 2.7.9
Linux64bit
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)

Here is my code:

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


2017-12-06 17:38:25,944 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:421] WARN - lookupUp service at http://www.ebi.ac.uk/interpro/match-lookup is accessible - code: 302,  using proxy: false
2017-12-06 17:38:26,167 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:421] WARN - lookupUp service at http://www.ebi.ac.uk/interpro/match-lookup is accessible - code: 302,  using proxy: false
2017-12-06 17:43:16,868 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2017_09/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2017_09/prosite_models /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobPrositeProfiles/000000000001_000000000214.fasta 
Error output from binary:
Segmentation fault
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2017_09/prosite_models/PS50001.prf /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobPrositeProfiles/000000000001_000000000214.fasta C=6.5 > /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobPrositeProfiles//yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop/tmpdir_000000000001_000000000214//ps426810-8.tmp at bin/prosite/ps_scan.pl line 1960.

2017-12-06 17:43:23,296 [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: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2017_09/prosite.dat -w bin/prosite/pfsearch -s -m -o gff -y data/prosite/2017_09/prosite_models /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobPrositeProfiles/000000000001_000000000214.fasta 
Error output from binary:
Segmentation fault
Could not execute bin/prosite/pfsearch -f -lxz data/prosite/2017_09/prosite_models/PS50001.prf /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobPrositeProfiles/000000000001_000000000214.fasta C=6.5 > /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobPrositeProfiles//yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop/tmpdir_000000000001_000000000214//ps426810-8.tmp at bin/prosite/ps_scan.pl line 1960.

    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.GeneratedMethodAccessor90.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)
2017-12-06 17:43:23,650 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2017-12-06 17:43:25,673 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN - StepInstance 27 is being re-run following a failure.
2017-12-06 17:48:28,493 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 137
Command: bin/hmmer/hmmer3/3.1b1/hmmscan -E 10 -Z 15438 --cpu 1 -o /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobSuperFamily-1.75/000000000001_000000000214.raw.out data/superfamily/1.75/hmmlib_1.75 /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobSuperFamily-1.75/000000000001_000000000214.fasta 

2017-12-06 17:49:46,027 [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: python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/bin/mobidb/binx /home/yz/文档/InterproScanT/newInterProScan5.27/my_interproscan/interproscan-5.27-66.0/temp/yz-iMac-Invalid-entry-length-DMI-table-is-broken-Stop_20171206_173803124_47nh//jobMobiDBLite/000000000001_000000000214.fasta 
Error output from binary:
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
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/local/lib/python2.7/multiprocessing/pool.py", line 558, in get
    raise self._value
OSError: [Errno 7] Argument list too long



ERROR: Calculation has exceeded maximum allowed complexity
Fingerprint KV14CHANNEL matches this sequence
ERROR: Calculation has exceeded maximum allowed complexity
Fingerprint ANTIFREEZEI matches this sequence

I think it's kind of a binary/compile problem but have no idea how to fix it.

It will be so kind to help me.

With regards,

yz

InterProScan5 binary protein sequences • 2.6k views
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Entering edit mode
2.9 years ago
george • 0

You probably need to recompile prosite. Check instructions here: https://github.com/ebi-pf-team/interproscan/wiki/CompilingBinaries And I believe interproscan requires Python 3.

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