java.lang.IllegalStateException: Attempting to create a Gene3D match that has no alignment data.

Google Groups | Unknown author | 5 years ago
  1. 0

    RC1 - Execution thrown when attempting to executeInTransaction the StepExecution. All database acti

    Google Groups | 5 years ago | Unknown author
    java.lang.IllegalStateException: Attempting to create a Gene3D match that has no alignment data.
  2. 0

    RC6 - Standalone run large batch of proteins generates errors

    Google Groups | 4 years ago | Unknown author
    java.lang.IllegalStateException: Command line failed with exit code: 134 Command: bin/hmmer/hmmer3/hmmsearch -Z 4023 --cut_tc data/tigrfam/13.0/TIGRFAMs_13.0_HMM.LIB temp/node16.cluster2.keygene.local_20130424_092824227_69cx/jobTIGRFAM-13.0/000000005601_000000005700.fasta Error output from binary: Fatal exception (source file esl_threads.c, line 129): thread creation failed
  3. 0

    Used pfscan-binary is linked to outdated library libg2c.so.0

    Google Groups | 5 years ago | Josef Schmitz
    java.lang.IllegalStateException: Command line failed with exit code: 141 Command: bin/ps_scan.pl -d data/prosite/20.66/prosite.dat --pfscan bin/ pfscan -s -m -o gff temp/dell- node-4.mpipz.mpg.de_20120515_120040054_154q/jobPrositeProfiles/ 000000000001_000000000001.fasta Error output from binary: bin/pfscan: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory
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  5. 0

    pantherScore.pl error

    GitHub | 6 months ago | dlepp
    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:
  6. 0

    IllegalStateException: Afterburner internal error: BeanDeserializer for [simple type, class Envelope] has no properties that match expected ordering -- can not create optimized deserializer

    GitHub | 2 years ago | steveme
    java.lang.IllegalStateException: Afterburner internal error: BeanDeserializer for [simple type, class Envelope] has no properties that match expected ordering -- can not create optimized deserializer

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    Root Cause Analysis

    1. java.lang.IllegalStateException

      Attempting to create a Gene3D match that has no alignment data.

      at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Gene3DHmmer3ParserSupport.createMatch()
    2. uk.ac.ebi
      StepExecutionTransactionImpl.executeInTransaction
      1. uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Gene3DHmmer3ParserSupport.createMatch(Gene3DHmmer3ParserSupport.java:32)
      2. uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Gene3DHmmer3ParserSupport.createMatch(Gene3DHmmer3ParserSupport.java:16)
      3. uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.AbstractHmmer3ParserSupport.addMatch(AbstractHmmer3ParserSupport.java:85)
      4. uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Gene3DHmmer3ParserSupport.addMatch(Gene3DHmmer3ParserSupport.java:16)
      5. uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3SearchMatchParser.parse(Hmmer3SearchMatchParser.java:183)
      6. uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:66)
      7. uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:82)
      7 frames
    3. Java RT
      Method.invoke
      1. sun.reflect.GeneratedMethodAccessor62.invoke(Unknown Source)
      2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
      3. java.lang.reflect.Method.invoke(Method.java:597)
      3 frames
    4. Spring AOP
      ReflectiveMethodInvocation.proceed
      1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:318)
      2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
      3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
      3 frames
    5. Spring Tx
      TransactionInterceptor.invoke
      1. org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
      1 frame
    6. Spring AOP
      JdkDynamicAopProxy.invoke
      1. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
      2. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
      2 frames
    7. Unknown
      $Proxy90.executeInTransaction
      1. $Proxy90.executeInTransaction(Unknown Source)
      1 frame
    8. uk.ac.ebi
      AmqInterProScanWorker.onMessage
      1. uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanWorker.onMessage(AmqInterProScanWorker.java:96)
      1 frame
    9. Spring Framework
      DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run
      1. org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:561)
      2. org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:499)
      3. org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:467)
      4. org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:325)
      5. org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
      6. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1059)
      7. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1051)
      8. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:948)
      8 frames
    10. Java RT
      Thread.run
      1. java.lang.Thread.run(Thread.java:662)
      1 frame