java.lang.IllegalStateException: Command line failed with exit code: 134 Command: bin/hmmer/hmmer3/hmmsearch -Z 13672 --cut_ga data/pfam/26.0/Pfam-A.hmm temp/node16.cluster2.keygene.local_20130424_092824227_69cx/jobPfamA-26.0/000000034601_000000034700.fasta Error output from binary: Fatal exception (source file esl_threads.c, line 129): thread creation failed

Google Groups | Unknown author | 4 years ago
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  1. 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 13672 --cut_ga data/pfam/26.0/Pfam-A.hmm temp/node16.cluster2.keygene.local_20130424_092824227_69cx/jobPfamA-26.0/000000034601_000000034700.fasta Error output from binary: Fatal exception (source file esl_threads.c, line 129): thread creation failed
  2. 0

    pantherScore.pl error

    GitHub | 12 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:
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    Google Groups | 5 years ago | Unknown author
    java.lang.IllegalStateException: Attempting to create a Gene3D match that has no alignment data.
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  5. 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    Used pfscan-binary is linked to outdated library libg2c.so.0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
  6. 0

    GitHub comment 19#285092407

    GitHub | 3 months ago | tcfhcdg
    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)

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    Root Cause Analysis

    1. java.lang.IllegalStateException

      Command line failed with exit code: 134 Command: bin/hmmer/hmmer3/hmmsearch -Z 13672 --cut_ga data/pfam/26.0/Pfam-A.hmm temp/node16.cluster2.keygene.local_20130424_092824227_69cx/jobPfamA-26.0/000000034601_000000034700.fasta Error output from binary: Fatal exception (source file esl_threads.c, line 129): thread creation failed

      at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute()
    2. uk.ac.ebi
      StepExecutionTransactionImpl.executeInTransaction
      1. uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:126)
      2. uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:84)
      2 frames
    3. Java RT
      Method.invoke
      1. sun.reflect.GeneratedMethodAccessor66.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:319)
      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
      $Proxy94.executeInTransaction
      1. $Proxy94.executeInTransaction(Unknown Source)
      1 frame
    8. uk.ac.ebi
      WorkerListener.onMessage
      1. uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
      1 frame
    9. Spring Framework
      DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run
      1. org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
      2. org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
      3. org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
      4. org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
      5. org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
      6. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1071)
      7. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1063)
      8. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:960)
      8 frames
    10. Java RT
      Thread.run
      1. java.lang.Thread.run(Thread.java:662)
      1 frame