GoogleCodeExporter
commented
9 years ago Original comment by Mr.Matth...@gmail.com on 30 Jun 2015 at 2:10
- Changed title: [interhelp #46031] Problems
Open GoogleCodeExporter opened 9 years ago
GoogleCodeExporter
commented
9 years ago Original comment by Mr.Matth...@gmail.com on 30 Jun 2015 at 2:10
GoogleCodeExporter
commented
9 years ago Hi,
The error would suggest the supplied coils binary does not work on your
system...
"Cannot run program "bin/coils/ncoils": java.io.IOException: error=2, No such
file or directory"
The way to fix that is as you mention, however you didn't get it working?
https://code.google.com/p/interproscan/wiki/CompilingBinaries
There are a couple of other things you could check:
1. If you compiled the new coils binary in a different location then did you
also update your interproscan.properties file to use the new location? You may
need to edit these properties (relative or absolute paths are allowed)...
binary.coils.path=bin/coils/ncoils
coils.new_coil.mat.path.2.2=data/coils/2.2/new_coil.mat
2. Does the coils binary run OK on it's own, e.g. you could try something
like...
# cd to InterProScan installation directory
./bin/coils/ncoils -c -m data/coils/2.2/new_coil.mat < test_proteins.fasta
Did that help you make any progress?
Thanks,
Matt
InterPro team
Original comment by Mr.Matth...@gmail.com on 30 Jun 2015 at 2:47
GoogleCodeExporter
commented
9 years ago Hi! I could solve this problem, thank you very much.
However, now I get another problem when I try to analyse nucleotide sequences:
bruna@bruna-POS-ECIG41BS ~/Downloads/interproscan-5.13-52.0 $
./interproscan.sh -t n -i ../pequeno.fasta -o ../saida_teste -f XML
03/07/2015 20:06:53:439 Welcome to InterProScan-5.13-52.0
03/07/2015 20:07:12:919 Running InterProScan v5 in STANDALONE mode...
2015-07-03 20:07:20,927
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:156]
ERROR - Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sf pearson -sequence
/home/bruna/Downloads/interproscan-5.13-52.0/../pequeno.fasta -outseq
/home/bruna/Downloads/interproscan-5.13-52.0/temp/bruna-POS-ECIG41BS_20150703_20
0712916_2f29//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries:
libmysqlclient.so.16: cannot open shared object file: No such file or directory
2015-07-03 20:07:20,929
[uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:192] ERROR -
Execution thrown when attempting to executeInTransaction the StepExecution.
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sf pearson -sequence
/home/bruna/Downloads/interproscan-5.13-52.0/../pequeno.fasta -outseq
/home/bruna/Downloads/interproscan-5.13-52.0/temp/bruna-POS-ECIG41BS_20150703_20
0712916_2f29//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries:
libmysqlclient.so.16: cannot open shared object file: No such file or directory
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:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy95.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:180)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1071)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1063)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:960)
at java.lang.Thread.run(Thread.java:662)
Loading file /home/bruna/Downloads/interproscan-5.13-52.0/../pequeno.fasta
03/07/2015 20:07:20:985 Running the following analyses:
[jobHAMAP,jobProDom-2006.1,jobPIRSF-3.01,jobPfamA-27.0,jobSMART-6.2,jobPrositePr
ofiles,jobTIGRFAM-15.0,jobPRINTS-42.0,jobSuperFamily-1.75,jobPrositePatterns,job
Coils-2.2,jobGene3d-3.5.0]
2015-07-03 20:07:21,084
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL
- Analysis step 4 : Run GetOrf to predict open reading frames from nucleic acid
sequence for proteins null to null has failed irretrievably. Available
StackTraces follow.
2015-07-03 20:07:21,091
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL
- The JVM will now exit with a non-zero exit status.
2015-07-03 20:07:21,091
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:107] 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:49)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:261)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster.
Check the log file for details
I have tried to compile getorf, however I receive this message when I try to
configure ("./configure"):
"X11 graphics have been selected but no X11 header files have been found.
This error usually happens on Linux/MacOSX distributions where the optional X11
development files have not been installed. On Linux RPM systems this package is
usually called something like xorg-x11-proto-devel whereas on Debian/Ubuntu it
may be called x-dev. On MacOSX installation DVDs the X11 files can usually be
found as an explicitly named optional installation."
What should I do?
Thank you very much.
Original comment by bzamit...@gmail.com on 3 Jul 2015 at 11:10
Original issue reported on code.google.com by
bzamit...@gmail.comon 28 Jun 2015 at 1:12