GoogleCodeExporter
commented
8 years ago Original comment by Mr.Matth...@gmail.com on 30 Jun 2015 at 2:10
- Changed title: [interhelp #46031] Problems
Open GoogleCodeExporter opened 8 years ago
GoogleCodeExporter
commented
8 years ago Original comment by Mr.Matth...@gmail.com on 30 Jun 2015 at 2:10
GoogleCodeExporter
commented
8 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
8 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
GoogleCodeExporter
commented
8 years ago Looks as if you might be missing some development files. If so you'll need to
install these (for which you'll need superuser access to install system wide).
The ubuntu command for this might be
sudo apt-get install libx11-dev
though I stress that's a guess. I can't tell without more information.Original comment by s...@ebi.ac.uk on 27 Jul 2015 at 2:03
GoogleCodeExporter
commented
8 years ago Hi:
In my case (ubuntu-12.04.5 and interproscan-5.14-53.0) the problem (error "127"
was the getorf version that comes with interproscan package, but I had my own
getorf on the system (because I installed emboss [sudo apt-get install emboss])
If you have emboss, use this command to locate the local getorf path:
>whereis getorf
(in my case /usr/bin/getorf)
Then, go the interproscan home (where you unzipped/installed the program) and
enter to this internal directory:
>cd bin/nucleotide
and move the old inteproscan getorf to getorf.bak
>mv getorf getorf.bak
Finally, create a symbolic link to your "system" getorf
>ln -s /usr/bin/getorf .
After this, the program run without the "error 127" problem
good luck!Original comment by jomal...@gmail.com on 18 Aug 2015 at 8:34
GoogleCodeExporter
commented
8 years ago Hi:
In my case (ubuntu-12.04.5 and interproscan-5.14-53.0) the problem (error "127"
was the getorf version that comes with interproscan package, but I had my own
getorf on the system (because I installed emboss [sudo apt-get install emboss])
If you have emboss, use this command to locate the local getorf path:
>whereis getorf
(in my case /usr/bin/getorf)
Then, go the interproscan home (where you unzipped/installed the program) and
enter to this internal directory:
>cd bin/nucleotide
and move the old inteproscan getorf to getorf.bak
>mv getorf getorf.bak
Finally, create a symbolic link to your "system" getorf
>ln -s /usr/bin/getorf .
After this, the program run without the "error 127" problem
good luck!Original comment by jomal...@gmail.com on 18 Aug 2015 at 8:34
GoogleCodeExporter
commented
8 years ago ...or just change the path to the local getorf in the file
"interproscan.properties".
binary.getorf.path=
CheersOriginal comment by jomal...@gmail.com on 18 Aug 2015 at 8:42
Original issue reported on code.google.com by
bzamit...@gmail.comon 28 Jun 2015 at 1:12