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[interhelp #47530] Problems with libdg.so.2 #68

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Try a nucleic sequence
2. I've already searched for "libdg.so" and that's what I get:
/usr/lib/i386-linux-gnu/libdg.so.2
/usr/lib/x86_64-linux-gnu/libdg.so.2

What version of the product are you using? On what operating system?
Linux Mint

Please provide any additional information below.
bruna@bruna-POS-ECIG41BS ~/Downloads/interproscan-5.13-52.0 $ ./interproscan.sh 
-t n -i ../pequeno.fasta -o ../saida_teste -f XML
15/07/2015 14:28:22:988 Welcome to InterProScan-5.13-52.0
15/07/2015 14:28:45:857 Running InterProScan v5 in STANDALONE mode...
2015-07-15 14:28:55,009 
[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_20150715_14
2845856_l1jo//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50 
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: libgd.so.2: cannot 
open shared object file: No such file or directory

2015-07-15 14:28:55,013 
[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_20150715_14
2845856_l1jo//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50 
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: libgd.so.2: 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
15/07/2015 14:28:55:051 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]
2015-07-15 14:28:55,165 
[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.
2015-07-15 14:28:55,215 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.
2015-07-15 14:28:55,215 
[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

Original issue reported on code.google.com by bzamit...@gmail.com on 15 Jul 2015 at 5:33

GoogleCodeExporter commented 9 years ago

Original comment by Mr.Matth...@gmail.com on 21 Jul 2015 at 1:10

GoogleCodeExporter commented 9 years ago 
Hi,

We have detailed the steps to go through if you encounter this problem at 
http://code.google.com/p/interproscan/wiki/CompilingBinaries#EMBOSS_getorf

Let us know if this helps.
Gift

Original comment by nuka....@gmail.com on 27 Jul 2015 at 9:04

GoogleCodeExporter commented 9 years ago 
Issue 66 has been merged into this issue.

Original comment by Mr.Matth...@gmail.com on 27 Jul 2015 at 1:38

GoogleCodeExporter commented 9 years ago 
First of all, thanks for your answer.
But no, it won't help. I've already tried doing all that is explained on 
https://code.google.com/p/interproscan/wiki/CompilingBinaries#EMBOSS_getorf.
Any other sugestions?

Regards,
Bruna

Original comment by bzamit...@gmail.com on 28 Jul 2015 at 3:09

GoogleCodeExporter commented 9 years ago 
Hi Bruna,

What is the output when you run the following command in the interproscan 
installation directory?
/usr/bin/getorf -sf pearson -sequence test_nt_seqs.fasta -outseq nt-orfs.fasta 
-minsize 50

Check what you get in nt-orfs.fasta and let me know. Then we can see what else 
can be done.

You may also use an external program to translate your input. My colleague 
recommends  
emboss-transeq (http://emboss.open-bio.org/rel/rel6/apps/transeq.html)  
from emboss. If you use transeq use the -clean option to change STOP 
codon positions from '*' to 'X' as Interproscan doesnt accept sequences 
with '*' character.

Regards,
Gift

Original comment by nuka....@gmail.com on 28 Jul 2015 at 3:25

GoogleCodeExporter commented 9 years ago 
Hi,
Thanks for your reply.

The message which I get when I run the following command in the interproscan 
installation directory
/usr/bin/getorf -sf pearson -sequence test_nt_seqs.fasta -outseq nt-orfs.fasta 
-minsize 50, is "Find and extract open reading frames (ORFs)".

I do not get any output file. Am I doing something wrong? I've entered 
"bruna@bruna-POS-ECIG41BS ~/Downloads/interproscan-5.13-52.0 $ /usr/bin/getorf 
-sf pearson -sequence test_nt_seqs.fasta -outseq nt-orfs.fasta -minsize 50"

Still I am improving my knowleadge in Linux and bioinformatics.

Waiting for any help you can provide to me, thanks in advance.

Best regards,
Bruna

Original comment by bzamit...@gmail.com on 3 Aug 2015 at 11:43

Attachments:

GoogleCodeExporter commented 9 years ago 
Hi Bruna,
Can you do the following in the interproscan installation directory?
 ls -l nt-orfs.fasta

and 
 cat nt-orfs.fasta

Regards,
Gift

Original comment by nuka....@gmail.com on 3 Aug 2015 at 11:55