Interproscan nucleotide sequence scanning

Question

[waqasnayab]

Dear All,

I have fasta file of nucleotide sequences (~ 30,000). My command is:

./interproscan.sh -t n -i /home/kamran/Working/waqas/trinityrnaseq_r20140717/pak.fasta

The error is:

10/11/2015 12:41:13:264 Welcome to InterProScan-5.15-54.0
10/11/2015 12:41:33:904 Running InterProScan v5 in STANDALONE mode...
2015-11-10 12:41:43,938
[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: IOException thrown when attempting to run binary
        at
uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:140)
        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:57)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        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:745)
Caused by: java.io.IOException: Cannot run program
"/home/kamran/Desktop/interproscan-5.15-54.0/bin/nucleotide/": error=13, Permission
denied
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1047)
        at
uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:144)
        at
uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:138)
        ... 22 more
Caused by: java.io.IOException: error=13, Permission denied
        at java.lang.UNIXProcess.forkAndExec(Native Method)
        at java.lang.UNIXProcess.<init>(UNIXProcess.java:187)
        at java.lang.ProcessImpl.start(ProcessImpl.java:130)
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1028)
        ... 24 more
Loading file /home/kamran/Working/waqas/trinityrnaseq_r20140717/pak.fasta
10/11/2015 12:41:44:053 Running the following analyses:
[jobHAMAP,jobProDom-2006.1,jobPIRSF-3.01,jobPfam,jobSMART-6.2,jobGene3d,jobCoils,jobPrositeProfiles,jobTIGRFAM-15.0,jobPRINTS-42.0,jobSuperFamily-1.75,jobPrositePatterns]
2015-11-10 12:41:44,487
[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.
2015-11-10 12:41:44,491
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL -
The JVM will now exit with a non-zero exit status.
2015-11-10 12:41:44,511
[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:290)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check
the log file for details

My system details are:

Linux kamran-OptiPlex-755 3.13.0-46-generic #77-Ubuntu SMP Mon Mar 2 18:23:39 UTC
2015 x86_64 x86_64 x86_64 GNU/Linux

java version "1.7.0_85"
OpenJDK Runtime Environment (IcedTea 2.6.1) (7u85-2.6.1-5ubuntu0.14.04.1)
OpenJDK 64-Bit Server VM (build 24.85-b03, mixed mode)

This is perl 5, version 18, subversion 2 (v5.18.2) built for
x86_64-linux-gnu-thread-multi
(with 41 registered patches, see perl -V for more detail)

Copyright 1987-2013, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the

Python 2.7.6

Kindly help me in this regard. Looking forward for you kind response.

Regards,
Waqasuddin Khan.

Answer 1

[Jon]

Looks like a permissions problem? Have you looked at the documentation for running nucleotide sequences, specifically translations, as it seems in some circumstances you may need to modify the interproscan.sh file for getorf from EMBOSS. https://github.com/ebi-pf-team/interproscan/wiki/ScanNucleicAcidSeqs

[waqasnayab]

i solved this by:

First check if you have the correct paths in the interproscan.properties 
file. The getorf path should look like
binary.getorf.path=bin/nucleotide/getorf

and then test with the test sequences.
./interproscan.sh -t n -i test_nt_seqs.fasta

Other possible solutions:

For nucleotide sequence input like yours (~ 30,000), we generally advise 
you either
   1) chunk the input or
   2) first 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.

Interproscan team told me this