[InterProScan] Binary problem?

Question

[Olajucan]

Dear all,

I have a trouble in using InterProScan.

I downloaded InterProScan5 and checked with md5sum and it worked fine.

However, when I tried with the test file, I had a problem from the first line.

Here is my code:

jung@jung-H170-HD3:~/my_interproscan/interproscan-5.25-64.0$ ./interproscan.sh -i test_proteins.fasta -f tsv

27/09/2017 12:07:47:145 Welcome to InterProScan-5.25-64.0

27/09/2017 12:07:56:250 Running InterProScan v5 in STANDALONE mode... on Linux

27/09/2017 12:08:10:306 Loading file /home/jung/my_interproscan/interproscan-5.25-64.0/test_proteins.fasta

27/09/2017 12:08:10:308 Running the following analyses:

[CDD-3.16,Coils-2.2.1,Gene3D-4.1.0,Hamap-201701.18,MobiDBLite-1.0,PANTHER-11.1,Pfam-31.0,PIRSF-3.02,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-20.132,ProSiteProfiles-20.132,SFLD-2,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0] Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally.

2017-09-27 12:08:19,017 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1

Command: python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /home/jung/my_interproscan/interproscan-5.25-64.0/bin/mobidb/binx /home/jung/my_interproscan/interproscan-5.25-64.0/temp/jung-H170-HD3_20170927_120756250_c3m5//jobMobiDBLite/000000000001_000000000006.fasta


Error output from binary: Traceback (most recent call last):   File "bin/mobidb/mobidb-lite.py", line 455, in <module>
    out = run_mobidb(binDirectory, args.threads, args.longOutput, acc, seq, args.architecture, verbose = args.verbose)   File "bin/mobidb/mobidb-lite.py", line 169, in run_mobidb
    disbinFile, flatFile = generate_files(acc, seq)   File "bin/mobidb/mobidb-lite.py", line 149, in generate_files
    f_disbin.write("1\n{0}\n{1}".format(len(seq),seq))   File "/home/jung/miniconda3/lib/python3.5/tempfile.py", line 483, in func_wrapper
    return func(*args, **kwargs)

TypeError: a bytes-like object is required, not 'str'

2017-09-27 12:08:19,023 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 1 Command: python bin/mobidb/mobidb-lite.py -a 64 -t 1 -bin /home/jung/my_interproscan/interproscan-5.25-64.0/bin/mobidb/binx /home/jung/my_interproscan/interproscan-5.25-64.0/temp/jung-H170-HD3_20170927_120756250_c3m5//jobMobiDBLite/000000000001_000000000006.fasta Error output from binary: Traceback (most recent call last):   File "bin/mobidb/mobidb-lite.py", line 455, in <module>
    out = run_mobidb(binDirectory, args.threads, args.longOutput, acc, seq, args.architecture, verbose = args.verbose)   File "bin/mobidb/mobidb-lite.py", line 169, in run_mobidb
    disbinFile, flatFile = generate_files(acc, seq)   File "bin/mobidb/mobidb-lite.py", line 149, in generate_files
    f_disbin.write("1\n{0}\n{1}".format(len(seq),seq))   File "/home/jung/miniconda3/lib/python3.5/tempfile.py", line 483, in func_wrapper
    return func(*args, **kwargs) TypeError: a bytes-like object is required, not 'str'

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
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:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy106.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:748)
2017-09-27 12:08:19,024 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepMobiDBRunBinary 2017-09-27 12:08:19,121 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:137] WARN
- StepInstance 18 is being re-run following a failure. 2017-09-27 12:08:19,217 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 127 Command: bin/blast/ncbi-blast-2.6.0+/rpsblast -query /home/jung/my_interproscan/interproscan-5.25-64.0/temp/jung-H170-HD3_20170927_120756250_c3m5//jobCDD/000000000001_000000000006.fasta
-db data/cdd/3.16/db/Cdd_NCBI -evalue 0.01 -seg no -outfmt 5  Error output from binary: bin/blast/ncbi-blast-2.6.0+/rpsblast: error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory

I think it's kind of a binary/compile problem but have no idea how to fix it.

It will be so kind to help me.

With regards,

Woo Joo

Answer 1

[Philipp Bayer]

This error usually happens between Python2 and Python3 - could you check which version your system has?

If you just run 'python' on that system it should open the Python prompt and say the version there.

My guess is that you have Python 3 as your 'default' Python, you may want to change that (for this run) back to Python2. How you do that depends on your system, for example you could do this:

In the interproscan folder there is a file called 'interproscan.properties' which contains an argument where you can overwrite the path to Python ('binary.prosite.python.path='), it may be installed on your system as 'python2' or similar.

You could also, for the duration of your run, alias python to go to python2:

alias python='python2'

or

alias python='python2.7'

depending on how your Python2 is installed. This alias will disappear once you close your terminal.

[Olajucan]

I appreciate your thoughtful comments, Philipp.

It was about PATH. First, my device's path to python was directed by miniconda, so I fixed it to python2. Second, rpsblast didn't seem to work properly, so I also changed the path to rpsblast with latest rpsblast+.

Your hint helped me to solve the problem. Thank you.

[Philipp Bayer]

Happy to hear that it worked!