Delivered pfscan-binary is linked to outdated library libg2c.so.0

[GoogleCodeExporter]

What steps will reproduce the problem?
1. On latest Debian and Ubuntu >= 10.04 running standalone Interproscan-5 with 
options: -F TSV -goterms -iprlookup -pa on a query protein produces the 
following error:

java -Xmx2g -jar interproscan-5.jar -F TSV -goterms -iprlookup -pa -i 
test_1_prot.fasta test_1_prot_iprscan_out.tsv

Welcome to InterProScan v5.
Running InterProScan v5 in STANDALONE mode...
2012-05-15 12:02:28,028 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:123] 
ERROR - Command line failed with exit code: 141
Command: bin/ps_scan.pl -d data/prosite/20.66/prosite.dat --pfscan bin/pfscan 
-s -m -o gff 
temp/dell-node-4.mpipz.mpg.de_20120515_120040054_154q/jobPrositeProfiles/0000000
00001_000000000001.fasta
Error output from binary:
bin/pfscan: error while loading shared libraries: libg2c.so.0: cannot open 
shared object file: No such file or directory

2012-05-15 12:02:28,032 
[uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanWorker:100] ERROR - 
Execution thrown when attempting to executeInTransaction the StepExecution.  
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 141
Command: bin/ps_scan.pl -d data/prosite/20.66/prosite.dat --pfscan bin/pfscan 
-s -m -o gff 
temp/dell-node-4.mpipz.mpg.de_20120515_120040054_154q/jobPrositeProfiles/0000000
00001_000000000001.fasta
Error output from binary:
bin/pfscan: error while loading shared libraries: libg2c.so.0: cannot open 
shared object file: No such file or directory

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:125)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:83)
    at sun.reflect.GeneratedMethodAccessor54.invoke(Unknown Source)
    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:309)
    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 $Proxy78.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanWorker.onMessage(AmqInterProScanWorker.java:96)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:560)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:498)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:467)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:325)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1058)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1050)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:947)
    at java.lang.Thread.run(Thread.java:662)
2012-05-15 12:02:28,266 
[uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanMaster:163] WARN - 
StepInstance 4 is being re-run following a failure.

The input fasta file looks like this:
cat test_1_prot.fasta 
>Protein 1
MEGVQVTSRVSSPKATGLWKPGYDCRLTGLWNPSMCLAAAFSACARVCQARGRISSDWMV
LNNVSSRLRRKSVAQDVQRGAFFTPAIFLAEVSDRCSCRAEIGLILGRPGKSLAVRTHLA
PIAA

The cause of this is an outdated binary of pfscan:
ldd bin/pfscan 
    linux-vdso.so.1 =>  (0x00007fff0fdff000)
    libg2c.so.0 => not found
    libm.so.6 => /lib/libm.so.6 (0x00007f3115c98000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f3115a82000)
    libc.so.6 => /lib/libc.so.6 (0x00007f3115721000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f3115f2c000)

libg2c.so.0 depends on GCC 3.4, not the current 4.x

Downloading pftools source and compiling them manually runs fine and links as 
follows:
ldd bin/pfscan
    linux-vdso.so.1 =>  (0x00007fff15090000)
    libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f1e0dc44000)
    libm.so.6 => /lib/libm.so.6 (0x00007f1e0d9c1000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f1e0d7ab000)
    libc.so.6 => /lib/libc.so.6 (0x00007f1e0d44a000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f1e0df41000)

Please rebuild the binaries of pftools using the latest libraries, e.g. on a 
current version of Debian or Ubuntu!

Kind regards!

Original issue reported on code.google.com by asis.hal...@gmail.com on 15 May 2012 at 2:42

[GoogleCodeExporter]

Same here, steps used for work-around (on ubuntu 10.04):

* if you have "libg2c.so.0 not found", you'll need GFortran for this:
   sudo apt-get install gfortran

* download PF-tools sources from 
ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/
as of 2012-08-02, latest release is 2.3.5 (released: 2011-05-25), direct link:
   wget ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/pft2.3.5.d.tar.gz

* extract and build::
   tar -xzf pft2.3.5.d.tar.gz
   cd pftools/
   make io.o pfscan pfsearch

(or, if you prefer:   make all )

* replace old version with new:
   cp ./pfscan ./pfsearch /your_interpro_dir/bin/prosite/

(overwrites existing pfscan and pfsearch)

Original comment by jules.ke...@googlemail.com on 2 Aug 2012 at 1:47

[GoogleCodeExporter]

Dear interproscan users, 

Thanks for reporting the problem, and thanks also for providing the solution. 
The binaries we include work for most users, but there are always cases where 
the binary we include does not work on someone's particular setup. The reasons 
for this aren't always obvious - internally we run Interproscan 5 on Ubuntu 
version 10.04 and up and we never encounter this particular problem.

We have now added a documentation section on how to compile binaries if you 
have a problem:
http://code.google.com/p/interproscan/wiki/CompilingBinaries

Also, instead of copying the binary to the interproscan binary directory you 
can update the following line of the interproscan.properties file to point to 
the pfscan binary:
binary.prosite.pfscan.path=

Thanks,
Craig

Original comment by newboycr...@gmail.com on 27 Mar 2013 at 2:02

[GoogleCodeExporter]

Original comment by Maxim.Sc...@gmail.com on 15 May 2014 at 9:29

• Changed state: Done
• Added labels: Subject-Binaries