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libssl.so.10 missing #11

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. try to search a nucleotide fasta
2. export to GFF3
3.

What is the expected output? What do you see instead?
The program gives me an error

What version of the product are you using? On what operating system?
INterproscan rc1 or 2 under centos

Please provide any additional information below.
with protein sequences it runs smoothly

Original issue reported on code.google.com by brandao.marcelo on 17 Jul 2012 at 6:02

GoogleCodeExporter commented 9 years ago 
I had a problem in both RC1 and RC2 with nucleotides. In my case it seemed to 
an unnecessary dependency on libmysqlclient.so.16 in the getorf binary 
(bin/nucleotide).

However, I found this program existed in my ubuntu 12 install anyway 
(/usr/lib/emboss/getorf) - if you don't have it, you made need to get it and 
compile if necessary.

Original comment by simon.po...@eaglegenomics.com on 8 Aug 2012 at 1:27

GoogleCodeExporter commented 9 years ago 
When I run 
./interproscan.sh -t n -i 
'/media/C/Cecile/contigs_abundances/GTrinity_1P.fasta' 
==>
Running InterProScan v5 in STANDALONE mode...
2013-02-20 13:18:56,746 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:124] 
ERROR - Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sequence 
/media/C/Cecile/contigs_abundances/GTrinity_1P.fasta -outseq 
temp/christen-z800_20130220_131856430_bshg/jobLoadNucleicAcidSequence/orfs.fasta
 -minsize 50 
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: libcrypto.so.10: 
cannot open shared object file: No such file or directory

However:
/bin/nucleotide/getorf -sequence 
/media/C/Cecile/contigs_abundances/GTrinity_1P.fasta -outseq 
temp/christen-z800_20130220_131344228_i5oj/jobLoadNucleicAcidSequence/orfs.fasta
 -minsize 50

runs fine

thus I tried
sudo ln -s /usr/lib/libcrypto.so.0.9.8 /usr/lib/libcrypto.so.10

this time, an other error

lcome to InterProScan 5RC4
Running the following analyses:
[jobPIRSF-2.82, jobPrositeProfiles-20.83, jobGene3d-3.3.0, jobProDom-2006.1, 
jobSMART-6.2, jobHAMAP-201207.04, jobPfamA-26.0, jobTIGRFAM-12.0, 
jobPRINTS-42.0, jobPrositePatterns-20.83, jobSuperFamily-1.75, jobCoils-2.2]
Running InterProScan v5 in STANDALONE mode...
2013-02-20 13:37:13,356 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:124] 
ERROR - Command line failed with exit code: 1
Command: bin/nucleotide/getorf -sequence 
/media/C/Cecile/contigs_abundances/GTrinity_1P.fasta -outseq 
temp/christen-z800_20130220_133713209_do5k/jobLoadNucleicAcidSequence/orfs.fasta
 -minsize 50 
Error output from binary:
Error: File usr/bin/getorf.acd line 0: ACD file not opened

2013-02-20 13:37:13,359 
[uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener:106] 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: bin/nucleotide/getorf -sequence 
/media/C/Cecile/contigs_abundances/GTrinity_1P.fasta -outseq 
temp/christen-z800_20130220_133713209_do5k/jobLoadNucleicAcidSequence/orfs.fasta
 -minsize 50 
Error output from binary:
Error: File usr/bin/getorf.acd line 0: ACD file not opened

(Ubuntu 10.04)
christen@unice.fr

Original comment by christen...@gmail.com on 20 Feb 2013 at 12:40

GoogleCodeExporter commented 9 years ago 
Dear Interproscan users,

It looks like you will need to compile getorf on your system in order to get it 
to work - this means you will need to compile the whole EMBOSS package. The 
instructions for downloading and installing the EMBOSS package can be found at:
http://emboss.sourceforge.net/download/#Stable/

You should only meed to do the compilations step, it is not necessary to 
configure your system for EMBOSS.

After compilation, update this line in the interproscan.properties file to 
point to the getorf binary:
binary.getorf.path=

Kid regards,
Craig

Original comment by newboycr...@gmail.com on 27 Mar 2013 at 2:28

GoogleCodeExporter commented 9 years ago 
On Debian based systems (e.g. Ubuntu or Linux Mint) EMBOSS is available as a 
package (see http://packages.debian.org/sid/emboss) produced by Debain Med 
(http://www.debian.org/devel/debian-med/) and can be installed with:

$ sudo apt-get install emboss

Or using your favourite package manager.

FWIW Debian Med provide a meta-package: med-bio, which can be used to install a 
selection of commonly used microbiology, molecular biology and bioinformatics 
applications (see http://debian-med.alioth.debian.org/tasks/bio), including 
EMBOSS.

Original comment by hpmcw...@gmail.com on 19 Sep 2013 at 2:47

GoogleCodeExporter commented 9 years ago 
BTW this can be avoided by compiling EMBOSS with appropriate 'configure' 
options (see configure --help for a list of the available options). For example:

./configure --disable-shared --without-x --without-java --without-hpdf 
--without-pngdriver --without-mysql --without-postgresql

Note: additional options may be required with other versions of EMBOSS, this 
example uses EMBOSS 6.3.1.

To disable, and thus remove dependencies on, MySQL, Postgres, Axis 2, X11, PDF 
support (libhpdf) and PNG support (libpng), and thus reduce the dependencies 
from:

$ ldd interproscan-5-RC7/bin/nucleotide/getorf
    linux-vdso.so.1 =>  (0x00007fff033ff000)
    libmysqlclient.so.16 => /usr/lib64/mysql/libmysqlclient.so.16 (0x0000003bf0600000)
    libcrypt.so.1 => /lib64/libcrypt.so.1 (0x0000003492000000)
    libnsl.so.1 => /lib64/libnsl.so.1 (0x00000034e7a00000)
    libssl.so.10 => /usr/lib64/libssl.so.10 (0x00000034df600000)
    libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00000034dd200000)
    libpq.so.5 => /usr/lib64/libpq.so.5 (0x0000003bf0e00000)
    libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000034db200000)
    libgd.so.2 => /usr/lib64/libgd.so.2 (0x0000003bf0a00000)
    libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00000034dee00000)
    libz.so.1 => /lib64/libz.so.1 (0x00000034d9200000)
    libm.so.6 => /lib64/libm.so.6 (0x00000034d8200000)
    libc.so.6 => /lib64/libc.so.6 (0x00000034d8600000)
    libfreebl3.so => /lib64/libfreebl3.so (0x0000003491800000)
    libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00000034de600000)
    libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00000034de200000)
    libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00000034dc600000)
    libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00000034dca00000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00000034d8a00000)
    libldap_r-2.4.so.2 => /lib64/libldap_r-2.4.so.2 (0x00007f8b99cbf000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00000034d8e00000)
    libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000034dba00000)
    libXpm.so.4 => /usr/lib64/libXpm.so.4 (0x000000348dc00000)
    libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00000034eb000000)
    libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x00000034dfa00000)
    libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00000034df200000)
    /lib64/ld-linux-x86-64.so.2 (0x00000034d7e00000)
    libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00000034dde00000)
    libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00000034dc200000)
    libresolv.so.2 => /lib64/libresolv.so.2 (0x00000034da200000)
    liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x00000034eb800000)
    libssl3.so => /usr/lib64/libssl3.so (0x00000034eac00000)
    libsmime3.so => /usr/lib64/libsmime3.so (0x00000034ea800000)
    libnss3.so => /usr/lib64/libnss3.so (0x00000034ea400000)
    libnssutil3.so => /usr/lib64/libnssutil3.so (0x00000034e9c00000)
    libplds4.so => /lib64/libplds4.so (0x00000034ea000000)
    libplc4.so => /lib64/libplc4.so (0x00000034e9400000)
    libnspr4.so => /lib64/libnspr4.so (0x00000034e9800000)
    libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x0000003490000000)
    libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000034db600000)
    libexpat.so.1 => /lib64/libexpat.so.1 (0x00000034dea00000)
    libselinux.so.1 => /lib64/libselinux.so.1 (0x00000034d9a00000)

to a more portable:

$ ldd emboss/getorf
    linux-vdso.so.1 =>  (0x00007fff88bff000)
    libm.so.6 => /lib64/libm.so.6 (0x00000034d8200000)
    libc.so.6 => /lib64/libc.so.6 (0x00000034d8600000)
    /lib64/ld-linux-x86-64.so.2 (0x00000034d7e00000)

Original comment by hpmcw...@gmail.com on 20 Sep 2013 at 8:40

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 20 Sep 2013 at 9:37

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
Also documented now on 
https://code.google.com/p/interproscan/wiki/CompilingBinaries#EMBOSS_getorf.

Original comment by Maxim.Sc...@gmail.com on 20 Sep 2013 at 9:57