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itsmeludo / PhylOligo

Bioinformatics / Explore oligonucleotide composition similarity between assembly contigs or scaffolds to detect contaminant DNA.
GNU General Public License v3.0
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error while loading shared libraries: libimf.so: cannot open shared object file: No suc h file or directory #6

Closed U201412486 closed 5 years ago

U201412486 commented 6 years ago

Hi, I have a question and need your help. I ran the program like this below. phyloligo.py -c 8 -i $assembly -k 4 -d JSD --method joblib -o JSD_4.mat It produced the report like this below. infoseq: error while loading shared libraries: libimf.so: cannot open shared object file: No suc h file or directory Error in system(paste("infoseq -auto -nocolumns -only -noheading -length ", : error in running command Execution halted Any advice? Looking forwarding to your reply.

itsmeludo commented 6 years ago

Hi, Thanks for your message, It seems that emboss has to be tested in the command line shell and maybe reinstalled. that would be my first guess.

The libimf seems not linked to phyloligo but rather a linux mishap, try addind he right path to LD_LIBRARY_PATH, according to your distribution: https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/268431

May i ask you which operating system and version you are using?

Best,

U201412486 commented 6 years ago

Hi, I am using CentOS release 6.6.And I had the LD_LIBRARY_PATH environment variable set to include the correct compiler library according to your advice,it did not work.And It reported the same error. export PATH=/public/software/compiler/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64/lib imf.so:$PATH Any advice?

itsmeludo commented 6 years ago

Hi, Thanks for your message, It seems that emboss has to be reinstalled, that would be my first guess.

Le sam. 28 avr. 2018 17:15, U201412486 notifications@github.com a écrit :

Hi, I have a question and need your help. I ran the program like this below. phyloligo.py -c 8 -i $assembly -k 4 -d JSD --method joblib -o JSD_4.mat It produced the report like this below. infoseq: error while loading shared libraries: libimf.so: cannot open shared object file: No suc h file or directory Error in system(paste("infoseq -auto -nocolumns -only -noheading -length ", : error in running command Execution halted Any advice? Looking forwarding to your reply.

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