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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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libjellyfish-2.0.so.2: cannot open shared object file error #25

Open npbhavya opened 10 years ago

npbhavya commented 10 years ago

So i have been trying to use jellyfish to count kmers of size 4, so i have been using the following command jellyfish count -s 400000 -t 32 -C -m 4 -o 4mers.txt But i keep getting the following error libjellyfish-2.0.so.2: cannot open shared object file error. Can you help me understand this error and how to get past it

gmarcais commented 10 years ago

On Tue, Oct 28, 2014 at 5:23 PM, npbhavya notifications@github.com wrote:

So i have been trying to use jellyfish to count kmers of size 4, so i have been using the following command jellyfish count -s 400000 -t 32 -C -m 4 -o 4mers.txt But i keep getting the following error libjellyfish-2.0.so.2: cannot open shared object file error. Can you help me understand this error and how to get past it

— Reply to this email directly or view it on GitHub https://github.com/gmarcais/Jellyfish/issues/25.

Most likely you moved the binary instead of installing it. Suppose you want to install jellyfish in your home directory, configure and install this way:

$ ./configure --prefix=$HOME $ make $ make install

Now jellyfish should be in $HOME/bin and it will find the share library without problem.

Guillaume.

npbhavya commented 10 years ago

Hey I did try installing it again using the commands you have given me. This time i have installed the jellyfish-1.1.11, however the same error seems to occur. Once again ellyfish: error while loading shared libraries: libjellyfish-2.0.so.2: cannot open shared object file: No such file or directory

Since i am using the jellyfish-1.1.11 but the error suggests the libjellyfish-2.0.so.2 file cannot be shared. Do you know where i am going wrong. Thank You

npbhavya commented 10 years ago

Hey thanks got it, used this method to get it working /jellyfish-1.1.11$ ps PID TTY TIME CMD 3463 pts/2 00:00:00 bash 12863 pts/2 00:00:00 ps /jellyfish-1.1.11$ export LD_LIBRARY_PATH="/usr/local/lib" So i have the output files but, they are in the 4mer.text_0 file which i cant open. Could you tell me if that is the correct output format and if it is, what application should i use to open these files

pminx commented 6 years ago

Thanks. export LD_LIBRARY_PATH="/usr/local/lib" then 'jellyfish' worked for me as well. No more libjellyfish-2.0.so.2 error. (v2.2.7) Pat

gmarcais commented 6 years ago

I do not think that the proper way to go. Setting up LD_LIBRARY_PATH is last resort hack in my opinion. If you installed in /usr/local/lib, run as root ldconfig and it should work.