can't find the shared object file (./sel392v2.so)

[wanjinhu]

dear @dcouvin

when i try to run CRISPRCasFinder, but it showed the erro like below:
"The shared object file (./sel392v2.so) must be available in your current directory"

i want to give a path of the shared object file (./sel392v2.so) , but i can't find that file in the whole folder.

can you help out this problem?

thanks a lot

[dcouvin]

Dear @wanjinhu
Thank you for your message.
Before using the tool, you should run the bash installer file (installer_UBUNTU.sh if you are on Linux Ubuntu) to install the program.
Normally, when the installation is complete, the shared object file (./sel392v2.so) must be present in the current directory. It is generated as follows during the installation:
gcc -Wall -Werror -fPIC -O3 -shared vmatch-2.3.0-${distribution}-64bit/SELECT/sel392.c -o $CURDIR/sel392v2.so
Please note that you can also use the dedicated singularity image (downloadable at: https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=CrisprCasFinder.simg) as follows:
singularity exec -B $PWD CrisprCasFinder.simg perl /usr/local/CRISPRCasFinder/CRISPRCasFinder.pl -so /usr/local/CRISPRCasFinder/sel392v2.so -cf /usr/local/CRISPRCasFinder/CasFinder-2.0.3 -drpt /usr/local/CRISPRCasFinder/supplementary_files/repeatDirection.tsv -rpts /usr/local/CRISPRCasFinder/supplementary_files/Repeat_List.csv -cas -def G -out RESULTfolder -in sequence.fasta

Hope this will help!
Best regards

[wanjinhu]

dear @dcouvin
thanks for your response , i solved my problem. I find sel392.c file in Vmatch path, and set -so parameter.

here are another problem when i run CRISPRCasFinder with test data:
macsyfinder: error: unrecognized arguments: all
No Cas results
Nb of Cas in this sequence = 0

i alread installed the software macsyfinder, can you help me out this problem?

thanks again

[dcouvin]

Dear @wanjinhu ,
Thank you for your message. Maybe you are using another version of macsyfinder. Please install Singularity and try the command in the previous message with your fasta file.
If you are using Linux Ubuntu, you can install singularity as:
sudo apt-get install -y singularity-container
You can find documentation here: https://sylabs.io/guides/3.0/user-guide/installation.html
Best regards