Comments (3)
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
from crisprcasfinder.
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
from crisprcasfinder.
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
from crisprcasfinder.
Related Issues (20)
- CRISPRCasFinder.pl: command not found HOT 5
- Using new version of MacSyFinder on CRISPRCasFinder.pl HOT 7
- Too many intermediate files HOT 2
- CRISPERCasFinder does not handle vmatch results with multi line sequence correctly HOT 2
- Recent Singularity container is not recognized by Singularity versions <2.6.1 HOT 1
- Installation of Date::Calc failed HOT 3
- Dependency issues using Singularity image HOT 1
- Flank sequence near contig edge has negative coordinate HOT 1
- MSG: No file or directory called HOT 1
- Error in `muscle': double free or corruption (out): 0x00007ffceb581bf0 HOT 12
- How to use CRISPRCasFinder through singularity container HOT 4
- error in using crisprcasfinder with subprocess, snakemake and Rscript HOT 10
- The result of CRISPR-Cas_summary.tsv don't have Cas Types/Subtypes HOT 1
- No CRISPR/CAS detection on fasta files with more than 100 contigs HOT 1
- CRISPRCasFinder.pl did not report any errors but produced three unknown core files HOT 2
- [FEATURE REQUEST] macsyfinder models custom dir
- Could not open output GFF in result/result2/ because No such file or directory
- json output sometimes "forgets" closing ] in "Cas": [] line
- a particular set of parameters for CCF fails to produce results for all genomes we tried HOT 3
- Error when result folder is not in source folder
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from crisprcasfinder.