Using new version of MacSyFinder on CRISPRCasFinder.pl

[mhyleung]

Dear all

I ran CRISPRCasFinder on some contig sequences that I know contains Cas proteins of various subtypes with the options -cas -def G, but am still getting no Cas type information in my [output]/TSV/CRISPR-Cas_summary.tsv. I just want to make sure I am not missing any optional flags in the command:

perl CRISPRCasFinder.pl --version
version 4.2.20

perl CRISPRCasFinder.pl -log \
-out [output_dir] \
-so [/path/to]/sel392v2.so \
-cas -cf CasFinder-2.0.3 -getSummaryCasfinder -def S \
./input.fasta

With this command I am able to detect a large number of CRISPRs, but no indication of any Cas proteins.

Thanks

Marcus

[mhyleung]

So it turns out that I do not have MacSyFinder installed properly. I went back to install the newest version of MacSyFinder, but I believe some of the macsyfinder options in the CRISPRCasFinder.pl script (-d and -p) are outdated, and it is giving me an error

macsyfinder: error: unrecognized arguments: -d and -p

Instead of downloading and installing the older version of MacSyFinder (I had been encountering problems getting the old version 1.0.5 to set up following https://github.com/gem-pasteur/macsyfinder/issues/11), can we change the bit of the CRISPRCasFinder.pl script where macsyfinder is called, precisely remove/updating the -d and -p options? Comparing the option menus for the two MacSyFinder versions (1.0.5 and 2.0rc6), I can't see to figure out what the -d and -p from 1.0.5 is replaced by in the new version

From the CRISPRCasFinder.pl script:

 if ( (-d $casfinder) and (-d $casdb) and (-d $profiles) ) {
          #if($default){
            $macsyfinder = "macsyfinder -w $cpuMacSyFinder -d $casdb -p $profiles --sequence-db $proteome all --out-dir $casDir ";
            #$macsyfinder = "macsyfinder -w $cpuMacSyFinder -d $casdb -p $profiles --sequence-db $proteome all --out-dir $casDir ";
            $macsyfinder .= $addToMacSy; # --multi-loci General-CAS
          #}
          #else{
            #$macsyfinder = "macsyfinder -w $cpuMacSyFinder -d $casdb -p $profiles --sequence-db $proteome all --out-dir $casDir "; #--multi-loci 'CAS*' --min-genes-required 'CAS*' 1";
          #}
    }
    #elsif($default){
        #$macsyfinder = "macsyfinder -w $cpuMacSyFinder --sequence-db $proteome all --out-dir $casDir"; #MacSyfinder without new definitions/profiles
    #}
    else{
        $macsyfinder = "macsyfinder -w $cpuMacSyFinder --sequence-db $proteome all --out-dir $casDir"; #MacSyfinder without new definitions/profiles

Thank you

Marcus

[dcouvin]

Hi Marcus, Thank you for your message. We will try to update with the new version of MacSyFinder as soon as possible... Best, David

[mhyleung]

Thank you very much David. Greatly appreciated!

[mhyleung]

Dear all. Was wondering if there is an update on the status of this thread? Thanks

Marcus

[Nazmul1991]

Hi all, is there any update? I have been facing the same problem. Please let me know if anyone figured it out already.

[dcouvin]

Dear All, thank you for your messages. Please be patient. A new version is coming soon. Best, David

[dcouvin]

Dear All, please note that CRISPRCasFinder vers 4.3.2 is now available and it includes the new version of MacSyFinder. Please see the new installation through the conda environment (https://github.com/dcouvin/CRISPRCasFinder#condabiocondamamba). Best, David