Open mhyleung opened 2 years ago
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version of MacSyFinder, but I believe some of the macsyfinder options in the CRISPRCasFinder.pl script (-d and -p) are outdated, and it is giving me an error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
Hi Marcus, Thank you for your message. We will try to update with the new version of MacSyFinder as soon as possible... Best, David
Thank you very much David. Greatly appreciated!
Dear all. Was wondering if there is an update on the status of this thread? Thanks
Marcus
Hi all, is there any update? I have been facing the same problem. Please let me know if anyone figured it out already.
Dear All, thank you for your messages. Please be patient. A new version is coming soon. Best, David
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
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:
With this command I am able to detect a large number of CRISPRs, but no indication of any Cas proteins.
Thanks
Marcus