run command locally and submission to website generate different results.

[limin321]

Hi I installed CRISPRCasFinder in my mac and run perl ./../CRISPRCasFinder.pl -in ../../hybrid_assembly/assembly_fasta\&gfa/hybrid_fasta/Yol001.fasta -cas -cf CasFinder-2.0.2 -def G -keep locally, and it is not able to find any cas genes and crispr system. However, when I submit the same genome to websit, https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Viewing/637185279057211761. It is able to find 2 CRISPR and 1 CAS. Could anyone please help what might be the resson of my issue? your help will be greatly appreciated.

By the way, when I install CRISPRCasFinder , I have to run $ export PERL5LIB=/usr/local/libexec/crisprcas/lib/perl5:/Users/dklabuser/Scripts/cgview_comparison_tool/lib/bioperl-1.2.3:/Users/dklabuser/Scripts/cgview_comparison_tool/lib/perl_modules:

Then, run $ perl ./../CRISPRCasFinder.pl -in ../../hybrid_assembly/assembly_fasta\&gfa/hybrid_fasta/Yol001.fasta -cas -cf CasFinder-2.0.2 -def G -keep

I don't know what is wrong with this issue either. If anyone can help, that will be really great.

Best Limin

[dcouvin]

Dear Limin, Thank you for your message. This difference in results between your Mac and the website could be due to differences in versions of software dependencies:

• on the website, version v2.0.3 of CasFinder is potentially used (this version is not yet available).
• results concerning CRISPR prediction may also differ in function of the version of several dependencies such as EMBOSS.

Please try on another system like Linux if possible.

Best, David

[graceblackwell]

Hi David, I am also having a similar problem, where the website is detecting cas genes but when using the singularity image to run the analysis on the same assembly, it doesn't find any. When do you expect v2.0.3 to be released? Best, Grace

[dcouvin]

Hi Grace, Thank you for your message. Unfortunately I do not know the release date of the next version of CasFinder. I will try to ask colleagues from Pasteur Institute in Paris for more information. Maybe Bertrand (@bneron ) could provide more precision on this issue. I will let you know when I have more information. Best, David

[graceblackwell]

Hi David, Thanks that would be great! I am hoping to apply it to quite a large database of assemblies and thought it would be best to apply it with the most up to date database if possible. Best, Grace

[graceblackwell]

Hi David, Any updates? Best, Grace

[dcouvin]

Dear Grace, Good news! We have just received the new version of CasFinder. The updated CRISPRCasFinder will be available soon. Best, David

[limin321]

Thanks. everyone . I am still waiting for the new version to release. That's an exciting news.

Best, limin

On Mon, May 4, 2020, 00:48 graceblackwell notifications@github.com wrote:

Hi David, Any updates? Best, Grace

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dcouvin/CRISPRCasFinder/issues/16#issuecomment-623310936, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGHTXJGYT3THRZEDHV2BK3RPZXL3ANCNFSM4LCCWQFA .

[graceblackwell]

Great news! Will keep my eye out :) Thanks for following it up. Best, Grace

[dcouvin]

Dear Grace and Limin, The updated CasFinder has been added to the tool. Do not hesitate if you encounter a problem using the updated tool. Best, David

[limin321]

excellent. Thank you very much. That's really an exciting news. I am gonna try soon.

Great appreciation for your work. Best.

On Mon, May 25, 2020, 08:33 David Couvin notifications@github.com wrote:

Dear Grace and Limin, The updated CasFinder has been added to the tool. Do not hesitate if you encounter a problem using the updated tool. Best, David

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dcouvin/CRISPRCasFinder/issues/16#issuecomment-633624777, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGHTXKGF4EY7DIMRRK6IOLRTKFVPANCNFSM4LCCWQFA .

[dcouvin]

Thank you Limin, Please note that this version of CasFinder (2.0.3) does not correspond to the last update (Makarova et al., 2020 ; https://doi.org/10.1038/s41579-019-0299-x). This change will be performed soon thanks to colleagues from Institut Pasteur in Paris. Thank you for your patience. Best, David

[limin321]

Thank you Limin, Please note that this version of CasFinder (2.0.3) does not correspond to the last update (Makarova et al., 2020 ; https://doi.org/10.1038/s41579-019-0299-x). This change will be performed soon thanks to colleagues from Institut Pasteur in Paris. Thank you for your patience. Best, David

Hi David, Thank you so much for the notes.
I just installed the new version of CasFinder (2.0.3). The installation process goes pretty well, but when I test, I run into some issue.

dklabuser$ perl CRISPRCasFinder.pl -h

here is the output.

Sysexits.c: loadable library and perl binaries are mismatched (got handshake key 0xd800080, needed 0xdb00080)

any thoughts what might be the issue? and how to solve it?

Thanks. Best, Limin

[dcouvin]

Hi Limin, Thank you for your message. I have not seen this error before, but I will try to solve it. Which operating system are you using? this error could be caused by the fact that your libperl version and your perl version are not the same. Maybe these links could help: https://stackoverflow.com/questions/45000585/listutil-c-loadable-library-and-perl-binaries-are-mismatched-got-handshake-key ; https://askubuntu.com/questions/1175697/loadable-library-and-perl-binaries-are-mismatched ; https://github.com/pgbackrest/pgbackrest/issues/687
I hope these links will help Best, David

[limin321]

Hi Limin, Thank you for your message. I have not seen this error before, but I will try to solve it. Which operating system are you using? this error could be caused by the fact that your libperl version and your perl version are not the same. Maybe these links could help: https://stackoverflow.com/questions/45000585/listutil-c-loadable-library-and-perl-binaries-are-mismatched-got-handshake-key ; https://askubuntu.com/questions/1175697/loadable-library-and-perl-binaries-are-mismatched ; pgbackrest/pgbackrest#687 I hope these links will help Best, David

Hi Limin, Thank you for your message. I have not seen this error before, but I will try to solve it. Which operating system are you using? this error could be caused by the fact that your libperl version and your perl version are not the same. Maybe these links could help: https://stackoverflow.com/questions/45000585/listutil-c-loadable-library-and-perl-binaries-are-mismatched-got-handshake-key ; https://askubuntu.com/questions/1175697/loadable-library-and-perl-binaries-are-mismatched ; pgbackrest/pgbackrest#687 I hope these links will help Best, David

Hi David, Mine is macOS Version 10.15.2, I tried to solve the issue following the link you sent to me, but I don't think I understand that at all.
When I run the following code:

$ ls -lah /usr/lib/x86_64-linux-gnu/libperl.so

Here is the output:

ls: /usr/lib/x86_64-linux-gnu/libperl.so: No such file or directory

feels like my mac doesn't have libper.

while running the

$ perl -v

This is perl 5, version 26, subversion 2 (v5.26.2) built for darwin-thread-multi-2level

Copyright 1987-2018, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.

the perl is there. When I installed the old version of CRISPRCaseFinder, I didn't have this problem.

Thanks.

[dcouvin]

Hi Limin, Thank you for your message. Indeed, I didn't try it on MacOS. Maybe @bneron could help us on this issue. There is a specific installation for Mac users. Maybe you could try to run directly "CRISPRCasFinder.pl -h" or "CRISPRCasFinder -h" without the perl command. please look at the user manuel "CRISPRCasFinder_Viewer_manual.pdf". You could also try to copy directly the main perl script and the new CasFinder folder in your previous installation repository. I hope these will help. Best, David

[limin321]

Hi Limin, Thank you for your message. Indeed, I didn't try it on MacOS. Maybe @bneron could help us on this issue. There is a specific installation for Mac users. Maybe you could try to run directly "CRISPRCasFinder.pl -h" or "CRISPRCasFinder -h" without the perl command. please look at the user manuel "CRISPRCasFinder_Viewer_manual.pdf". You could also try to copy directly the main perl script and the new CasFinder folder in your previous installation repository. I hope these will help. Best, David

Hi Davis, You are right. I followed your suggestion: copy directly the main perl script and the new CasFinder folder in your previous installation repository. and it works. I am able to get the same results as the one i got from website. Really appreciate that.

Best, Limin

[dcouvin]

Great ! ;-)