Error running Phylosift

[nhudag]

#Hi I have a hard time running PhyloSift.
Firstly the link given to download the file is not working. Alternatively, I cloned the Zip file.
Now I am getting this error when i try to execute the file
./phylosift search non_chimeric-seqs.fna
Can't locate App/Cmd/Setup.pm in @inc (you may need to install the App::Cmd::Setup module) (@inc contains: /home/huda/PhyloSift/bin/../lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.0 /usr/local/share/perl/5.26.0 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /home/huda/PhyloSift/bin/../lib/Phylosift.pm line 2.
BEGIN failed--compilation aborted at /home/huda/PhyloSift/bin/../lib/Phylosift.pm line 2.
Compilation failed in require at /home/huda/PhyloSift/bin/phylosift line 6.
BEGIN failed--compilation aborted at /home/huda/PhyloSift/bin/phylosift line 6.
Please help I am new to command line dont really know how to trouble shoot

[LoryBkr]

Hello @nhudag,

I have the same issue and I don't know what to do. Did you succeed and ran Phylosift after this problem ?

[gjospin]

Which link are you referring to? The DB should be downloaded from figshare manually https://figshare.com/articles/PhyloSift_markers_database/5755404 Use the marker.tgz that should be the most recent version. By default PS looks for the 2 DB directories (ncbi and markers) in the directory /$HOME/share/phylosift You can modify that path by uncommenting the $markers and $ncbi variables in the phylosiftrc file. The lines should look like the following: $marker_dir="/$HOME/share/phylosift/markers"; $ncbi_dir="/$HOME/share/phylosift/ncbi"; I hope this helps.

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On Tue, Aug 6, 2019 at 2:41 AM LoryBkr ***@***.***> wrote: Hello @nhudag <https://github.com/nhudag>, I have the same issue and I don't know what to do. Did you succeed and ran Phylosift after this problem ? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#490?email_source=notifications&email_token=AADQKTNW7W4FRDUUSRXDDCLQDFBLTA5CNFSM4ETL5VN2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3USATY#issuecomment-518594639>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AADQKTN4XLUG5BITZCWKLZLQDFBLTANCNFSM4ETL5VNQ> .

[LoryBkr]

@gjospin my error was to download some files that were at the link: https://figshare.com/articles/PhyloSift_markers_database/5755404 and not all of them. Thank you for your answer.
I have another one: Does phylosift work on a 32-bit OS ?

[gjospin]

I don't actually know. I don't remember ever trying it on a 32bit system.

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On Wed, Aug 7, 2019 at 4:07 AM LoryBkr ***@***.***> wrote: @gjospin <https://github.com/gjospin> my error was to download some files that were at the link: https://figshare.com/articles/PhyloSift_markers_database/5755404 and not all of them. Thank you for your answer. I have another one: Does phylosift work on a 32-bit OS ? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#490?email_source=notifications&email_token=AADQKTI6XHEMAWLUPEXA6T3QDKUFVA5CNFSM4ETL5VN2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3YBKBA#issuecomment-519050500>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AADQKTIPJBG7WZMPJ2QSLWDQDKUFVANCNFSM4ETL5VNQ> .

[LoryBkr]

Ok, I found a solution and I was able to try it on a 64-bit OS. Thank you for your reply. Kind regards.

[koadman]

just for sake of completeness of the record, the binaries in the phylosift releases were all built for 64-bit x86 CPUs. It may be possible to manually replace all the binaries that are bundled with phylosift (e.g. LAST, HMMER, Infernal, pplacer, etc) with 32-bit builds but building those would not be a small job.