Open ramnageena11 opened 3 years ago
a new error is coming makeblastdb upgarde required
I also had this issue, when using a conda (version 4.10.1) install into an existing environment. I found that if I created a new environment (i.e. conda create -n my_prokka_env) then I didn't experience this issue.
Alternatively, see this comment which provides a possible solution based on the perl version
You have to make sure you have BioPerl version 1.72 or above installed. Can you try updating/upgrading BioPerl? It seems the earlier recipes on Conda have a bug.
I also had this issue, when using a conda (version 4.10.1) install into an existing environment. I found that if I created a new environment (i.e. conda create -n my_prokka_env) then I didn't experience this issue.
Alternatively, see this comment which provides a possible solution based on the perl version
Thanks for the suggestions, i will try this.
You have to make sure you have BioPerl version 1.72 or above installed. Can you try updating/upgrading BioPerl? It seems the earlier recipes on Conda have a bug.
Yes, I have updated the and upgraded Bioperl. upgarde did not executed but updated.
@ramnageena11 is it ok to close the issue then?
i checked the Bioperl version is 1.007002 It did not updated how could i do that?
Did you try:
conda install -c bioconda perl-bioperl=1.7.2
Now this msg came
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Sorry. I had the incorrect version number. I edited the original post to fix that.
okay, am trying
Hey andersgs, I think that worked but now [13:49:40] This is prokka 1.14.6 [13:49:40] Written by Torsten Seemann torsten.seemann@gmail.com [13:49:40] Homepage is https://github.com/tseemann/prokka [13:49:40] Local time is Fri Apr 30 13:49:40 2021 [13:49:40] You are powersequence [13:49:40] Operating system is linux [13:49:40] You have BioPerl 1.007002 [13:49:40] System has 28 cores. [13:49:40] Will use maximum of 8 cores. [13:49:40] Annotating as >>> Bacteria <<< [13:49:40] The sequence databases have not been indexed. Please run 'prokka --setupdb' first.
Follow the instructions on the last line and you should be good to go
On Fri, 30 Apr 2021 at 12:54 pm, ramnageena11 @.***> wrote:
Hey andersgs, I think that worked but now [13:49:40] This is prokka 1.14.6 [13:49:40] Written by Torsten Seemann @.*** [13:49:40] Homepage is https://github.com/tseemann/prokka [13:49:40] Local time is Fri Apr 30 13:49:40 2021 [13:49:40] You are powersequence [13:49:40] Operating system is linux [13:49:40] You have BioPerl 1.007002 [13:49:40] System has 28 cores. [13:49:40] Will use maximum of 8 cores. [13:49:40] Annotating as >>> Bacteria <<< [13:49:40] The sequence databases have not been indexed. Please run 'prokka --setupdb' first.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/tseemann/prokka/issues/566#issuecomment-830345227, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA5IVO6TFWLTFHD5NVNTX2TTLMDFVANCNFSM43LFESNQ .
(my_prokka_env) powersequence@CH-CB-POWERSEQ:~/prokka/bin$ prokka --setupdb
Command 'prokka' not found, did you mean:
command 'propka' from deb pdb2pqr
Had the same issues :
streptidy git:(master) ✗ prokka -h Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains:
And I directly tried what @andersgs suggested : conda install -c bioconda perl-bioperl=1.7.2
And it solves the issue for me. At least I can run prokka -h :)
hi andersgs system got crashed. I am re-installing. will update. Thanks
Hi, Pls see and suggest.
(base) powersequencing@CH-CB-RS-P5820:~$ prokka --version Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /home/powersequencing/anaconda3/bin/../perl5 /home/powersequencing/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/powersequencing/anaconda3/lib/site_perl/5.26.2 /home/powersequencing/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /home/powersequencing/anaconda3/lib/5.26.2 .) at /home/powersequencing/anaconda3/bin/prokka line 32. BEGIN failed--compilation aborted at /home/powersequencing/anaconda3/bin/prokka line 32. (base) powersequencing@CH-CB-RS-P5820:~$ ^C (base) powersequencing@CH-CB-RS-P5820:~$ conda install -c bioconda perl-bioperl=1.7.2 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package zlib conflicts for: python=3.9 -> zlib[version='>=1.2.11,<1.3.0a0'] perl-bioperl=1.7.2 -> perl-bio-samtools -> zlib[version='>=1.2.11,<1.3.0a0']The following specifications were found to be incompatible with your system:
Your installed version is: 2.27
Hi andersgs, could you suggest, how to resolve?
Thanks ram
Hi, Its done.
Thanks
powersequence@CH-CB-POWERSEQ:~$ prokka --help Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /home/powersequence/anaconda3/bin/../perl5 /home/powersequence/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/powersequence/anaconda3/lib/site_perl/5.26.2 /home/powersequence/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /home/powersequence/anaconda3/lib/5.26.2 .) at /home/powersequence/anaconda3/bin/prokka line 32. BEGIN failed--compilation aborted at /home/powersequence/anaconda3/bin/prokka line 32.
I had run the command sudo cpan Bio::Perl and it was succesful.
Pls help me rectify the issue.
Thanks Ram