Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module)

[ramnageena11]

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

[ramnageena11]

a new error is coming makeblastdb upgarde required

[benrhodes26]

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

[andersgs]

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.

[ramnageena11]

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.

[ramnageena11]

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.

[andersgs]

@ramnageena11 is it ok to close the issue then?

[ramnageena11]

i checked the Bioperl version is 1.007002 It did not updated how could i do that?

[andersgs]

Did you try:

conda install -c bioconda perl-bioperl=1.7.2

[ramnageena11]

Now this msg came

Current channels:

• https://conda.anaconda.org/bioconda/linux-64
• https://conda.anaconda.org/bioconda/noarch
• https://conda.anaconda.org/conda-forge/linux-64
• https://conda.anaconda.org/conda-forge/noarch
• https://conda.anaconda.org/r/linux-64
• https://conda.anaconda.org/r/noarch
• https://repo.anaconda.com/pkgs/main/linux-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/linux-64
• https://repo.anaconda.com/pkgs/r/noarch

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.

[andersgs]

Sorry. I had the incorrect version number. I edited the original post to fix that.

[ramnageena11]

okay, am trying

[ramnageena11]

Hey andersgs, I think that worked but now [13:49:40] This is prokka 1.14.6 [13:49:40] Written by Torsten Seemann [email protected] [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.

[andersgs]

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 .

[ramnageena11]

(my_prokka_env) powersequence@CH-CB-POWERSEQ:~/prokka/bin$ prokka --setupdb

Command 'prokka' not found, did you mean:

command 'propka' from deb pdb2pqr

[RxLoutre]

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 :)

[ramnageena11]

hi andersgs system got crashed. I am re-installing. will update. Thanks

[ramnageena11]

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:

• feature:/linux-64::__glibc==2.27=0
• python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.27

[ramnageena11]

Hi andersgs, could you suggest, how to resolve?

Thanks ram

[ramnageena11]

Hi, Its done.

Thanks