Can't locate Bio/SeqIO.pm

Question

[zoe.meziere]

Hi everyone,

I'm totally new in programming, and I'm just trying to use Phyla_AMPHORA to get sequences of a specific marker, for all bacterial phyla to make a phylogenetic tree.

But after installing so many things, including Perlbrew and Bio Perl, I now get this message while trying to run the tests on Phyla_AMPHORA:

MacBook-Air-de-Zoe:Scripts ZoeMeziere$ perl MarkerScanner.pl -Phylum 3 TestData/ecoli.pep
Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2/darwin-thread-multi-2level /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at MarkerScanner.pl line 23.

Could you please tell me what I should do? And please remember I'm a total newbie, Thanks!! :))

[Ivan]

You probably need to sign in as the root user before installing missing modules. Set superuser password sudo passwd root and sign in through su

[Ram]

Bad idea, don't do this.

[Ivan]

I am sure you are right. I guess you mean the issues related to system stability and security. However, as Windows user I am used to the programs once installed start working. The only thing I care about is my work and this was the only way to circumvent the described problem and obtain the results.

[Ram]

Windows users need to "run as administrators" on a lot of applications. That is not the case in Linux. "once installed start working" only works if installation is done properly, which in your case is not true. You've "installed" Prokka but not its dependencies. ("Installation" on Linux is having executables and libraries in known locations, and your Bio::Root::Version is not in a location known to your user)

[Joe]

Environments like conda will allow you to install without needing admin rights

[Ivan]

It is not about the installation. The program doesn't work without su rights.

(base) arcella@Dulderscomp:~/miniconda3/pkgs/prokka-1.13-2$ bin/prokka

Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /home/arcella/miniconda3/pkgs/prokka-1.13-2/bin/../perl5 /home/arcella/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/arcella/miniconda3/lib/site_perl/5.26.2 /home/arcella/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/arcella/miniconda3/lib/5.26.2 .) at bin/prokka line 32.
BEGIN failed--compilation aborted at bin/prokka line 32.

(base) arcella@Dulderscomp:~/miniconda3/pkgs/prokka-1.13-2$ su
Password: 
root@Dulderscomp:/home/arcella/miniconda3/pkgs/prokka-1.13-2# bin/prokka

Name:
  Prokka 1.13 by Torsten Seemann <[e-mail]>
Synopsis:
  rapid bacterial genome annotation
Usage:
  prokka [options] <contigs.fasta>

Answer 1

[Joe]

cpanm Bio::Perl

Answer 2

[Ram]

Are you sure bioperl was installed using conda in the environment? There are very few utilities that need super user rights to work - bioperl is not one of them. Getting something working on conda can take a bit of know-how, but you'll almost never need su.

EDIT with explanation:

My experience has been that conda does not play well with other package managers. Maybe it can get along with pip, given how they're both python-based, but it does not play well with R's install.packages, and from your post, it looks like it doesn't play well with cpan either. The safest way for everything in a conda environment to work together is for all of it to be installed using conda. Installing perl-bioperl from the bioconda channel might fix the problem.

[Ivan]

It seems to be the true solution of the issue. This comment deserves the top position in the discussion.

[Ram]

This is commonly seen in R packages - this is the first I'm hearing of such problems in BioPerl. I'll move my comment to an answer and please accept it if it worked for you.

[Ivan]

Not so easy, unfortunately. I tried two ways of installing bioperl through conda and both didn't lead to success. There is an extensive discussion of the issue at another place https://github.com/tseemann/prokka/issues/519. It seems the participants finally found the solution. I personally and confidentially will continue with su. Still, thank you all for the replies.

Answer 3

[Arup Ghosh]

Install the Bio::SeqIO module from cpan.