Bioperl SeqIO.pm cannot be found

Question

[bart]

Hello,

I am trying to run this command line in the terminal from Mac OS, which is copied from a protocol:

FEELnc_codpot.pl –i <unannotated_transcript.fa> -a <mRNA_sequence.fa> -g <reference_genome.fa> -m ’shuffle’ –o <unannotated_transcript>

However, I get the following error: command not found, probably because I am not using perl, so I entered:

perl FEELnc_codpot.pl 

which gives me the following error:

Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/site_perl/5.26.2 /opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/5.26.2 .) at FEELnc_codpot.pl line 14.

So I copied seqio.pm from the bioperl directory which I had downloaded and placed it in /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level directory. However, this does not resolve the error. When I tried to run this command:

perl seqio.pm

I get this message:

Can't locate Bio/Factory/FTLocationFactory.pm in @INC (you may need to install the Bio::Factory::FTLocationFactory module) (@INC contains: /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/site_perl/5.26.2 /opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/5.26.2 .) at seqio.pm line 339. BEGIN failed--compilation aborted at seqio.pm line 339.

So I copied FTLocationFactory.pm into /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level.

Again this did not resolve the error. But gives the message that I also need Simple.pm in @INC. Which I copied into the correct directory (darwin-thread-multi-2level)

However, again this is not sufficient.

Does anyone know how to get FEELnc_codpot.pl working and resolve this error?

[bart]

For future FEELnc users: see also the issue section of the GitHub feelnc which contains solutions on this question and others: https://github.com/tderrien/FEELnc

Answer 1

[Kevin Blighe]

Hi,

As you are using conda, I would install BioPerl via that:

conda install -c bioconda perl-bioperl

Installing BioPerl separately, which I think that you have done, will mean that conda does not know where the BioPerl libraries are located.

Kevin

[bart]

Hi Kevin,

Thanks for your response. I have also tried installing BioPerl via Conda and I can find with Conda list. Unfortunately, I still get the same error message.

Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/site_perl/5.26.2 /opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/5.26.2 .) at FEELnc_codpot.pl line 14.

Do you have another suggestion I can try maybe? Thanks!

[Kevin Blighe]

From within the conda env, have you tried to install via CPAN? - see Can't locate Bio/SeqIO.pm

[bart]

I used Conda to install the CPAN shell, started it and entered:

install BioPerl

Then it gives me this error:

Reading '/Users/username/.cpan/Metadata'
  Database was generated on Sun, 08 Aug 2021 05:55:47 GMT
Running install for module 'BioPerl'
Checksum for /Users/username/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.8.tar.gz ok

==> Couldn't mkdir '/Users/username/.cpan/build/tmp-8658': Permission denied

==> Cannot continue: Please find the reason why I cannot make the <==
==> directory                                                     <==
==> /Users/username/.cpan/build/tmp-8658                             <==
==> and fix the problem, then retry.                              <==

So I get a permission denied. I tried to find a .cpan directory in the Users/username directory to give it permission (using chmod 755 filename) but I cannot find it. Do you have an idea where it might be located?