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I tried to run this command in the terminal from my Mac OS, which I 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 an error that the command cannot be 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 this perl script working and resolve this error?

Edit:

Test Summary Report
-------------------
t/00-compile.t                    (Wstat: 7168 Tests: 511 Failed: 28)
  Failed tests:  51, 64, 69, 81, 158, 170, 179-184, 331
                337-342, 358, 365, 375, 430, 467, 470, 482
                494, 507
  Non-zero exit status: 28
t/Root/RootIO.t                   (Wstat: 512 Tests: 1 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 3 tests but ran 1.
Files=211, Tests=13892, 138 wallclock secs ( 2.50 usr  0.72 sys + 100.25 cusr 18.37 csys = 121.84 CPU)
Result: FAIL
Failed 2/211 test programs. 28/13892 subtests failed.
make: *** [test_dynamic] Error 255
  CJFIELDS/BioPerl-1.7.8.tar.gz
9 dependencies missing (Graph::Directed,LWP::UserAgent,List::MoreUtils,Test::Memory::Cycle,XML::DOM,XML::LibXML,XML::LibXML::Reader,XML::Parser::PerlSAX,XML::Twig); additionally test harness failed
  /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/BioPerl-1.7.8.tar.gz**

The full output is several pages long so for now I just inserted the summary output.

Håkon Hægland
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Jasmin Jonson
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  • *"I tried to run this command (`FEELnc_codpot.pl`) ..."* : How did you install that command, what is the command doing? – Håkon Hægland Aug 09 '21 at 10:53
  • You can install bioperl with anaconda, see [this](https://anaconda.org/bioconda/perl-bioperl) link – Håkon Hægland Aug 09 '21 at 10:54
  • It's a perl script that can be used to find long non coding RNA from a FASTA file. I installed it using this link from github: https://github.com/tderrien/ FEELnc but also using this link from anaconda: https://anaconda.org/bioconda/feelnc. I have also tried installing bioperl from anaconda but it did not resolve the error (seqIO cannot be found in @INC) – Jasmin Jonson Aug 09 '21 at 12:34
  • See also [this](https://stackoverflow.com/q/58290190/2173773) question – Håkon Hægland Aug 09 '21 at 13:57
  • Added [bug report](https://github.com/bioconda/bioconda-recipes/issues/29984) – Håkon Hægland Aug 09 '21 at 17:40

1 Answers1

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It is not a good idea to try to resolve these errors by simply copying modules around your filesystem. You need to install them into your Perl module library correctly.

Both of the modules you mention are part of the BioPerl distribution, so it's likely that you can solve your problems by installing that.

$ sudo cpan BioPerl

See cpan for more details.

Dave Cross
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  • BioPerl was installing for a minute or so but at the end the test summary report says: Result: FAIL Failed 2/211 test programs. 28/13892 subtests failed. make: *** [test_dynamic] Error 255. – Jasmin Jonson Aug 09 '21 at 09:10
  • @JasminJonson: If you post the full output from the failed installation, then someone will probably be able to help you more. – Dave Cross Aug 09 '21 at 09:14
  • Sorry for some reason I can only write a limited number of characters in my comment. I will edit the full output into my original post – Jasmin Jonson Aug 09 '21 at 09:16
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    @JasminJonson: Putting in your comment would be a terrible idea - comments are unformatted :-) Editing it into your question is a much better idea. – Dave Cross Aug 09 '21 at 09:47