CODEWITHSUNDEEP
perl
Jasmin Jonson
Jasmin Jonson

Reputation: 39

Bioperl Seqio perl module cannot be found

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.

Upvotes: 0

Views: 1139

Answers (1)

Dave Cross
Dave Cross

Reputation: 69264

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.

Upvotes: 2

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