Question: Bioperl Generating Error, Please Help To Configure Bioperl!!
0
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5.7 years ago by
biostar150
biostar150 wrote:

Hi I am a novice perl programmer. I just installed bioperl in my mac and when I tried to invoke some programs it generates this king of error. Could you guys please help me understand what is the problem here?? Thanks!!

  Mac:Desktop darwin$ perl bioperl.pl 
    Use of uninitialized value $inFile in string at bioperl.pl line 7.
    Use of uninitialized value $outFile in concatenation (.) or string at bioperl.pl line 8.

    ------------- EXCEPTION: Bio::Root::Exception -------------
    MSG: Could not open >: No such file or directory
    STACK: Error::throw
    STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:486
    STACK: Bio::Root::IO::_initialize_io /Library/Perl/5.12/Bio/Root/IO.pm:351
    STACK: Bio::SeqIO::_initialize /Library/Perl/5.12/Bio/SeqIO.pm:491
    STACK: Bio::SeqIO::fasta::_initialize /Library/Perl/5.12/Bio/SeqIO/fasta.pm:87
    STACK: Bio::SeqIO::new /Library/Perl/5.12/Bio/SeqIO.pm:372
    STACK: Bio::SeqIO::new /Library/Perl/5.12/Bio/SeqIO.pm:413
    STACK: bioperl.pl:8
    -----------------------------------------------------------
bioperl • 3.2k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by biostar150
4

how is your code looks like? it seems like an IO error not related to BioPerl, feed your code to the critic - it may explain what is wrong.

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by Pavel Senin1.9k
4

There is no way to answer this without seeing the code in bioperl.pl.

ADD REPLYlink written 5.7 years ago by Neilfws48k
2

That isn't an installation problem, that stack trace tells you it cannot open a file that it cannot find and compilation warnings for Infile & Outfile. The modules are being loaded properly.

ADD REPLYlink written 5.7 years ago by Vivek2.3k

Thanks Guys!! The problem was that I did not install the cpanm module using sudo -s. It was not root execution, tha's why the error....

ADD REPLYlink written 5.7 years ago by biostar150
2

No, this is not related to what you posted above. If this were the case you would have seen a compile-time error that said Can't locate Bio/SeqIO.pm in @INC ... and the script would have halted. Clearly, BioPerl is installed because it generated a stack trace. The comments above are correct, the issue is that you are trying to initialize an object with a file that can't be found; that's what the Perl warnings tell you and the BioPerl stack trace below points to the same issue.

ADD REPLYlink written 5.7 years ago by SES8.2k
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