Cannot run FEELnc_codpot.pl

[bodhi84]

Hi I am working on the Zebrafish lncRNA and have recently installed your software. The first step of the pipeline is running smoothly and producing the desired output. But, whenever I am trying to run the next step i.e. FEELnc_codpot.pl I am getting the following error:

Undefined subroutine &Bio::DB::IndexedBase::_strip_crnl called at /usr/local/share/perl/5.26.1/Bio/DB/Fasta.pm line 295.

I have tried running the test with toy samples and there also I am getting the same error.

I would appreciate your help very much.

[vwucher]

Hi,

Thanks for using FEELnc. Concerning your error, it seems to me that it is maybe related to a previous error. Now, in order to avoid this error, the affectation of the PERL5LIB variable should be done in the following order (taking from the FEELnc GitHub main page): export PERL5LIB=$PERL5LIB:${FEELNCPATH}/lib/ #order is important to avoid &Bio::DB::IndexedBase::_strip_crnl error with bioperl >=v1.7

Do you export your variable in this order? If not, can you try and tell us if it is working correctly?

Thanks! Have a good day, Valentin

[bodhi84]

Hello, Thank you for your prompt reply. As per your suggestion, I have again exported the variables in the same order as mentioned in the FEELnc GitHub main page. But, it is again giving the same error.

Regards, Bodhisattwa

[vwucher]

Hi,

What is your version of BioPerl? Is it at least BioPerl-1.6.924? Sorry for those questions but it is to check 'usual' mistakes.

Thanks, Valentin

[bodhi84]

Hi Valentin, I have checked the BioPerl version and it is the recent version i.e. 1.007002. Thanks and Regards, Bodhisattwa

[tderrien]

Hi @bodhi84, Coul you paste the output of this command line: echo $PERL5LIB

Thanks

[bodhi84]

Hi tderrien, Please find the output of the command line: echo $PERL5LIB

:/home/zoology/Documents/FEELnc/lib/

Thanks, Bodhisattwa

[tderrien]

Ok, then to be sure both FEELnc lib and bioperl lib are exported correctly, you could try :

export PERL5LIB=/usr/local/share/perl/5.26.1:/home/zoology/Documents/FEELnc/lib/

Let us know if this helped.

Best

[bodhi84]

Hi tderrien,

Thank you very much for the solution. After exporting, it is working like a charm. It is indeed a great software and I am looking forward to get wonderful results using it.

Thanks again. Bodhisattwa

[tderrien]

Great, happy it helped