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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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Undefined subroutine &Parser::parseGTF when running FEELnc_filter.pl #30

Closed mxiang1 closed 6 years ago

mxiang1 commented 6 years ago

Hi, I ran in to this error while running the sample code:

FEELnc_filter.pl -i transcript_chr38.gtf -a annotation_chr38.gtf -b transcript_biotype=protein_coding Filtered transcripts will be available in file: 'transcript_chr38.feelncfilter.log' Undefined subroutine &Parser::parseGTF called at /home/ke.zhang/Programs/miniconda3/envs/conda_env/bin/FEELnc_filter.pl line 87.

I was able to see the help page when running the script without any arguments. Could anyone help me identify the problem? Thank you.

vwucher commented 6 years ago

Hi,

Apparently this is related to the fact that 'perl' can not find the parseGTF function. Do you install FEELnc with 'conda' or by taking the version from 'github'? And did you try to export the global variables (see below)?

export FEELNCPATH=${PWD}
export PERL5LIB=$PERL5LIB:${FEELNCPATH}/lib/ #order is important to avoid &Bio::DB::IndexedBase::_strip_crnl error with bioperl >=v1.7

export PATH=$PATH:${FEELNCPATH}/scripts/
export PATH=$PATH:${FEELNCPATH}/utils/

Thanks, Valentin

mxiang1 commented 6 years ago

Hi Valentin, The issue was due to having conda installed to multiple directories and I was able to resolve it by deleting the path which did not contain the libraries. Thank you, Menglan

vwucher commented 6 years ago

Hi,

It's nice that you found the solution!

Valentin