Issue in the installing of FEELnc

[charleslywang]

Dear, I have a problem on the installing process of FEELnc. [wkj@localhost FEELnc-master]$ FEELnc_classifier.pl Can't locate DB_File.pm in @INC (@INC contains: /home/wkj/wkj_software/FEELnc/FEELnc-master//lib/ /home/wkj/wkj_software/FEELnc/FEELnc-master/lib/ /home/wkj/perl5/lib/perl5/x86_64-linux-thread-multi /home/wkj/perl5/lib/perl5 /home/wkj/perl5/lib/perl5/x86_64-linux-thread-multi /home/wkj/perl5/lib/perl5 /home/wkj/perl5/lib/perl5/x86_64-linux-thread-multi /home/wkj/perl5/lib/perl5 /home/wkj/perl5/lib/perl5/x86_64-linux-thread-multi /home/wkj/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/wkj/perl5/lib/perl5/Bio/DB/SeqFeature/Store/LoadHelper.pm line 37. BEGIN failed--compilation aborted at /home/wkj/perl5/lib/perl5/Bio/DB/SeqFeature/Store/LoadHelper.pm line 37. Compilation failed in require at /home/wkj/perl5/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. BEGIN failed--compilation aborted at /home/wkj/perl5/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. Compilation failed in require at /home/wkj/wkj_software/FEELnc/FEELnc-master//lib//Bio/SeqFeature/database_part.pm line 6. BEGIN failed--compilation aborted at /home/wkj/wkj_software/FEELnc/FEELnc-master//lib//Bio/SeqFeature/database_part.pm line 6. Compilation failed in require at /home/wkj/wkj_software/FEELnc/FEELnc-master/scripts/FEELnc_classifier.pl line 12. BEGIN failed--compilation aborted at /home/wkj/wkj_software/FEELnc/FEELnc-master/scripts/FEELnc_classifier.pl line 12.

I tried a lot of things, but it did not work. What should I do ? Please help me! Best regards Kejun 2018-1-14

[tderrien]

Dear Kejun,

First of all, thank you for using FEELnc. Regarding this issue, it is more likely related to a pb of installation of (bio)perl. The missing file is "DB_File.pm" and should be included your install dir. If it helps, it is available on cpan here:

Also, and as indicated in the FEELnc README, did you correctly export the PERL5LIB variable? e.g

export FEELNCPATH=${PWD}
export PERL5LIB=${FEELNCPATH}/lib/:$PERL5LIB

Best,

Thomas

[charleslywang]

Dear Thomas Thank your for your reply! $ pwd /home/wkj/wkj_software/FEELnc/FEELnc-master export FEELNCPATH=/home/wkj/wkj_software/FEELnc/FEELnc-master export PERL5LIB=${FEELNCPATH}/lib/:$PERL5LIB export PATH=$PATH:${FEELNCPATH}/scripts/ export PATH=$PATH:${FEELNCPATH}/utils/ export PATH=$PATH:${FEELNCPATH}/bin/LINUX/ Is any problem in environment setting ? After installing "DB_File.pm" according to your suggested website， the new error is comming. $ FEELnc_classifier.pl FEELnc_classifier.pl /usr/bin/perl: symbol lookup error: /home/wkj/perl5/lib/perl5/x86_64-linux-thread-multi/auto/DB_File/DB_File.so: undefined symbol: Perl_xs_handshake

I do not know how to to next. Best regards kejun

[charleslywang]

another question is: if the lncRNA gtf is not avaiable for the test species, whether the lncRNA fasta file could be used to perform FEELnc_codpot.pl like this, No annotated lncRNAs are available but annotated lncRNAs from a closest species (< ~100 Myr) are available: FEELnc codpot will use them to learn its random forest model.
FEELnc_codpot.pl -i candidate_model.gtf -a reference_mrna.gtf -l close_species_lncrna.fasta -g genome.fasta
Is there any other method to tansfer the bed file to gtf file ?

Thanks a lot!

[tderrien]

For the first question, I'm afraid it is more related to your installation of perl/bioperl rather than to FEELnc. Maybe this link could help but a clean install may probably help. In addition, could you check your bioperl version:
perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n" '

Best,

Thomas

[tderrien]

I'm not sure to correctly understand the second question . But if you need to convert a bed/gtf to fasta from a closely related species , you could use this home-made script: https://github.com/tderrien/IGDR/blob/master/script/gtf2fasta.pl

Best,

Thomas

[charleslywang]

$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n" ' 1.007002 Is there any question in installing of bioperl ? If I installed the "DB_File.pm" you suggested, all three tools FEELnc_filter.pl，FEELnc_codpot.pl and FEELnc_classifier.pl are not available. If I removed the DB_File, FEELnc_filter.pl and FEELnc_codpot.pl are available. The second question is: I only have the reference_lncrna.fa and reference_lncRNA.bed file, not reference_lncrna.gtf in noncode database. In the second step FEELnc_codpot.pl, how to deal with it? Is there any tool to transfer bed file to gtf file?

[tderrien]

The error you mentioned is likely due to a problem of the DB_File package that's why a clean install of the complete package could help. To check this: perldoc -l DB_File In addition, FEELnc has been tested with BioPerl-1.006924 (not yet 1.007002).

For the second question, many tools can convert bed6 or bed12 to gtf.

Let me known if this helps

Thomas

[charleslywang]

Hi Thomas sorry later to reply. according to your suggestion, I installed DB file but occurs same problem. I do not known whether the version of BioPerl-1.006924 is right. Now, I could performed the first two steps FEELnc_filter.pl and FEELnc_codpot.pl. Thanks you for your help always.

[tderrien]

In case, it could help, I have updated the install section for the issue related to DB::File See this post : https://github.com/tderrien/FEELnc/issues/10

[brainfo]

so how can we install specific version BioPerl?? thx!