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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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Can't locate Parser.pm in @INC #23

Closed silvewheat closed 5 years ago

silvewheat commented 6 years ago

I install FEELnc by conda, and when I run test command: FEELnc_filter.pl -i transcript_chr38.gtf -a annotation_chr38.gtf -b transcript_biotype=protein_coding > candidate_lncRNA.gtf an error occurred:

Can't locate Parser.pm in @INC (you may need to install the Parser module) (@INC contains: /home/CYD/perl5/lib/perl5/5.26.0/x86_64-linux-thread-multi /home/CYD/perl5/lib/perl5/5.26.0 /home/CYD/perl5/lib/perl5/x86_64-linux-thread-multi /home/CYD/perl5/lib/perl5 /home/CYD/perl5/lib/perl5/5.26.0/x86_64-linux-thread-multi /home/CYD/perl5/lib/perl5/5.26.0 /home/CYD/perl5/lib/perl5/x86_64-linux-thread-multi /home/CYD/perl5/lib/perl5 /home/CYD/software/anaconda3/lib/site_perl/5.26.0/x86_64-linux-thread-multi /home/CYD/software/anaconda3/lib/site_perl/5.26.0 /home/CYD/software/anaconda3/lib/5.26.0/x86_64-linux-thread-multi /home/CYD/software/anaconda3/lib/5.26.0 .) at /home/CYD/software/anaconda3/bin/FEELnc_filter.pl line 14. BEGIN failed--compilation aborted at /home/CYD/software/anaconda3/bin/FEELnc_filter.pl line 14.

what Module should I install?

tderrien commented 6 years ago

Hi silvewheat,

Tx for using FEELnc and reporting the issue! It's probably related to a wrong export of the PERL5LIB variable, could you try to find the Parser.pm module in your FEELnc conda install: find /home/CYD/software/anaconda3/ -name "Parser.pm"

Then export the PERL5LIB accordingly: export PERL5LIB=$PERL5LIB:/condadir/of/Parser.pm

I'll update the README Best

a4free commented 6 years ago

Hi, I encountered the same problem, but FEELnc prompt： ./FEELnc_filter.pl -h Can't locate Parallel/ForkManager.pm in \@INC

But when I export PERL5LIB, another error occured: ./FEELnc_filter.pl --man DB_File.c: loadable library and perl binaries are mismatched (got handshake key 0xdb00080, needed 0xde00080)

What should I do ? Thx ;-)

perl -V @INC: lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi lib/perl5/site_perl/5.22.0 lib/site_perl/5.26.0/x86_64-linux-thread-multi lib/site_perl/5.26.0 lib/5.26.0/x86_64-linux-thread-multi lib/5.26.0

There seems 2 perl lib edition, but I only use conda to install FEELnc according the Readme.md.

tderrien commented 6 years ago

Hi @a4free, Indeed, it seems that the 2 perl versions trigger this error. Using conda install, the perl version 5.22.0 should be installed. You could try to export PERL5LIB with only 5.22.0 paths, smthg like: export PERL5LIB=lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi:lib/perl5/site_perl/5.22.0

Let me know if this helps. Best

Tichaboni commented 6 years ago

Hi @tderrien, @a4free @flegeai @vwucher I installed FEELnc on a new machine using conda. perl -v This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi Copyright 1987-2018, Larry Wall... When I run

FEELnc_filter.pl -i transcript_chr38.gtf -a annotation_chr38.gtf -b transcript_biotype=protein_coding > candidate_lncRNA.gtf to test FEELnc, I get the error message Can't locate Parser.pm in @INC (you may need to install the Parser module) (@INC contains: /home/bkimathi/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/bkimathi/miniconda3/lib/site_perl/5.26.2 /home/bkimathi/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/bkimathi/miniconda3/lib/5.26.2 .) at /home/bkimathi/miniconda3/bin/FEELnc_filter.pl line 14. BEGIN failed--compilation aborted at /home/bkimathi/miniconda3/bin/FEELnc_filter.pl line 14.

find /home/bkimathi/miniconda3/ -name "Parser.pm" Has the following output /home/bkimathi/miniconda3/pkgs/perl-xml-xpath-1.33-pl526_1/lib/site_perl/5.26.2/XML/XPath/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-xml-libxml-2.0132-pl526hbc14f71_0/lib/site_perl/5.26.2/x86_64-linux-thread-multi/XML/LibXML/SAX/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-cgi-4.22-pl526h470a237_4/lib/site_perl/5.26.2/x86_64-linux-thread-multi/HTML/Parser.pm /home/bkimathi/miniconda3/pkgs/feelnc-0.1.1-r3.4.1_1/lib/perl5/site_perl/5.22.0/Parser.pm /home/bkimathi/miniconda3/pkgs/feelnc-0.1.1-r3.4.1_2/lib/perl5/site_perl/5.22.0/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-xml-parser-2.44-pl526h3a4f0e9_6/lib/site_perl/5.26.2/x86_64-linux-thread-multi/XML/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-5.26.2-h470a237_0/lib/5.26.2/Pod/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-5.26.2-h470a237_0/lib/5.26.2/TAP/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-html-parser-3.72-pl526_3/lib/site_perl/5.26.2/x86_64-linux-thread-multi/HTML/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-types-standard-1.002001-pl526_1/lib/site_perl/5.26.2/Type/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-5.26.2-h14c3975_0/lib/5.26.2/Pod/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-5.26.2-h14c3975_0/lib/5.26.2/TAP/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-mime-tools-5.507-pl526_1/lib/site_perl/5.26.2/MIME/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-template-toolkit-2.26-pl526_1/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Template/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-lwp-simple-6.15-pl526h470a237_4/lib/site_perl/5.26.2/x86_64-linux-thread-multi/HTML/Parser.pm /home/bkimathi/miniconda3/pkgs/perl-test-harness-3.36-pl526_1/lib/site_perl/5.26.2/TAP/Parser.pm /home/bkimathi/miniconda3/lib/5.26.2/Pod/Parser.pm

What library should I export?

Your help will be highly appreciated p.s. I tried to run a nextflow program (lncRNA-Annotation-nf ) that has FEELnc but run into the same problem.

tderrien commented 6 years ago

Hi @Tichaboni,

It seems that you have different versions of FEELnc installed (r3.4.1_1 and r3.4.1_2) together with different versions of Perl (5.26.2 and 5.22.0). Using Perl version 5.22.0, you could try to export one of each : export PERL5LIB=/home/bkimathi/miniconda3/pkgs/feelnc-0.1.1-r3.4.1_1/lib/perl5/site_perl/5.22.0/Parser.pm:/home/bkimathi/miniconda3/pkgs/feelnc-0.1.1-r3.4.1_2/lib/perl5/site_perl/5.22.0

Alternatively, you could try to install via conda: https://github.com/tderrien/FEELnc#install-via-conda

Best

Thomas

abretaud commented 6 years ago

Hi, The conda package is currently broken due to complicated changes in the bioconda architecture. We're trying to repair it in https://github.com/bioconda/bioconda-recipes/pull/10725

abretaud commented 6 years ago

The conda package should be repaired now, you can try reinstalling it

sangeeta-25 commented 5 months ago

I am facing the same issue mention above. Can't locate Parallel/ForkManager.pm in @INC (you may need to install the Parallel::ForkManager module) (@INC contains: /home/bkimathi/miniconda3/pkgs/feelnc-0.1.1-r3.4.1_1/lib/perl5/site_perl/5.22.0/Parser.pm /home/bkimathi/miniconda3/pkgs/feelnc-0.1.1-r3.4.1_2/lib/perl5/site_perl/5.22.0 /home/user/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/user/miniconda3/lib/site_perl/5.26.2 /home/user/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/user/miniconda3/lib/5.26.2 .) at FEELnc_filter.pl line 10. BEGIN failed--compilation aborted at FEELnc_filter.pl line 10. I am struggling from the past 4 days. Can you please help me through this. I will be thankful to you.

tderrien commented 5 months ago

@sangeeta-25 Could you tell us if you were using conda install?

Tx

sangeeta-25 commented 4 months ago

I have install perl 5.18 version and export the path still getting this error . please help me through this .

Can't locate Bio/DB/Fasta.pm in @INC (you may need to install the Bio::DB::Fasta module) (@INC contains: /home/csir/Downloads/FEELnc/lib/ /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /home/csir/Downloads/FEELnc/lib/StringUtils.pm line 7. BEGIN failed--compilation aborted at /home/csir/Downloads/FEELnc/lib/StringUtils.pm line 7. Compilation failed in require at /home/csir/Downloads/FEELnc/lib/ExtractFromHash.pm line 9. BEGIN failed--compilation aborted at /home/csir/Downloads/FEELnc/lib/ExtractFromHash.pm line 9. Compilation failed in require at /home/csir/Downloads/FEELnc/lib/Parser.pm line 10. BEGIN failed--compilation aborted at /home/csir/Downloads/FEELnc/lib/Parser.pm line 10. Compilation failed in require at FEELnc_filter.pl line 14. BEGIN failed--compilation aborted at FEELnc_filter.pl line 14.

sangeeta-25 commented 4 months ago

Perl latest version has been install in the root. please let me know how can i trigger this problem

sangeeta-25 commented 4 months ago

If i am installing the module separately . then there is a compliation error.

sangeeta-25 commented 4 months ago

BEGIN failed--compilation aborted at /home/user/perl5/lib/perl5/ExtractFromHash.pm line 8. Compilation failed in require at FEELnc_filter.pl line 15.

i am getting this error can you please help me through this

tderrien commented 4 months ago

Did you correctly export the $PERL5LIB path?

and why don't you want to install it via conda : https://github.com/tderrien/FEELnc#install-via-conda ?