Error after installation of AGAT
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13 months ago
L_bioinfo • 0

I succesfully installed AGAT tools using conda.

Command: conda create agat -c conda-forge -c bioconda agat

It showed all the packages and dependencies. Installation was successful yet when I initate agat in the activated agat environment I get

perl: symbol lookup error: /var/bin/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Sub/Name/Name.so: undefined symbol: Perl_xs_apiversion_bootcheck                                                                      

Please suggest what could be a potential way out of this error.

Perl AGAT • 1.6k views
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Could you try which perl to see if it is the perl from Conda that is used?

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I tried which perl:

/home2/Lau/.local/miniconda3/envs/H_majoris_alignment/bin/perl

which is my current environment where agat was installed

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/var/bin/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Sub/Name/Name.so

This path also looks kinda weird. Why is there a bin directory under /var and why is there a Perl lib under it?

Could you also run ls /var and env | grep -i perl?

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env | grep -i perl 

PERL5LIB=/home2/Lau/perl5/lib/perl5:/var/bin/perl5/lib/perl5:/var/bin/perl5/lib/perl5/x86_64-linux-thread multi:/var/bin/PfamScan::/var/bin/perl5/lib/perl5 PERL_MB_OPT=--install_base /home2/Lau/perl5 PATH=/home2/Lau/.local/miniconda3/envs/H_majoris_alignment/bin:/home2/Lau/.local/miniconda3/condabin:/usr/lib64/qt-3.3/bin:/home2/Lau/perl5/bin:/var/bin/vcftools-vcftools-b240116/bin:/var/bin:/var/bin/trinityrnaseq-Trinity -v2.4.0:/var/bin/tophat-2.1.1.Linux_x86_64:/var/bin/stringtie-1.3.4d.Linux_x86_64:/var/bin/SPAdes-3.9.1-Linux/bin:/var/bin/IGVTools:/var/bin/seqtk-master:/var/bin/samtools-1. 3.1:/var/bin/Salmon-0.8.2_linux_x86_64/bin:/var/bin/ribopicker-standalone-0.4.3:/var/bi n/RAxML:/var/bin/proteinortho_v5.11:/var/bin/PfamScan:/var/bin/paml4.8/bin:/var/bin/mot hur:/var/bin/KaKs_Calculator1.2/src:/var/bin/ima2-8.27.12/src:/var/bin/IGVTools:/var/bi n/IGV_2.3.44:/var/bin/hmmer-3.1b2-linux-intel-x86_64/binaries:/var/bin/hisat2-2.1.0:/va r/bin/gff_scripts:/var/bin/freebayes/bin:/var/bin/fastx:/var/bin/fastq_screen_v0.11.1:/var/bin/bowtie2-2.3.1:/var/bin/x86_64:/var/bin/x86_64-redhat-linux-gnu:/var/bin/mothur/blast/bin:/var/bin/bedtools-2.17.0/bin:/var/bin/bcftools-1.4:/var/bin/barrnap-master/bi n:/var/bin/angsd:/var/bin/ITSx_1.0.11:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin :/home2/Lau/.local/bin:/home2/Lau/bin PERL_LOCAL_LIB_ROOT=:/home2/Lau/perl5 PERL_MM_OPT=INSTALL_BASE=/home2/Lau/perl5

Yes there is bin under var directory and it has perl5

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This is from your original post:

perl: symbol lookup error: /var/bin/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Sub/Name/Name.so: undefined symbol: Perl_xs_apiversion_bootcheck

Directory x86_64-linux-thread-multi has a hyphen between thread and multi.

This is from your env variable:

PERL5LIB=/home2/Lau/perl5/lib/perl5:/var/bin/perl5/lib/perl5:/var/bin/perl5/lib/perl5/x86_64-linux-thread multi:

Directory x86_64-linux-thread multi has a space between thread and multi.

What is the name of this directory? Did you set the PERL5LIB manually?

Could you export this export PERL5LIB="/var/bin/perl5/lib/perl5/x86_64-linux-thread-multi:$PERL5LIB" before activating your environment.

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Apologies. It doesn't have space, I couldn't edit it when the content was copied and pasted. I already have perl in my environment incase if I export from root won't it cause conflicts.root has perl -v : 5.16

My conda environment has perl -v: 5.32

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Could you check the bioperl version now? perl -MBio::Root::Version -e 'print "$Bio::Root::Version::VERSION\n"'

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1.006924 is the version I got after running the command you suggested.

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