Closed cmajones closed 6 years ago
Hi, It looks like the conda installation did not suceed, or the conda environment is not properly loaded, since the "perl-bioperl" should have been installed.
Did you have any error message when running "conda create --name virsorter -c bioconda mcl=14.137 muscle blast perl-bioperl perl-file-which hmmer=3.1b2 perl-parallel-forkmanager perl-list-moreutils diamond=0.9.14"
Hi Simon,
I did a fresh install of the conda environment and I'm still getting the following output:
So the error is different now, it looks like the scripts used by VirSorter are not in your path. Did you follow these two steps in the installation:
ln -s ~/Applications/VirSorter/wrapper_phage_contigs_sorter_iPlant.pl ~/miniconda/envs/virsorter/bin ln -s ~/Applications/VirSorter/Scripts ~/miniconda/envs/virsorter/bin
and replaced "~/miniconda/envs/" by your conda installation folder ?
Hi Simon,
Sorry about that - I did a fresh install of the conda environment again and am still getting the Can't locate Bio/Seq.pm in @INC
error. I did not get an error message when installing the environment.
Error log: err.txt Terminal out: VirSorter_out_2.txt
Can you double check if Bio::Seq is correctly installed in the conda environment ? This can be done by loading the environment and then trying to load only this module, e.g.:
source activate virsorter
perl -e "use Bio::Seq;"
If you get an error message, it means it's unfortunately an issue with conda, not VirSorter.
Yes I still get the same error message:
Can't locate Bio/Seq.pm in @INC (you may need to install the Bio::Seq module) (@INC contains: /home/casey/miniconda3/envs/virsorter_3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/casey/miniconda3/envs/virsorter_3/lib/site_perl/5.26.2 /home/casey/miniconda3/envs/virsorter_3/lib/5.26.2/x86_64-linux-thread-multi /home/casey/miniconda3/envs/virsorter_3/lib/5.26.2 .) at -e line 1. BEGIN failed--compilation aborted at -e line 1.
I will try to find a fix and let you know here.
Hi Simon, @gavinmdouglas in my lab found a fix for this:
ln -s /home/casey/perl5/lib/perl5/Bio/ /home/casey/miniconda3/envs/virsorter_3/lib/site_perl/5.26.2/x86_64-linux-thread-multi
And adding the following to my .bashrc file
export PERL5LIB=/home/casey/perl5/lib/perl5/
Thanks for helping me locate the issue.
I'm still surprised that conda couldn't install BioPerl by itself, but happy that you found a fix to this issue !
Best, Simon
More than a year later, I also had this issue with Conda and this post was very helpful! Though, I couldn't link to the perl files on my lab's server. Just in case other people have this issue, here's another solution by pulling the actual perl files from GitHub:
Clone the BioPerl GitHub repo.
Copy the lib/Bio/
folder and all of it's contents to the lib
folder in the VirSorter conda environment:
cp -r relPath/to/lib/Bio relPath/to/miniconda3/envs/virsorter/lib/5.26.2/
Now onto VirSort-ing! :)
Thanks for sharing this tip !
Hi all, I also run into such an issue with bioperl and was able to solve it like this:
conda create -n virsorter -c bioconda perl-bioperl-core=1.007002 virsorter=1.0.6
I hope that also helps others. cheers
Hi all, I also run into such an issue with bioperl and was able to solve it like this:
conda create -n virsorter -c bioconda perl-bioperl-core=1.007002 virsorter=1.0.6
I hope that also helps others. cheers
This one worked for me, thank you
I solved the same problem recently,
In my case, this problem occurs since the conda installed Bioperl into the "minicondaPath/pkgs/perl-bioperl-1.6.924-4" instead of "minicondaPath/envs/virsorter/lib/site_perl/5.26.2" even though the @INC is only include the "minicondaPath/envs/virsorter/lib/site_perl/5.26.2"
Therefore, I solved the problem by adding the following commands into the minicondaPath/envs/virsorter/etc/conda/activate.d/update_perllib.sh
export OLD_PERL5LIB=$PERL5LIB export PERL5LIB=$PERL5LIB:minicondaPath/pkgs/perl-bioperl-1.6.924-4/lib/perl5/site_perl/5.22.0
I hope my solution is helpful to others.
Thanks for sharing !
Hi all, I also run into such an issue with bioperl and was able to solve it like this:
conda create -n virsorter -c bioconda perl-bioperl-core=1.007002 virsorter=1.0.6
I hope that also helps others. cheers
this one works for me thxthx
Hi Simon,
Thanks for all your work on VirSorter. I'm having trouble running the command line version using a conda environment.
When putting in this command:
wrapper_phage_contigs_sorter_iPlant.pl -f V-MRN-001-12_scaffolds.fasta --db 2 --ncpu 4 --data-dir /home/casey/local/virsorter/virsorter-data
I get back the two files attached.
err.txt VirSorter_terminal_output.txt
'Namely, in the err output, I get:
Can't locate Bio/Seq.pm in @INC (you may need to install the Bio::Seq module)
and
Error: Failed to open sequence file /home/casey/casey_backup/mareen/MAREEN_virome_all/concat_data/V-MRN-001-12_S21_R1_assembly/virsorter-out/fasta/VIRSorter_prots.fasta for reading
I've installed bioperl and metagenemark to try and fix these problems.
Do you have any other suggestions to get this to work? I would use CyVerse but have 100+ files to run in parallel on our cluster.
Thanks!