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Virsorter running error

Hello all, After downloading the virsorter tools using conda environment, I checked whether th command is running or not with ./wrapper_phage_contigs_sorter_iPlant.pl --help and it work all fine, but when running with my File.fna file format it shows the following error.

Step 1 failed, we stop there: either /home/lab202/VISHAL/TOOLS/VirSorter/virsorter-out/fasta/VIRSorter_prots.fasta or /home/lab202/VISHAL/TOOLS/VirSorter/virsorter-out/fasta/VIRSorter_nett_filtered.fasta were not found

I checked out the directory and i literally don't have those two files.

So can anyone help me as where I can get those files.?

next-gen sequencing
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updated by ericaholdridge • ericaholdridge • written by vishalchanda364 • vishalchanda364

I have checked with all possible ways, and checked with other files as well but end up getting the same error. The command which is used is:

perl wrapper_phage_contigs_sorter_iPlant.pl -f ../F_V_0_29_R.contigs.genes.faa --data-dir ../virsorter-data

And yes the files are totally fine, I am able to run 

head file.fna
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written by vishalchanda364 • vishalchanda364

If you install it correctly and add the shortcuts you don't need to add perl. I haven't used VirSorter but sometimes using python pyscript.py and ./pyscript.py generate different results. Maybe you can try ./wrapper instead of perl wrapper.

By head File.fna I meant make sure you are using the correct input (assembly/contigs) and headers do not have special characters.

And use ls -s to make sure the paths to other files work. Also you can try providing the full path to the databases like the other user in this github issue link.

https://github.com/simroux/VirSorter/issues/57

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written by Fatima Fatima

2 answers

What you get when you type which wrapper_phage_contigs_sorter_iPlant.pl? Maybe try wrapper_phage_contigs_sorter_iPlant.pl --help, conda should add the tool to the path so having ./ is probably not required.

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written by onestop_data onestop_data

I am getting this following error while running which wrapper_phage_contigs_sorter_iPlant.pl command.

/usr/bin/which: no wrapper_phage_contigs_sorter_iPlant.pl in (/home/usr/miniconda3/envs/virsorter/bin:/home/usr/miniconda3/condabin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/usr/.local/bin:/home/usr/bin)

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written by vishalchanda364 • vishalchanda364

and when I am running the following command wrapper_phage_contigs_sorter_iPlant.pl --help I am getting the following error:

bash: wrapper_phage_contigs_sorter_iPlant.pl: command not found...

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written by vishalchanda364 • vishalchanda364

I see. So I wonder if you named your conda environment. If you followed the tutorial on their Github page, you probably named it virsorter, Do you remember installing it with the following command conda install --name virsorter -c bioconda metagene_annotator?

If so, you need to activate the environment calling source activate virsorter and then you should be able to run it.

Please check out Using a conda virtual environment

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written by onestop_data onestop_data

Yes, I followed the tutorial in the github and I am running it inside the envirnment. But still the error is same. And while installing from github, I have skipped this step

To run VirSorter from any directory, you can make symbolic links to

Does this make any change?

Can you please tell me if this is the issue of the command, environment or the missing file. So that I would have a clear picture and rectify the issue.?

Thank you, Vishal

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written by vishalchanda364 • vishalchanda364

Hi there! I know this was from a long time ago but I wanted to provide a potential solution in case someone stumbles across this post.

First, make sure MetaGeneAnnotator is correctly installed to your conda environment:

conda install --name virsorter -c bioconda metagene_annotator

Next, you want to make sure that the folder Bio is in one of the directories that are listed in the variable @INC. For example, I found Bio in the path /anaconda3/envs/virsorter/lib/perl5/site-perl/5.22.0/Bio and copied it to the directory /anaconda3/envs/virsorter/lib/site-perl/5.26.2/darwin-thread-multi-2level.

scp -r /anaconda3/envs/virsorter/lib/perl5/site-perl/5.22.0/Bio /anaconda3/envs/virsorter/lib/site-perl/5.26.2/darwin-thread-multi-2level/

This solution is outlined on the VirSorter GitHub: https://github.com/simroux/VirSorter/issues/74.

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written by ericaholdridge • ericaholdridge

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