Question: Virsorter running error
0
gravatar for vishalchanda364
8 months ago by
vishalchanda36420 wrote:

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.?

sequencing next-gen • 318 views
ADD COMMENTlink modified 8 months ago by onestop_data260 • written 8 months ago by vishalchanda36420
1

Could you provide the command that you used?

Maybe VirSorter can't handle .fna file?

cp File.fna File.fasta

I haven't used VirSorter but it seems that the protein creating step has failed therefore no VirSorter_prots.fasta can be found.

Could you run

head File.fna

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

https://github.com/simroux/VirSorter/issues/3

ADD REPLYlink modified 8 months ago • written 8 months ago by Fatima720

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
ADD REPLYlink modified 8 months ago • written 8 months ago by vishalchanda36420
1

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

ADD REPLYlink modified 8 months ago • written 8 months ago by Fatima720
1
gravatar for onestop_data
8 months ago by
onestop_data260
onestop_data260 wrote:

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.

ADD COMMENTlink written 8 months ago by onestop_data260

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)

ADD REPLYlink written 8 months ago by vishalchanda36420

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...

ADD REPLYlink written 8 months ago by vishalchanda36420
1

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

ADD REPLYlink written 8 months ago by onestop_data260

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

ADD REPLYlink modified 8 months ago • written 8 months ago by vishalchanda36420

I think the best way to see if adding the symbolic links makes any changes is to try adding them:

to create

ln -s source_file link

to delete

unlink link

https://baptiste-wicht.com/posts/2012/09/linux-symbolic-links-hard-links.html

http://merenlab.org/2018/02/08/importing-virsorter-annotations/

ADD REPLYlink modified 8 months ago • written 8 months ago by Fatima720

Thank you for the help, still the error remains.

ADD REPLYlink written 8 months ago by vishalchanda36420
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