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.?
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.
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.
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)
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.
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.?
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.
Could you provide the command that you used?
Maybe VirSorter can't handle .fna file?
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
https://github.com/simroux/VirSorter/issues/57
https://github.com/simroux/VirSorter/issues/3
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:
And yes the files are totally fine, I am able to run
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.pyand./pyscript.pygenerate different results. Maybe you can try ./wrapper instead of perl wrapper.By
head File.fnaI meant make sure you are using the correct input (assembly/contigs) and headers do not have special characters.And use
ls -sto 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