I have some bins. And I want to use viralrecall to screen them.
The ideal output could be a csv(tsv), one column for the MAG, one column for scores.
I want to ask how to get the score of entire bin just like the result in your essay

And I don't understand the parameter "-c"
it also retrun many replicons

Hi, there. Thank you for developing this wonderful tool.

I was trying to get Viral Recall up and running using the general VOG database, but ran into the error:

Traceback (most recent call last):
  File "viralrecall.py", line 733, in <module>
    status = main()
  File "viralrecall.py", line 728, in main
    run_program(input, project, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, 
summary_file, contiglevel)
  File "viralrecall.py", line 383, in run_program
    vdesc = get_annot(database)
  File "viralrecall.py", line 41, in get_annot
    input = open("hmm/vog.annotations.tsv", "r")
FileNotFoundError: [Errno 2] No such file or directory: 'hmm/vog.annotations.tsv'

As I understand, this should be present in the hmm/ folder from Zenodo as per the README, but it isn't there. Can you direct me where to find it, or help find an alternative?

Thank you for your help,

Regards,

Luke

Thank you for creating this tool! Helps me a lot.

I noticed I was missing this output file when I ran ViralRecall:
*.fasta: The DNA coding sequence of the predicted proteins from Prodigal

Running, for instance,
python viralrecall.py -i bin.10.fa -p bin.10 -t 8 -c

would only give me
bin.10.faa
bin.10.full_annot.tsv
bin.10.markerout
bin.10.pfamout
bin.10.summary.tsv
bin.10.vogout

I have obtained hundreds of promising NCLDV genomes from the Lake Cadagno metagenomics dataset. However, I am struggling in assigning taxonomy to them. There are missing names in the "spreadsheet of annotated genomes" which are present in the GVDB databases.
https://faylward.github.io/GVDB/

Please suggest some steps/script for assigning taxonomy on prospective NCLDV genomes. Thank you.

Hi,

I want to point out a simple issue that I resolved. I am on a Linux machine running Ubuntu and the python script is interpreting "\n" characters as "\r" and causing issues. I resolved the issue by replacing the characters with sed.

sed -i 's/\r/\n/' viralrecall.py

Hello,

I tried running the example data with the command python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f in the ViralRecall conda environment and was returned this error message after it ran to completion:

Traceback (most recent call last): File "viralrecall.py", line 733, in <module> status = main() File "viralrecall.py", line 728, in main run_program(input, project, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel) File "viralrecall.py", line 655, in run_program plt.ylim(minval, numpy.nanmax(df2["rolling"])) File "/media/imperator/bross/miniconda3/envs/ViralRecall/lib/python3.5/site-packages/matplotlib/pyplot.py", line 1478, in ylim ret = ax.set_ylim(*args, **kwargs) File "/media/imperator/bross/miniconda3/envs/ViralRecall/lib/python3.5/site-packages/matplotlib/axes/_base.py", line 3470, in set_ylim if bottom == top: File "/media/imperator/bross/miniconda3/envs/ViralRecall/lib/python3.5/site-packages/pandas/core/generic.py", line 1576, in __nonzero__ .format(self.__class__.__name__))

Is this an issue regarding the installed versions of matplotlib (3.0.0) and pandas (0.23.4) in the environment?

Hello，

Will the databases of HMMs ( cellular organisms and GVOG) be updated?
If I want to build my own database, how to configure it to be compatible with viralrecall?
How can I skip the prodigal and use the .faa file as the input file directly? (the genome of some cellular organisms are too large）

Thanks for your time and consideration !

Hi
I tried to run your tool on a metagenome (~80 k sequences) with the marker option

python viralrecall.py -i MG.fna -p MG -db marker -t 20 -c

but it apparently gets stuck for a very long time at the cumsum2 function.
As this function is not useful in the case of a metagenome, I was wondering if there a way to treat the contigs independently from one another to just find signatures of viruses?
Thanks
Greg

Hello，
I am getting an error when trying to run viralrecall using the NCLDV database. The error is :

Traceback (most recent call last):
File "viralrecall.py", line 523, in
status = main()
File "viralrecall.py", line 518, in main
run_program(input, project, database, window, phagesize, minscore, minvog, evalue, cpus, plotflag, redo, flanking, batch, summary_file)
File "viralrecall.py", line 335, in run_program
subset = df3.ix[reg]
File "/public/work/jianfei/soft/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py", line 5274, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'

I find that panda "ix" is deprecated, My panda version is pandas-1.0.5. Any idea could solve this problem?

Thank you,

JianFei

Hello,

I recently tried running a local install of viralrecall. However, I got the following error message:

Traceback (most recent call last):
  File "viralrecall.py", line 733, in <module>
    status = main()
  File "viralrecall.py", line 728, in main
    run_program(input, project, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel)
  File "viralrecall.py", line 655, in run_program
    plt.ylim(minval, numpy.nanmax(df2["rolling"]))
  File "/scratch2/software/anaconda/envs/viralrecall-preq/lib/python3.5/site-packages/matplotlib/pyplot.py", line 1478, in ylim
    ret = ax.set_ylim(*args, **kwargs)
  File "/scratch2/software/anaconda/envs/viralrecall-preq/lib/python3.5/site-packages/matplotlib/axes/_base.py", line 3470, in set_ylim
    if bottom == top:
  File "/scratch2/software/anaconda/envs/viralrecall-preq/lib/python3.5/site-packages/pandas/core/generic.py", line 1576, in __nonzero__
    .format(self.__class__.__name__))
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

My understanding is that this is due to pandas treating booleans as ambiguous. I was wondering if there is a simple way to resolve this issue?

Thank you!
Cédric

After installing into the Conda environment i am facing following problem,

Traceback (most recent call last):
File "viralrecall.py", line 733, in
status = main()
File "viralrecall.py", line 728, in main
run_program(input, project, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel)
File "viralrecall.py", line 401, in run_program
df = pandas.concat([df, s1], axis=1, sort=True)
TypeError: concat() got an unexpected keyword argument 'sort'

Hi，
Thanks for your amazing tool!
I have successfully run this tool. But how could I get the taxonomy of NCLDV seqs? It's not found around the result files.
Look forward to your favourable reply.

This problem is not related to the code, but the database is not available:
https://data.lib.vt.edu/downloads/6h440s637

Hi,
I would like to know the appropriate threshold (min score and minvog) that I should set to mine the signal of giant viruses from many viral contigs. Thank you!

My python version:
Python 3.5.6
The command that has been run:
python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f
The output file did not generate the seven files in the README, only the following four files:
test_outdir.faa
test_outdir.markerout
test_outdir.pfamout
test_outdir.vogout
Error is as follows:
Traceback (most recent call last):
File "viralrecall.py", line 733, in <module>
status = main()
File "viralrecall.py", line 728, in main
run_program(input, project, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel)
File "viralrecall.py", line 401, in run_program
df = pandas.concat([df, s1], axis=1, sort=True)
TypeError: concat() got an unexpected keyword argument 'sort'

Hello,

I am getting an error when trying to run viralrecall using the NCLDV database. The general database seems to be OK. The error is:

Error: File existence/permissions problem in trying to open HMM file hmm/pfam.for_ncvog.hmm.
HMM file hmm/pfam.for_ncvog.hmm not found (nor an .h3m binary of it)

I have hmm/NCVOG.hmm. Any idea what could be causing this problem?

Thank you,
Sarah

Hi there,
For context, I'm new to python and shell coding in general.
I installed the required packages and directories alongside ViralRecall. As suggested, I tested to see if everything was working using python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f .
Sadly, I get the following messages:
"Intel MKL FATAL ERROR: This system does not meet the minimum requirements for use of the Intel(R) Math Kernel Library.
The processor must support the Intel(R) Supplemental Streaming SIMD Extensions 3 (Intel(R) SSSE3) instructions.
The processor must support the Intel(R) Streaming SIMD Extensions 4.2 (Intel(R) SSE4.2) instructions.
The processor must support the Intel(R) Advanced Vector Extensions (Intel(R) AVX) instructions."

I suspect these messages may be due to the fact that I have a new gen MacBook Pro with an Apple M1 Pro chip. Rosetta is installed and working.

Has anyone else had similar issues? Is there perhaps an easy solution that I am not aware of yet?

When I use -db "marker" -c

 bacphagenetwork@watson:/mnt/raid7/Dachuang/Achuan/viralrecall$ python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -db "marker" -c
viralrecall.py:400: DeprecationWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  s1 = pandas.DataFrame(pandas.Series(i, name = names[index]))

It's not an issue, but I just wanted to share an experience of making viralrecall run from any directory.
The solution is straightforward and consists of having one additional wrapper script that converts relative paths to the input and the project into absolute ones and launches viralrecall.py from its location, e.g. /opt/viralrecall/:

$ cat /opt/viralrecall/viralrecall
#!/bin/bash

SCRIPT_DIR="$( cd "$( dirname "$( realpath "${BASH_SOURCE[0]}" )" )" &> /dev/null && pwd )"

args=()
while test $# -gt 0; do
	arg=$1
	args+=("$arg")
	case "$arg" in
		-i|--input|-p|--project)
			args+=("$(realpath -ms "$2")")
			shift
		;;
	esac
	shift
done

cd "$SCRIPT_DIR"
python viralrecall.py "${args[@]}"

The wrapper can be soft-linked to a location on the PATH, and then viralrecall can be run intuitively as:

cd path/to/my/inputs/
viralrecall -i input.fasta -p project

One small problem is that viralrecall.py writes two files in the directory where it resides - err.txt and out.txt. To prevent this from happening in directories that are not supposed to have write permissions for regular users (and running viralrecall on different inputs compromises these files either way), they can be redirected preemptively to /dev/null:

$ readlink -f /opt/viralrecall/{out,err}.txt
/dev/null
/dev/null

although of course a more elegant solution would be to modify viralrecall.py to make it write those files relative to project.

Hello!

I am trying to recover NCLDV sequences from metagenomes and metaviromes. I was using virsorter2 with --include-groups "NCLDV" and I also want to use viral recall to ensure that the contigs are effectively from "NCLDV". I am not sure if filtering the contigs using score > 0 is enough (having in mind that I have also used virsorter2) or being more stringent and using 1 of the 10 marker genes presence + score > 0.

Thank you very much!

Hello, sorry to open this as an issue but it is more of a query. Is it possible to use ViralRecall to get viruses of the specific algal genome (chlorella) from the metagenomics dataset? Thank you for your suggestions.

Hello,
I've been trying to run ViralRecall, both using the test provided and with my own data, but it always gives me the following error:

Traceback (most recent call last):
File "/opt/viralrecall/viralrecall.py", line 733, in <module>
status = main()
File "/opt/viralrecall/viralrecall.py", line 725, in main
run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel)
File "/opt/viralrecall/viralrecall.py", line 475, in run_program
summary = summary.append(data)
File "/opt/Anaconda3/envs/viralrecall/lib/python3.10/site-packages/pandas/core/generic.py", line 5989, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

Any idea what the issue might be?

Hi team,

When trying to run viralrecall on some genomes with both --db GVOG and --db general, I noticed that several output files are lacking for the latter. Notably, it lacks the "*.full_annot.tsv", which is what I am most interested in. I am possibly also interested in viral regions that can be detected based on the generic VOG database, with default settings, but no regions are reported, although I'm not sure what this is caused by. For example, the '.summary.tsv' file is also lacking. Below you find an overview of what is produced with --db general. Note that the hmmscan outputs look okay, as well as the predicted protein sequences.

I hope you can help me finding out what might go wrong here.

Best,
Jolien

*.faa
*.markerout
*.pdf (I was using the '-f' flag)
*.pfamout
*.vogout

• .vregion_annot.tsv (no regions reported)

Hello,

This is not an issue but more of a request that if the markerout files can be made into .csv it would make a lot of downstream analysis and counting a lot easier :)

I've been trying to make a python script that does this task (*.markerout -> .csv) and its proving to be above my skills.

Thanks for your time and consideration !

I've been using your tool and find it very useful. However, I couldn't find any information about the license. Could you please clarify under what license this project is distributed?

Thank you