feargalr/demovir

Taxonomic classification of viruses at Order and Family level

demovir's Issues

Error in data.frame(levels(results3$contig), taxassO, margin_o, taxassF, :

When I run the command "Rscript demovir.R",the error shows:
Error in data.frame(levels(results3$contig), taxassO, margin_o, taxassF, :
arguments imply differing number of rows: 0, 100
Execution halted

I have print out the "margin_f",there is blank information,
Mimiviridae Siphoviridae Myoviridae Myoviridae Siphoviridae
100 100 100 100 100
Siphoviridae Myoviridae Poxviridae Siphoviridae
NA 100 100 100 100
how should I do to make it normally?

Demovir doesn't seem to count votes for contigs

Hi there,

I'm under the impression that demovir is supposed to assign taxonomy to each ORF predicted by prodigal and then assign tax to the contig based on the most common classification. From my output it seems that each ORF is just given a classifiction and that the percentage of votes is always 100%. Is this the intended result?

Sequence_ID Order Percent_of_votes Family Percent_of_votes
NODE_10001_length_1717_cov_4.338147_1 # 11 # 274 # -1 # ID=30947_1;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.386 Caudovirales 100 Siphoviridae 100
NODE_10001_length_1717_cov_4.338147_2 # 289 # 1716 # -1 # ID=30947_2;partial=01;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.477 Caudovirales 100 Siphoviridae 100
NODE_10007_length_1396_cov_4.014914_2 # 314 # 1396 # -1 # ID=10115_2;partial=01;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.351 Caudovirales 100 Siphoviridae 100
NODE_1000_length_8519_cov_4.104915_1 # 39 # 2021 # 1 # ID=3790_1;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.493 Herpesvirales 100 Herpesviridae 100
NODE_1000_length_8519_cov_4.104915_2 # 2038 # 3909 # 1 # ID=3790_2;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.540 Caudovirales 100 Siphoviridae 100
NODE_1000_length_8519_cov_4.104915_4 # 4613 # 5713 # 1 # ID=3790_4;partial=00;start_type=TTG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.478 Caudovirales 100 Myoviridae 100
NODE_1000_length_8519_cov_4.104915_8 # 6598 # 6870 # 1 # ID=3790_8;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.491 Caudovirales 100 Siphoviridae 100
NODE_1000_length_8519_cov_4.104915_9 # 6877 # 7881 # 1 # ID=3790_9;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.529 Caudovirales 100 Siphoviridae 100

I can not understand result file

At result file, sequence iD is contig ID or ORF ID?

Demovir's output is blank?

Hello,

I'm wondering if there's any 'test' data set I can use with Demovir to see if my installation is working? All of the contigs I run which contain viral sequences (linear, some 40kb+) consistently produce an empty output file from Demovir, when I'm sure at least some of them should be classifiable.

These are bacteriophage viral contigs. I am using the database linked to on the main README page.

Please advise. Thank you.

Michael

FIXED in pull req #2 #2

Cannot understand the error.!!

Hello, While running the tool, I got the following error, which is out of the box for me as I am new to bioinformatics with a little knowledge about programming. Can some one help me with this issue please.?

I am working on a metagenomic data, and need to run this tool for getting taxonomic annotation of the viral contigs.

The error which I got is:

Genes predicted
UBLAST complete
sort: cannot read: trembl_ublast.viral.txt: No such file or directory
rm: cannot remove ‘AA.fasta’: No such file or directory
rm: cannot remove ‘trembl_ublast.viral.txt’: No such file or directory
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: read.delim -> read.table
Execution halted
Done!

Thanks in advance, Vishal

Error in data.frame(levels(results3$contig), taxassO, margin_o, taxassF,

demovir.sh 8*.fa 4
Genes predicted
UBLAST complete
Error in data.frame(levels(results3$contig), taxassO, margin_o, taxassF, :
arguments imply differing number of rows: 0, 123
Execution halted
Done!

help me,please...thanks!!!

Problem in the demovir.R script

Hello there, I was working over this script, I figured out most of the part of this script, but please can you help me understand the error I am committing while running this.

The actual problem is the demovir.R is producing the DemoVir_assignments.txt, but inside this file there are only header i.e.;

Sequence_ID Order Percent_of_votes Family Percent_of_votes

and nothing else. So, is it an error from my side or I have to change something in the script, I can't understand the script as I am totally new to R script and Bioinformatics.!
Thanks, Vishal

empty output after installing, how can I solve this?

Dear all, I would like to use this software since a colleague recommended it to me and I have seen it applied in several publications. I have thousands of configs already filtered with virfinder and I have the following installed in a Fedora installation:

R version 3.6.3
Prodigal V2.6.3: February, 2016
usearch v11.0.667_i86linux32 (I put the binary in the bin folder I called it usearch)
bz2 is already installed

I followed the installation and after downloading the nr.95.fasta.bz2 I used some data as an example. I then used format_db.sh first.

After several tries I am trying it against this sequence of a known virus to see if I can get a match.
Could you help me diagnose this error or how to solve this issue? Thanks in advance!

Andrés

Error in running Demovir

Hi,

While running this tool in macOS 11.5.2, I got the following error but couldn't understand it as I am new to bioinformatics with a little knowledge about coding/programming. Can someone help me with this issue please?

I am working on a viral metagenomic data and so would like to use it for getting taxonomic annotation on my viral contigs.

The error which I got is as follows:

Genes predicted
UBLAST complete
sort: No such file or directory
rm: trembl_ublast.viral.txt: No such file or directory
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: read.delim -> read.table
Execution halted
Done!

I installed required components, downloaded nr.95.fasta.bz2 database from FigShare and put it in the Demovir directory, followed by using chmod 777 to get all permissions for all files in Demovir directory including format_db.sh, and then ran the programme in a folder at the desktop: /path_to_demovir/demovir.sh input.fasta threads.

If there's anything wrong or I misunderstood it please help me correct it. Many thanks!

Ernie

Database can't download

hello,
I find that the database can't download, which indicated 403 Forbidden. How to solve this problem? Thanks!