Closed sahilrishav2 closed 3 months ago
Hi, VS2 is design to tell if a sequence is virus or non-virus, not optimized to assigning specific virus groups which is a classification task. But, the "hallmark" column (>0) is strong signal that the assigned virus group in "max-score-group" is correct. In your example, you have a high confidence RNA virus:
k141_16734||full 0.560 0.950 0.950 RNA 3788 1 66.700 0.000
For more detailed viral gene annotation, you can take a look at DRAM-v. You can see an example in this SOP.
Thank you so much, sir. I check this and come again if any further assistance is required.
Hi, I want to ask if there is a way to speed up the processing. I am running vs2 using 40 threads, still, it is taking too much time
Other than -j
, you could split up your data and run them in parallel.
ok, thank you for your response
Hello, As per your suggestions, I am following the SOP tutorial for the annotation process but it gave an error on one of the files while the analysis on the other files is completed. This is the error:
virsorter run --seqname-suffix-off --viral-gene-enrich-off --provirus-off --prep-for-dramv -i SRR2083773.out/final-viral-combined_output_directory/combined.fna -w SRR2083773.out/final-viral-combined_output_directory/vs2-pass2 --include-groups dsDNAphage,RNA --min-score 0.5 -j 20 all
sed: can't read for-dramv/final-viral-combined-for-dramv.fa: No such file or directory
[Tue Apr 23 10:03:19 2024]
Error in rule finalize:
jobid: 7
output: final-viral-combined.fa, final-viral-score.tsv
conda-env: /jbod_new/home4_jbod/rishav1/VirSorter2/virsorter_db/conda_envs/72fd9e48
shell:
echo iter-0/*/all.pdg.gff.splitdir/all.pdg.gff.*.split | xargs rm -f
python /jbod_new/home4_jbod/rishav1/VirSorter2/virsorter/./scripts/filter-score-table.py config.yaml iter-0/viral-combined-proba-more-cols.tsv iter-0/viral-combined.fa final-viral-score.tsv final-viral-combined.fa
if [ True = "True" ]; then
mkdir -p for-dramv
python /jbod_new/home4_jbod/rishav1/VirSorter2/virsorter/./scripts/modify-seqname-for-dramv.py final-viral-combined.fa final-viral-score.tsv -o for-dramv/final-viral-combined-for-dramv.fa
cp iter-0/viral-affi-contigs-for-dramv.tab for-dramv
fi
N_viral_fullseq=$(grep -c '^>.*||full$' final-viral-combined.fa || :)
N_viral_lt2gene=$(grep -c '^>.*||lt2gene$' final-viral-combined.fa || :)
if [ True = True ]; then
Dramv_notes="for-dramv ==> dir with input files for dramv"
Dramv_notes2="For seqnames in files for dramv,
| is replaced with _ to be compatible with DRAMv"
else
Dramv_notes=""
Dramv_notes2=""
fi
if [ True = True ]; then
sed -i -E 's/(\|\|full([[:space:]]+)|\|\|[0-9]+_partial([[:space:]]+)|\|\|lt2gene([[:space:]]+))/\2\3\4/;' final-viral-score.tsv
sed -i -E 's/(\|\|full$|\|\|[0-9]+_partial$|\|\|lt2gene$)//;' final-viral-combined.fa
if [ True = True ]; then
sed -i -E 's/(__full(\|[0-9]+\|(c|l)$)|__[0-9]+_partial(\|[0-9]+\|(c|l)$)|__lt2gene(\|[0-9]+\|(c|l)$))/\2\4\6/;' for-dramv/viral-affi-contigs-for-dramv.tab
sed -i -E 's/(__full(__[0-9]+\|)|__[0-9]+_partial(__[0-9]+\|)|__lt2gene(__[0-9]+\|))/\2\3\4/;' for-dramv/viral-affi-contigs-for-dramv.tab
sed -i -E 's/(__full(-cat_[1-6]$)|__[0-9]+_partial(-cat_[1-6]$)|__lt2gene(-cat_[1-6]$))/\2\3\4/;' for-dramv/final-viral-combined-for-dramv.fa
fi
Suffix_notes=""
else
Suffix_notes="
Suffix is added to seq names in final-viral-combined.fa:
contigs (>=2 genes) as viral: ||full
contigs (< 2 genes) as viral: ||lt2gene
$Dramv_notes2
"
fi
printf "
====> VirSorter run (non-provirus mode) finished.
# of contigs w/ >=2 genes as viral: $N_viral_fullseq
# of contigs w/ < 2 genes as viral: $N_viral_lt2gene
Useful output files:
final-viral-score.tsv ==> score table
final-viral-combined.fa ==> all viral seqs
$Dramv_notes
$Suffix_notes
NOTES:
Users can further screen the results based on the
following columns in final-viral-score.tsv
- contig length (length)
- hallmark gene count (hallmark)
- viral gene %% (viral)
- cellular gene %% (cellular)
The "group" field in final-viral-score.tsv should NOT be used
as reliable taxonomy info
We recommend this SOP/tutorial for quality control
(make sure to use the lastest version):
https://dx.doi.org/10.17504/protocols.io.bwm5pc86
<====
" | python /jbod_new/home4_jbod/rishav1/VirSorter2/virsorter/./scripts/echo.py
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Exiting because a job execution failed. Look above for error message
Could you please help me with this concern ? Thank you
There might be not viral seqs found. You can take a look at the following two files in output directory to check.
final-viral-combined.fa
final-viral-score.tsv
Ok Sir, thank you so much
Hi,
I am using metatranscriptome data to identify bacteriophages using the vs2 tool. The problem is that I am unable to understand how to know, which virus is identified from the viral contigs. Also, which viral genes have been identified? This is the output file:
Please help me regarding this concern, thank you