metaviralspades output - standard metaspades output not found

[rbtoscan]

Description of bug

Hello,

Thank you very much for developing this tool.

I am interested in running metaviralspades in metagenomics datasets and comparing the viral contigs to the standard metaspades output, as pointed out in the paper - last paragraph of section 2.1: https://academic.oup.com/bioinformatics/article/36/14/4126/5837667 .

When I run the tool, I only get scaffolds.fasta and contigs.fasta, assumedly from metaviralspades only.

Were the scaffolds.fasta/contigs.fasta also generated for the standard metaspades run or perhaps I misunderstood the manuscript?

Thank you!
Best
Rodolfo

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes genome assembler v3.15.5

Operating System

Ubuntu 20.04.4 LTS

Python Version

Python 3.10.6

Method of SPAdes installation

conda

No errors reported in spades.log

• Yes

[asl]

Tagging @Dmitry-Antipov

[rbtoscan]

Hi @Dmitry-Antipov,

is metaviralspades supposed to generate the outputs, metaspades and viral verify?

Thank you!

Best
Rudi