No complete extrachromosomal contigs assembled!!

[MonicaSteffi]

Description of bug

I tried spades for my viral genome assembly. After the end of the assembly, I just received "No complete extrachromosomal contigs assembled!!" in the log file. Also, I couldn't find any contigs or scaffold files. Does this message mean that there is no viral genome present in that particular sample?

Thank you in advance

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.4

Operating System

Linux-4.12.14-197.40-default-x86_64-with-glibc2.26

Python Version

3.10.9

Method of SPAdes installation

conda

No errors reported in spades.log

• Yes

[asl]

Tagging @Dmitry-Antipov

[Dmitry-Antipov]

Hi
No, this means that for some reasons we were not able to assemble complete viral genomes - metaviralSPAdes is focused on them only. Usual problems are coverage gaps or ultra-high coverage, but other issues can appear too.

You can just try regular (meta) SPAdes to get the complete assembly and extract viral fragments from it.

[MonicaSteffi]

Hi No, this means that for some reasons we were not able to assemble complete viral genomes - metaviralSPAdes is focused on them only. Usual problems are coverage gaps or ultra-high coverage, but other issues can appear too.

You can just try regular (meta) SPAdes to get the complete assembly and extract viral fragments from it.

Thank you. Ill check with metaspade and post it back

[MonicaSteffi]

Hi No, this means that for some reasons we were not able to assemble complete viral genomes - metaviralSPAdes is focused on them only. Usual problems are coverage gaps or ultra-high coverage, but other issues can appear too.

You can just try regular (meta) SPAdes to get the complete assembly and extract viral fragments from it.

Hi,
Ive tried metaspade and with similar sample and I got 2047 contigs and I tried filtering out based on virVerify and checkV. Got good quality contigs.
Thank you