Kmers and the Assembly Graph: "GFA used k-mer length (k=55) must match the command line settings (k=21)"

[nickp60]

Description of bug

I am working on a pipeline of running a metagenomic assembly with metaSPAdes, followed by metaViralSPAdes. I am attempting to use the assembly graph as input to metaviralspades to save time. The error I get is stating that the kmer length in the assembly graph does not match the cli settings (I guess the default for metaviralSPAdes is 21. How do I retrieve the kmer size from the assembly graph, so I can use it to set k properly for metaViralSpades? I can tell it gets parsed here, but I can't make heads nor tails of it.

Thanks in adnvance

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes-3.15.4

Operating System

Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-glibc2.29

Python Version

3.8.10

Method of SPAdes installation

Docker

No errors reported in spades.log

• Yes

[asl]

Hello

You need to use last k-mer length if the input is assembly graph. If you have used default set of k-mers for metaSPAdes (did not alter -k option), then it would be 55.

[nickp60]

Great, thanks so much!