Anton Korobeynikov comments

Results 792 comments of


                                            Anton Korobeynikov

no difference between hybrid mode and short read only

Still, have you assembled the complete genome (in `gene_clusters.fasta` file)?

Metaspades, finished abnormally, err code: -6

Hello Looks like someone's killed your SPAdes job from outside. Is there any possibility for this?

Metaspades, finished abnormally, err code: -6

Do you have any OOM manager installed and active?

metaspades with single-end reads?

No particular ETA / plans so far.

MetaSpades Error code 11

Hello Does the problem reproduce with the latest SPAdes 3.14.1?

cloudspades: spades-core finished abnormally, err code: -8

@nick-youngblut cloudSPAdes is planned to be a part of SPAdes release eventually. The problem is standard: paper & conferences deadlines made it so that cloudSPAdes codebase diverged a lot from...

How to deal with local modifications of llvm, specifically non-free ConvertUTF.*

SPAdes is open source and the repo is open, so you could easily see the history of all our local changes to LLVM (usually – workarounds or fixes for different...

Assembly missing ~300 kbp

How have you found that something is missing?

Assembly missing ~300 kbp

So, have you checked that the region is question indeed has some read coverage? Will you please post your spades.log file

Assembly missing ~300 kbp

Well, judging from the coverage histogram, the genome size is ~3.9 Mbp. I would suggest you to use --isolate mode and skip the read error correction (though, it would be...