David Pellow

Note - I observed this too, but managed to successfully install directly from bioconda rather than through the smaegol channel. I suggest leaving this open until other users can confirm.

I don't see k-mers reported in the std output. In the .hf5 file there's a field that says estimated k-mer number: 69880669047 - just under 70 billion. (k=31, would trying...

I've pasted it below. It's for a metagenomic simulation - the concatenated reference genomes are ~70Gbp, so this matches the k-mer count assuming almost all are unique. From what I...

Yes exactly - it's a multifasta of reference genomes. The longest is 16Mbp

Yes, I've tried 500GB-650GB, and also various values for max-disk. Are there parameters that you think would get it to work? Or another assembler that you would recommend?

Thanks

OK - It could be a good idea as a number of recent k-mer indexing/querying tools recommend using bcalm, not necessarily in the usual context of assembly of sequencing reads....

> David, This may be a use-case for TwoPaCo: Thanks! I'll look into it.

@sdewell Did you figure out how to solve this issue?

@jvollme - did this work? For me it seems to be installing 2.9 by default and I need 2.10.1 (there's a bug fix for multithreading according to the release notes).