Stephen Nayfach

Did you ever find a solution? I'm running into this issue using only 500 genomes.

Yes it works with --no_pairwise. But that defeats the main purpose of Scoary, which is to control for the population structure, no?

I have run into the same issue as @geboro. I tested several spades modules on 25 isolate miseq viral libraries. All modules produce a contigs.fasta file except when using --metaviral...

I don't think the high coverage is a problem. Many other libraries had similar coverage (500-1000x) and finished without issues. I've attached the assembly graph file. I'd be very interested...

Thanks, this is resolved as far as I'm concerned. I might suggest adding a warning or something to the log file that indicates why no final assembly is output. That...

For the last assembly (shown above) I downsampled the library to 650x coverage and the program output a circular genome. However, I'm dealing with one last tricky phage library for...

Thanks! I'd suggest adding this info to the docs for those who are impatient and using the tool just for this value :)

I've gotten the same error. For me, what caused the error was one sequence composed entirely of G and T nucleotides. Adding a single A and C nucleotide resulted in...

Is there any update on this? Suggestions for creating a mmseqs2 database of this size?

The HGM dataset contains MAGs from human gut metagenomes. The PATRIC and IMG datasets are mainly isolate genomes, both from gut and non-gut environments. You'll have to refer to the...