Steven.

Are you loading in a .gfa file?

Sounds like a job for [command line blast.](https://www.ncbi.nlm.nih.gov/books/NBK279680/) You can download the non-redundant database and execute searches locally. I also like to wrap some databases into [Abricate](https://github.com/tseemann/abricate), which has a...

Looks like you might be running out of memory causing the kernel to terminate the process. Easy way to tell for sure is to rerun it, watch htop, and then...

Have you tried subsampling your reads?

Check out [NanoStat](https://github.com/wdecoster/nanostat) to get an idea of how many bases you have for each sample. Then use something like [FiltLong](https://github.com/rrwick/Filtlong) to filter your reads. In general, I find it's...

That’s still a lot of bases, ~300X coverage of an E. coli. What are you trying to assemble?

Their total genome sizes are both in the ballpark of 4.5 Mb. So if you have Illumina reads sub sample to 180000000 bases (~40X). If you only have long reads...

Have you checked [out Climb](https://www.climb.ac.uk/)? They offer free access to servers for academic institutions.

Spades uses 512 Mb of RAM per thread, so you could try invoking with a single core. You could also manually set the memory limit as described in #215, which...

#153 describes this issue, complete with a fix.