Help with SGA

[condomitti]

Hi fellows,

I'm assembling a Denovo genome with SGA, using reads generated by Illumina HiScan.
Everything seems to be ok, although it's been running for 10 days now (in a 40 dual-core processors / 1TB RAM single machine). Is that normal?

Also, as this is my first assemble with SGA, I'm in doubt with the files already generated... it produced files like:

merged.k41.rmdup-thread0.hits.gz
...
...
...
merged.k41.rmdup-thread77.hits.gz
merged.k41.rmdup-thread78.hits.gz
and so on...


I guess it's being produced by each of the 80 threads I've said SGA to work with.

Are all those files expected or should it be only a single merged file?

I tried looking at the references but couldn't find any plausible answer.

Thank you in advance!

George Condomitti.

[GenoMax]

Probably not the direct answer you are looking for ..

If the program is still running (that you can actually see it accumulate CPU time and the files are growing in size) you should leave it alone. De novo assemblies can take a long time (depending on the genome size) and this would be normal behavior.

[condomitti]

Thank you GenoMax.

It's still running. I'll wait then.

Cheers