load-graph.py runtime

[Mewgia]

Hello.

My question is similar to that #1352
but exactly about load-graph. We have a sample of soil whole metagenome shotgun sequencing. 75 millions of reads, trimmed, normalized. Now we are trying to run load-graph.py for further partitioning. The PC has debian8, 40G ram

load-graph.py - k 31 -N 4 -T 8 -M 36G

it was run yesterday 3 pm and still working. does it even work? we understand that 36G is not enough for fast work, but it would be better if it had issued an error at the beginning, and now we are waiting for who knows what. should we wait for it to finish?

[ctb]

hello! That seems like a long time, I agree; we haven't changed anything in khmer in a while so I'm reasonably sure it hasn't been broken recently, but I'm still surprised. The memory has relatively little to do with the speed, and load-graph is linear in time with the data... is it providing any output? regardless, I am not sure I would recommend using load-graph any more, especially if you've run digital normalization (which should give you most of the benefits of khmer-style treatment). What problems are you trying to resolve? thanks, --titus

On Wed, Mar 17, 2021 at 02:20:31AM -0700, Mewgia wrote: Hello. My question is similar to that #1352 but exactly about load-graph. We have a sample of soil whole metagenome shotgun sequencing. 75 millions of reads, trimmed, normalized. Now we are trying to run load-graph.py for further partitioning. The PC has debian8, 40G ram load-graph.py - k 31 -N 4 -T 8 -M 36G it was run yesterday 3 pm and still working. does it even work? we understand that 36G is not enough for fast work, but it would be better if it had issued an error at the beginning, and now we are waiting for who knows what. should we wait for it to finish? -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: #1911

-- C. Titus Brown, ***@***.***