Closed Phelimb closed 7 years ago
Hi @Phelimb,
The McCortex clean command guesses out how many colours it can handle at once given the memory constraints and an estimate of the number of kmers. This means it can clean a (for example) 1,000 colour graph by pooling the samples and cleaning this single colour population graph, then cleaning n
colours against the pop graph at a time. The effect is the same as loading all colours at once. I think the issue is that it's guessing that n=0
is optimal - which is obviously crazy. Try setting the number of colours to use with -N 1
. I think that will fix it - let me know if it doesn't.
I'm putting together a patch to fix this behaviour.
@phelimb is cleaning a single colour graph, so seems like this is a degenerate case where your calculation/estimate is unnecessary
Yep - should be fixed on develop
branch now.
Your fix in principle allows the code to choose to clean in 2 colours even in a 1 colour graph though ? Anyway sounds good
Thanks @noporpoise. Will give the develop version a try and let you know if it fixes the issue.
Hi @noporpoise,
I'm running mccortex building and cleaning on a bunch of samples from the ENA and a small percentage are failing on the cleaning step without much information as to why.
Here's a dump of the log. Building works fine but then cleaning dies with
Assert Failed db_graph_alloc(): num_of_cols > 0
Any ideas?