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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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Aligning contigs from deNovo Assembly with ngm-lr #29

Open mdkeehan opened 7 years ago

mdkeehan commented 7 years ago

Hi,

I have recently tried using ngmlr to align contigs against a reference. The contigs come from 10x Chromium Supernova deNovo assemblies. I get the following warnings in my output

Warning: Couldn't allocate alignment matrix. Required memory (13823) > max matrix size (10000)

I have found the line in IConfig.h 

ulong maxMatrixSizeMB = 350000;

to crank up the memory limit used for the alignment Matrix.

I wonder if you have any other suggestions for parameters I could try to change to handle very long contigs acting as reads.

fritzsedlazeck commented 7 years ago

Hi, I personally did not use NGMLR ever to do that. I think Philipp tried it once or twice, but he is now on holidays for almost 2 weeks. Thanks Fritz

cabbagesofdoom commented 6 years ago

Hi, This is also something that I would like to do with NGMLR and have the same issue. Would it be possible to make the max matrix size a settable parameter? How does this relate to memory requirements? (I can run on a 1TB RAM node, so hopefully not likely to be a constraint.) Thanks, Rich

ggstatgen commented 5 years ago

Hi all,

I am trying to do the same thing as OP and am stumbling in the same warning.

Warning: Couldn't allocate alignment matrix. Required memory (30689) > max matrix size (10000)

Any recommended parameters for aligning to a reference the contigs out of a de novo assembly program (canu in my case, if it matters) ?