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maickrau / GraphAligner

MIT License
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Memory and threads suggested - Core dump when building minimizer seeder from the graph #72

Open lingliao opened 1 year ago

lingliao commented 1 year ago

Hi,

I am trying to align a .fastq file(16GB) to a genome graph(4GB). Could you please suggest me how many memory and threads should be prepared for successful running?

Thanks!

lingliao commented 1 year ago

I met the same issue "Core dump when building minimizer seeder from the graph"

maickrau commented 1 year ago

Could you share the graph?

lingliao commented 1 year ago

SURE! Thank you for the quick response!!

The graph is downloaded from here https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-grch38.gfa.gz I unzipped it before aligning.

maickrau commented 1 year ago

Which parameters did you use?

lingliao commented 1 year ago

Sooo nice to hear from you!!

Here is my command line, GraphAligner -g input.gfa -f input.fastq -a out.gaf -x vg. And I call GraphAligner with docker image quay.io/biocontainers/graphaligner:1.0.16--hd03093a_1. Please let me know if there is any other info might be needed.

Thank you!

maickrau commented 1 year ago

I couldn't reproduce this bug using either compiled from source or bioconda installation. Could you please try the installing via bioconda, or compiling from source, instead of biocontainer?

About the memory use and threads, with version 1.0.16 (bioconda) 45Gb RAM should be enough. The more threads the faster but 16 threads will probably run in less than a day. With the most recent development commit 30Gb RAM should be enough.

lingliao commented 1 year ago

I will give it a try soon and share a feed back here!

Thank you Mikko!!

clemgoub commented 1 year ago

some insight in this thread: https://github.com/maickrau/GraphAligner/issues/68