blat for genome size larger than 6GB (Segmentation fault (core dumped))

[Pengcheng Yang]

Dear colleagues,

I want to use blat for the target genome database with size 6Gb. But
encountered "Segmentation fault (core dumped)" error. I have
successfully run blat when I split the genome into two equal size, i.e
each 3Gb. So I guess the blat aligner not support the target database
with size greater than 4Gb, isn't it?

Best,

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Pengcheng Yang (杨鹏程)

Research Associate
Beijing Institute of Life Science,
Chinese Academy of Sciences
Beijing, People's Republic of China
Email: yan...@mail.biols.ac.cn

[Steve Heitner]

Hello, Pengchang.

The way the software is designed, it is optimized for speed and memory usage, but as you found, it is limited by database/query size. As you also found, larger databases/queries can easily be broken into smaller parts, run in parallel, and then recombined.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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