memory error with -R parameter

[shakti83kumar]

Dear Sir, I have run ragoo with -R parameter by executing as ragoo.py contigs.fasta reference.fasta -R short reads -T sr -C -g 111. It run well but it showed memory Error. I herewith attached screenshot with red leveled memory Error. Kindly help me solve this problem. Thanks in advanced

Shakti Kumar NIAB, Hyderabad, India

[malonge]

Hi there,

Thanks for sharing. What is the size of your draft assembly? And how much short-read coverage do you have? Also, how much memory do you have available on your system?

[shakti83kumar]

Dear Malonge/Ragoo Sir,

Thank you for prompt reply. The size of your draft assembly is 2.57 Gb has been generated of 10x chromium data and supernova assembly program has shown 42.07 x as RAW COVERAGE.

On Wed, Jul 17, 2019 at 6:46 PM Michael Alonge [email protected] wrote:

Hi there,

Thanks for sharing. What is the size of your draft assembly? And how much short-read coverage do you have?

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[malonge]

Thanks for the info. This python implementation is not very memory efficient and short read alignments can use quite a lot of memory. If you don't have access to a machine with more memory, perhaps you can downsample your reads. I think 30X is probably a good number. Of course, using error-corrected long reads uses much less memory, though you may not have that available.

In the future, I may consider creating a more efficient implementation, but probably not any time soon.

[mictadlo]

What is the best way to downsample the short reads to 30X?

Thank you in advance,

Michal

[malonge]

I would use seqtk

[malonge]

Hi there,

RagTag, the successor to RaGOO, is now available here:

https://github.com/malonge/RagTag

RagTag uses pysam for read-mapping validation, thus dramatically decreasing the memory requirements.

Thanks