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.

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On Wed, Jul 17, 2019 at 6:46 PM Michael Alonge ***@***.***> wrote: Hi there, Thanks for sharing. What is the size of your draft assembly? And how much short-read coverage do you have? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#21?email_source=notifications&email_token=ALKFRSC2BTJLDDNCZDZHRSTP74LTFA5CNFSM4IEQGGL2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2EE55A#issuecomment-512249588>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALKFRSCDA4SFFEEGE7UFPVTP74LTFANCNFSM4IEQGGLQ> .

[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