Question: Falcon - Estimation of free disc space needed
0
gravatar for alslonik
4 days ago by
alslonik10
Israel
alslonik10 wrote:

Hi, I am running a de novo assembly of a plant ~500Mb genome from PacBio reads of 120X coverage with Falcon. It runs for about 5 days now, done ~20% of the 160000 jobs that it has, and the disc space it takes is 2.5T currently. My free disc is up to 6T, meaning that I have 3.5T free. I am trying to estimate the size that I will need. What is the behaviour of Falcon regarding the temp files that it creates and how much free space on a disc it will need...? Is it something that can be calculated?

pacbio falcon assembly • 74 views
ADD COMMENTlink modified 3 days ago by Roxane Boyer620 • written 4 days ago by alslonik10
1
gravatar for Roxane Boyer
3 days ago by
Roxane Boyer620
France / Toulouse / GeT-Plage
Roxane Boyer620 wrote:

Hello alslonik !

Even if I did not used Falcon but Canu, I once had a similar issue while trying to assemble a large genome with PacBio data and a large depth. I think that calculate the memory needed is higly dependant on the parameters you used for your run, but is not that easy to predict.

I'm not sure if Falcon delete temporary files, and if yes, when will he do so. In order you to avoid waiting for several days of assembling, and then abort spaces issue, you could try to read this : https://github.com/marbl/canu/issues/193 , an old post where I could have a lot of feed back from the Canu dev, they helped me understanding why I was producing so much data and how I could lower the volume of produced data (filtering the raw reads for example using a histogram of reads length for example).

In conclusion, buying a disc is not the only solution, you may be able to produce less data by filterings your reads, and playing with some assembly parametrs (like the minimum size for overlapp of 2 reads.) , I'll be glad to do my best to discuss about this !

Hope this was a bit helpfull,

Cheers,

Roxane

ADD COMMENTlink written 3 days ago by Roxane Boyer620

Thanks, Falcon does some internal filtering at the beginning, but yes - I guess you are right, and if there will no be additional option I will filter the reads! I ll look deeper into these settings parameters...Thank you!

ADD REPLYlink written 3 days ago by alslonik10
1

You are welcome :) Glad I could help

ADD REPLYlink written 3 days ago by Roxane Boyer620
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