Question: Minia assembler restart after error?
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gravatar for avismirabilis
9 days ago by
avismirabilis40 wrote:

My genome assembly was running fine with 22% completed on the 'Assembly' step. It had already taken 72 hours to get here. My system had to be shutdown for some critical security updates, and I had to interrupt the Minia run. Anyway to re-start from where I aborted, or back to square one?

minia assembly • 109 views
ADD COMMENTlink modified 6 days ago by Rayan Chikhi1.3k • written 9 days ago by avismirabilis40
3
gravatar for Rayan Chikhi
6 days ago by
Rayan Chikhi1.3k
France, Lille, CNRS
Rayan Chikhi1.3k wrote:

Hi, due to the use of HDF5, the intermediate files do not get properly saved during a run, hence it's generally not possible to restart a minia run. What sort of organism took 72+ hours to assemble? This might be a good occasion to use the latest version of minia (https://github.com/GATB/minia, compile from sources) for improved quality of results.

ADD COMMENTlink written 6 days ago by Rayan Chikhi1.3k

The genome is a of a Crane species - approx 1.3Gb expected genome size. We have about 800 million reads, so I was wondering if that was the reason for how long it was taking.

ADD REPLYlink written 6 days ago by avismirabilis40

Are you running it on a network drive? also, how many threads and free disk space?

ADD REPLYlink written 15 hours ago by Rayan Chikhi1.3k

Nothing unusual regarding setup. linux server (not cluster), 80 cores with 60 TB free space, and 512Gb RAM.

I took you advice and ran the latest version of Minia- actually using the GATB pipeline. That one completed through all K's within 48 hours. Strange phenomenon was that i got better assembly stats with a single pair of reads (~100 million reads), but was really poor with additional reads and mate pairs added. Perhaps that's a discussion for another thread.

ADD REPLYlink written 7 hours ago by avismirabilis40
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