Question: Minia assembler restart after error?
0
gravatar for avismirabilis
10 months 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 • 383 views
ADD COMMENTlink modified 9 months ago by Rayan Chikhi1.4k • written 10 months ago by avismirabilis40
3
gravatar for Rayan Chikhi
9 months ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k 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 9 months ago by Rayan Chikhi1.4k

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 9 months ago by avismirabilis40

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

ADD REPLYlink written 9 months ago by Rayan Chikhi1.4k

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 9 months ago by avismirabilis40

Good to know the assembly completed with the latest version. Did you compare contigs between those two runs, or scaffolds?

ADD REPLYlink written 9 months ago by Rayan Chikhi1.4k
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