Re: [MUMmer-help] ERROR: mummer and/or mgaps returned non-zero

[Adam P. <aph...@gm...>]

Hello,
This error typically occurs when your computer runs out of memory. You can
either switch to a computer with more RAM or divide your genome into parts
and align each separately to cut down on the memory usage.

Best,
-Adam


On Fri, Sep 4, 2015 at 10:34 PM, xiejianbo1860 <xie...@16...>
wrote:

> Dear Professor,
>
> Now i am using mummer to do alignment work, but i met a problem that i
> can't solve.  I will appreciate if you could help me!
>
> Here i describe the error i met, i want to find reliable set of snps in
> ref plant genomes (less than 500M), and it is less than the maximum
> reference length. the error messages are showed as below:
>
> The command : nucmer -maxmatch -c 90 -l 40   --prefix=ref_3 2_ref.fa
> 3_qry.fa
>
> # reading input file "ref_3.ntref" of length 394507750
> # construct suffix tree for sequence of length 394507750
> # (maximum reference length is 536870908)
> # (maximum query length is 4294967295)
> # process 3945077 characters per dot
> #................................................................................................ERROR:
> mummer and/or mgaps returned non-zero
>
>
> Could you help me to solve this problem?
>
> Best wishes.
>
> Thanks!
>
> No.35 Qinghua East Road, Haidian District
> BEIJING 100083
> P.R.CHINA
>
>
>
>
>
>
> 2015-09-05
> ------------------------------
> xiejianbo1860
>
>
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