Hi Elena,
How much RAM does the computer running progressiveMauve have? The
software's memory requirements grow quickly with additional sequences,
and with the degree of divergence among those sequences, and it seems
likely that running out of memory could cause the problems you are
observing. I would suggest trying this alignment on a machine with at
least 32GB RAM. However, I can't rule out an implementation bug from the
error messages you indicated. Finally, please note that as you go beyond
50 bacterial genomes you will quickly reach the practical limits of the
current algorithm as the running time and memory required become
excessive.
Best,
-Aaron
On Mon, 2016-02-15 at 00:38 +0000, Maria Martinez Diaz wrote:
> Dear All Mauve users,
>
>
>
>
> I have been trying to run an alignment in mauve but it is continuously
> finishing with an error message when I scale the number of isolates.
>
> I have 34 genomes from M. abscessus (one annotated reference , two
> complete genenomes, contigs download from NCBI, and contigs generated
> by me from fastq). I have arranged the contigs using the tools in
> mauve and check that the gbk from the reference has the sequence at
> the end as suggested in blogs. I run a test with only two of each kind
> of files in the snapshot_2015-02-25 in a mac pro computer and it
> finish without error. However, when I scale to 34 or even 20 samples
> it has finish once with error 11 and another time with error 134 after
> running for more than 6 hours.
>
>
>
>
>
>
> Greedy BPE
> Scoring with scaled breakpoint penalty: 86146.9
> 1%..2%..3%..4%..5%..6%..7%..8%..9%..
> 10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
> 20%..21%..22%..23%..24%..25%..26%..done
> Arrived at 24 intervals
> Adding unaligned intervals
> addUnalignedIntervals yields 67 intervals
> Merging unaligned intervals
> Marbling gaps
> Propagating descendant breakpoints
> descendant 0(29) has 48 intervals
> descendant 1(36) has 1 intervals
> propagateDescendantBreakpoints yields 71 intervals
> Creating ancestral ordering
> Previous anchoring score: 6.71385e+08, new anchor score: 1.31356e+09
> Backing up alignment tree...
> propagating ancestral breakpoints
> recursive anchor search
> 0,0 have 821 new matches outside LCBs
> 1,0 have 1100 new matches outside LCBs
> 2,0 have 1097 new matches outside LCBs
> 3,0 have 1483 new matches outside LCBs
> libc++abi.dylib: terminating
> Exited with error code: 134
>
>
>
> Much appreciate your help.
>
>
>
> Thanks,
>
>
>
>
> Elena Martinez
> Postdoctoral Research Fellow
>
> Centre for Infectious Diseases and Microbiology
> Level 3, ICPMR Building, Westmead Hospital
> PO Box 533 Wentworthville NSW 2145
>
> Ph (+612) 9845 5541
>
> maria.martinezd...@sydney.edu.au
>
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--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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