Dear Aaron,
Thanks for answering. At the moment I'm trying in the HPC system of the
university and I could run 20 genomes in one core with 20 cpu in less than two
hours. So it seems that it was a problem of computer resources. But is good to
know that I should keep my comparison under 50 genomes.
Thanks again.
Elena
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
________________________________
From: Aaron Darling [aaron.darl...@uts.edu.au]
Sent: Tuesday, February 16, 2016 6:14 AM
To: mauve-users@lists.sourceforge.net
Subject: Re: [Mauve-users] problems when scaling number of samples error 134,
libc++abi.dylib: terminating
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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