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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