Good morning,
Wondering if anyone has a suggestion for me.
I used progressivemauve to align 48 genomes and got a gibberish alignment
because, silly me, I did not order my contigs first.
So re-ordered the contigs using Mauve Contig Mover (one at a time, using the
same reference) and then tried to realign the 48 genomes with progressivemauve.
No luck.
After two hours progressivemauve exited with this error:
Greedy BPE
Scoring with scaled breakpoint penalty: 150573
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%..27%..28%..29%..
30%..31%..done
Arrived at 5 intervals
Adding unaligned intervals
addUnalignedIntervals yields 15 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(61) has 3 intervals
descendant 1(64) has 1 intervals
propagateDescendantBreakpoints yields 7 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.31866e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 62 new matches outside LCBs
1,0 have 77 new matches outside LCBs
Caught signal 11
Cleaning up and exiting!
Temporary files deleted.
Then I tried it again, no changes, just to see if maybe progressivemauve had
simply crashed as it sometimes does for me for no apparent reason and got this
error after two hours:
Greedy BPE
Scoring with scaled breakpoint penalty: 150573
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%..27%..28%..29%..
30%..31%..done
Arrived at 5 intervals
Adding unaligned intervals
addUnalignedIntervals yields 15 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(61) has 3 intervals
descendant 1(64) has 1 intervals
propagateDescendantBreakpoints yields 7 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.31866e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
libc++abi.dylib: terminating
0,0 have 62 new matches outside LCBs
1,0 have 77 new matches outside LCBs
Very similar but a little different.
I'm using the MCM output files totally unchanged. The data is the same but now
in theory better suited for alignment since it's been reordered. Other such
errors people have mentioned are due to the format of the files. Could that be
a problem and so late into the program - 2 hours? What else could it be? Would
really love to see this work.
Thank you,
Paulina
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