Hi Aaron,
Thanks for the fix, but it ended up crashing again at a different
location. It looks like it is looking for a library that is in your
directory.
Do you think you could provide a fix?
Here is the error:
Greedy BPE
Scoring with scaled breakpoint penalty: 22036.4
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..done
Arrived at 115 intervals
Adding unaligned intervals
addUnalignedIntervals yields 344 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 481 intervals
descendant 1(10) has 241 intervals
propagateDescendantBreakpoints yields 835 intervals
Creating ancestral ordering
Previous anchoring score: 6.51848e+07, new anchor score: 6.45947e+07
propagating ancestral breakpoints
performing a gapped alignment
0%..
27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..
82%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..Fix left ends
done.
performing iterative refinement
0%..
33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..cga doesn't fit
cga.RightEnd(cga_seq) 73994
RightEnd(my_seq): 4223132
cga.LeftEnd(cga_seq) 1
LeftEnd(my_seq): 4149139
cga.AlignmentLength(): 73994
AlignmentLength(): 89033
Unhandled gnException: Exception SeqIndexOutOfBounds thrown from
Unknown() in
/home/a.darling/development/build_2.1.1/include/libMems-1.5/libMems/CompactGappedAlignment.h
527
terminate called after throwing an instance of 'genome::gnException'
Aborted
Aaron Darling wrote:
Hi Morgan,
Indeed, you have discovered a problem specific to the 64-bit linux build
of Progressive Mauve 2.1.1. It starts "waiting" and never stops. The
root of the problem is that the Mauve release build and testing system
has not yet been automated across all compute architectures (i.e. 32/64
bit, windows, linux, etc), and a bug slipped through in the 64-bit linux
build.
As near-term workaround I have built a replacement for the 64-bit linux
progressiveMauve binary, and have made it available here:
http://gel.ahabs.wisc.edu/mauve/downloads/progressiveMauve_2.1.1_linux_x64.gz
simply download, gunzip, and replace the original 64-bit
progressiveMauve.
Regards,
-Aaron
On Fri, 2008-02-22 at 16:52 -0800, Morgan Langille wrote:
I am trying to aligning 13 pseudomonas genomes, but I am having some
problems. I first tried this on a 4GB 32 bit machine and received out of
memory errors. I then tried running the 64 bit version of
progressiveMauve on a 64 bit machine with 16GB memory (dual quad core
Xeon processor) and I get the error below. Regular mauveAligner (64 bit
version) works without any problems. I also tried running it with the
--disable-cache option and still received the same error. Note that the
process does not actually end, but just stays there "waiting" (I waited
4 hours at least before killing it).
Any suggestions?
Morgan
Sequence loaded successfully.
NC_002516.gbk 6264404 base pairs.
Sequence loaded successfully.
NC_002947.gbk 6181863 base pairs.
Sequence loaded successfully.
NC_004129.gbk 7074893 base pairs.
Sequence loaded successfully.
NC_004578.gbk 6397126 base pairs.
Sequence loaded successfully.
NC_005773.gbk 5928787 base pairs.
Sequence loaded successfully.
NC_007005.gbk 6093698 base pairs.
Sequence loaded successfully.
NC_007492.gbk 6438405 base pairs.
Sequence loaded successfully.
NC_008027.gbk 5888780 base pairs.
Sequence loaded successfully.
NC_008463.gbk 6537648 base pairs.
Sequence loaded successfully.
NC_009434.gbk 4567418 base pairs.
Sequence loaded successfully.
NC_009439.gbk 5072807 base pairs.
Sequence loaded successfully.
NC_009512.gbk 5959964 base pairs.
Sequence loaded successfully.
NC_009656.gbk 6588339 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 2 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
Creating sorted mer list
Create time was: 4 seconds.
0%..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%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..done.
waiting
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