Hi there,
I am unable to run Mauve 2.3.1 since it always exits with error code 3. Can
anybody tell me the meaning of this error code and how I could fix this
problem?
Your help is very appreciated! See console output below.
Best, Gerald
OS name is: Windows 8 arch: x86
Executing:
progressiveMauve --output=C:\Users\glackner\Docs\alignment1\alignment1
--skip-refinement --weight=200
--output-guide-tree=C:\Users\glackner\Docs\alignment1\alignment1.guide_tree
--backbone-output=C:\Users\glackner\Docs\alignment1\alignment1.backbone
C:\Users\glackner\Docs\alignment1\bla1.gbk
C:\Users\glackner\Docs\alignment1\bla2.gbk
Storing raw sequence at C:\Users\glackner\AppData\Local\Temp\raw28B5.tmp
Sequence loaded successfully.
C:\Users\glackner\Docs\alignment1\bla1.gbk 18823367 base pairs.
Storing raw sequence at C:\Users\glackner\AppData\Local\Temp\raw2AAA.tmp
Sequence loaded successfully.
C:\Users\glackner\Docs\alignment1\bla2.gbk 19151376 base pairs.
Using weight 17 mers for initial seeds
Creating sorted mer list
Create time was: 8 seconds.
Creating sorted mer list
Create time was: 8 seconds.
0%..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.
using default bp penalty: 200
using default bp estimate min score: 507749
Starting with 717 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.991032
0.991032 0
Writing guide tree to C:\Users\glackner\Docs\alignment1\alignment1.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 573 initial LCBs
Using scaled bp penalty: 4000
Pair (0,1) has 1 well-supported breakpoints
genome content distance matrix:
0 0.991032
0.991032 0
bp distance matrix:
0.9 0.00316901
0.00316901 0.9
Aligning...
Aligning node 1 to 2 via 0!
Working set size: 284 Mb
Pagefile usage: 82 Mb
get ancestral matches
Working set size: 284 Mb
Pagefile usage: 82 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 284 Mb
Pagefile usage: 82 Mb
construct LCB tracking matches
There are 583 tracking matches
There are 1166 / 1749 components used
Working set size: 284 Mb
Pagefile usage: 82 Mb
init tracking match LCB tracking
Working set size: 284 Mb
Pagefile usage: 82 Mb
pairwise score tracking matches
Working set size: 285 Mb
Pagefile usage: 82 Mb
get pairwise LCBs
there are 576 pairwise LCBs
Working set size: 285 Mb
Pagefile usage: 82 Mb
scaling bp penalty by conservation weight:
0.991032
scaling bp penalty by bp weight:
0.00316901
Greedy BPE
Scoring with scaled breakpoint penalty: 4000
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%..done
Working set size: 285 Mb
Pagefile usage: 82 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 5 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 503 new matches outside LCBs
0,0 has an additional 92316 matches
Restoring backed up alignment tree...
1,0 has 92316 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 412 Mb
Pagefile usage: 219 Mb
construct LCB tracking matches
There are 91947 tracking matches
There are 183894 / 275841 components used
Working set size: 444 Mb
Pagefile usage: 253 Mb
init tracking match LCB tracking
Working set size: 444 Mb
Pagefile usage: 253 Mb
pairwise score tracking matches
Working set size: 549 Mb
Pagefile usage: 254 Mb
get pairwise LCBs
there are 25707 pairwise LCBs
Working set size: 558 Mb
Pagefile usage: 263 Mb
scaling bp penalty by conservation weight:
0.991032
scaling bp penalty by bp weight:
0.00316901
Greedy BPE
Scoring with scaled breakpoint penalty: 4000
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%..done
Working set size: 530 Mb
Pagefile usage: 237 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 5 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: 3, new anchor score: -7
Working set size: 575 Mb
Pagefile usage: 307 Mb
propagating ancestral breakpoints
Working set size: 575 Mb
Pagefile usage: 307 Mb
performing a gapped alignment
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%..
100%..Working set size: 592 Mb
Pagefile usage: 324 Mb
Fix left ends
Working set size: 592 Mb
Pagefile usage: 324 Mb
done.
Working set size: 592 Mb
Pagefile usage: 324 Mb
root alignment has 1 superintervals
root alignment length: 37974643
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Exited with error code: 3
------------------------------------------------------------------------------
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