Hi.
I'm re-posting with just header and footer of the console log:
I'm trying to align 19 closely related genomes + 1 distantly related with
progressiveMauve 2.1.1 on a MacOSX 10.4 box.
It runs for about 14 hours, sending to the console meaningful logs, than
crashes with "error code 132".
It happens after a recursive anchor search, but several recursive anchor
searches had already been performed successfully.
The box is equipped with 2GB RAM, and the maximum Mauve RAM usage appears to
be 1.4GB, so it should not be a memory shortage problem.
What "error code 132" stands for?
Any suggestions on how to fix it?
The complete console log follows.
Thanks a lot in advance!
Duccio Medini
OS name is: Mac OS X arch: i386
Executing:
/Applications/Mauve/Mauve.app/Contents/MacOS/progressiveMauve --seed-family
--output=/data/all_merged
--backbone-output=/data/all_merged.backbone
--output-guide-tree=/data/all_merged.guide_tree --muscle-args=-maxmb 900
/data/genome1.fna
[....]
/data/genome20.fna
Sequence loaded successfully.
/data/genome1.fna 4751080 base pairs.
Sequence loaded successfully.
/data/genome2.fna 2153922 base pairs.
Sequence loaded successfully.
[...]
/data/genome20.fna 2184406 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 3 seconds.
[....]
Searching with seed pattern 11110011010101011001111
Creating sorted mer list
Create time was: 3 seconds.
[...]
Creating sorted mer list
Create time was: 2 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%..
Searching with seed pattern 11110110010101001101111
[.........] Footer:
Previous anchoring score: 1.39838e+08, new anchor score: 1.39496e+08
propagating ancestral breakpoints
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..9%..
10%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..22%..23%..25%..26%..27%..28%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..47%..48%..49%..
50%..52%..53%..54%..55%..56%..57%..59%..
60%..62%..63%..64%..65%..66%..67%..69%..
70%..72%..73%..74%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..87%..88%..89%..
91%..92%..93%..95%..97%..
100%..Fix left ends
done.
Aligning node 25 to 28 via 24!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 12897 tracking matches
There are 51084 / 502983 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 2761 pairwise LCBs
scaling bp penalty by conservation weight:
0.142939
0.168289
scaling bp penalty by bp weight:
0.176786
0.3375
Greedy BPE
Scoring with scaled breakpoint penalty: 54237.2
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%..done
Arrived at 22 intervals
Adding unaligned intervals
addUnalignedIntervals yields 62 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(25) has 16 intervals
descendant 1(28) has 1 intervals
propagateDescendantBreakpoints yields 37 intervals
Creating ancestral ordering
Previous anchoring score: - 1.79769e+308, new anchor score: 2.38672e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
Exited with error code: 132
---- End of console log ----
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