Hi,
I tried to align 7 rhodopseudomonas genomes with Mauve. The application
terminated with error code 3 at the same point each time I tried. I've
tried to increase the Java memory on my computer, but that doesn't seem to
help.
However the alignment did run successfully earlier with 3 bradyrhizobium
genomes. I do not understand the problem here. Attached is the log. Thanks
for your help.
Regards,
Duke
OS name is: Windows 7 arch: x86
Executing:
progressiveMauve --output=E:\Duke\Brady\mauve output\rhodopseudomonas only
alignment mauve --output-guide-tree=E:\Duke\Brady\mauve output\rhodopseudomonas
only alignment mauve.guide_tree --backbone-output=E:\Duke\Brady\mauve
output\rhodopseudomonas only alignment mauve.backbone
E:\Duke\Brady\Rhodopseudomonas palustris BisA53\Rhodopseudomonas palustris
BisA53.gb E:\Duke\Brady\Rhodopseudomonas palustris BisB18\Rhodopseudomonas
palustris BisB18.gb E:\Duke\Brady\Rhodopseudomonas palustris
BisB5\Rhodopseudomonas palustris BisB5.gb E:\Duke\Brady\Rhodopseudomonas
palustris CGA009\Rhodopseudomonas palustris CGA009.gb
E:\Duke\Brady\Rhodopseudomonas palustris DX-1\Rhodopseudomonas palustris
DX-1.gb E:\Duke\Brady\Rhodopseudomonas palustris HaA2\Rhodopseudomonas
palustris HaA2.gb E:\Duke\Brady\Rhodopseudomonas palustris
TIE-1\Rhodopseudomonas palustris TIE-1.gb
Storing raw sequence at C:\Users\REBECC~1\AppData\Local\Temp\raw330F.tmp
Sequence loaded successfully.
E:\Duke\Brady\Rhodopseudomonas palustris BisA53\Rhodopseudomonas palustris
BisA53.gb 5505494 base pairs.
Storing raw sequence at C:\Users\REBECC~1\AppData\Local\Temp\raw360C.tmp
Sequence loaded successfully.
E:\Duke\Brady\Rhodopseudomonas palustris BisB18\Rhodopseudomonas palustris
BisB18.gb 5513844 base pairs.
Storing raw sequence at C:\Users\REBECC~1\AppData\Local\Temp\raw38AC.tmp
Sequence loaded successfully.
E:\Duke\Brady\Rhodopseudomonas palustris BisB5\Rhodopseudomonas palustris
BisB5.gb 4892717 base pairs.
Storing raw sequence at C:\Users\REBECC~1\AppData\Local\Temp\raw3BD8.tmp
Sequence loaded successfully.
E:\Duke\Brady\Rhodopseudomonas palustris CGA009\Rhodopseudomonas palustris
CGA009.gb 5459213 base pairs.
Storing raw sequence at C:\Users\REBECC~1\AppData\Local\Temp\raw3ED6.tmp
Sequence loaded successfully.
E:\Duke\Brady\Rhodopseudomonas palustris DX-1\Rhodopseudomonas palustris
DX-1.gb 5404117 base pairs.
Storing raw sequence at C:\Users\REBECC~1\AppData\Local\Temp\raw4195.tmp
Sequence loaded successfully.
E:\Duke\Brady\Rhodopseudomonas palustris HaA2\Rhodopseudomonas palustris
HaA2.gb 5331656 base pairs.
Storing raw sequence at C:\Users\REBECC~1\AppData\Local\Temp\raw44C1.tmp
Sequence loaded successfully.
E:\Duke\Brady\Rhodopseudomonas palustris TIE-1\Rhodopseudomonas palustris
TIE-1.gb 5744041 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 44 seconds.
Creating sorted mer list
Create time was: 44 seconds.
Creating sorted mer list
Create time was: 40 seconds.
Creating sorted mer list
Create time was: 45 seconds.
Creating sorted mer list
Create time was: 45 seconds.
Creating sorted mer list
Create time was: 43 seconds.
Creating sorted mer list
Create time was: 47 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.
using default bp penalty: 156565
using default bp estimate min score: 469696
Starting with 3057223 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.270778 0.289481 0.285407 0.283794 0.27191
0.287463
0.270778 0 0.287221 0.280233 0.280375
0.267325 0.284703
0.289481 0.287221 0 0.249522 0.249511
0.204503 0.247523
0.285407 0.280233 0.249522 0 0.164392
0.224788 0.0831734
0.283794 0.280375 0.249511 0.164392 0
0.222619 0.171496
0.27191 0.267325 0.204503 0.224788 0.222619 0
0.229654
0.287463 0.284703 0.247523 0.0831734 0.171496
0.229654 0
Writing guide tree to E:\Duke\Brady\mauve output\rhodopseudomonas only
alignment mauve.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 2, 3 has 123171 initial LCBs
Pair 0, 1 has 131109 initial LCBs
Using scaled bp penalty: 148994
Using scaled bp penalty: 132817
Pair (2,3) has 20 well-supported breakpoints
Pair (0,1) has 27 well-supported breakpoints
Pair 2, 4 has 123736 initial LCBs
Pair 0, 2 has 129060 initial LCBs
Using scaled bp penalty: 149003
Using scaled bp penalty: 119707
Pair (2,4) has 29 well-supported breakpoints
Pair (0,2) has 38 well-supported breakpoints
Pair 2, 5 has 113263 initial LCBs
Pair 0, 3 has 136616 initial LCBs
Using scaled bp penalty: 188092
Using scaled bp penalty: 122476
Pair (2,5) has 26 well-supported breakpoints
Pair (0,3) has 31 well-supported breakpoints
Pair 2, 6 has 123776 initial LCBs
Pair 0, 4 has 136060 initial LCBs
Using scaled bp penalty: 150588
Using scaled bp penalty: 123586
Pair (2,6) has 21 well-supported breakpoints
Pair (0,4) has 36 well-supported breakpoints
Pair 3, 4 has 112918 initial LCBs
Pair 0, 5 has 134791 initial LCBs
Using scaled bp penalty: 228995
Pair (3,4) has 17 well-supported breakpoints
Using scaled bp penalty: 131995
Pair 3, 5 has 136949 initial LCBs
Pair (0,5) has 31 well-supported breakpoints
Pair 0, 6 has 138976 initial LCBs
Using scaled bp penalty: 169629
Pair (3,5) has 22 well-supported breakpoints
Using scaled bp penalty: 121073
Pair 3, 6 has 13267 initial LCBs
Using scaled bp penalty: 331868
Pair (3,6) has 1 well-supported breakpoints
Pair (0,6) has 29 well-supported breakpoints
Pair 4, 5 has 133148 initial LCBs
Pair 1, 2 has 132074 initial LCBs
Using scaled bp penalty: 171535
Using scaled bp penalty: 121237
Pair (4,5) has 25 well-supported breakpoints
Pair (1,2) has 27 well-supported breakpoints
Pair 1, 3 has 137702 initial LCBs
Pair 4, 6 has 114563 initial LCBs
Using scaled bp penalty: 221307
Using scaled bp penalty: 126062
Pair (4,6) has 17 well-supported breakpoints
Pair (1,3) has 30 well-supported breakpoints
Pair 5, 6 has 138551 initial LCBs
Pair 1, 4 has 137848 initial LCBs
Using scaled bp penalty: 165410
Using scaled bp penalty: 125962
Pair (5,6) has 22 well-supported breakpoints
Pair (1,4) has 27 well-supported breakpoints
Pair 1, 5 has 136832 initial LCBs
Using scaled bp penalty: 135352
Pair (1,5) has 31 well-supported breakpoints
Pair 1, 6 has 140405 initial LCBs
Using scaled bp penalty: 122959
Pair (1,6) has 26 well-supported breakpoints
genome content distance matrix:
0 0.270778 0.289481 0.285407 0.283794 0.27191
0.287463
0.270778 0 0.287221 0.280233 0.280375
0.267325 0.284703
0.289481 0.287221 0 0.249522 0.249511
0.204503 0.247523
0.285407 0.280233 0.249522 0 0.164392
0.224788 0.0831734
0.283794 0.280375 0.249511 0.164392 0
0.222619 0.171496
0.27191 0.267325 0.204503 0.224788 0.222619 0
0.229654
0.287463 0.284703 0.247523 0.0831734 0.171496
0.229654 0
bp distance matrix:
0.9 0.3 0.422222 0.344444 0.4 0.344444 0.322222
0.3 0.9 0.3 0.333333 0.3 0.344444 0.288889
0.422222 0.3 0.9 0.222222 0.322222 0.288889
0.233333
0.344444 0.333333 0.222222 0.9 0.188889
0.244444 0.0111111
0.4 0.3 0.322222 0.188889 0.9 0.277778 0.188889
0.344444 0.344444 0.288889 0.244444 0.277778
0.9 0.244444
0.322222 0.288889 0.233333 0.0111111 0.188889
0.244444 0.9
Aligning...
Aligning node 8 to 9 via 7!
Working set size: 840 Mb
Pagefile usage: 605 Mb
get ancestral matches
Working set size: 877 Mb
Pagefile usage: 610 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 878 Mb
Pagefile usage: 611 Mb
construct LCB tracking matches
There are 136396 tracking matches
There are 272792 / 1773148 components used
Working set size: 989 Mb
Pagefile usage: 722 Mb
init tracking match LCB tracking
Working set size: 989 Mb
Pagefile usage: 723 Mb
pairwise score tracking matches
Working set size: 991 Mb
Pagefile usage: 724 Mb
get pairwise LCBs
there are 14170 pairwise LCBs
Working set size: 1000 Mb
Pagefile usage: 734 Mb
scaling bp penalty by conservation weight:
0.0831734
scaling bp penalty by bp weight:
0.0111111
Greedy BPE
Scoring with scaled breakpoint penalty: 108178
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%..done
Working set size: 893 Mb
Pagefile usage: 635 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 4 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(8) has 1 intervals
descendant 1(9) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.16507e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2 new matches outside LCBs
0,0 has an additional 3057 matches
Restoring backed up alignment tree...
6,3 has 3057 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 899 Mb
Pagefile usage: 639 Mb
construct LCB tracking matches
There are 131381 tracking matches
There are 262762 / 1707953 components used
Working set size: 991 Mb
Pagefile usage: 726 Mb
init tracking match LCB tracking
Working set size: 992 Mb
Pagefile usage: 727 Mb
pairwise score tracking matches
Working set size: 993 Mb
Pagefile usage: 728 Mb
get pairwise LCBs
there are 2407 pairwise LCBs
Working set size: 995 Mb
Pagefile usage: 730 Mb
scaling bp penalty by conservation weight:
0.0831734
scaling bp penalty by bp weight:
0.0111111
Greedy BPE
Scoring with scaled breakpoint penalty: 108178
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%..done
Working set size: 897 Mb
Pagefile usage: 637 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 3 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(8) has 1 intervals
descendant 1(9) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: 2.16507e+008, new anchor score: 2.26595e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1 new matches outside LCBs
0,0 has an additional 1892 matches
Restoring backed up alignment tree...
6,3 has 1892 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 901 Mb
Pagefile usage: 638 Mb
construct LCB tracking matches
There are 131045 tracking matches
There are 262090 / 1703585 components used
Working set size: 991 Mb
Pagefile usage: 726 Mb
init tracking match LCB tracking
Working set size: 992 Mb
Pagefile usage: 726 Mb
pairwise score tracking matches
Working set size: 993 Mb
Pagefile usage: 728 Mb
get pairwise LCBs
there are 1916 pairwise LCBs
Working set size: 995 Mb
Pagefile usage: 730 Mb
scaling bp penalty by conservation weight:
0.0831734
scaling bp penalty by bp weight:
0.0111111
Greedy BPE
Scoring with scaled breakpoint penalty: 108178
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%..done
Working set size: 898 Mb
Pagefile usage: 637 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 3 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(8) has 1 intervals
descendant 1(9) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: 2.26595e+008, new anchor score: 2.26645e+008
Working set size: 896 Mb
Pagefile usage: 635 Mb
propagating ancestral breakpoints
Working set size: 896 Mb
Pagefile usage: 635 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: 971 Mb
Pagefile usage: 725 Mb
Fix left ends
Working set size: 971 Mb
Pagefile usage: 725 Mb
done.
Working set size: 971 Mb
Pagefile usage: 725 Mb
Aligning node 7 to 10 via 6!
Working set size: 967 Mb
Pagefile usage: 721 Mb
get ancestral matches
Working set size: 1087 Mb
Pagefile usage: 832 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1088 Mb
Pagefile usage: 833 Mb
construct LCB tracking matches
There are 177748 tracking matches
There are 691784 / 2310724 components used
Working set size: 1228 Mb
Pagefile usage: 973 Mb
init tracking match LCB tracking
Working set size: 1229 Mb
Pagefile usage: 974 Mb
pairwise score tracking matches
Working set size: 1232 Mb
Pagefile usage: 977 Mb
get pairwise LCBs
there are 239606 pairwise LCBs
Working set size: 1261 Mb
Pagefile usage: 1009 Mb
scaling bp penalty by conservation weight:
0.164392
0.171496
scaling bp penalty by bp weight:
0.188889
0.188889
Greedy BPE
Scoring with scaled breakpoint penalty: 50218.7
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%..done
Working set size: 1092 Mb
Pagefile usage: 867 Mb
Arrived at 46 intervals
Adding unaligned intervals
addUnalignedIntervals yields 140 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(7) has 1 intervals
descendant 1(10) has 1 intervals
propagateDescendantBreakpoints yields 46 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 8.5825e+006
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 11761 new matches outside LCBs
1,0 have 7900 new matches outside LCBs
0,0 has an additional 48153 matches
1,0 has an additional 44276 matches
Restoring backed up alignment tree...
3,4 has 48153 pairwise matches
6,4 has 44276 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1123 Mb
Pagefile usage: 879 Mb
construct LCB tracking matches
There are 50227 tracking matches
There are 196993 / 652951 components used
Working set size: 1124 Mb
Pagefile usage: 880 Mb
init tracking match LCB tracking
Working set size: 1124 Mb
Pagefile usage: 880 Mb
pairwise score tracking matches
Working set size: 1125 Mb
Pagefile usage: 880 Mb
get pairwise LCBs
there are 48487 pairwise LCBs
Working set size: 1128 Mb
Pagefile usage: 884 Mb
scaling bp penalty by conservation weight:
0.164392
0.171496
scaling bp penalty by bp weight:
0.188889
0.188889
Greedy BPE
Scoring with scaled breakpoint penalty: 50218.7
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%..done
Working set size: 1123 Mb
Pagefile usage: 878 Mb
Arrived at 89 intervals
Adding unaligned intervals
addUnalignedIntervals yields 240 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(7) has 1 intervals
descendant 1(10) has 1 intervals
propagateDescendantBreakpoints yields 89 intervals
Creating ancestral ordering
Previous anchoring score: 8.5825e+006, new anchor score: 2.76153e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2177 new matches outside LCBs
1,0 have 2266 new matches outside LCBs
0,0 has an additional 13415 matches
1,0 has an additional 12415 matches
Restoring backed up alignment tree...
3,4 has 13415 pairwise matches
6,4 has 12415 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1093 Mb
Pagefile usage: 843 Mb
construct LCB tracking matches
There are 46280 tracking matches
There are 181131 / 601640 components used
Working set size: 1095 Mb
Pagefile usage: 844 Mb
init tracking match LCB tracking
Working set size: 1095 Mb
Pagefile usage: 844 Mb
pairwise score tracking matches
Working set size: 1096 Mb
Pagefile usage: 845 Mb
get pairwise LCBs
there are 25359 pairwise LCBs
Working set size: 1100 Mb
Pagefile usage: 850 Mb
scaling bp penalty by conservation weight:
0.164392
0.171496
scaling bp penalty by bp weight:
0.188889
0.188889
Greedy BPE
Scoring with scaled breakpoint penalty: 50218.7
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%..done
Working set size: 1097 Mb
Pagefile usage: 847 Mb
Arrived at 131 intervals
Adding unaligned intervals
addUnalignedIntervals yields 330 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(7) has 1 intervals
descendant 1(10) has 1 intervals
propagateDescendantBreakpoints yields 131 intervals
Creating ancestral ordering
Previous anchoring score: 2.76153e+008, new anchor score: 2.84494e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 6802 new matches outside LCBs
1,0 have 3904 new matches outside LCBs
0,0 has an additional 13371 matches
1,0 has an additional 9758 matches
Restoring backed up alignment tree...
3,4 has 13371 pairwise matches
6,4 has 9758 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1101 Mb
Pagefile usage: 853 Mb
construct LCB tracking matches
There are 48059 tracking matches
There are 185804 / 624767 components used
Working set size: 1103 Mb
Pagefile usage: 854 Mb
init tracking match LCB tracking
Working set size: 1103 Mb
Pagefile usage: 854 Mb
pairwise score tracking matches
Working set size: 1104 Mb
Pagefile usage: 855 Mb
get pairwise LCBs
there are 24258 pairwise LCBs
Working set size: 1108 Mb
Pagefile usage: 858 Mb
scaling bp penalty by conservation weight:
0.164392
0.171496
scaling bp penalty by bp weight:
0.188889
0.188889
Greedy BPE
Scoring with scaled breakpoint penalty: 50218.7
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%..done
Working set size: 1105 Mb
Pagefile usage: 856 Mb
Arrived at 127 intervals
Adding unaligned intervals
addUnalignedIntervals yields 314 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(7) has 1 intervals
descendant 1(10) has 1 intervals
propagateDescendantBreakpoints yields 127 intervals
Creating ancestral ordering
Previous anchoring score: 2.84494e+008, new anchor score: 2.84926e+008
Working set size: 1105 Mb
Pagefile usage: 856 Mb
propagating ancestral breakpoints
Working set size: 1105 Mb
Pagefile usage: 856 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: 1066 Mb
Pagefile usage: 830 Mb
Fix left ends
Working set size: 1066 Mb
Pagefile usage: 830 Mb
done.
Working set size: 1066 Mb
Pagefile usage: 830 Mb
Aligning node 11 to 12 via 1!
Working set size: 1060 Mb
Pagefile usage: 826 Mb
get ancestral matches
Working set size: 1062 Mb
Pagefile usage: 828 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1062 Mb
Pagefile usage: 828 Mb
construct LCB tracking matches
There are 142786 tracking matches
There are 285572 / 1856218 components used
Working set size: 1133 Mb
Pagefile usage: 894 Mb
init tracking match LCB tracking
Working set size: 1134 Mb
Pagefile usage: 894 Mb
pairwise score tracking matches
Working set size: 1135 Mb
Pagefile usage: 895 Mb
get pairwise LCBs
there are 113263 pairwise LCBs
Working set size: 1156 Mb
Pagefile usage: 916 Mb
scaling bp penalty by conservation weight:
0.204503
scaling bp penalty by bp weight:
0.288889
Greedy BPE
Scoring with scaled breakpoint penalty: 31704.8
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%..done
Working set size: 1058 Mb
Pagefile usage: 822 Mb
Arrived at 58 intervals
Adding unaligned intervals
addUnalignedIntervals yields 176 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(11) has 1 intervals
descendant 1(12) has 1 intervals
propagateDescendantBreakpoints yields 58 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.42529e+007
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 9860 new matches outside LCBs
0,0 has an additional 35679 matches
Restoring backed up alignment tree...
2,5 has 35679 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1075 Mb
Pagefile usage: 839 Mb
construct LCB tracking matches
There are 92204 tracking matches
There are 184408 / 1198652 components used
Working set size: 1099 Mb
Pagefile usage: 861 Mb
init tracking match LCB tracking
Working set size: 1099 Mb
Pagefile usage: 861 Mb
pairwise score tracking matches
Working set size: 1100 Mb
Pagefile usage: 862 Mb
get pairwise LCBs
there are 24054 pairwise LCBs
Working set size: 1106 Mb
Pagefile usage: 868 Mb
scaling bp penalty by conservation weight:
0.204503
scaling bp penalty by bp weight:
0.288889
Greedy BPE
Scoring with scaled breakpoint penalty: 31704.8
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%..done
Working set size: 1058 Mb
Pagefile usage: 821 Mb
Arrived at 77 intervals
Adding unaligned intervals
addUnalignedIntervals yields 233 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(11) has 1 intervals
descendant 1(12) has 1 intervals
propagateDescendantBreakpoints yields 77 intervals
Creating ancestral ordering
Previous anchoring score: 3.42529e+007, new anchor score: 5.00634e+007
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 8915 new matches outside LCBs
0,0 has an additional 16404 matches
Restoring backed up alignment tree...
2,5 has 16404 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1070 Mb
Pagefile usage: 837 Mb
construct LCB tracking matches
There are 86282 tracking matches
There are 172564 / 1121666 components used
Working set size: 1090 Mb
Pagefile usage: 854 Mb
init tracking match LCB tracking
Working set size: 1090 Mb
Pagefile usage: 854 Mb
pairwise score tracking matches
Working set size: 1091 Mb
Pagefile usage: 855 Mb
get pairwise LCBs
there are 15184 pairwise LCBs
Working set size: 1095 Mb
Pagefile usage: 858 Mb
scaling bp penalty by conservation weight:
0.204503
scaling bp penalty by bp weight:
0.288889
Greedy BPE
Scoring with scaled breakpoint penalty: 31704.8
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%..done
Working set size: 1087 Mb
Pagefile usage: 851 Mb
Arrived at 62 intervals
Adding unaligned intervals
addUnalignedIntervals yields 188 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(11) has 1 intervals
descendant 1(12) has 1 intervals
propagateDescendantBreakpoints yields 62 intervals
Creating ancestral ordering
Previous anchoring score: 5.00634e+007, new anchor score: 5.08628e+007
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 7980 new matches outside LCBs
0,0 has an additional 13774 matches
Restoring backed up alignment tree...
2,5 has 13774 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1069 Mb
Pagefile usage: 832 Mb
construct LCB tracking matches
There are 84515 tracking matches
There are 169030 / 1098695 components used
Working set size: 1091 Mb
Pagefile usage: 853 Mb
init tracking match LCB tracking
Working set size: 1091 Mb
Pagefile usage: 853 Mb
pairwise score tracking matches
Working set size: 1092 Mb
Pagefile usage: 854 Mb
get pairwise LCBs
there are 12922 pairwise LCBs
Working set size: 1096 Mb
Pagefile usage: 858 Mb
scaling bp penalty by conservation weight:
0.204503
scaling bp penalty by bp weight:
0.288889
Greedy BPE
Scoring with scaled breakpoint penalty: 31704.8
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%..done
Working set size: 1091 Mb
Pagefile usage: 853 Mb
Arrived at 65 intervals
Adding unaligned intervals
addUnalignedIntervals yields 197 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(11) has 1 intervals
descendant 1(12) has 1 intervals
propagateDescendantBreakpoints yields 65 intervals
Creating ancestral ordering
Previous anchoring score: 5.08628e+007, new anchor score: 5.07901e+007
Working set size: 1091 Mb
Pagefile usage: 853 Mb
propagating ancestral breakpoints
Working set size: 1091 Mb
Pagefile usage: 853 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: 1108 Mb
Pagefile usage: 866 Mb
Fix left ends
Working set size: 1108 Mb
Pagefile usage: 866 Mb
done.
Working set size: 1108 Mb
Pagefile usage: 866 Mb
Aligning node 1 to 6 via 2!
Working set size: 1055 Mb
Pagefile usage: 815 Mb
get ancestral matches
Working set size: 1309 Mb
Pagefile usage: 1127 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1310 Mb
Pagefile usage: 1128 Mb
construct LCB tracking matches
There are 225495 tracking matches
There are 1661746 / 2931435 components used
Working set size: 1401 Mb
Pagefile usage: 1279 Mb
init tracking match LCB tracking
Working set size: 1407 Mb
Pagefile usage: 1284 Mb
pairwise score tracking matches
Working set size: 1390 Mb
Pagefile usage: 1294 Mb
get pairwise LCBs
there are 854029 pairwise LCBs
Working set size: 1392 Mb
Pagefile usage: 1382 Mb
scaling bp penalty by conservation weight:
0.222619 0.224788 0.229654
0.249511 0.249522 0.247523
scaling bp penalty by bp weight:
0.277778 0.244444 0.244444
0.322222 0.222222 0.233333
Greedy BPE
Scoring with scaled breakpoint penalty: 29824.4
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
1%..2%..3%..4%..5%..
Exited with error code: 3
------------------------------------------------------------------------------
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