Hi Mark,
I'm not sure either of these will help, but they've both bitten
me in the past with fasta files; I honestly don't recall the
particular error message(s):
(1) Non-native or mixed end-of-line characters: In my experience
the Mac OS X version of Mauve expects Unix (LF) files, so if a Classic
Mac (CR) or Windows (CRLF) line slips in it has problems. You mention
TextWrangler, which I can think can convert end-of-lines as well as
its sibling, BBEdit.
(2) Blank lines in the fasta file (between sequences, not within
them). Again, I think TextWrangler can fix these: do a search-and
replace, replacing all \r\r with \r
Hope that helps,
Guy
On 5/19/11, Mark Mandel wrote:
Dear Mauve lovers,
I am attempting to use Mauve Contig Mover to rearrange ~100 fasta-formatted contigs in a draft genome assembly, using a GenBank-formatted reference assembly. Using default parameters + "iterative refinement" in the Mauve GUI on a Mac (OS X 10.6, default settings) the first 3 assemblies works fine, but on the 4th assembly MCM exits with an error code 11. The following details suggest to me that the formatting of the fasta file is the problem:
- Different reference genome with same fasta formatted draft produces error code 11.
- Same reference genome with other fasta-formatted draft produces output with no error.
However, I have not been able to identify any obvious error in this fasta file. I opened it in TextWrangler and re-saved it. In the DNA sequence there are only A/C/G/T, plus a handful (<30) of recognized ambiguous bases. The headers are all simple.
Any tips would be appreciated. The only note on this list I saw about an error 11 was back in 2007 and didn't provide additional insight. Log below.
Thanks,
Mark Mandel
P.S. ....and kudos to Anna, Aaron, Nicole, et al. for this wonderful part of Mauve.
shown
OS name is: Mac OS X arch: x86_64
Executing:
/Applications/Mauve.app/Contents/MacOS/progressiveMauve --output=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/alignment1 --weight=200 --output-guide-tree=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/alignment1.guide_tree --backbone-output=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/alignment1.backbone /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/1059.gbk /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/G0CEFIC01_assembly.fasta
Storing raw sequence at /var/folders/Bf/BfmUsD9IEK0z0edfb3CYzU+++TI/-Tmp-/rawseq406.000
Sequence loaded successfully.
/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/1059.gbk 4503336 base pairs.
Storing raw sequence at /var/folders/Bf/BfmUsD9IEK0z0edfb3CYzU+++TI/-Tmp-/rawseq406.001
Sequence loaded successfully.
/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/G0CEFIC01_assembly.fasta 4274522 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 2 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%..done.
using default bp penalty: 200
using default bp estimate min score: 463374
Starting with 23381 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.119988
0.119988 0
Writing guide tree to /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/alignment1.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 15467 initial LCBs
Using scaled bp penalty: 277899
Pair (0,1) has 22 well-supported breakpoints
genome content distance matrix:
0 0.119988
0.119988 0
bp distance matrix:
0.9 0.304615
0.304615 0.9
Aligning...
Aligning node 1 to 2 via 0!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 17131 tracking matches
There are 34262 / 51393 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 15471 pairwise LCBs
scaling bp penalty by conservation weight:
0.119988
scaling bp penalty by bp weight:
0.304615
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%..done
Arrived at 64 intervals
Adding unaligned intervals
addUnalignedIntervals yields 194 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 64 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 5.98418e+07
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2228 new matches outside LCBs
0,0 has an additional 9484 matches
Restoring backed up alignment tree...
1,0 has 9484 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 13809 tracking matches
There are 27618 / 41427 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 4891 pairwise LCBs
scaling bp penalty by conservation weight:
0.119988
scaling bp penalty by bp weight:
0.304615
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%..done
Arrived at 48 intervals
Adding unaligned intervals
addUnalignedIntervals yields 131 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 48 intervals
Creating ancestral ordering
Previous anchoring score: 5.98418e+07, new anchor score: 2.84664e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2064 new matches outside LCBs
0,0 has an additional 5000 matches
Restoring backed up alignment tree...
1,0 has 5000 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 13540 tracking matches
There are 27080 / 40620 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 4357 pairwise LCBs
scaling bp penalty by conservation weight:
0.119988
scaling bp penalty by bp weight:
0.304615
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%..done
Arrived at 50 intervals
Adding unaligned intervals
addUnalignedIntervals yields 139 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 50 intervals
Creating ancestral ordering
Previous anchoring score: 2.84664e+08, new anchor score: 2.8467e+08
propagating ancestral breakpoints
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%..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%..Fix left ends
done.
Performing final pass iterative refinement
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%..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%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
root alignment has 48 superintervals
root alignment length: 4917198
Organisms have 38.3% GC
Completed without error.
shown
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
printing
printing
done: /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/G0CEFIC01_assembly_contigs.tab
group determined empty
size 0: 4169570
removed lcb: 4169570
group determined empty
size 0: 4187767
removed lcb: 4187767
new lcbs: 41
placing conflicts
matching edges
new group: 3060696, 4098859 true
rev1: falserev2: true
new group: 3275602, 4114017 true
rev1: falserev2: false
new group: 1830475, 3085061 true
rev1: falserev2: false
unmatched length: 0
done with ordered. 60
unmatched length: 0
done with conflicted. 60
unmatched length: 0
done with unordered. 0
printing
printing
printing
done: /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment1/contigs/G0CEFIC01_assembly_contigs.tab
C: 1
shown
OS name is: Mac OS X arch: x86_64
Executing:
/Applications/Mauve.app/Contents/MacOS/progressiveMauve --output=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/alignment2 --weight=200 --output-guide-tree=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/alignment2.guide_tree --backbone-output=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/alignment2.backbone /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/1059.gbk /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/G0CEFIC01_assembly.fasta
Storing raw sequence at /var/folders/Bf/BfmUsD9IEK0z0edfb3CYzU+++TI/-Tmp-/rawseq410.000
Sequence loaded successfully.
/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/1059.gbk 4503336 base pairs.
Storing raw sequence at /var/folders/Bf/BfmUsD9IEK0z0edfb3CYzU+++TI/-Tmp-/rawseq410.001
Sequence loaded successfully.
/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/G0CEFIC01_assembly.fasta 4274522 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 2 seconds.
Creating sorted mer list
Create time was: 1 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: 200
using default bp estimate min score: 463374
Starting with 23391 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.119956
0.119956 0
Writing guide tree to /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/alignment2.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 15441 initial LCBs
Using scaled bp penalty: 277939
Pair (0,1) has 3 well-supported breakpoints
genome content distance matrix:
0 0.119956
0.119956 0
bp distance matrix:
0.9 0.0415385
0.0415385 0.9
Aligning...
Aligning node 1 to 2 via 0!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 17164 tracking matches
There are 34328 / 51492 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 15476 pairwise LCBs
scaling bp penalty by conservation weight:
0.119956
scaling bp penalty by bp weight:
0.0415385
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%..done
Arrived at 11 intervals
Adding unaligned intervals
addUnalignedIntervals yields 34 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 11 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 5.68676e+07
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1161 new matches outside LCBs
0,0 has an additional 7970 matches
Restoring backed up alignment tree...
1,0 has 7970 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 12870 tracking matches
There are 25740 / 38610 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 4162 pairwise LCBs
scaling bp penalty by conservation weight:
0.119956
scaling bp penalty by bp weight:
0.0415385
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%..done
Arrived at 11 intervals
Adding unaligned intervals
addUnalignedIntervals yields 32 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 11 intervals
Creating ancestral ordering
Previous anchoring score: 5.68676e+07, new anchor score: 2.85376e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1047 new matches outside LCBs
0,0 has an additional 3918 matches
Restoring backed up alignment tree...
1,0 has 3918 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 12588 tracking matches
There are 25176 / 37764 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 3594 pairwise LCBs
scaling bp penalty by conservation weight:
0.119956
scaling bp penalty by bp weight:
0.0415385
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%..done
Arrived at 13 intervals
Adding unaligned intervals
addUnalignedIntervals yields 38 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 13 intervals
Creating ancestral ordering
Previous anchoring score: 2.85376e+08, new anchor score: 2.85358e+08
propagating ancestral breakpoints
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
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%..Fix left ends
done.
Performing final pass iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..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%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
root alignment has 11 superintervals
root alignment length: 4923049
Organisms have 38.3% GC
Completed without error.
shown
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
not enought overlap: genome1_c20 (1,255050)
not enought overlap: genome1_c20 (1,255050)
not enought overlap: genome1_c20 (1,255050)
not enought overlap: genome1_c20 (1,255050)
not enought overlap: genome1_c20 (1,255050)
group determined empty
size 0: 4186740
removed lcb: 4186740
new lcbs: 10
placing conflicts
matching edges
unmatched length: 0
done with ordered. 61
unmatched length: 0
done with conflicted. 61
unmatched length: 0
done with unordered. 0
printing
printing
printing
done: /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment2/contigs/G0CEFIC01_assembly_contigs.tab
C: 2
shown
OS name is: Mac OS X arch: x86_64
Executing:
/Applications/Mauve.app/Contents/MacOS/progressiveMauve --output=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/alignment3 --weight=200 --output-guide-tree=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/alignment3.guide_tree --backbone-output=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/alignment3.backbone /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/1059.gbk /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/G0CEFIC01_assembly.fasta
Storing raw sequence at /var/folders/Bf/BfmUsD9IEK0z0edfb3CYzU+++TI/-Tmp-/rawseq412.000
Sequence loaded successfully.
/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/1059.gbk 4503336 base pairs.
Storing raw sequence at /var/folders/Bf/BfmUsD9IEK0z0edfb3CYzU+++TI/-Tmp-/rawseq412.001
Sequence loaded successfully.
/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/G0CEFIC01_assembly.fasta 4274522 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 2 seconds.
Creating sorted mer list
Create time was: 1 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: 200
using default bp estimate min score: 463374
Starting with 23388 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.11996
0.11996 0
Writing guide tree to /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/alignment3.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 15449 initial LCBs
Using scaled bp penalty: 277934
Pair (0,1) has 3 well-supported breakpoints
genome content distance matrix:
0 0.11996
0.11996 0
bp distance matrix:
0.9 0.0415385
0.0415385 0.9
Aligning...
Aligning node 1 to 2 via 0!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 17157 tracking matches
There are 34314 / 51471 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 15470 pairwise LCBs
scaling bp penalty by conservation weight:
0.11996
scaling bp penalty by bp weight:
0.0415385
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%..done
Arrived at 11 intervals
Adding unaligned intervals
addUnalignedIntervals yields 34 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 11 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 5.68651e+07
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1747 new matches outside LCBs
0,0 has an additional 8180 matches
Restoring backed up alignment tree...
1,0 has 8180 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 13081 tracking matches
There are 26162 / 39243 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 4374 pairwise LCBs
scaling bp penalty by conservation weight:
0.11996
scaling bp penalty by bp weight:
0.0415385
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%..done
Arrived at 13 intervals
Adding unaligned intervals
addUnalignedIntervals yields 38 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 13 intervals
Creating ancestral ordering
Previous anchoring score: 5.68651e+07, new anchor score: 2.85356e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1737 new matches outside LCBs
0,0 has an additional 4072 matches
Restoring backed up alignment tree...
1,0 has 4072 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 12689 tracking matches
There are 25378 / 38067 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 3702 pairwise LCBs
scaling bp penalty by conservation weight:
0.11996
scaling bp penalty by bp weight:
0.0415385
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%..done
Arrived at 12 intervals
Adding unaligned intervals
addUnalignedIntervals yields 35 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 12 intervals
Creating ancestral ordering
Previous anchoring score: 2.85356e+08, new anchor score: 2.85317e+08
propagating ancestral breakpoints
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..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%..Fix left ends
done.
Performing final pass iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..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%..Fix left ends
done.
root alignment has 13 superintervals
root alignment length: 4929228
Organisms have 38.3% GC
Completed without error.
shown
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
not enought overlap: genome1_c20 (1,255050)
not enought overlap: genome1_c20 (1,255050)
not enought overlap: genome1_c20 (1,255050)
not enought overlap: genome1_c20 (1,255050)
not enought overlap: genome1_c20 (1,255050)
new lcbs: 13
placing conflicts
matching edges
unmatched length: 0
done with ordered. 59
unmatched length: 0
done with conflicted. 59
unmatched length: 0
done with unordered. 0
printing
printing
printing
done: /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment3/contigs/G0CEFIC01_assembly_contigs.tab
C: 3
shown
OS name is: Mac OS X arch: x86_64
Executing:
/Applications/Mauve.app/Contents/MacOS/progressiveMauve --output=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment4/alignment4 --weight=200 --output-guide-tree=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment4/alignment4.guide_tree --backbone-output=/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment4/alignment4.backbone /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment4/1059.gbk /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment4/G0CEFIC01_assembly.fasta
Storing raw sequence at /var/folders/Bf/BfmUsD9IEK0z0edfb3CYzU+++TI/-Tmp-/rawseq416.000
Sequence loaded successfully.
/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment4/1059.gbk 4503336 base pairs.
Storing raw sequence at /var/folders/Bf/BfmUsD9IEK0z0edfb3CYzU+++TI/-Tmp-/rawseq416.001
Sequence loaded successfully.
/Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment4/G0CEFIC01_assembly.fasta 4274522 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 2 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%..done.
using default bp penalty: 200
using default bp estimate min score: 463374
Starting with 23389 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.119957
0.119957 0
Writing guide tree to /Users/markmandel/Documents/Molecules/mauve/110502 - 1059-1125 MCM/alignment4/alignment4.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 15452 initial LCBs
Using scaled bp penalty: 277937
Pair (0,1) has 3 well-supported breakpoints
genome content distance matrix:
0 0.119957
0.119957 0
bp distance matrix:
0.9 0.0415385
0.0415385 0.9
Aligning...
Aligning node 1 to 2 via 0!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 17162 tracking matches
There are 34324 / 51486 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 15473 pairwise LCBs
scaling bp penalty by conservation weight:
0.119957
scaling bp penalty by bp weight:
0.0415385
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%..done
Arrived at 19 intervals
Adding unaligned intervals
addUnalignedIntervals yields 58 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 19 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 5.68612e+07
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1652 new matches outside LCBs
0,0 has an additional 8497 matches
Restoring backed up alignment tree...
1,0 has 8497 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 13277 tracking matches
There are 26554 / 39831 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 4552 pairwise LCBs
scaling bp penalty by conservation weight:
0.119957
scaling bp penalty by bp weight:
0.0415385
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%..done
Arrived at 15 intervals
Adding unaligned intervals
addUnalignedIntervals yields 44 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 15 intervals
Creating ancestral ordering
Previous anchoring score: 5.68612e+07, new anchor score: 2.85344e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1479 new matches outside LCBs
Caught signal 11
Cleaning up and exiting!
Temporary files deleted.
Exited with error code: 11
------------------------------
Mark J. Mandel, Ph.D.
Assistant Professor
Department of Microbiology-Immunology
Northwestern University Feinberg School of Medicine
320 E. Superior St., Searle 3-403
Chicago, IL 60611
[email protected]
https://sites.google.com/site/markjmandel/
(312) 503-4138 Office
(312) 503-2915 Lab
(312) 503-9594 Fax
------------------------------------------------------------------------------
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools to help Windows* and Linux* C/C++ and Fortran
developers boost performance applications - including clusters.
http://p.sf.net/sfu/intel-dev2devmay
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------------------------------------------------------------------------------ What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay
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