Dear Aaron,
Sorry for constantly bothering you.
I've been running alignment of complete bacterial genomes that I have
downloaded from ncbi. Not a big work, only 5 genomes ob about 4Mb maximum.
After successfully aligned the 5 of them and a subset of 3... I wanted to align
only 2 of them and an error occurred at the beginning of the task.
I copy here the whole console text:
Running alignment.
Executing
/Applications/Mauve 2.4.0/Mauve.app/Contents/MacOS/progressiveMauve
--output=/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome
Comparison/DDBJ_WGS/MAUVE alignemnts/Complete Apast (2s)
--output-guide-tree=/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome
Comparison/DDBJ_WGS/MAUVE alignemnts/Complete Apast (2s).guide_tree
--backbone-output=/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome
Comparison/DDBJ_WGS/MAUVE alignemnts/Complete Apast (2s).backbone
/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome Comparison/DDBJ_WGS/MAUVE
Input sequences/Acetobacter pasteurianus IFO 3283-01.gb
/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome Comparison/DDBJ_WGS/MAUVE
Input sequences/Acetobacter pasteurianus 386B.gb
Storing raw sequence at
/var/folders/sr/w5fjtzj91t72f0kjm0s3ny9m0000gn/T/rawseq7102.000
Sequence loaded successfully.
/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome Comparison/DDBJ_WGS/MAUVE Input
sequences/Acetobacter pasteurianus IFO 3283-01.gb 2907495 base pairs.
Storing raw sequence at
/var/folders/sr/w5fjtzj91t72f0kjm0s3ny9m0000gn/T/rawseq7102.001
Sequence loaded successfully.
/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome Comparison/DDBJ_WGS/MAUVE Input
sequences/Acetobacter pasteurianus 386B.gb 2818679 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 1 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: 150144
using default bp estimate min score: 450432
Starting with 2928 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.0942431
0.0942431 0
Writing guide tree to /Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome
Comparison/DDBJ_WGS/MAUVE alignemnts/Complete Apast (2s).guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 759 initial LCBs
Using scaled bp penalty: 303163
Pair (0,1) has 2 well-supported breakpoints
genome content distance matrix:
0 0.0942431
0.0942431 0
bp distance matrix:
0.9 0.0428571
0.0428571 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 2261 tracking matches
There are 4522 / 6783 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 768 pairwise LCBs
scaling bp penalty by conservation weight:
0.0942431
scaling bp penalty by bp weight:
0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 92578
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
Arrived at 5 intervals
Adding unaligned intervals
addUnalignedIntervals yields 16 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 5 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.27763e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 151 new matches outside LCBslibc++abi.dylib: terminating
Exited with error code: 134
Thank you for your help!!
Cristina
------------------------
Cristina Andres-Barrao, PhD.
cav00...@nodai.ac.jp
Laboratory of Fermentation Biochemistry
Department of Fermentation Sciences
Faculty of Applied Biosciences
Tokyo University of Agriculture
1-1-1 Sakuragaoka, Setagaya-ku
Tokyo 156-8502, Japan
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