hello,
I am trying to use Mauve to align my scaffolds.fa output from a Spades de novo
assembly against a reference, but received an error. I've attached the error
output file for your consideration and would greatly appreciate any feedback.
Thanks again and I hope to hear from you soon.
trying path ./linux-x64/progressiveMauve
Running alignment.
Executing
./linux-x64/progressiveMauve
--output=/home/molecularecology/Desktop/mauveSPadesREf
--output-guide-tree=/home/molecularecology/Desktop/mauveSPadesREf.guide_tree
--backbone-output=/home/molecularecology/Desktop/mauveSPadesREf.backbone
/home/molecularecology/Desktop/zcpb/refo/Ldec.genome.10062013.fa
/home/molecularecology/Desktop/zcpb/spades_outputs/scaffolds.fasta
Storing raw sequence at /tmp/rawseq21575.000
Sequence loaded successfully.
/home/molecularecology/Desktop/zcpb/refo/Ldec.genome.10062013.fa 1170241964
base pairs.
Storing raw sequence at /tmp/rawseq21575.001
Sequence loaded successfully.
/home/molecularecology/Desktop/zcpb/spades_outputs/scaffolds.fasta 597642283
base pairs.
Using weight 21 mers for initial seeds
Creating sorted mer list
Create time was: 154 seconds.
Creating sorted mer list
Create time was: 82 seconds.
0%..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%..
done.
using default bp penalty: 208036
using default bp estimate min score: 624107
Starting with 6987946 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.7505
0.7505 0
Writing guide tree to /home/molecularecology/Desktop/mauveSPadesREf.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 4841563 initial LCBs
Using scaled bp penalty: 4000
Pair (0,1) has 189698 well-supported breakpoints
genome content distance matrix:
0 0.7505
0.7505 0
bp distance matrix:
0.9 0.9
0.9 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 6381046 tracking matches
There are 12762092 / 19143138 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 4842018 pairwise LCBs
scaling bp penalty by conservation weight:
0.7505
scaling bp penalty by bp weight:
0.9
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%..done
Arrived at 188889 intervals
Adding unaligned intervals
addUnalignedIntervals yields 566486 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 188889 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 6.48718e+09
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
Creating dmSML for seqI 0
Wrote raw sequence for seqI 0
Loaded sequence 0363140026b.p.
MemTotal: 32840720 kB
Crap. It's broke, return value 1
terminate called after throwing an instance of 'genome::gnException'
Exited with error code: 134
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