Hello,
I am trying to reorder contigs of a couple of bacterial genomes using
MAUVE. It did work in the past with one of the strains and I got 6
alignments. Now I am using genebank files to keep annotation. With the same
strain that worked before, I am getting only one alignment and an error
message before the start of the second round. Could someone help me find
out what's wrong? I ran this on two computers, to check if it some software
problem, and got the same error with both.
Thanks a lot. The log is attached.
Shlomo
shown
OS name is: Windows Vista arch: x86
Executing:
progressiveMauve --seed-family --output=C:\Users\Tsutsi\Desktop\MAUVE
reorder\P4\alignment1\alignment1 --weight=200
--output-guide-tree=C:\Users\Tsutsi\Desktop\MAUVE
reorder\P4\alignment1\alignment1.guide_tree
--backbone-output=C:\Users\Tsutsi\Desktop\MAUVE
reorder\P4\alignment1\alignment1.backbone C:\Users\Tsutsi\Desktop\MAUVE
reorder\P4\alignment1\NC_000913.fasta C:\Users\Tsutsi\Desktop\MAUVE
reorder\P4\alignment1\UWO.gbk
Storing raw sequence at C:\Users\Tsutsi\AppData\Local\Temp\raw8F4E.tmp
Sequence loaded successfully.
C:\Users\Tsutsi\Desktop\MAUVE reorder\P4\alignment1\NC_000913.fasta 4639675
base pairs.
Storing raw sequence at C:\Users\Tsutsi\AppData\Local\Temp\raw9049.tmp
Sequence loaded successfully.
C:\Users\Tsutsi\Desktop\MAUVE reorder\P4\alignment1\UWO.gbk 4872465 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 6 seconds.
Creating sorted mer list
Create time was: 7 seconds.
Searching with seed pattern 11110011010101011001111
Creating sorted mer list
Create time was: 6 seconds.
Creating sorted mer list
Create time was: 6 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
Creating sorted mer list
Create time was: 5 seconds.
Creating sorted mer list
Create time was: 7 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 11110101100100110101111
Creating sorted mer list
Create time was: 6 seconds.
Creating sorted mer list
Create time was: 6 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: 465808
Starting with 3036 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.0772755
0.0772755 0
Writing guide tree to C:\Users\Tsutsi\Desktop\MAUVE
reorder\P4\alignment1\alignment1.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 1763 initial LCBs
Using scaled bp penalty: 337672
Pair (0,1) has 40 well-supported breakpoints
genome content distance matrix:
0 0.0772755
0.0772755 0
bp distance matrix:
0.9 0.507042
0.507042 0.9
Aligning...
Aligning node 1 to 2 via 0!
Working set size: 100 Mb
Pagefile usage: 27 Mb
get ancestral matches
Working set size: 100 Mb
Pagefile usage: 27 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 100 Mb
Pagefile usage: 27 Mb
construct LCB tracking matches
There are 2182 tracking matches
There are 4364 / 6546 components used
Working set size: 101 Mb
Pagefile usage: 27 Mb
init tracking match LCB tracking
Working set size: 101 Mb
Pagefile usage: 27 Mb
pairwise score tracking matches
Working set size: 103 Mb
Pagefile usage: 28 Mb
get pairwise LCBs
there are 1746 pairwise LCBs
Working set size: 103 Mb
Pagefile usage: 28 Mb
scaling bp penalty by conservation weight:
0.0772755
scaling bp penalty by bp weight:
0.507042
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%..done
Working set size: 103 Mb
Pagefile usage: 28 Mb
Arrived at 82 intervals
Adding unaligned intervals
addUnalignedIntervals yields 238 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 82 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.26511e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1780 new matches outside LCBs
0,0 has an additional 6577 matches
Restoring backed up alignment tree...
1,0 has 6577 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 117 Mb
Pagefile usage: 48 Mb
construct LCB tracking matches
There are 5144 tracking matches
There are 10288 / 15432 components used
Working set size: 118 Mb
Pagefile usage: 49 Mb
init tracking match LCB tracking
Working set size: 118 Mb
Pagefile usage: 49 Mb
pairwise score tracking matches
Working set size: 125 Mb
Pagefile usage: 50 Mb
get pairwise LCBs
there are 4106 pairwise LCBs
Working set size: 126 Mb
Pagefile usage: 51 Mb
scaling bp penalty by conservation weight:
0.0772755
scaling bp penalty by bp weight:
0.507042
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
Working set size: 126 Mb
Pagefile usage: 50 Mb
Arrived at 79 intervals
Adding unaligned intervals
addUnalignedIntervals yields 205 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 79 intervals
Creating ancestral ordering
Previous anchoring score: 2.26511e+008, new anchor score: 3.7318e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1382 new matches outside LCBs
0,0 has an additional 4110 matches
Restoring backed up alignment tree...
1,0 has 4110 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 128 Mb
Pagefile usage: 52 Mb
construct LCB tracking matches
There are 4908 tracking matches
There are 9816 / 14724 components used
Working set size: 128 Mb
Pagefile usage: 52 Mb
init tracking match LCB tracking
Working set size: 128 Mb
Pagefile usage: 52 Mb
pairwise score tracking matches
Working set size: 128 Mb
Pagefile usage: 52 Mb
get pairwise LCBs
there are 3762 pairwise LCBs
Working set size: 128 Mb
Pagefile usage: 53 Mb
scaling bp penalty by conservation weight:
0.0772755
scaling bp penalty by bp weight:
0.507042
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
Working set size: 128 Mb
Pagefile usage: 52 Mb
Arrived at 76 intervals
Adding unaligned intervals
addUnalignedIntervals yields 197 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 76 intervals
Creating ancestral ordering
Previous anchoring score: 3.7318e+008, new anchor score: 3.73213e+008
Working set size: 128 Mb
Pagefile usage: 52 Mb
propagating ancestral breakpoints
Working set size: 128 Mb
Pagefile usage: 52 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: 164 Mb
Pagefile usage: 99 Mb
Fix left ends
Working set size: 164 Mb
Pagefile usage: 99 Mb
done.
Working set size: 164 Mb
Pagefile usage: 99 Mb
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%..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: 164 Mb
Pagefile usage: 99 Mb
Fix left ends
Working set size: 164 Mb
Pagefile usage: 99 Mb
done.
root alignment has 79 superintervals
root alignment length: 5133684
Organisms have 50.7% GC
Completed without error.
shown
Error reading file.
org.biojava.bio.BioException: Could not read sequence
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:108)
at org.gel.mauve.format.BaseFormat$2.nextSequence(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.XmfaViewerModel.init(Unknown Source)
at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source)
at org.gel.mauve.ModelBuilder.buildModel(Unknown Source)
at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source)
at org.gel.mauve.gui.FrameLoader.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(Unknown Source)
at
org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankContext.java:292)
at
org.biojava.bio.seq.io.GenbankContext.processLine(GenbankContext.java:129)
at
org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java:146)
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)
... 10 more
printing
printing
done: C:\Users\Tsutsi\Desktop\MAUVE reorder\P4\alignment1\UWO.gbk_contigs.tab
Exception in thread "Thread-8" java.lang.NullPointerException
at org.gel.mauve.MauveHelperFunctions.getFeatures(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.output(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.initMauveData(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.initModelData(Unknown Source)
at
org.gel.mauve.contigs.ContigReorderer$ReordererMauveFrame$1.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
------------------------------------------------------------------------------
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