Hi Aron,
thank you very much for your reply. I have finally figured out that Mauve works
fine when I use other input files, e.g. multi fasta files of my genomes.
Genbank files from other test genomes work as well. Maybe something is illegal
in the Genbank files of my genomes. Indeed, I received the following error
message using a (reformatted) genbank file.
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)
I do you have any suggestions, how I could preserve me annotations?
Best,
Gerald
-----Original Message-----
From: Aaron Darling [mailto:aaron.darl...@uts.edu.au]
Sent: Mittwoch, 30. April 2014 01:14
To: mauve-users@lists.sourceforge.net
Subject: Re: [Mauve-users] Mauve error code: 3
Hello Gerald,
Thanks for providing the console log output, it's helpful. The aligner appears
to have exited with the error right at the end of the alignment process. It's
possible that it has actually finished all of the work and the output files
exist, but there was some problem arising when the program deallocated memory
and resources as it shut down. Can you check whether the genome alignment file
"alignment1" is non-empty and if so whether it can be opened by the Mauve
viewer?
If the alignment file is empty it's possible that the aligner ran out of memory
at the final stage of alignment. It appears that your run used the 32-bit
version of progressiveMauve, which is limited to using 2GB of RAM. Can you try
using the 64-bit version of the aligner? One way to do so is by installing a
64-bit Java VM then (re)installing Mauve. For testing it might be easier to
just do it from the command line:
win64\progressiveMauve --output=C:\Users\glackner\Docs\alignment1
\alignment1 --output-guide-tree=C:\Users\glackner\Docs\alignment1
\alignment1.guide_tree --backbone-output=C:\Users\glackner\Docs
\alignment1\alignment1.backbone C:\Users\glackner\Docs\alignment1 \bla1.gbk
C:\Users\glackner\Docs\alignment1\bla2.gbk
The 64-bit version of progressiveMauve is located in the win64 subdirectory in
the Mauve 2.3.1 folder, within the C:\Program Files
(x86) or wherever else you may have chosen to install it.
Hope that helps,
-Aaron
On Thu, 2014-04-24 at 17:01 +1000, Lackner Gerald wrote:
> Hi there,
>
>
>
> I am unable to run Mauve 2.3.1 since it always exits with error code
> 3. Can anybody tell me the meaning of this error code and how I could
> fix this problem?
>
> Your help is very appreciated! See console output below.
>
>
>
> Best, Gerald
>
>
>
> OS name is: Windows 8 arch: x86
>
> Executing:
>
> progressiveMauve --output=C:\Users\glackner\Docs\alignment1\alignment1
> --skip-refinement --weight=200 --output-guide-tree=C:\Users\glackner
> \Docs\alignment1\alignment1.guide_tree --backbone-output=C:\Users
> \glackner\Docs\alignment1\alignment1.backbone C:\Users\glackner\Docs
> \alignment1\bla1.gbk C:\Users\glackner\Docs\alignment1\bla2.gbk
>
> Storing raw sequence at C:\Users\glackner\AppData\Local\Temp
> \raw28B5.tmp
>
> Sequence loaded successfully.
>
> C:\Users\glackner\Docs\alignment1\bla1.gbk 18823367 base pairs.
>
> Storing raw sequence at C:\Users\glackner\AppData\Local\Temp
> \raw2AAA.tmp
>
> Sequence loaded successfully.
>
> C:\Users\glackner\Docs\alignment1\bla2.gbk 19151376 base pairs.
>
> Using weight 17 mers for initial seeds
>
> Creating sorted mer list
>
> Create time was: 8 seconds.
>
> Creating sorted mer list
>
> Create time was: 8 seconds.
>
> 0%..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: 507749
>
> Starting with 717 multi-matches
>
> Computing genome content distance matrix...
>
>
>
>
>
> Genome conservation distance matrix:
>
> 0 0.991032
>
> 0.991032 0
>
>
>
> Writing guide tree to C:\Users\glackner\Docs\alignment1
> \alignment1.guide_tree
>
> reading tree...
>
> initializing alignment tree...
>
> Constructing seed occurrence lists for repeat detection
>
> Calculating pairwise breakpoint distances
>
> Pair 0, 1 has 573 initial LCBs
>
> Using scaled bp penalty: 4000
>
> Pair (0,1) has 1 well-supported breakpoints
>
> genome content distance matrix:
>
> 0 0.991032
>
> 0.991032 0
>
>
>
> bp distance matrix:
>
> 0.9 0.00316901
>
> 0.00316901 0.9
>
>
>
> Aligning...
>
> Aligning node 1 to 2 via 0!
>
> Working set size: 284 Mb
>
> Pagefile usage: 82 Mb
>
> get ancestral matches
>
> Working set size: 284 Mb
>
> Pagefile usage: 82 Mb
>
> Performing Sum-of-pairs Greedy Breakpoint Elimination
>
> Working set size: 284 Mb
>
> Pagefile usage: 82 Mb
>
> construct LCB tracking matches
>
> There are 583 tracking matches
>
> There are 1166 / 1749 components used
>
> Working set size: 284 Mb
>
> Pagefile usage: 82 Mb
>
> init tracking match LCB tracking
>
> Working set size: 284 Mb
>
> Pagefile usage: 82 Mb
>
> pairwise score tracking matches
>
> Working set size: 285 Mb
>
> Pagefile usage: 82 Mb
>
> get pairwise LCBs
>
> there are 576 pairwise LCBs
>
> Working set size: 285 Mb
>
> Pagefile usage: 82 Mb
>
> scaling bp penalty by conservation weight:
>
> 0.991032
>
>
>
>
>
> scaling bp penalty by bp weight:
>
> 0.00316901
>
>
>
> 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%..94%..done
>
> Working set size: 285 Mb
>
> Pagefile usage: 82 Mb
>
> Arrived at 1 intervals
>
> Adding unaligned intervals
>
> addUnalignedIntervals yields 5 intervals
>
> Merging unaligned intervals
>
> Marbling gaps
>
> Propagating descendant breakpoints
>
> descendant 0(1) has 1 intervals
>
> descendant 1(2) has 1 intervals
>
> propagateDescendantBreakpoints yields 1 intervals
>
> Creating ancestral ordering
>
> Previous anchoring score: -1.79769e+308, new anchor score: 3
>
> Backing up alignment tree...
>
> propagating ancestral breakpoints
>
> recursive anchor search
>
> 0,0 have 503 new matches outside LCBs
>
> 0,0 has an additional 92316 matches
>
> Restoring backed up alignment tree...
>
> 1,0 has 92316 pairwise matches
>
> Performing Sum-of-pairs Greedy Breakpoint Elimination
>
> Working set size: 412 Mb
>
> Pagefile usage: 219 Mb
>
> construct LCB tracking matches
>
> There are 91947 tracking matches
>
> There are 183894 / 275841 components used
>
> Working set size: 444 Mb
>
> Pagefile usage: 253 Mb
>
> init tracking match LCB tracking
>
> Working set size: 444 Mb
>
> Pagefile usage: 253 Mb
>
> pairwise score tracking matches
>
> Working set size: 549 Mb
>
> Pagefile usage: 254 Mb
>
> get pairwise LCBs
>
> there are 25707 pairwise LCBs
>
> Working set size: 558 Mb
>
> Pagefile usage: 263 Mb
>
> scaling bp penalty by conservation weight:
>
> 0.991032
>
>
>
>
>
> scaling bp penalty by bp weight:
>
> 0.00316901
>
>
>
> 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%..94%..95%..96%..97%..done
>
> Working set size: 530 Mb
>
> Pagefile usage: 237 Mb
>
> Arrived at 1 intervals
>
> Adding unaligned intervals
>
> addUnalignedIntervals yields 5 intervals
>
> Merging unaligned intervals
>
> Marbling gaps
>
> Propagating descendant breakpoints
>
> descendant 0(1) has 1 intervals
>
> descendant 1(2) has 1 intervals
>
> propagateDescendantBreakpoints yields 1 intervals
>
> Creating ancestral ordering
>
> Previous anchoring score: 3, new anchor score: -7
>
> Working set size: 575 Mb
>
> Pagefile usage: 307 Mb
>
> propagating ancestral breakpoints
>
> Working set size: 575 Mb
>
> Pagefile usage: 307 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: 592 Mb
>
> Pagefile usage: 324 Mb
>
> Fix left ends
>
> Working set size: 592 Mb
>
> Pagefile usage: 324 Mb
>
>
>
> done.
>
> Working set size: 592 Mb
>
> Pagefile usage: 324 Mb
>
> root alignment has 1 superintervals
>
> root alignment length: 37974643
>
>
>
> This application has requested the Runtime to terminate it in an
> unusual way.
>
> Please contact the application's support team for more information.
>
> Exited with error code: 3
>
>
>
>
>
>
--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
UTS CRICOS Provider Code: 00099F
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