Thank you sir. But when I downloaded the recent version and tried the
alignment, I was returned with the following error.
trying path /home/mku/Downloads/mauve_2.4.0/linux-x64/mauveAligner
Running alignment.
Executing
/home/mku/Downloads/mauve_2.4.0/linux-x64/mauveAligner
--output=/media/New Volume_/mauvee
--island-size=50
--island-output=/media/New Volume_/mauvee.islands
--backbone-size=50
--max-backbone-gap=50
--backbone-output=/media/New Volume_/mauvee.backbone
--id-matrix=/media/New Volume_/mauvee.id_matrix
--output-alignment=/media/New Volume_/mauvee.alignment
--output-guide-tree=/media/New Volume_/mauvee.guide_tree
/media/SWETHA/My Project!/Sequences/M.brandtii/Mbrandtii rna.gbk
/media/SWETHA/My Project!/Sequences/M.brandtii/Mbrandtii rna.gbk.sslist
/media/SWETHA/My Project!/Sequences/P.alecto/Palecto rna.gbk
/media/SWETHA/My Project!/Sequences/P.alecto/Palecto rna.gbk.sslist
/home/mku/Downloads/mauve_2.4.0/linux-x64/mauveAligner: 1: Syntax
error: "(" unexpected
Exited with error code: 2
On 2/12/15, Aaron Darling <aarondarl...@ucdavis.edu> wrote:
> Hi Swetha,
>
> It looks like you've used the older 32-bit version of progressiveMauve.
> That version is limited to using 4GB of memory, which is not enough for
> your dataset. I'd suggest getting the current 2.4.0 release, which is
> 64-bit only. It is available here:
> http://darlinglab.org/mauve/download.html
>
> Hopefully that solves the problem but if you encounter more issues
> please get in touch again.
>
> Best,
> -Aaron
>
>
> On Thu, 2015-02-12 at 12:53 +0530, Swetha Gopal wrote:
>> Hello !
>>
>> Am a new user for Mauve and I tried aligning two mammalian bat
>> genomes (rna.gbk files) but the error code 134 was returned and I am
>> not able to find out a solution for the same. I used the Progressive
>> Mauve and retained the default values for parameters and scoring. Do
>> suggest a solution. The console log is as follows.
>>
>> OS name is: Linux arch: i386
>> trying path /home/mku/Downloads/mauve_2.3.1/progressiveMauve
>> Executing:
>> /home/mku/Downloads/mauve_2.3.1/progressiveMauve
>> --output=/home/mku/Pictures/mauve
>> --output-guide-tree=/home/mku/Pictures/mauve.guide_tree
>> --backbone-output=/home/mku/Pictures/mauve.backbone /media/SWETHA/My
>> Project!/Sequences/M.brandtii/M.brandtii rna.gbk /media/SWETHA/My
>> Project!/Sequences/P.alecto/P.alecto rna.gbk
>> Storing raw sequence at /tmp/rawseq7653.000
>> Sequence loaded successfully.
>> /media/SWETHA/My Project!/Sequences/M.brandtii/M.brandtii rna.gbk
>> 81248420 base pairs.
>> Storing raw sequence at /tmp/rawseq7653.001
>> Sequence loaded successfully.
>> /media/SWETHA/My Project!/Sequences/P.alecto/P.alecto rna.gbk
>> 57233395 base pairs.
>> Using weight 19 mers for initial seeds
>> Creating sorted mer list
>> Create time was: 77 seconds.
>> Creating sorted mer list
>> Create time was: 55 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: 182316
>> using default bp estimate min score: 546948
>> Starting with 189877 multi-matches
>> Computing genome content distance matrix...
>>
>>
>> Genome conservation distance matrix:
>> 0 0.786507
>> 0.786507 0
>>
>> Writing guide tree to /home/mku/Pictures/mauve.guide_tree
>> reading tree...
>> initializing alignment tree...
>> Constructing seed occurrence lists for repeat detection
>> Calculating pairwise breakpoint distances
>> Pair 0, 1 has 57809 initial LCBs
>> Using scaled bp penalty: 4000
>> Pair (0,1) has 7854 well-supported breakpoints
>> genome content distance matrix:
>> 0 0.786507
>> 0.786507 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 172041 tracking matches
>> There are 344082 / 516123 components used
>> init tracking match LCB tracking
>> pairwise score tracking matches
>> get pairwise LCBs
>> there are 57731 pairwise LCBs
>> scaling bp penalty by conservation weight:
>> 0.786507
>>
>>
>> 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%..done
>> Arrived at 8076 intervals
>> Adding unaligned intervals
>> addUnalignedIntervals yields 24211 intervals
>> Merging unaligned intervals
>> Marbling gaps
>> Propagating descendant breakpoints
>> descendant 0(1) has 1 intervals
>> descendant 1(2) has 1 intervals
>> propagateDescendantBreakpoints yields 8076 intervals
>> Creating ancestral ordering
>> Previous anchoring score: -1.79769e+308, new anchor score: 8.83463e+08
>> Backing up alignment tree...
>> propagating ancestral breakpoints
>> recursive anchor search
>> Creating dmSML for seqI 0
>> Wrote raw sequence for seqI 0
>> Loaded sequence 023837698b.p.
>> MemTotal: 3966888 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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>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
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> Mauve-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mauve-users
>
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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