Hello Aaron,
Thanks a lot for your quick response. I’ve checked and there was a problem
apparently with sequence IDs; after sequence renaming MCM works fine.
All the best
Eugeni
> On 9 Jan 2017, at 12:26, Aaron Darling <aaron.darl...@uts.edu.au> wrote:
>
> Hi Eugeni,
> Before the malloc error, the aligner issued a warning message about the file
> CAG00011_hs9.9_v3.fna, which contains characters or formatting that the
> software was not expecting in a FastA file. I suggest carefully checking that
> file first.
>
> -Aaron
>
> On Mon, 2017-01-09 at 10:44 +0100, Eugeni Belda wrote:
>> Hello,
>> I’m trying to reorder a set of E.coli contigs from a draft metagenomic
>> assembly (5000 contigs approximately) against the reference E. coli
>> K12-MG1335 sequence using the MCM option of Mauve, but the following error
>> message appears on Mauve console:
>>
>> Copying...
>>
>> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/GCF_000005845.2_ASM584v2_genomic.fna
>> to
>>
>> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna
>> Copying...
>>
>> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/CAG00011_hs9.9_v3.fna
>> to
>>
>> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna
>> Running alignment.
>> Executing
>> /Applications/Mauve.app/Contents/MacOS/progressiveMauve
>>
>> --output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1
>> --skip-refinement
>> --weight=200
>>
>> --output-guide-tree=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1.guide_tree
>>
>> --backbone-output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1.backbone
>>
>> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna
>>
>> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna
>> Storing raw sequence at
>> /var/folders/68/q1l_zkrx2ll01m7rq3y3cl900000gn/T/rawseq44633.000
>> Sequence loaded successfully.
>> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna
>> 4641652 base pairs.
>> Storing raw sequence at
>> /var/folders/68/q1l_zkrx2ll01m7rq3y3cl900000gn/T/rawseq44633.001
>> Sequence loaded successfully.ERROR! gap character encountered at genome
>> sequence position 201558
>>
>> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna
>> 4278085 base pairs.Input sequences must be unaligned and ungapped!
>>
>> Using weight 15 mers for initial seeds
>> Creating sorted mer list
>> Create time was: 2 seconds.
>> Creating sorted mer list
>> progressiveMauve(44633,0x7fffa7cd83c0) malloc: *** error for object
>> 0x7f9810531b50: pointer being freed was not allocated
>> *** set a breakpoint in malloc_error_break to debug
>> Exited with error code: 134
>>
>> I’ve looked on the mauve-users mailing list for similar problem but I
>> haven’t found anything related. Any support will be very appreciated.
>> Yours sincerely
>> Eugeni Belda
>>
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> --
> Aaron E. Darling, Ph.D.
> Associate Professor, ithree institute
> University of Technology Sydney
> Australia
>
> http://darlinglab.org
> twitter: @koadman
>
>
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