Re: [Mauve-users] malloc error with Mauve Contig Mover-

[Aaron D. <aar...@ut...>]

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/escherich
> ia/GCF_000005845.2_ASM584v2_genomic.fna
> to
> 	/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherich
> ia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna
> Copying...
> 	/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherich
> ia/CAG00011_hs9.9_v3.fna
> to
> 	/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherich
> ia/testdir5/alignment1/CAG00011_hs9.9_v3.fna
> Running alignment.
> Executing 
> /Applications/Mauve.app/Contents/MacOS/progressiveMauve
>   --
> output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escheric
> hia/testdir5/alignment1/alignment1
>   --skip-refinement
>   --weight=200
>   --output-guide-
> tree=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichi
> a/testdir5/alignment1/alignment1.guide_tree
>   --backbone-
> output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escheric
> hia/testdir5/alignment1/alignment1.backbone
>  
> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/tes
> tdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna
>  
> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/tes
> tdir5/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/tes
> tdir5/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/tes
> tdir5/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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