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
>
> -------------------------------------------------------------------
> -----------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Mauve-users mailing list
> Mauve-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mauve-users
--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
UTS CRICOS Provider Code: 00099F
DISCLAIMER: This email message and any accompanying attachments may contain
confidential information.
If you are not the intended recipient, do not read, use, disseminate,
distribute or copy this message or
attachments. If you have received this message in error, please notify the
sender immediately and delete
this message. Any views expressed in this message are those of the individual
sender, except where the
sender expressly, and with authority, states them to be the views of the
University of Technology Sydney.
Before opening any attachments, please check them for viruses and defects.
Think. Green. Do.
Please consider the environment before printing this email.
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
