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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