[Mauve-users] malloc error with Mauve Contig Mover-
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From: Eugeni B. <eug...@gm...> - 2017-01-09 09:44:36
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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 |