Hello Hongxian,
Where/how did you obtain those GBK files? Downloads from the NCBI web
site in GBK format can fail to include the actual genome sequence. Can
you check whether your gbk files have the actual nucleotide sequence at
the end? The file sizes should each be around 9Mb for those two
genomes.
To test it out, I obtained copies of those two genomes from the GenBank
ftp archive:
ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/Bacillus_li
cheniformis_ATCC_14580_uid12388/CP000002.gbk
ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/Bacillus_li
cheniformis_9945A_uid49115/CP005965.gbk
and it appears to work as expected with Mauve (the snapshot for linux),
so perhaps you can try again with the files from those ftp links?
Best,
-Aaron
On Thu, 2016-06-30 at 11:28 -0400, Hongxian He wrote:
>
>
> Hi,
>
> I am new to Mauve. I've downloaded both stable 2.4.0 release and
> latest snapshot, but I am running into problems while trying to align
> two genomes in GenBank formats. Both genomes were downloaded from
> NCBI (full gbk files with nucleotide sequences). I've tried both
> versions, and tried both regular aligner and progressiveMauve
> aligner, and I got errors in both cases. I have increased the default
> memory setting with "JAVA_ARGS="-Xms8000M -Xmx32000M" (I have 32GB
> RAM on my workstation). There is 16GB free space in /tmp.
>
> However, when I aligned them using their raw FASTA files, it worked.
>
> Has anyone seen this kind of error before?
>
> Thanks very much,
> Hongxian
>
> [Error Message]
>
> trying path /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve
> Running alignment.
> Executing
> /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve
> --
> output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS
> M13_vs_9945A
> --output-guide-
> tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM1
> 3_vs_9945A.guide_tree
> --backbone-
> output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS
> M13_vs_9945A.backbone
>
> /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.
> gbk
>
> /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.
> gbk
> Storing raw sequence at /tmp/rawseq15048.000
> Sequence loaded successfully.
> /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.
> gbk 4222645 base pairs.
> Storing raw sequence at /tmp/rawseq15048.001
> Sequence loaded successfully.
> Error creating sorted mer list
> /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.
> gbk 4376305 base pairs.
>
> terminate called after throwing an instance of 'genome::gnException
> 'Using weight 15 mers for initial seeds
> Creating sorted mer list
> Exited with error code: 134
>
> trying path /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner
> Running alignment.
> Executing
> /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner
> --
> output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS
> M13_vs_9945A
> --island-size=50
> --island-
> output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS
> M13_vs_9945A.islands
> --backbone-size=50
> --max-backbone-gap=50
> --backbone-
> output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS
> M13_vs_9945A.backbone
> --id-
> matrix=/home/hongxian/projects/bacillus_platform/genome_comparison/DS
> M13_vs_9945A.id_matrix
> --output-
> alignment=/home/hongxian/projects/bacillus_platform/genome_comparison
> /DSM13_vs_9945A.alignment
> --output-guide-
> tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM1
> 3_vs_9945A.guide_tree
>
> /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.
> gbk
>
> /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.
> gbk.sslist
>
> /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.
> gbk
>
> /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.
> gbk.sslist
> Error creating sorted mer listSequence loaded successfully.
>
> /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.
> gbk 4222645 base pairs.
> Sequence loaded successfully.
> /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.
> gbk 4376305 base pairs.
> Using weight 15 mers for initial seeds
> Creating sorted mer list
> Unhandled gnException: Exception FileNotOpened thrown from
> Unknown() in FileSML.cpp 125
> Unable to open file for writing.
>
> Exited with error code: 246
>
>
>
> -------------------------------------------------------------------
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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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