Hi Aaron,
Thanks for your reply. Coincidentally I found out why I was getting the
error. The gbk files checked out just fine. The problem was that I did not
have the write permission to the directory where one of the GenBank files
was located (it turned out that the program would create the .sslist file
in the same directory where the gbk file is located - instead of /tmp or
the output directory which I was thinking of). The program works now! Thank
you for all help!
Best,
Hongxian
On Fri, Jul 1, 2016 at 1:31 AM, Aaron Darling <aaron.darl...@uts.edu.au>
wrote:
> 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_licheniformis_ATCC_14580_uid12388/CP000002.gbk
>
> ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/Bacillus_licheniformis_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/DSM13_vs_9945A
>
> --output-guide-tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.guide_tree
>
> --backbone-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_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/DSM13_vs_9945A
> --island-size=50
>
> --island-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.islands
> --backbone-size=50
> --max-backbone-gap=50
>
> --backbone-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.backbone
>
> --id-matrix=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_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/DSM13_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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