Re: [Mauve-users] Error in aligning GenBank files

[Peter H. <pet...@ok...>]

Hi Hongxian,

I was able to do those alignments on a windows desktop with 16GB RAM, so 
my recommendation is to re-download the genebank files from NCBI, and 
try again using the DEFAULT parameters (including NOT renaming the 
output files). the error

"Unhandled gnException: Exception FileNotOpened thrown from Unknown()  
in FileSML.cpp 125

Suggests the software was looking for a file it couldn't find.... maybe 
because you renamed some output files.

My Java settings were:

"C:\Program Files\Java\jre1.8.0_91\bin\javaw.exe" -jar -XX:NewSize=4000m 
-XX:MaxNewSize=4000m -XX:+UseParallelGC -XX:NewRatio=8 -Xmx8000m 
-Xss512M -Xms8000m Mauve.jar

Hope that helps.

Peter


On 06/30/2016 10:28 AM, 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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