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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