Hello,
I used the stripSubsetLCBs program to extract the core genome of 27 bacteria
genomes. I used these paramethers:
>./stripSubsetLCBs clost_inpatients.xfma clost_inpatients.xfma.bbcols core.xfma
>500
and the run was successful...
"Read 28320 backbone entries
seq_count is: 27
output_ivs.size() 789"
However, when I tried to use Mauve to produce the SNPs using the core.xfma
file, the run failed.
java -cp
/home/gybazeta/Documents/Programs/mauve_snapshot_2012-06-07/mauve_snapshot_2012-06-07/Mauve.jar
org.gel.mauve.analysis.SnpExporter -f core.xfma -o aln_snp.out
Loading alignment file...This line could not be parsed: seq:caa)
This line could not be parsed: seq:tgt)
This line could not be parsed: seq:tgt)
This line could not be parsed: seq:tac)
This line could not be parsed: seq:ttc)
This line could not be parsed: seq:ttt)
java.lang.ArrayIndexOutOfBoundsException: genome genome1.gbk position 1
at org.gel.mauve.XMFAAlignment.getLCB(Unknown Source)
at org.gel.mauve.XMFAAlignment.getRange(Unknown Source)
at org.gel.mauve.SimilarityIndex.calculateIndex(Unknown Source)
at org.gel.mauve.SimilarityIndex.<init>(Unknown Source)
at org.gel.mauve.XmfaViewerModel.init(Unknown Source)
at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source)
at org.gel.mauve.analysis.SnpExporter.main(Unknown Source)
Perhaps I am missing something? may be another way to extract the SNPs from the
core.xfma file?
Cheers
Gustavo
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