Hello!
I have an xml output of the blast, which would be used to analyze the Blast2go, however, as early analysis, always comes up the following error message:
Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit
I was suggested to divide the xml file into smaller files, like I could do this?
I quickly wrote a tool to split a XML file: https://github.com/lindenb/jvarkit/wiki/Biostar165777
$ java -jar dist-1.139/biostar165777.jar -o out__SPLIT__.xml -T Hit -N 5 ~/blastn.xml
$ ls -la ~/blastn.xml out*.xml
-rw-rw-r-- 1 lindenb lindenb 422606 nov. 14 12:47 /home/lindenb/blastn.xml
-rw-rw-r-- 1 lindenb lindenb 86319 nov. 14 16:17 out001.xml
-rw-rw-r-- 1 lindenb lindenb 83570 nov. 14 16:17 out002.xml
-rw-rw-r-- 1 lindenb lindenb 85096 nov. 14 16:17 out003.xml
-rw-rw-r-- 1 lindenb lindenb 88297 nov. 14 16:17 out004.xml
-rw-rw-r-- 1 lindenb lindenb 87123 nov. 14 16:17 out005.xml
$ grep -cF "<Hit>" ~/blastn.xml out*.xml
/home/lindenb/blastn.xml:100
out001.xml:20
out002.xml:20
out003.xml:20
out004.xml:20
out005.xml:20
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version 2.3.6
did you try to increase the JVM memory with -XmX ? http://stackoverflow.com/questions/14763079
Hi Pierre,
I used Xmx60000m, I believe that I can not increase more =(
Yess! o //
Thank you Pierre, I will test the tool.
Hi Pierre,
The tool works for separation, However, the files Appear to all be the same, everyone starts describing the hits for the same gene, this is possible? it is possible to fix?
look at your question; You never talked about 'gene'. The tool only split the XML.