Re: [igv-help] I am trying to convert MAF to SAM, but it runs into java error.
Jim Robinson
It looks like you are running out of memory, you need to allocate
more. To do so edit the file “igvtools”, which is a shell
script. And edit this parameter -Xmx1500m. For example, to
allocate 4gb change it to
java -Djava.awt.headless=true -Xmx4g -jar `dirname $0`/igvtools.jar "$@“
If you are on a large memory machine you can make that 8g. Hopefully you are not trying this on Windows.
Jim
I have a 20GB MAF file and I am using the following command to convert it to SAM file. It generates about 5GB of output data and then crashes. Please let me know how I can fix it.--
igvtools MAFtoSAM filtered_all_chr_122.maf filtered_all_chr_122.sam
error after it runs for a few hours:
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOfRange(Arrays.java:3664)
at java.lang.String.<init>(String.java:207)
at java.lang.String.substring(String.java:1969)
at java.lang.String.subSequence(String.java:2003)
at java.util.regex.Pattern.split(Pattern.java:1216)
at org.broad.igv.tools.sort.Parser.createRecord(Parser.java:85)
at org.broad.igv.tools.sort.Parser.readNextRecord(Parser.java:74)
at org.broad.igv.tools.sort.AsciiSorter.run(AsciiSorter.java:109)
at org.broad.igv.maf.MAFtoSAM.addSATags(MAFtoSAM.java:102)
at org.broad.igv.maf.MAFtoSAM.convert(MAFtoSAM.java:90)
at org.broad.igv.tools.IgvTools.run(IgvTools.java:455)
at org.broad.igv.tools.IgvTools.main(IgvTools.java:259)
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