MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
I always have issue in ClusterESP step (no enough heap memory), even though I used the command line as follow:
java -Xmx30g -jar /home/medhat/source/gasv//bin/GASV.jar --cluster --batch --maximal --output regions --nohead --minClusterSize 1 --outputdir ./multibread_sv_result/tolerant-RunGASV/ --verbose ./multibread_sv_result/tolerant-RunGASV/gasv.in Using window size of 84946
ClusterESP: processing chr 1, chr1
but I still have this error:
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.nio.HeapByteBuffer.(HeapByteBuffer.java:57)
at java.nio.ByteBuffer.allocate(ByteBuffer.java:335)
at sun.nio.cs.StreamDecoder.(StreamDecoder.java:251)
at sun.nio.cs.StreamDecoder.(StreamDecoder.java:231)
at sun.nio.cs.StreamDecoder.forInputStreamReader(StreamDecoder.java:69)
at java.io.InputStreamReader.(InputStreamReader.java:74)
at java.io.FileReader.(FileReader.java:58)
at gasv.main.ReadESP.(Unknown Source)
at gasv.main.ReadInput.createReadFiles(Unknown Source)
at gasv.main.ReadInput.readWindowFromFiles(Unknown Source)
at gasv.main.ClusterESP.clusterESP(Unknown Source)
at gasv.main.GASVMain.main(Unknown Source)
I always have issue in ClusterESP step (no enough heap memory), even though I used the command line as follow:
java -Xmx30g -jar /home/medhat/source/gasv//bin/GASV.jar --cluster --batch --maximal --output regions --nohead --minClusterSize 1 --outputdir ./multibread_sv_result/tolerant-RunGASV/ --verbose ./multibread_sv_result/tolerant-RunGASV/gasv.in Using window size of 84946 ClusterESP: processing chr 1, chr1 but I still have this error:
any solution?