addnorm: Requested array size exceeds VM limit

[jiangshan529]

Hi, I am creating a hic file with 1.7 billion reads to 50 bp res map, but the addnorm always failed in the last step. How could this be resolved? I requested a google cloud server with 700gb memory and the used memory never exceeds 100g.

Calculating norms for zoom BP_50
Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit
at java.base/java.util.Arrays.copyOf(Arrays.java:3537)
at java.base/java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:100)
at java.base/java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:111)
at org.broad.igv.tdf.BufferedByteWriter.putLong(BufferedByteWriter.java:134)
at org.broad.igv.tdf.BufferedByteWriter.putDouble(BufferedByteWriter.java:115)
at juicebox.tools.utils.original.NormalizationVectorUpdater.writeNormalizationVector(NormalizationVectorUpdater.java:859)
at juicebox.tools.utils.original.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:174)
at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:84)
at juicebox.tools.HiCTools.main(HiCTools.java:96)

[moshe-olshansky]

Hello,
Which norm are you trying to add? KR may not work, but SCALE and its derivatives should.