BAM Statistics - LifeScope

[Alfonso-Rourich]

Hi everyone,

In our company, we use LifeScope to do the mapping and SNP (and other variations) call, but doing a targeted resequencing analysis, the Mapping.BamStats module fails because a java.lang.NumberFormatException. This is part of one of the logs in the folder module:

22 jun 2013 12:35:16,384 FATAL [main] PluginRunner:87 - java.lang.NumberFormatException: For input string: "95,4136"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1222)
java.lang.Double.parseDouble(Double.java:510)
com.apldbio.aga.analysis.secondary.plugin.writer.ChtFileWriter.getReadPairedTypeStats(ChtFileWriter.java:1355)
com.apldbio.aga.analysis.secondary.plugin.writer.ChtFileWriter.writeMatrixData(ChtFileWriter.java:1071)
com.apldbio.aga.analysis.secondary.plugin.writer.ChtFileWriter.writeStatsMatrix(ChtFileWriter.java:559)
com.apldbio.aga.analysis.secondary.plugin.writer.ChtFileWriter.writeContigMatrix(ChtFileWriter.java:385)
com.apldbio.aga.analysis.secondary.plugin.merge.SamplewiseStatsMerger.merge(SamplewiseStatsMerger.java:74)
com.apldbio.aga.analysis.secondary.plugin.BamStatsGatherer.gather(BamStatsGatherer.java:52)
com.apldbio.aga.analysis.secondary.plugin.BAMStatsDistributionHelper.doGather(BAMStatsDistributionHelper.java:250)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
java.lang.reflect.Method.invoke(Method.java:597)
com.apldbio.aga.analysis.jobms.AbstractDistributionHelper.invoke(AbstractDistributionHelper.java:66)
com.apldbio.aga.analysis.jobms.PluginRunner.doMain(PluginRunner.java:467)
com.apldbio.aga.analysis.jobms.PluginRunner.safeMain(PluginRunner.java:722)
com.apldbio.aga.analysis.jobms.PluginRunner.main(PluginRunner.java:700)

I think the problem is that there could be a file with an incompatible format, but I don't find the solution. Does anyone know anything about this problem?

Thank you very much for your help.