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.
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.