Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Alfonso-Rourich
    started a topic BAM Statistics - LifeScope

    BAM Statistics - LifeScope

    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.

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:52 AM
0 responses
21 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
50 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-12-2024, 03:37 PM
0 responses
437 views
0 likes
Last Post seqadmin  
Working...
X