multi-bamqc java.lang.NumberFormatException error

[Henri-Jean Garchon]

Hi,

I consistently get a java error message when I run multi-bamqc on my onw bamqc ffile/folers:

hjg@aurigny:/home/NGS/spa3/run_2015_02_12/14_qualimap_stats$ /usr/local/bin/qualimap_v2.1.2/qualimap multi-bamqc -d qualimap.input -outdir multibam_qc
QualiMap v.2.1.2
Built on 2015-09-23 14:22

Selected tool: multi-bamqc
Running multi-sample BAM QC

Checking input paths
Loading sample data
Failed to run multi-bamqc
java.lang.NumberFormatException: For input string: "38,19"
        at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1250)
        at java.lang.Double.parseDouble(Double.java:540)
        at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.loadSummaryStats(MultisampleBamQcAnalysis.java:174)
        at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.createSummaryTable(MultisampleBamQcAnalysis.java:213)
        at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.run(MultisampleBamQcAnalysis.java:84)
        at org.bioinfo.ngs.qc.qualimap.main.MultisampleBamQcTool.execute(MultisampleBamQcTool.java:157)
        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:186)
        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)
 
Mon Oct 19 16:54:49 CEST 2015           WARNING Cleanup output dir

I know nothing about java.
Would you have any idea of what the problem is?
Note that the "gh2ax_chip_seq" example files run perfectly fine!
In anticipation many thanks for your help
Best wishes

Henri-Jean

[Konstantin Okonechnikov]

Hi!

Thanks a lot for the report!

Most likely the problem is related to the default format of generated numbers in genome_results.txt report file (comma separator for a float number instead of a dot).  

Could you please share several Qualimap BAM QC reports (*_stats folders), so I can check this issue? Typically these reports are rather small.

--

  Konstantin

[Henri-Jean Garchon]

Hi Konstantin,

Thanks very much for your prompt reply.
You're absolutely right! I checked the genome_results.txt file: the decimal separators are commas instead of dots.
As a quick fix, I substituted the commas with dots and now multi-bamqc run fine.
However, it's probably not the definitive solution: there are some issues like mean qualities at 0.14 for the 5 samples etc.
I am going to transfer you the files.
Many thanks again

Henri-Jean

PS: I was surprised to learn that thare more countries using the comma as the decimal mark than the dot.

[Konstantin Okonechnikov]

Hi Henri-Jean,

yep, the comma-dot is a problem sometimes! 

To share the data it's easy to use dropbox.com or drive.google.com. You can send it directly to my e-mail: k.okonechnikov[at]gmail[dot]com

-- 

  Konstantin

--
You received this message because you are subscribed to the Google Groups "QualiMap" group.
To unsubscribe from this group and stop receiving emails from it, send an email to qualimap+u...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.