java.lang.NullPointerException

[Arnold Liao]

I'm getting this error with my bamqc 

bam is in https://drive.google.com/folderview?id=0B4x0rK6clrNnT2NLcVI3TzdyVTA&usp=sharing 

java.lang.NullPointerException

ubuntu:~/qualimap_v2.2$ ./qualimap bamqc -bam ~/bam/100ngHmBrainA2_I9_S1.bam

Java memory size is set to 1200M

Launching application...

QualiMap v.2.2

Built on 2016-01-29 12:10

Selected tool: bamqc

Available memory (Mb): 32

Max memory (Mb): 1216

Starting bam qc....

Loading sam header...

Loading locator...

Loading reference...

Number of windows: 400, effective number of windows: 424

Chunk of reads size: 1000

Number of threads: 1

Processed 50 out of 424 windows...

Processed 100 out of 424 windows...

Processed 150 out of 424 windows...

Processed 200 out of 424 windows...

Processed 250 out of 424 windows...

Processed 300 out of 424 windows...

Processed 350 out of 424 windows...

Processed 400 out of 424 windows...

Total processed windows:424

Number of reads: 163111916

Number of valid reads: 77199200

Number of correct strand reads:0

Inside of regions...

Num mapped reads: 77199200

Num mapped first of pair: 77199200

Num mapped second of pair: 0

Num singletons: 77199200

Time taken to analyze reads: 853

Computing descriptors...

numberOfMappedBases: 7456072454

referenceSize: 3095693983

numberOfSequencedBases: 5747636461

numberOfAs: 1632355311

Computing per chromosome statistics...

Computing histograms...

Overall analysis time: 854

end of bam qc

Computing report...

Failed to run bamqc

java.lang.NullPointerException

        at org.bioinfo.ngs.qc.qualimap.beans.BamQCXYHistogramChart.render(BamQCXYHistogramChart.java:150)

        at org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.computeChartsBuffers(BamQCRegionReporter.java:821)

        at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:263)

        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:187)

        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)

[Konstantin Okonechnikov]

Hi!

Thanks a lot for the report! The bug occurred because in the alignment file there were paired-end reads, however from each pair only the first read was aligned and this was leading to fail in the generation of insert size histogram.

Novel version with the fix can be downloaded from here:
https://bitbucket.org/kokonech/qualimap/downloads/qualimap-build-28-02-16.tar.gz

Attached is the report for the shared file computed by the fixed version.

Let me know if there are any other questions.

--

  Konstantin

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[Arnold Liao]

I'm glad it wasn't user error.  Thanks for the fix

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