bamqc error: Range(double, double): require lower (66.5) <= upper (50.5)

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SLF

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Jun 1, 2012, 8:45:52 AM6/1/12
to QualiMap

Hi there,

I'm getting this exception when trying to run qualimap with R 2.15.0
and JRE 1.6.0_12 or JRE 1.7.0

java.lang.IllegalArgumentException: Range(double, double): require
lower (66.5) <= upper (50.5).
at org.jfree.data.Range.<init>(Range.java:90)
at org.jfree.chart.axis.ValueAxis.setRange(ValueAxis.java:
1283)
at
org.bioinfo.ngs.qc.qualimap.beans.BamQCXYHistogramChart.render(BamQCXYHistogramChart.java:
187)
at
org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.computeChartsBuffers(BamQCRegionReporter.java:
464)
at
org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:181)
at
org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:
131)
at
org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:
67)


Is this a know issue?

Cheers,
Samjavaz

Konstantin Okonechnikov

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Jun 1, 2012, 9:09:10 AM6/1/12
to qual...@googlegroups.com
Hey Samuel,

this is not a known issue.

Did you encounter the problem only with some specific dataset or is it
reoccuring?

--
Konstantin

Thoraval, Samuel

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Jun 1, 2012, 9:18:50 AM6/1/12
to qual...@googlegroups.com
Hi Konstantin,

With some specific dataset. It is a PGM ion Torrent dataset. The reference sequence is only 30kb and there are

samtools flagstat:
576240 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
508841 + 0 mapped (88.30%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

The full output from bamqc is (it complains that the bal file might not be sorted, I sorted it using "samtools sort" just to ensure it is):
./qualimap bamqc -bam R_2012_05_30_17_07_23_sorted.bam -gff /data/results/Sam/SyntheticDNA/region.gff -nt 1
QualiMap v.0.3
Built on 2012-05-18 11:35

Selected tool: bamqc
Available memory (Mb): 32
Max memory (Mb): 954
Starting bam qc....
loading sam header header
Fri Jun 01 11:34:42 BST 2012 WARNING According to header the BAM file is not sorted by coordinate!
loading locator
loading reference
effectiveNumberOfWindows 400
Number of threads: 1
initializing regions from /data/results/Sam/SyntheticDNA/region.gff.....
found 1 regions
initializing memory...
filling region references...
Processed 50 out of 400 windows...
Processed 100 out of 400 windows...
Processed 150 out of 400 windows...
Processed 200 out of 400 windows...
Processed 250 out of 400 windows...
Processed 300 out of 400 windows...
Processed 350 out of 400 windows...
Processed 400 out of 400 windows...
Total processed windows:400
Number of reads: 576240
Number of valid reads: 508841
Number of duplicated reads: 0

Inside of regions...
Num mapped reads: 508841
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 22
Computing descriptors...
numberOfMappedBases: 63097020
referenceSize: 31564
numberOfSequencedBases: 63097020
numberOfAs: 16824312
Computing histograms...
Overall analysis time: 22
end of bam qc
Computing report...
java.lang.IllegalArgumentException: Range(double, double): require lower (66.5) <= upper (50.5).
at org.jfree.data.Range.<init>(Range.java:90)
at org.jfree.chart.axis.ValueAxis.setRange(ValueAxis.java:1283)
at org.bioinfo.ngs.qc.qualimap.beans.BamQCXYHistogramChart.render(BamQCXYHistogramChart.java:187)
at org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.computeChartsBuffers(BamQCRegionReporter.java:464)
at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:181)
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:131)
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:67)


Best regards,
Sam

Thoraval, Samuel

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Jun 1, 2012, 9:20:08 AM6/1/12
to qual...@googlegroups.com
By the way, it has high coverage (2000x on average).

Best regards,
Sam

NGS Support: ngs-eu...@lifetech.com
java.lang.IllegalArgumentException: Range(double, double): require lower (66.5) <= upper (50.5).
at org.jfree.data.Range.<init>(Range.java:90)
at org.jfree.chart.axis.ValueAxis.setRange(ValueAxis.java:1283)
at org.bioinfo.ngs.qc.qualimap.beans.BamQCXYHistogramChart.render(BamQCXYHistogramChart.java:187)
at org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.computeChartsBuffers(BamQCRegionReporter.java:464)
at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:181)
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:131)
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:67)


Best regards,
Sam


-----Original Message-----
From: qual...@googlegroups.com [mailto:qual...@googlegroups.com] On Behalf Of Konstantin Okonechnikov
Sent: vendredi 1 juin 2012 15:09
To: qual...@googlegroups.com

Konstantin Okonechnikov

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Jun 1, 2012, 10:32:44 AM6/1/12
to qual...@googlegroups.com
Samuel,

I've figured out what is going on.

The problem is related to the Coverage Histogram 0-50x, which is
provided additionally to Coverage Histogram. This histogram is
especially useful for samples with low coverage. However in your
sample minimum coverage is more than 50, and this results in a crash.

We'll fix this issue ASAP, I'll update this thread when the new
version of Qualimap is available for download.

Thanks for your report,
Konstantin

Thoraval, Samuel

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Jun 1, 2012, 10:40:38 AM6/1/12
to qual...@googlegroups.com
That was quick!
Indeed minimum coverage is around 100x...

Thanks for the support,

Konstantin Okonechnikov

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Jun 4, 2012, 10:18:38 AM6/4/12
to qual...@googlegroups.com
Hey Samuel,

we have just released a new minor version of Qualimap, which includes
fixes for high coverage data.

Let me know, if you still have problems.

Best regards,
Konstantin

On Fri, Jun 1, 2012 at 4:40 PM, Thoraval, Samuel

Thoraval, Samuel

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Jun 4, 2012, 11:01:25 AM6/4/12
to qual...@googlegroups.com
Thanks Konstantin,

I tested and it worked fine now!

Cheers,
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