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