Qualimap v.1.0 on bit BAM file - java.lang.ArrayIndexOutOfBoundsException: -432634231

[Marsa]

Dear QualiMap authors and users,

I am trying to run bamqc from QualiMap v.1.0 on quite a big BAM (WGS data with 1.5 billion reads) and I am getting the following  java.lang.ArrayIndexOutOfBoundsException error:

Java memory size is set to 128G

Launching application...

QualiMap v.1.0

Built on 2014-05-29 11:34

Selected tool: bamqc

Available memory (Mb): 32

Max memory (Mb): 122168

Fri Dec 05 09:31:04 EST 2014            WARNING output folder already exists

Starting bam qc....

Loading sam header...

Loading locator...

Loading reference...

Number of windows: 400, effective number of windows: 483

Chunk of reads size: 1000

Number of threads: 40

Processed 50 out of 483 windows...

Processed 100 out of 483 windows...

Processed 150 out of 483 windows...

Processed 200 out of 483 windows...

Processed 250 out of 483 windows...

Processed 300 out of 483 windows...

Processed 350 out of 483 windows...

Processed 400 out of 483 windows...

Processed 450 out of 483 windows...

Total processed windows:483

Number of reads: 1477874142

Number of valid reads: 1477874142

Number of duplicated reads: 0

Number of correct strand reads:0

Inside of regions...

Num mapped reads: 1477874142

Num mapped first of pair: 734603929

Num mapped second of pair: 743270213

Num singletons: 40751869

Time taken to analyze reads: 11492

Computing descriptors...

numberOfMappedBases: 134388071242

referenceSize: 3101804741

numberOfSequencedBases: 133657463976

numberOfAs: 40136063368

Computing per chromosome statistics...

Computing histograms...

java.lang.ArrayIndexOutOfBoundsException: -432634231

        at java.util.ArrayList.elementData(ArrayList.java:371)

        at java.util.ArrayList.get(ArrayList.java:384)

        at org.bioinfo.ngs.qc.qualimap.beans.BamStats.computeInsertSizeHistogram(BamStats.java:975)

        at org.bioinfo.ngs.qc.qualimap.beans.BamStats.computeHistograms(BamStats.java:793)

        at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:488)

        at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:211)

        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:177)

        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:102)

I randomly sampled this BAM file and Qualimap run fine on small sampled file. I also was able to run bamqc on each chromosome by splitting BAM file into chromosome-based bam files. 

Looks like Qualimap has problem with big BAM file. I was researching the web for this qualimap error but wasn't able to find anything related to my issue.

Does anyone know what is causing this error and how to fix it? 

Regards,

Marsa

[Konstantin Okonechnikov]

Dear Marsa,

thanks for the report!

Try using the latest version, most likely this issue was fixed:

https://www.dropbox.com/sh/0zpbl8b2yw5doxp/AADY6S7NEUEyLlzZH_kBFJmza/qualimap-build-26-09-14.tar.gz?dl=0

More details here:

https://groups.google.com/forum/#!topic/qualimap/7itxJ6VjJts 

-- 

  Konstantin